Warning: Permanently added '172.25.85.76' (ECDSA) to the list of known hosts. Cloning into 'coot'... Note: checking out 'bfedf58f3192f0dc17566ed19d737f00bb7e34a0'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at bfedf58... import_srpm % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 18.5M 100 18.5M 0 0 73.1M 0 --:--:-- --:--:-- --:--:-- 73.4M coot-0.8.8.tar.gz: OK % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 6571k 100 6571k 0 0 47.4M 0 --:--:-- --:--:-- --:--:-- 47.5M reference-structures.tar.gz: OK WARNING: Could not find required logging config file: /var/lib/copr-rpmbuild/results/configs/logging.ini. Using default... INFO: mock.py version 1.4.2 starting (python version = 3.6.1)... Start: init plugins INFO: tmpfs initialized INFO: selinux disabled INFO: compress_logs: initialized Finish: init plugins Start: run INFO: Start(coot.spec) Config(579072-fedora-rawhide-i386) Start: clean chroot Finish: clean chroot Start: chroot init INFO: mounting tmpfs at /var/lib/mock/579072-fedora-rawhide-i386/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled HW Info plugin Mock Version: 1.4.2 INFO: Mock Version: 1.4.2 Start: dnf install "Copr repository" 0% [ ] --- B/s | 0 B --:-- ETA "Copr repository" 467 kB/s | 23 kB 00:00 fedora 0% [ ] --- B/s | 0 B --:-- ETA fedora 43% [========- ] 72 MB/s | 22 MB 00:00 ETA fedora 94% [==================- ] 73 MB/s | 47 MB 00:00 ETA fedora 67 MB/s | 50 MB 00:00 Last metadata expiration check: 0:00:00 ago on Thu 13 Jul 2017 08:08:24 PM UTC. Dependencies resolved. ================================================================================ Group Packages ================================================================================ Marking packages as installed by the group: @Buildsystem building group xz redhat-rpm-config grep bzip2 shadow-utils findutils rpm-build sed gzip util-linux diffutils gcc-c++ bash info tar gawk patch gcc coreutils cpio unzip which make fedora-release ================================================================================ Package Arch Version Repository Size ================================================================================ Installing dependencies: audit-libs i686 2.7.7-1.fc27 fedora 110 k basesystem noarch 11-3.fc26 fedora 8.8 k bash i686 4.4.12-6.fc27 fedora 1.6 M binutils i686 2.28-9.fc27 fedora 5.9 M bzip2 i686 1.0.6-22.fc26 fedora 57 k bzip2-libs i686 1.0.6-22.fc26 fedora 44 k ca-certificates noarch 2017.2.14-2.fc27 fedora 478 k chkconfig i686 1.10-1.fc27 fedora 186 k coreutils i686 8.27-10.fc27 fedora 1.2 M coreutils-common i686 8.27-10.fc27 fedora 1.9 M cpio i686 2.12-4.fc26 fedora 267 k cpp i686 7.1.1-5.fc27 fedora 9.1 M cracklib i686 2.9.6-5.fc26 fedora 85 k crypto-policies noarch 20170606-1.git7c32281.fc27 fedora 35 k curl i686 7.54.1-2.fc27 fedora 308 k cyrus-sasl-lib i686 2.1.26-32.fc27 fedora 166 k diffutils i686 3.6-1.fc27 fedora 361 k dwz i686 0.12-3.fc26 fedora 109 k elfutils i686 0.169-3.fc27 fedora 319 k elfutils-default-yama-scope noarch 0.169-3.fc27 fedora 38 k elfutils-libelf i686 0.169-3.fc27 fedora 209 k elfutils-libs i686 0.169-3.fc27 fedora 312 k expat i686 2.2.1-2.fc27 fedora 93 k fedora-release noarch 27-0.2 fedora 25 k fedora-repos noarch 27-0.2 fedora 92 k fedora-repos-rawhide noarch 27-0.2 fedora 7.4 k fedora-rpm-macros noarch 26-2.fc26 fedora 6.5 k file i686 5.31-1.fc27 fedora 70 k file-libs i686 5.31-1.fc27 fedora 513 k filesystem i686 3.3-1.fc27 fedora 1.1 M findutils i686 1:4.6.0-12.fc27 fedora 529 k fpc-srpm-macros noarch 1.1-2.fc26 fedora 7.0 k gawk i686 4.1.4-3.fc26 fedora 1.1 M gc i686 7.6.0-4.fc27 fedora 112 k gcc i686 7.1.1-5.fc27 fedora 20 M gcc-c++ i686 7.1.1-5.fc27 fedora 11 M gdb-headless i686 8.0-17.fc27 fedora 3.5 M gdbm i686 1.13-1.fc27 fedora 159 k ghc-srpm-macros noarch 1.4.2-5.fc26 fedora 7.7 k glib2 i686 2.53.3-1.fc27 fedora 2.5 M glibc i686 2.25.90-22.fc27 fedora 4.7 M glibc-all-langpacks i686 2.25.90-22.fc27 fedora 7.0 M glibc-common i686 2.25.90-22.fc27 fedora 862 k glibc-devel i686 2.25.90-22.fc27 fedora 1.0 M glibc-headers i686 2.25.90-22.fc27 fedora 518 k gmp i686 1:6.1.2-4.fc27 fedora 276 k gnat-srpm-macros noarch 4-2.fc26 fedora 8.1 k gnupg2 i686 2.1.21-2.fc27 fedora 2.3 M gnutls i686 3.5.14-1.fc27 fedora 758 k go-srpm-macros noarch 2-9.fc27 fedora 7.9 k grep i686 3.1-1.fc27 fedora 276 k guile i686 5:2.0.14-1.fc26 fedora 3.5 M gzip i686 1.8-2.fc26 fedora 159 k info i686 6.4-2.fc27 fedora 192 k isl i686 0.16.1-1.fc26 fedora 890 k kernel-headers i686 4.13.0-0.rc0.git5.1.fc27 fedora 1.2 M keyutils-libs i686 1.5.10-1.fc27 fedora 31 k krb5-libs i686 1.15.1-14.fc27 fedora 791 k libacl i686 2.2.52-15.fc27 fedora 33 k libarchive i686 3.3.1-1.fc27 fedora 387 k libasan i686 7.1.1-5.fc27 fedora 388 k libassuan i686 2.4.3-2.fc26 fedora 77 k libatomic i686 7.1.1-5.fc27 fedora 33 k libatomic_ops i686 7.4.6-1.fc27 fedora 33 k libattr i686 2.4.47-18.fc26 fedora 23 k libbabeltrace i686 1.5.2-2.fc27 fedora 205 k libblkid i686 2.30-1.fc27 fedora 206 k libcap i686 2.25-5.fc26 fedora 53 k libcap-ng i686 0.7.8-3.fc26 fedora 29 k libcilkrts i686 7.1.1-5.fc27 fedora 72 k libcom_err i686 1.43.4-2.fc26 fedora 45 k libcrypt-nss i686 2.25.90-22.fc27 fedora 58 k libcurl i686 7.54.1-2.fc27 fedora 287 k libdb i686 5.3.28-24.fc27 fedora 805 k libdb-utils i686 5.3.28-24.fc27 fedora 147 k libfdisk i686 2.30-1.fc27 fedora 254 k libffi i686 3.1-12.fc27 fedora 33 k libgcc i686 7.1.1-5.fc27 fedora 96 k libgcrypt i686 1.7.8-1.fc27 fedora 406 k libgomp i686 7.1.1-5.fc27 fedora 200 k libgpg-error i686 1.27-1.fc27 fedora 186 k libidn2 i686 2.0.2-1.fc27 fedora 96 k libipt i686 1.6.1-2.fc27 fedora 57 k libksba i686 1.3.5-3.fc26 fedora 137 k libmetalink i686 0.1.3-2.fc26 fedora 30 k libmount i686 2.30-1.fc27 fedora 223 k libmpc i686 1.0.2-6.fc26 fedora 57 k libmpx i686 7.1.1-5.fc27 fedora 39 k libnghttp2 i686 1.24.0-1.fc27 fedora 76 k libpkgconf i686 1.3.7-1.fc27 fedora 31 k libpsl i686 0.17.0-2.fc26 fedora 48 k libpwquality i686 1.4.0-1.fc27 fedora 100 k libselinux i686 2.6-6.fc27 fedora 175 k libsemanage i686 2.6-4.fc27 fedora 156 k libsepol i686 2.6-1.fc26 fedora 308 k libsigsegv i686 2.11-1.fc26 fedora 28 k libsmartcols i686 2.30-1.fc27 fedora 163 k libssh2 i686 1.8.0-2.fc26 fedora 100 k libstdc++ i686 7.1.1-5.fc27 fedora 494 k libstdc++-devel i686 7.1.1-5.fc27 fedora 1.9 M libtasn1 i686 4.12-1.fc27 fedora 76 k libtool-ltdl i686 2.4.6-18.fc27 fedora 56 k libubsan i686 7.1.1-5.fc27 fedora 163 k libunistring i686 0.9.7-1.fc26 fedora 416 k libusbx i686 1.0.21-2.fc26 fedora 68 k libutempter i686 1.1.6-9.fc26 fedora 29 k libuuid i686 2.30-1.fc27 fedora 82 k libverto i686 0.2.6-7.fc26 fedora 21 k libxml2 i686 2.9.4-2.fc26 fedora 714 k lua-libs i686 5.3.4-3.fc27 fedora 126 k lz4-libs i686 1.7.5-4.fc27 fedora 50 k make i686 1:4.2.1-2.fc26 fedora 497 k mpfr i686 3.1.5-3.fc27 fedora 221 k ncurses i686 6.0-10.20170520.fc27 fedora 366 k ncurses-base noarch 6.0-10.20170520.fc27 fedora 77 k ncurses-libs i686 6.0-10.20170520.fc27 fedora 328 k nettle i686 3.3-2.fc26 fedora 328 k npth i686 1.5-1.fc27 fedora 24 k nspr i686 4.15.0-1.fc27 fedora 144 k nss i686 3.31.0-2.fc27 fedora 899 k nss-pem i686 1.0.3-3.fc27 fedora 79 k nss-softokn i686 3.31.0-2.fc27 fedora 413 k nss-softokn-freebl i686 3.31.0-2.fc27 fedora 220 k nss-sysinit i686 3.31.0-2.fc27 fedora 61 k nss-util i686 3.31.0-2.fc27 fedora 89 k ocaml-srpm-macros noarch 4-2.fc26 fedora 7.5 k openblas-srpm-macros noarch 2-1.fc27 fedora 6.5 k openldap i686 2.4.45-1.fc27 fedora 365 k openssl-libs i686 1:1.1.0f-5.fc27 fedora 1.2 M p11-kit i686 0.23.7-1.fc27 fedora 255 k p11-kit-trust i686 0.23.7-1.fc27 fedora 130 k pam i686 1.3.0-3.fc27 fedora 757 k patch i686 2.7.5-4.fc26 fedora 133 k pcre i686 8.41-1.fc27 fedora 204 k perl-srpm-macros noarch 1-23.fc27 fedora 9.2 k pkgconf i686 1.3.7-1.fc27 fedora 30 k pkgconf-m4 noarch 1.3.7-1.fc27 fedora 13 k pkgconf-pkg-config i686 1.3.7-1.fc27 fedora 12 k popt i686 1.16-8.fc26 fedora 60 k publicsuffix-list-dafsa noarch 20170424-1.fc27 fedora 44 k python-srpm-macros noarch 3-20.fc27 fedora 9.2 k qt5-srpm-macros noarch 5.9.0-2.fc27 fedora 8.3 k readline i686 7.0-5.fc26 fedora 215 k redhat-rpm-config noarch 64-1.fc27 fedora 61 k rpm i686 4.13.0.1-31.fc27 fedora 524 k rpm-build i686 4.13.0.1-31.fc27 fedora 155 k rpm-build-libs i686 4.13.0.1-31.fc27 fedora 133 k rpm-libs i686 4.13.0.1-31.fc27 fedora 325 k rpm-plugin-selinux i686 4.13.0.1-31.fc27 fedora 61 k sed i686 4.4-1.fc26 fedora 289 k setup noarch 2.10.5-2.fc26 fedora 174 k shadow-utils i686 2:4.3.1-3.fc26 fedora 1.2 M sqlite-libs i686 3.19.3-1.fc27 fedora 493 k system-python-libs i686 3.6.1-10.fc27 fedora 6.3 M systemd-libs i686 233-6.fc27 fedora 492 k tar i686 2:1.29-4.fc26 fedora 830 k tzdata noarch 2017b-1.fc27 fedora 420 k unzip i686 6.0-33.fc26 fedora 182 k ustr i686 1.0.4-22.fc26 fedora 98 k util-linux i686 2.30-1.fc27 fedora 2.5 M which i686 2.21-2.fc26 fedora 46 k xz i686 5.2.3-2.fc26 fedora 152 k xz-libs i686 5.2.3-2.fc26 fedora 98 k zip i686 3.0-18.fc26 fedora 269 k zlib i686 1.2.11-2.fc26 fedora 101 k Transaction Summary ================================================================================ Install 165 Packages Total download size: 119 M Installed size: 452 M Downloading Packages: (1/165): gcc-c++-7.1 0% [ ] --- B/s | 0 B --:-- ETA (1/165): diffutils-3.6-1.fc27.i686.rpm 5.2 MB/s | 361 kB 00:00 (2-3/165): shadow-ut 0% [ ] 16 MB/s | 1.1 MB 00:07 ETA (2/165): shadow-utils-4.3.1-3.fc26.i686.rpm 13 MB/s | 1.2 MB 00:00 (3-4/165): util-linu 2% [- ] 16 MB/s | 3.1 MB 00:07 ETA (3/165): make-4.2.1-2.fc26.i686.rpm 18 MB/s | 497 kB 00:00 (4-5/165): util-linu 4% [- ] 17 MB/s | 5.8 MB 00:06 ETA (4/165): fedora-release-27-0.2.noarch.rpm 3.7 MB/s | 25 kB 00:00 (5-6/165): util-linu 5% [= ] 17 MB/s | 6.4 MB 00:06 ETA (5/165): util-linux-2.30-1.fc27.i686.rpm 32 MB/s | 2.5 MB 00:00 (6-7/165): sed-4.4-1 5% [= ] 17 MB/s | 7.1 MB 00:06 ETA (6/165): sed-4.4-1.fc26.i686.rpm 9.9 MB/s | 289 kB 00:00 (7-8/165): rpm-build 6% [= ] 17 MB/s | 7.8 MB 00:06 ETA (7/165): rpm-build-4.13.0.1-31.fc27.i686.rpm 11 MB/s | 155 kB 00:00 (8-9/165): which-2.2 6% [= ] 17 MB/s | 8.2 MB 00:06 ETA (8/165): which-2.21-2.fc26.i686.rpm 6.1 MB/s | 46 kB 00:00 (9-10/165): patch-2. 7% [= ] 17 MB/s | 8.5 MB 00:06 ETA (9/165): patch-2.7.5-4.fc26.i686.rpm 11 MB/s | 133 kB 00:00 (10-11/165): info-6. 7% [=- ] 17 MB/s | 9.0 MB 00:06 ETA (10/165): info-6.4-2.fc27.i686.rpm 14 MB/s | 192 kB 00:00 (11-12/165): gcc-7.1 7% [=- ] 17 MB/s | 9.5 MB 00:06 ETA (11/165): unzip-6.0-33.fc26.i686.rpm 9.2 MB/s | 182 kB 00:00 (12-13/165): gcc-7.1 9% [=- ] 18 MB/s | 11 MB 00:06 ETA (12/165): xz-5.2.3-2.fc26.i686.rpm 13 MB/s | 152 kB 00:00 (13-14/165): gcc-7.1 10% [== ] 18 MB/s | 12 MB 00:05 ETA (13/165): gawk-4.1.4-3.fc26.i686.rpm 12 MB/s | 1.1 MB 00:00 (14-15/165): gcc-7.1 16% [=== ] 19 MB/s | 20 MB 00:05 ETA (14/165): gzip-1.8-2.fc26.i686.rpm 9.3 MB/s | 159 kB 00:00 (15-16/165): gcc-7.1 18% [===- ] 19 MB/s | 22 MB 00:05 ETA (15/165): gcc-c++-7.1.1-5.fc27.i686.rpm 30 MB/s | 11 MB 00:00 (16-17/165): bash-4. 18% [===- ] 19 MB/s | 22 MB 00:05 ETA (16/165): redhat-rpm-config-64-1.fc27.noarch.rp 9.0 MB/s | 61 kB 00:00 (17-18/165): bash-4. 19% [===- ] 20 MB/s | 23 MB 00:04 ETA (17/165): findutils-4.6.0-12.fc27.i686.rpm 22 MB/s | 529 kB 00:00 (18-19/165): bash-4. 20% [==== ] 20 MB/s | 25 MB 00:04 ETA (18/165): grep-3.1-1.fc27.i686.rpm 20 MB/s | 276 kB 00:00 (19-20/165): bash-4. 22% [==== ] 20 MB/s | 26 MB 00:04 ETA (19/165): bash-4.4.12-6.fc27.i686.rpm 15 MB/s | 1.6 MB 00:00 (20-21/165): tar-1.2 23% [====- ] 20 MB/s | 27 MB 00:04 ETA (20/165): tar-1.29-4.fc26.i686.rpm 25 MB/s | 830 kB 00:00 (21-22/165): gcc-7.1 24% [====- ] 20 MB/s | 29 MB 00:04 ETA (21/165): cpio-2.12-4.fc26.i686.rpm 13 MB/s | 267 kB 00:00 (22-23/165): gcc-7.1 24% [====- ] 21 MB/s | 29 MB 00:04 ETA (22/165): bzip2-1.0.6-22.fc26.i686.rpm 1.2 MB/s | 57 kB 00:00 (23-24/165): gcc-7.1 27% [=====- ] 21 MB/s | 33 MB 00:04 ETA (23/165): coreutils-8.27-10.fc27.i686.rpm 15 MB/s | 1.2 MB 00:00 (24-25/165): gcc-7.1 30% [====== ] 22 MB/s | 36 MB 00:03 ETA (24/165): gmp-6.1.2-4.fc27.i686.rpm 17 MB/s | 276 kB 00:00 (25-26/165): gcc-7.1 32% [====== ] 22 MB/s | 38 MB 00:03 ETA (25/165): libmpc-1.0.2-6.fc26.i686.rpm 4.9 MB/s | 57 kB 00:00 (26-27/165): gcc-7.1 33% [======- ] 22 MB/s | 39 MB 00:03 ETA (26/165): libstdc++-7.1.1-5.fc27.i686.rpm 24 MB/s | 494 kB 00:00 (27-28/165): gcc-7.1 34% [======- ] 22 MB/s | 41 MB 00:03 ETA (27/165): libstdc++-devel-7.1.1-5.fc27.i686.rpm 26 MB/s | 1.9 MB 00:00 (28-29/165): gcc-7.1 39% [=======- ] 23 MB/s | 48 MB 00:03 ETA (28/165): gcc-7.1.1-5.fc27.i686.rpm 36 MB/s | 20 MB 00:00 (29-30/165): glibc-2 41% [======== ] 23 MB/s | 49 MB 00:02 ETA (29/165): mpfr-3.1.5-3.fc27.i686.rpm 2.7 MB/s | 221 kB 00:00 (30-31/165): glibc-2 41% [======== ] 23 MB/s | 50 MB 00:02 ETA (30/165): glibc-2.25.90-22.fc27.i686.rpm 18 MB/s | 4.7 MB 00:00 (31-32/165): zlib-1. 41% [======== ] 23 MB/s | 50 MB 00:02 ETA (31/165): zlib-1.2.11-2.fc26.i686.rpm 2.8 MB/s | 101 kB 00:00 (32-33/165): audit-l 41% [======== ] 23 MB/s | 50 MB 00:02 ETA (32/165): audit-libs-2.7.7-1.fc27.i686.rpm 3.2 MB/s | 110 kB 00:00 (33/165): libacl-2.2 41% [======== ] 23 MB/s | 50 MB 00:02 ETA (33/165): libacl-2.2.52-15.fc27.i686.rpm 1.9 MB/s | 33 kB 00:00 (34-35/165): libattr 41% [======== ] 23 MB/s | 50 MB 00:02 ETA (34/165): libattr-2.4.47-18.fc26.i686.rpm 1.5 MB/s | 23 kB 00:00 (35-36/165): libseli 42% [======== ] 23 MB/s | 50 MB 00:02 ETA (35/165): libselinux-2.6-6.fc27.i686.rpm 11 MB/s | 175 kB 00:00 (36/165): libsemanag 42% [======== ] 23 MB/s | 50 MB 00:02 ETA (36/165): libsemanage-2.6-4.fc27.i686.rpm 17 MB/s | 156 kB 00:00 (37-38/165): setup-2 42% [======== ] 23 MB/s | 50 MB 00:02 ETA (37/165): libblkid-2.30-1.fc27.i686.rpm 32 MB/s | 206 kB 00:00 (38-39/165): setup-2 42% [======== ] 23 MB/s | 51 MB 00:02 ETA (38/165): setup-2.10.5-2.fc26.noarch.rpm 21 MB/s | 174 kB 00:00 (39-40/165): libcap- 42% [========- ] 23 MB/s | 51 MB 00:02 ETA (39/165): libcap-ng-0.7.8-3.fc26.i686.rpm 4.4 MB/s | 29 kB 00:00 (40-41/165): libfdis 42% [========- ] 23 MB/s | 51 MB 00:02 ETA (40/165): libfdisk-2.30-1.fc27.i686.rpm 33 MB/s | 254 kB 00:00 (41-42/165): libmoun 42% [========- ] 23 MB/s | 51 MB 00:02 ETA (41/165): libmount-2.30-1.fc27.i686.rpm 28 MB/s | 223 kB 00:00 (42-43/165): libsmar 42% [========- ] 23 MB/s | 51 MB 00:02 ETA (42/165): libutempter-1.1.6-9.fc26.i686.rpm 9.6 MB/s | 29 kB 00:00 (43-44/165): libsmar 43% [========- ] 23 MB/s | 51 MB 00:02 ETA (43/165): libsmartcols-2.30-1.fc27.i686.rpm 16 MB/s | 163 kB 00:00 (44-45/165): libuuid 43% [========- ] 23 MB/s | 51 MB 00:02 ETA (44/165): libuuid-2.30-1.fc27.i686.rpm 7.5 MB/s | 82 kB 00:00 (45-46/165): ncurses 43% [========- ] 23 MB/s | 51 MB 00:02 ETA (45/165): ncurses-libs-6.0-10.20170520.fc27.i68 18 MB/s | 328 kB 00:00 (46-47/165): pam-1.3 43% [========- ] 23 MB/s | 52 MB 00:02 ETA (46/165): gc-7.6.0-4.fc27.i686.rpm 15 MB/s | 112 kB 00:00 (47-48/165): pam-1.3 44% [========- ] 24 MB/s | 53 MB 00:02 ETA (47/165): systemd-libs-233-6.fc27.i686.rpm 28 MB/s | 492 kB 00:00 (48-49/165): pam-1.3 44% [========- ] 24 MB/s | 53 MB 00:02 ETA (48/165): pam-1.3.0-3.fc27.i686.rpm 27 MB/s | 757 kB 00:00 (49-50/165): guile-2 44% [========- ] 24 MB/s | 53 MB 00:02 ETA (49/165): fedora-repos-27-0.2.noarch.rpm 14 MB/s | 92 kB 00:00 (50-51/165): guile-2 44% [========- ] 24 MB/s | 53 MB 00:02 ETA (50/165): bzip2-libs-1.0.6-22.fc26.i686.rpm 6.0 MB/s | 44 kB 00:00 (51-52/165): guile-2 45% [========= ] 24 MB/s | 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Verifying : gcc-7.1.1-5.fc27.i686 12/165 Verifying : unzip-6.0-33.fc26.i686 13/165 Verifying : xz-5.2.3-2.fc26.i686 14/165 Verifying : gawk-4.1.4-3.fc26.i686 15/165 Verifying : gzip-1.8-2.fc26.i686 16/165 Verifying : bash-4.4.12-6.fc27.i686 17/165 Verifying : redhat-rpm-config-64-1.fc27.noarch 18/165 Verifying : findutils-1:4.6.0-12.fc27.i686 19/165 Verifying : grep-3.1-1.fc27.i686 20/165 Verifying : tar-2:1.29-4.fc26.i686 21/165 Verifying : cpio-2.12-4.fc26.i686 22/165 Verifying : coreutils-8.27-10.fc27.i686 23/165 Verifying : bzip2-1.0.6-22.fc26.i686 24/165 Verifying : glibc-2.25.90-22.fc27.i686 25/165 Verifying : gmp-1:6.1.2-4.fc27.i686 26/165 Verifying : libmpc-1.0.2-6.fc26.i686 27/165 Verifying : libstdc++-7.1.1-5.fc27.i686 28/165 Verifying : libstdc++-devel-7.1.1-5.fc27.i686 29/165 Verifying : mpfr-3.1.5-3.fc27.i686 30/165 Verifying : zlib-1.2.11-2.fc26.i686 31/165 Verifying : audit-libs-2.7.7-1.fc27.i686 32/165 Verifying : libacl-2.2.52-15.fc27.i686 33/165 Verifying : libattr-2.4.47-18.fc26.i686 34/165 Verifying : libselinux-2.6-6.fc27.i686 35/165 Verifying : libsemanage-2.6-4.fc27.i686 36/165 Verifying : setup-2.10.5-2.fc26.noarch 37/165 Verifying : libblkid-2.30-1.fc27.i686 38/165 Verifying : libcap-ng-0.7.8-3.fc26.i686 39/165 Verifying : libfdisk-2.30-1.fc27.i686 40/165 Verifying : libmount-2.30-1.fc27.i686 41/165 Verifying : libsmartcols-2.30-1.fc27.i686 42/165 Verifying : libutempter-1.1.6-9.fc26.i686 43/165 Verifying : libuuid-2.30-1.fc27.i686 44/165 Verifying : ncurses-libs-6.0-10.20170520.fc27.i686 45/165 Verifying : pam-1.3.0-3.fc27.i686 46/165 Verifying : systemd-libs-233-6.fc27.i686 47/165 Verifying : gc-7.6.0-4.fc27.i686 48/165 Verifying : guile-5:2.0.14-1.fc26.i686 49/165 Verifying : fedora-repos-27-0.2.noarch 50/165 Verifying : binutils-2.28-9.fc27.i686 51/165 Verifying : bzip2-libs-1.0.6-22.fc26.i686 52/165 Verifying : elfutils-0.169-3.fc27.i686 53/165 Verifying : elfutils-libelf-0.169-3.fc27.i686 54/165 Verifying : elfutils-libs-0.169-3.fc27.i686 55/165 Verifying : file-5.31-1.fc27.i686 56/165 Verifying : file-libs-5.31-1.fc27.i686 57/165 Verifying : gdb-headless-8.0-17.fc27.i686 58/165 Verifying : libcap-2.25-5.fc26.i686 59/165 Verifying : libdb-5.3.28-24.fc27.i686 60/165 Verifying : lua-libs-5.3.4-3.fc27.i686 61/165 Verifying : openssl-libs-1:1.1.0f-5.fc27.i686 62/165 Verifying : pkgconf-pkg-config-1.3.7-1.fc27.i686 63/165 Verifying : popt-1.16-8.fc26.i686 64/165 Verifying : rpm-4.13.0.1-31.fc27.i686 65/165 Verifying : rpm-build-libs-4.13.0.1-31.fc27.i686 66/165 Verifying : rpm-libs-4.13.0.1-31.fc27.i686 67/165 Verifying : xz-libs-5.2.3-2.fc26.i686 68/165 Verifying : cpp-7.1.1-5.fc27.i686 69/165 Verifying : glibc-devel-2.25.90-22.fc27.i686 70/165 Verifying : isl-0.16.1-1.fc26.i686 71/165 Verifying : libasan-7.1.1-5.fc27.i686 72/165 Verifying : libatomic-7.1.1-5.fc27.i686 73/165 Verifying : libcilkrts-7.1.1-5.fc27.i686 74/165 Verifying : libgcc-7.1.1-5.fc27.i686 75/165 Verifying : libgomp-7.1.1-5.fc27.i686 76/165 Verifying : libmpx-7.1.1-5.fc27.i686 77/165 Verifying : libubsan-7.1.1-5.fc27.i686 78/165 Verifying : filesystem-3.3-1.fc27.i686 79/165 Verifying : libsigsegv-2.11-1.fc26.i686 80/165 Verifying : readline-7.0-5.fc26.i686 81/165 Verifying : dwz-0.12-3.fc26.i686 82/165 Verifying : fedora-rpm-macros-26-2.fc26.noarch 83/165 Verifying : fpc-srpm-macros-1.1-2.fc26.noarch 84/165 Verifying : ghc-srpm-macros-1.4.2-5.fc26.noarch 85/165 Verifying : gnat-srpm-macros-4-2.fc26.noarch 86/165 Verifying : go-srpm-macros-2-9.fc27.noarch 87/165 Verifying : ocaml-srpm-macros-4-2.fc26.noarch 88/165 Verifying : openblas-srpm-macros-2-1.fc27.noarch 89/165 Verifying : perl-srpm-macros-1-23.fc27.noarch 90/165 Verifying : python-srpm-macros-3-20.fc27.noarch 91/165 Verifying : qt5-srpm-macros-5.9.0-2.fc27.noarch 92/165 Verifying : zip-3.0-18.fc26.i686 93/165 Verifying : pcre-8.41-1.fc27.i686 94/165 Verifying : coreutils-common-8.27-10.fc27.i686 95/165 Verifying : ncurses-6.0-10.20170520.fc27.i686 96/165 Verifying : basesystem-11-3.fc26.noarch 97/165 Verifying : glibc-common-2.25.90-22.fc27.i686 98/165 Verifying : libsepol-2.6-1.fc26.i686 99/165 Verifying : ustr-1.0.4-22.fc26.i686 100/165 Verifying : ncurses-base-6.0-10.20170520.fc27.noarch 101/165 Verifying : cracklib-2.9.6-5.fc26.i686 102/165 Verifying : libpwquality-1.4.0-1.fc27.i686 103/165 Verifying : libgcrypt-1.7.8-1.fc27.i686 104/165 Verifying : libgpg-error-1.27-1.fc27.i686 105/165 Verifying : lz4-libs-1.7.5-4.fc27.i686 106/165 Verifying : libatomic_ops-7.4.6-1.fc27.i686 107/165 Verifying : libffi-3.1-12.fc27.i686 108/165 Verifying : libtool-ltdl-2.4.6-18.fc27.i686 109/165 Verifying : libunistring-0.9.7-1.fc26.i686 110/165 Verifying : fedora-repos-rawhide-27-0.2.noarch 111/165 Verifying : chkconfig-1.10-1.fc27.i686 112/165 Verifying : elfutils-default-yama-scope-0.169-3.fc27.noarch 113/165 Verifying : expat-2.2.1-2.fc27.i686 114/165 Verifying : libbabeltrace-1.5.2-2.fc27.i686 115/165 Verifying : libipt-1.6.1-2.fc27.i686 116/165 Verifying : system-python-libs-3.6.1-10.fc27.i686 117/165 Verifying : ca-certificates-2017.2.14-2.fc27.noarch 118/165 Verifying : crypto-policies-20170606-1.git7c32281.fc27.noarc 119/165 Verifying : pkgconf-1.3.7-1.fc27.i686 120/165 Verifying : pkgconf-m4-1.3.7-1.fc27.noarch 121/165 Verifying : libarchive-3.3.1-1.fc27.i686 122/165 Verifying : libdb-utils-5.3.28-24.fc27.i686 123/165 Verifying : gnupg2-2.1.21-2.fc27.i686 124/165 Verifying : rpm-plugin-selinux-4.13.0.1-31.fc27.i686 125/165 Verifying : glibc-headers-2.25.90-22.fc27.i686 126/165 Verifying : tzdata-2017b-1.fc27.noarch 127/165 Verifying : glib2-2.53.3-1.fc27.i686 128/165 Verifying : gdbm-1.13-1.fc27.i686 129/165 Verifying : sqlite-libs-3.19.3-1.fc27.i686 130/165 Verifying : p11-kit-0.23.7-1.fc27.i686 131/165 Verifying : p11-kit-trust-0.23.7-1.fc27.i686 132/165 Verifying : libpkgconf-1.3.7-1.fc27.i686 133/165 Verifying : libxml2-2.9.4-2.fc26.i686 134/165 Verifying : gnutls-3.5.14-1.fc27.i686 135/165 Verifying : libassuan-2.4.3-2.fc26.i686 136/165 Verifying : libksba-1.3.5-3.fc26.i686 137/165 Verifying : libusbx-1.0.21-2.fc26.i686 138/165 Verifying : npth-1.5-1.fc27.i686 139/165 Verifying : openldap-2.4.45-1.fc27.i686 140/165 Verifying : kernel-headers-4.13.0-0.rc0.git5.1.fc27.i686 141/165 Verifying : libtasn1-4.12-1.fc27.i686 142/165 Verifying : libidn2-2.0.2-1.fc27.i686 143/165 Verifying : nettle-3.3-2.fc26.i686 144/165 Verifying : cyrus-sasl-lib-2.1.26-32.fc27.i686 145/165 Verifying : nspr-4.15.0-1.fc27.i686 146/165 Verifying : nss-3.31.0-2.fc27.i686 147/165 Verifying : nss-util-3.31.0-2.fc27.i686 148/165 Verifying : krb5-libs-1.15.1-14.fc27.i686 149/165 Verifying : libcom_err-1.43.4-2.fc26.i686 150/165 Verifying : nss-pem-1.0.3-3.fc27.i686 151/165 Verifying : nss-softokn-3.31.0-2.fc27.i686 152/165 Verifying : nss-sysinit-3.31.0-2.fc27.i686 153/165 Verifying : keyutils-libs-1.5.10-1.fc27.i686 154/165 Verifying : libverto-0.2.6-7.fc26.i686 155/165 Verifying : nss-softokn-freebl-3.31.0-2.fc27.i686 156/165 Verifying : libcrypt-nss-2.25.90-22.fc27.i686 157/165 Verifying : curl-7.54.1-2.fc27.i686 158/165 Verifying : libmetalink-0.1.3-2.fc26.i686 159/165 Verifying : glibc-all-langpacks-2.25.90-22.fc27.i686 160/165 Verifying : libcurl-7.54.1-2.fc27.i686 161/165 Verifying : libnghttp2-1.24.0-1.fc27.i686 162/165 Verifying : libpsl-0.17.0-2.fc26.i686 163/165 Verifying : libssh2-1.8.0-2.fc26.i686 164/165 Verifying : publicsuffix-list-dafsa-20170424-1.fc27.noarch 165/165 Installed: audit-libs.i686 2.7.7-1.fc27 basesystem.noarch 11-3.fc26 bash.i686 4.4.12-6.fc27 binutils.i686 2.28-9.fc27 bzip2.i686 1.0.6-22.fc26 bzip2-libs.i686 1.0.6-22.fc26 ca-certificates.noarch 2017.2.14-2.fc27 chkconfig.i686 1.10-1.fc27 coreutils.i686 8.27-10.fc27 coreutils-common.i686 8.27-10.fc27 cpio.i686 2.12-4.fc26 cpp.i686 7.1.1-5.fc27 cracklib.i686 2.9.6-5.fc26 crypto-policies.noarch 20170606-1.git7c32281.fc27 curl.i686 7.54.1-2.fc27 cyrus-sasl-lib.i686 2.1.26-32.fc27 diffutils.i686 3.6-1.fc27 dwz.i686 0.12-3.fc26 elfutils.i686 0.169-3.fc27 elfutils-default-yama-scope.noarch 0.169-3.fc27 elfutils-libelf.i686 0.169-3.fc27 elfutils-libs.i686 0.169-3.fc27 expat.i686 2.2.1-2.fc27 fedora-release.noarch 27-0.2 fedora-repos.noarch 27-0.2 fedora-repos-rawhide.noarch 27-0.2 fedora-rpm-macros.noarch 26-2.fc26 file.i686 5.31-1.fc27 file-libs.i686 5.31-1.fc27 filesystem.i686 3.3-1.fc27 findutils.i686 1:4.6.0-12.fc27 fpc-srpm-macros.noarch 1.1-2.fc26 gawk.i686 4.1.4-3.fc26 gc.i686 7.6.0-4.fc27 gcc.i686 7.1.1-5.fc27 gcc-c++.i686 7.1.1-5.fc27 gdb-headless.i686 8.0-17.fc27 gdbm.i686 1.13-1.fc27 ghc-srpm-macros.noarch 1.4.2-5.fc26 glib2.i686 2.53.3-1.fc27 glibc.i686 2.25.90-22.fc27 glibc-all-langpacks.i686 2.25.90-22.fc27 glibc-common.i686 2.25.90-22.fc27 glibc-devel.i686 2.25.90-22.fc27 glibc-headers.i686 2.25.90-22.fc27 gmp.i686 1:6.1.2-4.fc27 gnat-srpm-macros.noarch 4-2.fc26 gnupg2.i686 2.1.21-2.fc27 gnutls.i686 3.5.14-1.fc27 go-srpm-macros.noarch 2-9.fc27 grep.i686 3.1-1.fc27 guile.i686 5:2.0.14-1.fc26 gzip.i686 1.8-2.fc26 info.i686 6.4-2.fc27 isl.i686 0.16.1-1.fc26 kernel-headers.i686 4.13.0-0.rc0.git5.1.fc27 keyutils-libs.i686 1.5.10-1.fc27 krb5-libs.i686 1.15.1-14.fc27 libacl.i686 2.2.52-15.fc27 libarchive.i686 3.3.1-1.fc27 libasan.i686 7.1.1-5.fc27 libassuan.i686 2.4.3-2.fc26 libatomic.i686 7.1.1-5.fc27 libatomic_ops.i686 7.4.6-1.fc27 libattr.i686 2.4.47-18.fc26 libbabeltrace.i686 1.5.2-2.fc27 libblkid.i686 2.30-1.fc27 libcap.i686 2.25-5.fc26 libcap-ng.i686 0.7.8-3.fc26 libcilkrts.i686 7.1.1-5.fc27 libcom_err.i686 1.43.4-2.fc26 libcrypt-nss.i686 2.25.90-22.fc27 libcurl.i686 7.54.1-2.fc27 libdb.i686 5.3.28-24.fc27 libdb-utils.i686 5.3.28-24.fc27 libfdisk.i686 2.30-1.fc27 libffi.i686 3.1-12.fc27 libgcc.i686 7.1.1-5.fc27 libgcrypt.i686 1.7.8-1.fc27 libgomp.i686 7.1.1-5.fc27 libgpg-error.i686 1.27-1.fc27 libidn2.i686 2.0.2-1.fc27 libipt.i686 1.6.1-2.fc27 libksba.i686 1.3.5-3.fc26 libmetalink.i686 0.1.3-2.fc26 libmount.i686 2.30-1.fc27 libmpc.i686 1.0.2-6.fc26 libmpx.i686 7.1.1-5.fc27 libnghttp2.i686 1.24.0-1.fc27 libpkgconf.i686 1.3.7-1.fc27 libpsl.i686 0.17.0-2.fc26 libpwquality.i686 1.4.0-1.fc27 libselinux.i686 2.6-6.fc27 libsemanage.i686 2.6-4.fc27 libsepol.i686 2.6-1.fc26 libsigsegv.i686 2.11-1.fc26 libsmartcols.i686 2.30-1.fc27 libssh2.i686 1.8.0-2.fc26 libstdc++.i686 7.1.1-5.fc27 libstdc++-devel.i686 7.1.1-5.fc27 libtasn1.i686 4.12-1.fc27 libtool-ltdl.i686 2.4.6-18.fc27 libubsan.i686 7.1.1-5.fc27 libunistring.i686 0.9.7-1.fc26 libusbx.i686 1.0.21-2.fc26 libutempter.i686 1.1.6-9.fc26 libuuid.i686 2.30-1.fc27 libverto.i686 0.2.6-7.fc26 libxml2.i686 2.9.4-2.fc26 lua-libs.i686 5.3.4-3.fc27 lz4-libs.i686 1.7.5-4.fc27 make.i686 1:4.2.1-2.fc26 mpfr.i686 3.1.5-3.fc27 ncurses.i686 6.0-10.20170520.fc27 ncurses-base.noarch 6.0-10.20170520.fc27 ncurses-libs.i686 6.0-10.20170520.fc27 nettle.i686 3.3-2.fc26 npth.i686 1.5-1.fc27 nspr.i686 4.15.0-1.fc27 nss.i686 3.31.0-2.fc27 nss-pem.i686 1.0.3-3.fc27 nss-softokn.i686 3.31.0-2.fc27 nss-softokn-freebl.i686 3.31.0-2.fc27 nss-sysinit.i686 3.31.0-2.fc27 nss-util.i686 3.31.0-2.fc27 ocaml-srpm-macros.noarch 4-2.fc26 openblas-srpm-macros.noarch 2-1.fc27 openldap.i686 2.4.45-1.fc27 openssl-libs.i686 1:1.1.0f-5.fc27 p11-kit.i686 0.23.7-1.fc27 p11-kit-trust.i686 0.23.7-1.fc27 pam.i686 1.3.0-3.fc27 patch.i686 2.7.5-4.fc26 pcre.i686 8.41-1.fc27 perl-srpm-macros.noarch 1-23.fc27 pkgconf.i686 1.3.7-1.fc27 pkgconf-m4.noarch 1.3.7-1.fc27 pkgconf-pkg-config.i686 1.3.7-1.fc27 popt.i686 1.16-8.fc26 publicsuffix-list-dafsa.noarch 20170424-1.fc27 python-srpm-macros.noarch 3-20.fc27 qt5-srpm-macros.noarch 5.9.0-2.fc27 readline.i686 7.0-5.fc26 redhat-rpm-config.noarch 64-1.fc27 rpm.i686 4.13.0.1-31.fc27 rpm-build.i686 4.13.0.1-31.fc27 rpm-build-libs.i686 4.13.0.1-31.fc27 rpm-libs.i686 4.13.0.1-31.fc27 rpm-plugin-selinux.i686 4.13.0.1-31.fc27 sed.i686 4.4-1.fc26 setup.noarch 2.10.5-2.fc26 shadow-utils.i686 2:4.3.1-3.fc26 sqlite-libs.i686 3.19.3-1.fc27 system-python-libs.i686 3.6.1-10.fc27 systemd-libs.i686 233-6.fc27 tar.i686 2:1.29-4.fc26 tzdata.noarch 2017b-1.fc27 unzip.i686 6.0-33.fc26 ustr.i686 1.0.4-22.fc26 util-linux.i686 2.30-1.fc27 which.i686 2.21-2.fc26 xz.i686 5.2.3-2.fc26 xz-libs.i686 5.2.3-2.fc26 zip.i686 3.0-18.fc26 zlib.i686 1.2.11-2.fc26 Complete! Finish: dnf install Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: Start: buildsrpm Start: rpmbuild -bs Building target platforms: i686 Building for target i686 Wrote: /builddir/build/SRPMS/coot-0.8.8-2.fc27.src.rpm Finish: rpmbuild -bs Finish: buildsrpm INFO: Done(coot.spec) Config(child) 1 minutes 5 seconds INFO: Results and/or logs in: intermediate-srpm Finish: run INFO: unmounting tmpfs. WARNING: Could not find required logging config file: /var/lib/copr-rpmbuild/results/configs/logging.ini. Using default... INFO: mock.py version 1.4.2 starting (python version = 3.6.1)... Start: init plugins INFO: tmpfs initialized INFO: selinux disabled INFO: compress_logs: initialized Finish: init plugins Start: run INFO: Start(intermediate-srpm/coot-0.8.8-2.fc27.src.rpm) Config(579072-fedora-rawhide-i386) Start: chroot init INFO: mounting tmpfs at /var/lib/mock/579072-fedora-rawhide-i386/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled HW Info plugin Mock Version: 1.4.2 INFO: Mock Version: 1.4.2 Finish: chroot init Start: build phase for coot-0.8.8-2.fc27.src.rpm Start: build setup for coot-0.8.8-2.fc27.src.rpm Building target platforms: i686 Building for target i686 Wrote: /builddir/build/SRPMS/coot-0.8.8-2.fc27.src.rpm "Copr repository" 0% [ ] --- B/s | 0 B --:-- ETA "Copr repository" 453 kB/s | 23 kB 00:00 fedora 0% [ ] --- B/s | 0 B --:-- ETA fedora 25% [===== ] 43 MB/s | 13 MB 00:00 ETA fedora 51% [========== ] 43 MB/s | 26 MB 00:00 ETA fedora 83% [================- ] 44 MB/s | 42 MB 00:00 ETA fedora 40 MB/s | 50 MB 00:01 Last metadata expiration check: 0:00:00 ago on Thu 13 Jul 2017 08:09:35 PM UTC. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: autoconf noarch 2.69-24.fc26 fedora 709 k automake noarch 1.15-9.fc26 fedora 695 k clipper-devel i686 2.1-20160709.1.fc26 fedora 235 k compat-guile18-devel i686 1.8.8-16.fc26 fedora 110 k desktop-file-utils i686 0.23-3.fc26 fedora 74 k doxygen i686 1:1.8.13-9.fc27 fedora 6.7 M freeglut-devel i686 3.0.0-4.fc26 fedora 119 k ghostscript i686 9.20-10.fc27 fedora 46 k goocanvas-devel i686 1.0.0-12.fc26 fedora 115 k gsl-devel i686 2.4-1.fc27 copr_base 563 k gtk2-devel i686 2.24.31-4.fc27 fedora 3.0 M gtkglext-devel i686 1.2.0-28.fc26 fedora 135 k guile-lib i686 0.2.4-2.fc26 fedora 235 k imlib-devel i686 1:1.9.15-29.fc26 fedora 114 k libappstream-glib i686 0.7.0-1.fc27 fedora 309 k libcurl-devel i686 7.54.1-2.fc27 fedora 739 k libgnomecanvas-devel i686 2.30.3-12.fc26 fedora 75 k libtool i686 2.4.6-18.fc27 fedora 706 k mmdb2-devel i686 2.0.1-7.fc26 fedora 107 k pygtk2-devel i686 2.24.0-16.fc26 fedora 150 k python2-devel i686 2.7.13-12.fc27 fedora 408 k python2-rdkit i686 2016.09.4-2.fc26 fedora 3.1 M rdkit-devel i686 2016.09.4-2.fc26 fedora 280 k refmac-dictionary noarch 5.41-6.fc26 fedora 21 M ssm-devel i686 1.4-5.fc26 fedora 23 k swig i686 3.0.12-8.fc27 fedora 1.5 M texinfo-tex i686 6.4-2.fc27 fedora 158 k texlive-collection-latexrecommended noarch 6:svn35765.0-35.20160520.fc27.1 fedora 33 k Installing dependencies: aajohan-comfortaa-fonts noarch 2.004-7.fc26 fedora 150 k acl i686 2.2.52-15.fc27 fedora 78 k atk i686 2.25.2-1.fc27 fedora 269 k atk-devel i686 2.25.2-1.fc27 fedora 189 k atlas i686 3.10.2-16.fc26 fedora 5.9 M avahi-libs i686 0.7-1.fc27 fedora 61 k boost i686 1.63.0-9.fc27 fedora 47 k boost-atomic i686 1.63.0-9.fc27 fedora 49 k boost-chrono i686 1.63.0-9.fc27 fedora 53 k boost-container i686 1.63.0-9.fc27 fedora 80 k boost-context i686 1.63.0-9.fc27 fedora 51 k boost-coroutine i686 1.63.0-9.fc27 fedora 64 k boost-date-time i686 1.63.0-9.fc27 fedora 63 k boost-devel i686 1.63.0-9.fc27 fedora 9.2 M boost-fiber i686 1.63.0-9.fc27 fedora 77 k boost-filesystem i686 1.63.0-9.fc27 fedora 82 k boost-graph i686 1.63.0-9.fc27 fedora 146 k boost-iostreams i686 1.63.0-9.fc27 fedora 74 k boost-locale i686 1.63.0-9.fc27 fedora 304 k boost-log i686 1.63.0-9.fc27 fedora 483 k boost-math i686 1.63.0-9.fc27 fedora 269 k boost-numpy i686 1.63.0-9.fc27 fedora 61 k boost-program-options i686 1.63.0-9.fc27 fedora 177 k boost-python i686 1.63.0-9.fc27 fedora 133 k boost-python3 i686 1.63.0-9.fc27 fedora 131 k boost-random i686 1.63.0-9.fc27 fedora 55 k boost-regex i686 1.63.0-9.fc27 fedora 324 k boost-serialization i686 1.63.0-9.fc27 fedora 165 k boost-signals i686 1.63.0-9.fc27 fedora 77 k boost-system i686 1.63.0-9.fc27 fedora 52 k boost-test i686 1.63.0-9.fc27 fedora 286 k boost-thread i686 1.63.0-9.fc27 fedora 94 k 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326 k texlive-palatino noarch 6:svn31835.0-35.fc27.1 fedora 403 k texlive-paralist noarch 6:svn39247-35.fc27.1 fedora 36 k texlive-parallel noarch 6:svn15878.0-35.fc27.1 fedora 36 k texlive-parskip noarch 6:svn19963.2.0-35.fc27.1 fedora 34 k texlive-pdfpages noarch 6:svn40638-35.fc27.1 fedora 48 k texlive-pdftex noarch 6:svn41149-35.fc27.1 fedora 74 k texlive-pdftex-bin i686 6:svn40987-35.20160520.fc27.1 fedora 392 k texlive-pdftex-def noarch 6:svn22653.0.06d-35.fc27.1 fedora 46 k texlive-pdftex-doc noarch 6:svn41149-35.fc27.1 fedora 1.5 M texlive-pgf noarch 6:svn40966-35.fc27.1 fedora 823 k texlive-plain noarch 6:svn40274-35.fc27.1 fedora 494 k texlive-powerdot noarch 6:svn38984-35.fc27.1 fedora 63 k texlive-psfrag noarch 6:svn15878.3.04-35.fc27.1 fedora 37 k texlive-pslatex noarch 6:svn16416.0-35.fc27.1 fedora 40 k texlive-psnfss noarch 6:svn33946.9.2a-35.fc27.1 fedora 61 k texlive-pspicture noarch 6:svn15878.0-35.fc27.1 fedora 34 k texlive-pst-3d noarch 6:svn17257.1.10-35.fc27.1 fedora 36 k texlive-pst-blur noarch 6:svn15878.2.0-35.fc27.1 fedora 35 k texlive-pst-coil noarch 6:svn37377.1.07-35.fc27.1 fedora 37 k texlive-pst-eps noarch 6:svn15878.1.0-35.fc27.1 fedora 36 k texlive-pst-fill noarch 6:svn15878.1.01-35.fc27.1 fedora 37 k texlive-pst-grad noarch 6:svn15878.1.06-35.fc27.1 fedora 37 k texlive-pst-math noarch 6:svn34786.0.63-35.fc27.1 fedora 38 k texlive-pst-node noarch 6:svn40743-35.fc27.1 fedora 60 k texlive-pst-ovl noarch 6:svn40873-35.fc27.1 fedora 35 k texlive-pst-pdf noarch 6:svn31660.1.1v-35.fc27.1 fedora 41 k texlive-pst-pdf-bin noarch 6:svn7838.0-35.20160520.fc27.1 fedora 33 k texlive-pst-plot noarch 6:svn41242-35.fc27.1 fedora 56 k texlive-pst-slpe noarch 6:svn24391.1.31-35.fc27.1 fedora 36 k texlive-pst-text noarch 6:svn15878.1.00-35.fc27.1 fedora 37 k texlive-pst-tools noarch 6:svn34067.0.05-35.fc27.1 fedora 38 k texlive-pst-tree noarch 6:svn24142.1.12-35.fc27.1 fedora 40 k texlive-pstricks noarch 6:svn41321-35.fc27.1 fedora 116 k texlive-pstricks-add noarch 6:svn40744-35.fc27.1 fedora 58 k texlive-pxfonts noarch 6:svn15878.0-35.fc27.1 fedora 514 k texlive-qstest noarch 6:svn15878.0-35.fc27.1 fedora 38 k texlive-rcs noarch 6:svn15878.0-35.fc27.1 fedora 46 k texlive-rotating noarch 6:svn16832.2.16b-35.fc27.1 fedora 35 k texlive-rsfs noarch 6:svn15878.0-35.fc27.1 fedora 91 k texlive-sansmath noarch 6:svn17997.1.1-35.fc27.1 fedora 36 k texlive-sansmathaccent noarch 6:svn30187.0-35.fc27.1 fedora 47 k texlive-sauerj noarch 6:svn15878.0-35.fc27.1 fedora 38 k texlive-section noarch 6:svn20180.0-35.fc27.1 fedora 42 k texlive-seminar noarch 6:svn34011.1.62-35.fc27.1 fedora 66 k texlive-sepnum noarch 6:svn20186.2.0-35.fc27.1 fedora 35 k texlive-setspace noarch 6:svn24881.6.7a-35.fc27.1 fedora 40 k texlive-showexpl noarch 6:svn32737.v0.3l-35.fc27.1 fedora 37 k texlive-soul noarch 6:svn15878.2.4-35.fc27.1 fedora 39 k texlive-subfig noarch 6:svn15878.1.3-35.fc27.1 fedora 40 k texlive-symbol noarch 6:svn31835.0-35.fc27.1 fedora 71 k texlive-tetex noarch 6:svn41059-35.fc27.1 fedora 119 k texlive-tetex-bin noarch 6:svn36770.0-35.20160520.fc27.1 fedora 34 k texlive-tex noarch 6:svn40793-35.fc27.1 fedora 39 k texlive-tex-bin i686 6:svn40987-35.20160520.fc27.1 fedora 194 k texlive-tex-gyre noarch 6:svn18651.2.004-35.fc27.1 fedora 7.0 M texlive-tex-gyre-math noarch 6:svn41264-35.fc27.1 fedora 1.4 M texlive-tex-ini-files noarch 6:svn40533-35.fc27.1 fedora 37 k texlive-texconfig noarch 6:svn40768-35.fc27.1 fedora 48 k texlive-texconfig-bin noarch 6:svn29741.0-35.20160520.fc27.1 fedora 33 k texlive-texlive-common-doc noarch 6:svn40682-35.fc27.1 fedora 231 k texlive-texlive-docindex noarch 6:svn41430-35.fc27.1 fedora 165 k texlive-texlive-en noarch 6:svn41185-35.fc27.1 fedora 89 k texlive-texlive-msg-translations noarch 6:svn41431-35.fc27.1 fedora 158 k texlive-texlive-scripts noarch 6:svn41433-35.fc27.1 fedora 49 k texlive-texlive-scripts-bin noarch 6:svn29741.0-35.20160520.fc27.1 fedora 33 k texlive-texlive.infra noarch 6:svn41280-35.fc27.1 fedora 165 k texlive-texlive.infra-bin i686 6:svn40312-35.20160520.fc27.1 fedora 32 k texlive-textcase noarch 6:svn15878.0-35.fc27.1 fedora 34 k texlive-thumbpdf noarch 6:svn34621.3.16-35.fc27.1 fedora 54 k texlive-thumbpdf-bin noarch 6:svn6898.0-35.20160520.fc27.1 fedora 33 k texlive-times noarch 6:svn35058.0-35.fc27.1 fedora 357 k texlive-tipa noarch 6:svn29349.1.3-35.fc27.1 fedora 2.8 M texlive-tools noarch 6:svn40934-35.fc27.1 fedora 79 k texlive-trimspaces noarch 6:svn15878.1.1-35.fc27.1 fedora 33 k texlive-txfonts noarch 6:svn15878.0-35.fc27.1 fedora 787 k texlive-type1cm noarch 6:svn21820.0-35.fc27.1 fedora 35 k texlive-typehtml noarch 6:svn17134.0-35.fc27.1 fedora 39 k texlive-ucharcat noarch 6:svn38907-35.fc27.1 fedora 34 k texlive-ucs noarch 6:svn35853.2.2-35.fc27.1 fedora 377 k texlive-underscore noarch 6:svn18261.0-35.fc27.1 fedora 37 k texlive-unicode-data noarch 6:svn39808-35.fc27.1 fedora 284 k texlive-unicode-math noarch 6:svn38462-35.fc27.1 fedora 77 k texlive-updmap-map noarch 6:svn41159-35.fc27.1 fedora 200 k texlive-url noarch 6:svn32528.3.4-35.fc27.1 fedora 38 k texlive-utopia noarch 6:svn15878.0-35.fc27.1 fedora 249 k texlive-varwidth noarch 6:svn24104.0.92-35.fc27.1 fedora 37 k texlive-wasy noarch 6:svn35831.0-35.fc27.1 fedora 58 k texlive-wasy2-ps noarch 6:svn35830.0-35.fc27.1 fedora 247 k texlive-wasysym noarch 6:svn15878.2.0-35.fc27.1 fedora 36 k texlive-xcolor noarch 6:svn41044-35.fc27.1 fedora 51 k texlive-xdvi noarch 6:svn40768-35.fc27.1 fedora 77 k texlive-xdvi-bin i686 6:svn40750-35.20160520.fc27.1 fedora 319 k texlive-xetex noarch 6:svn41438-35.fc27.1 fedora 382 k texlive-xetex-bin i686 6:svn41091-35.20160520.fc27.1 fedora 631 k texlive-xetex-def noarch 6:svn40327-35.fc27.1 fedora 39 k texlive-xetexconfig noarch 6:svn41133-35.fc27.1 fedora 33 k texlive-xkeyval noarch 6:svn35741.2.7a-35.fc27.1 fedora 49 k texlive-xunicode noarch 6:svn30466.0.981-35.fc27.1 fedora 60 k texlive-zapfchan noarch 6:svn31835.0-35.fc27.1 fedora 119 k texlive-zapfding noarch 6:svn31835.0-35.fc27.1 fedora 81 k ttmkfdir i686 3.0.9-49.fc26 fedora 57 k urw-fonts noarch 3:2.4-23.fc26 fedora 3.0 M xapian-core-libs i686 1.4.4-1.fc27 fedora 784 k xml-common noarch 0.6.3-45.fc26 fedora 30 k xorg-x11-font-utils i686 1:7.5-33.fc26 fedora 81 k xorg-x11-fonts-Type1 noarch 7.5-17.fc26 fedora 521 k xorg-x11-proto-devel noarch 7.7-22.fc27 fedora 287 k zlib-devel i686 1.2.11-2.fc26 fedora 56 k zziplib i686 0.13.62-8.fc26 fedora 86 k Transaction Summary ================================================================================ Install 582 Packages Total download size: 297 M Installed size: 1.0 G Downloading Packages: (1/582): autoconf-2. 0% [ ] --- B/s | 0 B --:-- ETA (1/582): clipper-devel-2.1-20160709.1.fc26.i686 2.8 MB/s | 235 kB 00:00 (2-3/582): autoconf- 0% [ ] 7.5 MB/s | 647 kB 00:39 ETA (2/582): automake-1.15-9.fc26.noarch.rpm 6.7 MB/s | 695 kB 00:00 (3-4/582): autoconf- 0% [ ] 7.6 MB/s | 1.2 MB 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[================ ] 270/582 Installing : texlive-amsfonts-6:svn2 [================= ] 270/582 Installing : texlive-amsfonts-6:svn2 [================== ] 270/582 Installing : texlive-amsfonts-6:svn2 [=================== ] 270/582 Installing : texlive-amsfonts-6:svn2 [==================== ] 270/582 Installing : texlive-amsfonts-6:svn2 [===================== ] 270/582 Installing : texlive-amsfonts-6:svn2 [====================== ] 270/582 Installing : texlive-amsfonts-6:svn2 [======================= ] 270/582 Installing : texlive-amsfonts-6:svn29208.3.04-35.fc27.1.noarc 270/582 Installing : texlive-ifluatex-6:svn4 [ ] 271/582 Installing : texlive-ifluatex-6:svn4 [======================= ] 271/582 Installing : texlive-ifluatex-6:svn41346-35.fc27.1.noarch 271/582 Installing : texlive-booktabs-6:svn4 [ ] 272/582 Installing : texlive-booktabs-6:svn4 [= ] 272/582 Installing : texlive-booktabs-6:svn4 [======================= ] 272/582 Installing : texlive-booktabs-6:svn40846-35.fc27.1.noarch 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texlive-mptopdf-bin-6:s [=================== ] 299/582 Installing : texlive-mptopdf-bin-6:svn18674.0-35.20160520.fc2 299/582 Installing : texlive-mptopdf-6:svn41 [ ] 300/582 Installing : texlive-mptopdf-6:svn41 [==== ] 300/582 Installing : texlive-mptopdf-6:svn41 [========= ] 300/582 Installing : texlive-mptopdf-6:svn41 [========== ] 300/582 Installing : texlive-mptopdf-6:svn41 [=============== ] 300/582 Installing : texlive-mptopdf-6:svn41 [==================== ] 300/582 Installing : texlive-mptopdf-6:svn41 [===================== ] 300/582 Installing : texlive-mptopdf-6:svn41 [======================= ] 300/582 Installing : texlive-mptopdf-6:svn41282-35.fc27.1.noarch 300/582 Running scriptlet: texlive-mptopdf-6:svn41282-35.fc27.1.noarch 300/582 Installing : texlive-euler-6:svn1726 [ ] 301/582 Installing : texlive-euler-6:svn1726 [======================= ] 301/582 Installing : texlive-euler-6:svn17261.2.5-35.fc27.1.noarch 301/582 Installing : texlive-fancybox-6:svn1 [ ] 302/582 Installing : texlive-fancybox-6:svn1 [======================= ] 302/582 Installing : texlive-fancybox-6:svn18304.1.4-35.fc27.1.noarch 302/582 Installing : texlive-float-6:svn1587 [ ] 303/582 Installing : texlive-float-6:svn1587 [= ] 303/582 Installing : texlive-float-6:svn1587 [======================= ] 303/582 Installing : texlive-float-6:svn15878.1.3d-35.fc27.1.noarch 303/582 Installing : texlive-index-6:svn2409 [ ] 304/582 Installing : texlive-index-6:svn2409 [======== ] 304/582 Installing : texlive-index-6:svn2409 [================ ] 304/582 Installing : texlive-index-6:svn2409 [================== ] 304/582 Installing : texlive-index-6:svn2409 [=================== ] 304/582 Installing : texlive-index-6:svn2409 [======================= ] 304/582 Installing : texlive-index-6:svn24099.4.1beta-35.fc27.1.noarc 304/582 Installing : texlive-setspace-6:svn2 [ ] 305/582 Installing : texlive-setspace-6:svn2 [======================= ] 305/582 Installing : texlive-setspace-6:svn24881.6.7a-35.fc27.1.noarc 305/582 Installing : texlive-underscore-6:sv [ ] 306/582 Installing : texlive-underscore-6:sv [======================= ] 306/582 Installing : texlive-underscore-6:svn18261.0-35.fc27.1.noarch 306/582 Installing : texlive-wasy-6:svn35831 [ ] 307/582 Installing : texlive-wasy-6:svn35831 [== ] 307/582 Installing : texlive-wasy-6:svn35831 [======== ] 307/582 Installing : texlive-wasy-6:svn35831 [============= ] 307/582 Installing : texlive-wasy-6:svn35831 [============== ] 307/582 Installing : texlive-wasy-6:svn35831 [=============== ] 307/582 Installing : texlive-wasy-6:svn35831 [================ ] 307/582 Installing : texlive-wasy-6:svn35831 [================= ] 307/582 Installing : texlive-wasy-6:svn35831 [================== ] 307/582 Installing : texlive-wasy-6:svn35831 [=================== ] 307/582 Installing : texlive-wasy-6:svn35831 [===================== ] 307/582 Installing : texlive-wasy-6:svn35831 [====================== ] 307/582 Installing : texlive-wasy-6:svn35831 [======================= ] 307/582 Installing : texlive-wasy-6:svn35831.0-35.fc27.1.noarch 307/582 Installing : texlive-latexconfig-6:s [ ] 308/582 Installing : texlive-latexconfig-6:s [= ] 308/582 Installing : texlive-latexconfig-6:s [== ] 308/582 Installing : texlive-latexconfig-6:s [==== ] 308/582 Installing : texlive-latexconfig-6:s [===== ] 308/582 Installing : texlive-latexconfig-6:s [======== ] 308/582 Installing : texlive-latexconfig-6:s [=============== ] 308/582 Installing : texlive-latexconfig-6:s [================= ] 308/582 Installing : texlive-latexconfig-6:s [====================== ] 308/582 Installing : texlive-latexconfig-6:s [======================= ] 308/582 Installing : texlive-latexconfig-6:svn40274-35.fc27.1.noarch 308/582 Installing : texlive-natbib-6:svn206 [ ] 309/582 Installing : texlive-natbib-6:svn206 [===== ] 309/582 Installing : texlive-natbib-6:svn206 [========== ] 309/582 Installing : texlive-natbib-6:svn206 [============== ] 309/582 Installing : texlive-natbib-6:svn206 [=============== ] 309/582 Installing : texlive-natbib-6:svn206 [===================== ] 309/582 Installing : texlive-natbib-6:svn206 [======================= ] 309/582 Installing : texlive-natbib-6:svn20668.8.31b-35.fc27.1.noarch 309/582 Installing : texlive-pdftex-def-6:sv [ ] 310/582 Installing : texlive-pdftex-def-6:sv [============== ] 310/582 Installing : texlive-pdftex-def-6:sv [======================= ] 310/582 Installing : texlive-pdftex-def-6:svn22653.0.06d-35.fc27.1.no 310/582 Installing : texlive-enumitem-6:svn2 [ ] 311/582 Installing : texlive-enumitem-6:svn2 [================== ] 311/582 Installing : texlive-enumitem-6:svn2 [======================= ] 311/582 Installing : texlive-enumitem-6:svn24146.3.5.2-35.fc27.1.noar 311/582 Installing : texlive-footmisc-6:svn2 [ ] 312/582 Installing : texlive-footmisc-6:svn2 [======================= ] 312/582 Installing : texlive-footmisc-6:svn23330.5.5b-35.fc27.1.noarc 312/582 Installing : texlive-pst-ovl-6:svn40 [ ] 313/582 Installing : texlive-pst-ovl-6:svn40 [= ] 313/582 Installing : texlive-pst-ovl-6:svn40 [== ] 313/582 Installing : texlive-pst-ovl-6:svn40 [====== ] 313/582 Installing : texlive-pst-ovl-6:svn40 [======= ] 313/582 Installing : texlive-pst-ovl-6:svn40 [=================== ] 313/582 Installing : texlive-pst-ovl-6:svn40 [======================= ] 313/582 Installing : texlive-pst-ovl-6:svn40873-35.fc27.1.noarch 313/582 Installing : texlive-bibtex-bin-6:sv [ ] 314/582 Installing : texlive-bibtex-bin-6:sv [====== ] 314/582 Installing : texlive-bibtex-bin-6:sv [============ ] 314/582 Installing : texlive-bibtex-bin-6:sv [================== ] 314/582 Installing : texlive-bibtex-bin-6:sv [======================= ] 314/582 Installing : texlive-bibtex-bin-6:svn40473-35.20160520.fc27.1 314/582 Installing : texlive-bibtex-6:svn407 [ ] 315/582 Installing : texlive-bibtex-6:svn407 [= ] 315/582 Installing : texlive-bibtex-6:svn407 [==== ] 315/582 Installing : texlive-bibtex-6:svn407 [======= ] 315/582 Installing : texlive-bibtex-6:svn407 [========== ] 315/582 Installing : texlive-bibtex-6:svn407 [============= ] 315/582 Installing : texlive-bibtex-6:svn407 [================ ] 315/582 Installing : texlive-bibtex-6:svn407 [================== ] 315/582 Installing : texlive-bibtex-6:svn407 [===================== ] 315/582 Installing : texlive-bibtex-6:svn407 [======================= ] 315/582 Installing : texlive-bibtex-6:svn40768-35.fc27.1.noarch 315/582 Installing : texlive-dvipdfmx-def-6: [ ] 316/582 Installing : texlive-dvipdfmx-def-6: [======================= ] 316/582 Installing : texlive-dvipdfmx-def-6:svn40328-35.fc27.1.noarch 316/582 Installing : texlive-glyphlist-6:svn [ ] 317/582 Installing : texlive-glyphlist-6:svn [======== ] 317/582 Installing : texlive-glyphlist-6:svn [================ ] 317/582 Installing : texlive-glyphlist-6:svn [=================== ] 317/582 Installing : texlive-glyphlist-6:svn [===================== ] 317/582 Installing : texlive-glyphlist-6:svn [======================= ] 317/582 Installing : texlive-glyphlist-6:svn28576.0-35.fc27.1.noarch 317/582 Installing : texlive-gsftopk-bin-6:s [ ] 318/582 Installing : texlive-gsftopk-bin-6:s [======================= ] 318/582 Installing : texlive-gsftopk-bin-6:svn40473-35.20160520.fc27. 318/582 Installing : texlive-gsftopk-6:svn40 [ ] 319/582 Installing : texlive-gsftopk-6:svn40 [======= ] 319/582 Installing : texlive-gsftopk-6:svn40 [======================= ] 319/582 Installing : texlive-gsftopk-6:svn40768-35.fc27.1.noarch 319/582 Installing : texlive-lua-alt-getopt- [ ] 320/582 Installing : texlive-lua-alt-getopt- [======================= ] 320/582 Installing : texlive-lua-alt-getopt-6:svn29349.0.7.0-35.fc27. 320/582 Installing : texlive-makeindex-bin-6 [ ] 321/582 Installing : texlive-makeindex-bin-6 [========= ] 321/582 Installing : texlive-makeindex-bin-6 [=================== ] 321/582 Installing : texlive-makeindex-bin-6 [======================= ] 321/582 Installing : texlive-makeindex-bin-6:svn40473-35.20160520.fc2 321/582 Installing : texlive-makeindex-6:svn [ ] 322/582 Installing : texlive-makeindex-6:svn [== ] 322/582 Installing : texlive-makeindex-6:svn [=== ] 322/582 Installing : texlive-makeindex-6:svn [==== ] 322/582 Installing : texlive-makeindex-6:svn [===== ] 322/582 Installing : texlive-makeindex-6:svn [====== ] 322/582 Installing : texlive-makeindex-6:svn [======= ] 322/582 Installing : texlive-makeindex-6:svn [======== ] 322/582 Installing : texlive-makeindex-6:svn [========= ] 322/582 Installing : texlive-makeindex-6:svn [========== ] 322/582 Installing : texlive-makeindex-6:svn [=========== ] 322/582 Installing : texlive-makeindex-6:svn [============ ] 322/582 Installing : texlive-makeindex-6:svn [============= ] 322/582 Installing : texlive-makeindex-6:svn [============== ] 322/582 Installing : texlive-makeindex-6:svn [================ ] 322/582 Installing : texlive-makeindex-6:svn [================= ] 322/582 Installing : texlive-makeindex-6:svn [================== ] 322/582 Installing : texlive-makeindex-6:svn [=================== ] 322/582 Installing : texlive-makeindex-6:svn [==================== ] 322/582 Installing : texlive-makeindex-6:svn [===================== ] 322/582 Installing : texlive-makeindex-6:svn [======================= ] 322/582 Installing : texlive-makeindex-6:svn40768-35.fc27.1.noarch 322/582 Installing : texlive-mfware-bin-6:sv [ ] 323/582 Installing : texlive-mfware-bin-6:sv [==== ] 323/582 Installing : texlive-mfware-bin-6:sv [====== ] 323/582 Installing : texlive-mfware-bin-6:sv [========= ] 323/582 Installing : texlive-mfware-bin-6:sv [============ ] 323/582 Installing : texlive-mfware-bin-6:sv [================= ] 323/582 Installing : texlive-mfware-bin-6:sv [================== ] 323/582 Installing : texlive-mfware-bin-6:sv [===================== ] 323/582 Installing : texlive-mfware-bin-6:sv [======================= ] 323/582 Installing : texlive-mfware-bin-6:svn40473-35.20160520.fc27.1 323/582 Installing : texlive-mfware-6:svn407 [ ] 324/582 Installing : texlive-mfware-6:svn407 [== ] 324/582 Installing : texlive-mfware-6:svn407 [==== ] 324/582 Installing : texlive-mfware-6:svn407 [===== ] 324/582 Installing : texlive-mfware-6:svn407 [======= ] 324/582 Installing : texlive-mfware-6:svn407 [======== ] 324/582 Installing : texlive-mfware-6:svn407 [========= ] 324/582 Installing : texlive-mfware-6:svn407 [========== ] 324/582 Installing : texlive-mfware-6:svn407 [============== ] 324/582 Installing : texlive-mfware-6:svn407 [=================== ] 324/582 Installing : texlive-mfware-6:svn407 [===================== ] 324/582 Installing : texlive-mfware-6:svn407 [======================= ] 324/582 Installing : texlive-mfware-6:svn40768-35.fc27.1.noarch 324/582 Installing : texlive-plain-6:svn4027 [ ] 325/582 Installing : texlive-plain-6:svn4027 [= ] 325/582 Installing : 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: texlive-plain-6:svn4027 [=================== ] 325/582 Installing : texlive-plain-6:svn4027 [==================== ] 325/582 Installing : texlive-plain-6:svn4027 [===================== ] 325/582 Installing : texlive-plain-6:svn4027 [====================== ] 325/582 Installing : texlive-plain-6:svn4027 [======================= ] 325/582 Installing : texlive-plain-6:svn40274-35.fc27.1.noarch 325/582 Installing : texlive-tex-bin-6:svn40 [ ] 326/582 Installing : texlive-tex-bin-6:svn40 [== ] 326/582 Installing : texlive-tex-bin-6:svn40 [==== ] 326/582 Installing : texlive-tex-bin-6:svn40 [====== ] 326/582 Installing : texlive-tex-bin-6:svn40 [======== ] 326/582 Installing : texlive-tex-bin-6:svn40 [========== ] 326/582 Installing : texlive-tex-bin-6:svn40 [============ ] 326/582 Installing : texlive-tex-bin-6:svn40 [=============== ] 326/582 Installing : texlive-tex-bin-6:svn40 [================= ] 326/582 Installing : texlive-tex-bin-6:svn40 [=================== ] 326/582 Installing : texlive-tex-bin-6:svn40 [===================== ] 326/582 Installing : texlive-tex-bin-6:svn40 [======================= ] 326/582 Installing : texlive-tex-bin-6:svn40987-35.20160520.fc27.1.i6 326/582 Installing : texlive-tex-6:svn40793- [ ] 327/582 Installing : texlive-tex-6:svn40793- [= ] 327/582 Installing : texlive-tex-6:svn40793- [======================= ] 327/582 Installing : texlive-tex-6:svn40793-35.fc27.1.noarch 327/582 Running scriptlet: texlive-tex-6:svn40793-35.fc27.1.noarch 327/582 Installing : texlive-tex-ini-files-6 [ ] 328/582 Installing : texlive-tex-ini-files-6 [= ] 328/582 Installing : texlive-tex-ini-files-6 [== ] 328/582 Installing : texlive-tex-ini-files-6 [==== ] 328/582 Installing : texlive-tex-ini-files-6 [===== ] 328/582 Installing : texlive-tex-ini-files-6 [=========== ] 328/582 Installing : texlive-tex-ini-files-6 [============ ] 328/582 Installing : texlive-tex-ini-files-6 [============== ] 328/582 Installing : texlive-tex-ini-files-6 [======================= ] 328/582 Installing : texlive-tex-ini-files-6:svn40533-35.fc27.1.noarc 328/582 Installing : texlive-texconfig-bin-6 [ ] 329/582 Installing : texlive-texconfig-bin-6 [====== ] 329/582 Installing : texlive-texconfig-bin-6 [============ ] 329/582 Installing : texlive-texconfig-bin-6 [=================== ] 329/582 Installing : texlive-texconfig-bin-6:svn29741.0-35.20160520.f 329/582 Installing : texlive-texconfig-6:svn [ ] 330/582 Installing : texlive-texconfig-6:svn [============= ] 330/582 Installing : texlive-texconfig-6:svn [================== ] 330/582 Installing : texlive-texconfig-6:svn [====================== ] 330/582 Installing : texlive-texconfig-6:svn [======================= ] 330/582 Installing : texlive-texconfig-6:svn40768-35.fc27.1.noarch 330/582 Installing : texlive-xdvi-bin-6:svn4 [ ] 331/582 Installing : texlive-xdvi-bin-6:svn4 [== ] 331/582 Installing : texlive-xdvi-bin-6:svn4 [=== ] 331/582 Installing : texlive-xdvi-bin-6:svn4 [==== ] 331/582 Installing : 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texlive-xdvi-bin-6:svn4 [====================== ] 331/582 Installing : texlive-xdvi-bin-6:svn4 [======================= ] 331/582 Installing : texlive-xdvi-bin-6:svn40750-35.20160520.fc27.1.i 331/582 Installing : texlive-xdvi-6:svn40768 [ ] 332/582 Installing : texlive-xdvi-6:svn40768 [=========== ] 332/582 Installing : texlive-xdvi-6:svn40768 [============ ] 332/582 Installing : texlive-xdvi-6:svn40768 [============= ] 332/582 Installing : texlive-xdvi-6:svn40768 [================== ] 332/582 Installing : texlive-xdvi-6:svn40768 [==================== ] 332/582 Installing : texlive-xdvi-6:svn40768 [======================= ] 332/582 Installing : texlive-xdvi-6:svn40768-35.fc27.1.noarch 332/582 Installing : texlive-wasy2-ps-6:svn3 [ ] 333/582 Installing : texlive-wasy2-ps-6:svn3 [= ] 333/582 Installing : texlive-wasy2-ps-6:svn3 [== ] 333/582 Installing : texlive-wasy2-ps-6:svn3 [=== ] 333/582 Installing : texlive-wasy2-ps-6:svn3 [====== ] 333/582 Installing : texlive-wasy2-ps-6:svn3 [========= ] 333/582 Installing : texlive-wasy2-ps-6:svn3 [============ ] 333/582 Installing : texlive-wasy2-ps-6:svn3 [=============== ] 333/582 Installing : texlive-wasy2-ps-6:svn3 [================== ] 333/582 Installing : texlive-wasy2-ps-6:svn3 [==================== ] 333/582 Installing : texlive-wasy2-ps-6:svn3 [======================= ] 333/582 Installing : texlive-wasy2-ps-6:svn35830.0-35.fc27.1.noarch 333/582 Installing : texlive-fancyref-6:svn1 [ ] 334/582 Installing : texlive-fancyref-6:svn1 [======================= ] 334/582 Installing : texlive-fancyref-6:svn15878.0.9c-35.fc27.1.noarc 334/582 Installing : texlive-mathtools-6:svn [ ] 335/582 Installing : texlive-mathtools-6:svn [======= ] 335/582 Installing : texlive-mathtools-6:svn [========== ] 335/582 Installing : texlive-mathtools-6:svn [================== ] 335/582 Installing : texlive-mathtools-6:svn [====================== ] 335/582 Installing : texlive-mathtools-6:svn [======================= ] 335/582 Installing : 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Installing : texlive-txfonts-6:svn15 [====================== ] 357/582 Installing : texlive-txfonts-6:svn15 [======================= ] 357/582 Installing : texlive-txfonts-6:svn15878.0-35.fc27.1.noarch 357/582 Installing : texlive-zapfchan-6:svn3 [ ] 358/582 Installing : texlive-zapfchan-6:svn3 [== ] 358/582 Installing : texlive-zapfchan-6:svn3 [====== ] 358/582 Installing : texlive-zapfchan-6:svn3 [======= ] 358/582 Installing : texlive-zapfchan-6:svn3 [======== ] 358/582 Installing : texlive-zapfchan-6:svn3 [========= ] 358/582 Installing : texlive-zapfchan-6:svn3 [=========== ] 358/582 Installing : texlive-zapfchan-6:svn3 [============= ] 358/582 Installing : texlive-zapfchan-6:svn3 [================== ] 358/582 Installing : texlive-zapfchan-6:svn3 [==================== ] 358/582 Installing : texlive-zapfchan-6:svn3 [===================== ] 358/582 Installing : texlive-zapfchan-6:svn3 [====================== ] 358/582 Installing : texlive-zapfchan-6:svn3 [======================= ] 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texlive-cm-6:svn32865.0 [================ ] 359/582 Installing : texlive-cm-6:svn32865.0 [================= ] 359/582 Installing : texlive-cm-6:svn32865.0 [================== ] 359/582 Installing : texlive-cm-6:svn32865.0 [=================== ] 359/582 Installing : texlive-cm-6:svn32865.0 [==================== ] 359/582 Installing : texlive-cm-6:svn32865.0 [===================== ] 359/582 Installing : texlive-cm-6:svn32865.0 [====================== ] 359/582 Installing : texlive-cm-6:svn32865.0 [======================= ] 359/582 Installing : texlive-cm-6:svn32865.0-35.fc27.1.noarch 359/582 Installing : texlive-anysize-6:svn15 [ ] 360/582 Installing : texlive-anysize-6:svn15 [== ] 360/582 Installing : texlive-anysize-6:svn15 [=== ] 360/582 Installing : texlive-anysize-6:svn15 [======================= ] 360/582 Installing : texlive-anysize-6:svn15878.0-35.fc27.1.noarch 360/582 Installing : texlive-cite-6:svn36428 [ ] 361/582 Installing : texlive-cite-6:svn36428 [========= ] 361/582 Installing : texlive-cite-6:svn36428 [=================== ] 361/582 Installing : texlive-cite-6:svn36428 [======================= ] 361/582 Installing : texlive-cite-6:svn36428.5.5-35.fc27.1.noarch 361/582 Installing : texlive-cmap-6:svn41168 [ ] 362/582 Installing : texlive-cmap-6:svn41168 [== ] 362/582 Installing : texlive-cmap-6:svn41168 [===== ] 362/582 Installing : texlive-cmap-6:svn41168 [======== ] 362/582 Installing : texlive-cmap-6:svn41168 [=========== ] 362/582 Installing : texlive-cmap-6:svn41168 [============ ] 362/582 Installing : texlive-cmap-6:svn41168 [============= ] 362/582 Installing : texlive-cmap-6:svn41168 [=============== ] 362/582 Installing : texlive-cmap-6:svn41168 [================= ] 362/582 Installing : texlive-cmap-6:svn41168 [================== ] 362/582 Installing : texlive-cmap-6:svn41168 [==================== ] 362/582 Installing : texlive-cmap-6:svn41168 [===================== ] 362/582 Installing : texlive-cmap-6:svn41168 [======================= ] 362/582 Installing : texlive-cmap-6:svn41168-35.fc27.1.noarch 362/582 Installing : texlive-euenc-6:svn1979 [ ] 363/582 Installing : texlive-euenc-6:svn1979 [= ] 363/582 Installing : texlive-euenc-6:svn1979 [== ] 363/582 Installing : texlive-euenc-6:svn1979 [==== ] 363/582 Installing : texlive-euenc-6:svn1979 [====== ] 363/582 Installing : texlive-euenc-6:svn1979 [======= ] 363/582 Installing : texlive-euenc-6:svn1979 [========= ] 363/582 Installing : texlive-euenc-6:svn1979 [=========== ] 363/582 Installing : texlive-euenc-6:svn1979 [============ ] 363/582 Installing : texlive-euenc-6:svn1979 [============= ] 363/582 Installing : texlive-euenc-6:svn1979 [================ ] 363/582 Installing : texlive-euenc-6:svn1979 [================== ] 363/582 Installing : texlive-euenc-6:svn1979 [===================== ] 363/582 Installing : texlive-euenc-6:svn1979 [======================= ] 363/582 Installing : texlive-euenc-6:svn19795.0.1h-35.fc27.1.noarch 363/582 Installing : texlive-mdwtools-6:svn1 [ ] 364/582 Installing : texlive-mdwtools-6:svn1 [= ] 364/582 Installing : texlive-mdwtools-6:svn1 [== ] 364/582 Installing : texlive-mdwtools-6:svn1 [=== ] 364/582 Installing : texlive-mdwtools-6:svn1 [==== ] 364/582 Installing : texlive-mdwtools-6:svn1 [===== ] 364/582 Installing : texlive-mdwtools-6:svn1 [======== ] 364/582 Installing : texlive-mdwtools-6:svn1 [========= ] 364/582 Installing : texlive-mdwtools-6:svn1 [========== ] 364/582 Installing : texlive-mdwtools-6:svn1 [================= ] 364/582 Installing : texlive-mdwtools-6:svn1 [=================== ] 364/582 Installing : texlive-mdwtools-6:svn1 [======================= ] 364/582 Installing : texlive-mdwtools-6:svn15878.1.05.4-35.fc27.1.noa 364/582 Installing : texlive-ntgclass-6:svn1 [ ] 365/582 Installing : texlive-ntgclass-6:svn1 [== ] 365/582 Installing : texlive-ntgclass-6:svn1 [===== ] 365/582 Installing : texlive-ntgclass-6:svn1 [======= ] 365/582 Installing : texlive-ntgclass-6:svn1 [========== ] 365/582 Installing : texlive-ntgclass-6:svn1 [============= ] 365/582 Installing : texlive-ntgclass-6:svn1 [================ ] 365/582 Installing : texlive-ntgclass-6:svn1 [================= ] 365/582 Installing : texlive-ntgclass-6:svn1 [================== ] 365/582 Installing : texlive-ntgclass-6:svn1 [==================== ] 365/582 Installing : texlive-ntgclass-6:svn1 [======================= ] 365/582 Installing : texlive-ntgclass-6:svn15878.2.1a-35.fc27.1.noarc 365/582 Installing : texlive-parskip-6:svn19 [ ] 366/582 Installing : texlive-parskip-6:svn19 [== ] 366/582 Installing : texlive-parskip-6:svn19 [=== ] 366/582 Installing : texlive-parskip-6:svn19 [======================= ] 366/582 Installing : texlive-parskip-6:svn19963.2.0-35.fc27.1.noarch 366/582 Installing : texlive-rcs-6:svn15878. [ ] 367/582 Installing : texlive-rcs-6:svn15878. [====================== ] 367/582 Installing : texlive-rcs-6:svn15878. [======================= ] 367/582 Installing : texlive-rcs-6:svn15878.0-35.fc27.1.noarch 367/582 Installing : texlive-sansmath-6:svn1 [ ] 368/582 Installing : texlive-sansmath-6:svn1 [= ] 368/582 Installing : texlive-sansmath-6:svn1 [======================= ] 368/582 Installing : texlive-sansmath-6:svn17997.1.1-35.fc27.1.noarch 368/582 Installing : texlive-section-6:svn20 [ ] 369/582 Installing : texlive-section-6:svn20 [======================= ] 369/582 Installing : texlive-section-6:svn20180.0-35.fc27.1.noarch 369/582 Installing : texlive-sepnum-6:svn201 [ ] 370/582 Installing : texlive-sepnum-6:svn201 [= ] 370/582 Installing : texlive-sepnum-6:svn201 [======================= ] 370/582 Installing : texlive-sepnum-6:svn20186.2.0-35.fc27.1.noarch 370/582 Installing : texlive-textcase-6:svn1 [ ] 371/582 Installing : texlive-textcase-6:svn1 [= ] 371/582 Installing : texlive-textcase-6:svn1 [== ] 371/582 Installing : texlive-textcase-6:svn1 [==== ] 371/582 Installing : texlive-textcase-6:svn1 [====================== ] 371/582 Installing : texlive-textcase-6:svn15878.0-35.fc27.1.noarch 371/582 Installing : texlive-epsf-6:svn21461 [ ] 372/582 Installing : texlive-epsf-6:svn21461 [============ ] 372/582 Installing : texlive-epsf-6:svn21461 [======================= ] 372/582 Installing : texlive-epsf-6:svn21461.2.7.4-35.fc27.1.noarch 372/582 Installing : texlive-charter-6:svn15 [ ] 373/582 Installing : texlive-charter-6:svn15 [= ] 373/582 Installing : texlive-charter-6:svn15 [== ] 373/582 Installing : texlive-charter-6:svn15 [=== ] 373/582 Installing : texlive-charter-6:svn15 [==== ] 373/582 Installing : texlive-charter-6:svn15 [===== ] 373/582 Installing : texlive-charter-6:svn15 [====== ] 373/582 Installing : texlive-charter-6:svn15 [======= ] 373/582 Installing : texlive-charter-6:svn15 [======== ] 373/582 Installing : texlive-charter-6:svn15 [========= ] 373/582 Installing : texlive-charter-6:svn15 [========== ] 373/582 Installing : texlive-charter-6:svn15 [=========== ] 373/582 Installing : texlive-charter-6:svn15 [============ ] 373/582 Installing : texlive-charter-6:svn15 [============== ] 373/582 Installing : texlive-charter-6:svn15 [================ ] 373/582 Installing : texlive-charter-6:svn15 [================== ] 373/582 Installing : texlive-charter-6:svn15 [==================== ] 373/582 Installing : texlive-charter-6:svn15 [===================== ] 373/582 Installing : texlive-charter-6:svn15 [====================== ] 373/582 Installing : texlive-charter-6:svn15 [======================= ] 373/582 Installing : texlive-charter-6:svn15878.0-35.fc27.1.noarch 373/582 Installing : texlive-cmextra-6:svn32 [ ] 374/582 Installing : texlive-cmextra-6:svn32 [= ] 374/582 Installing : texlive-cmextra-6:svn32 [== ] 374/582 Installing : texlive-cmextra-6:svn32 [=== ] 374/582 Installing : texlive-cmextra-6:svn32 [==== ] 374/582 Installing : texlive-cmextra-6:svn32 [===== ] 374/582 Installing : texlive-cmextra-6:svn32 [========== ] 374/582 Installing : texlive-cmextra-6:svn32 [============ ] 374/582 Installing : texlive-cmextra-6:svn32 [============= ] 374/582 Installing : texlive-cmextra-6:svn32 [============== ] 374/582 Installing : texlive-cmextra-6:svn32 [=============== ] 374/582 Installing : texlive-cmextra-6:svn32 [================ ] 374/582 Installing : texlive-cmextra-6:svn32 [================= ] 374/582 Installing : texlive-cmextra-6:svn32 [================== ] 374/582 Installing : texlive-cmextra-6:svn32 [=================== ] 374/582 Installing : texlive-cmextra-6:svn32 [==================== ] 374/582 Installing : texlive-cmextra-6:svn32 [===================== ] 374/582 Installing : texlive-cmextra-6:svn32 [====================== ] 374/582 Installing : texlive-cmextra-6:svn32 [======================= ] 374/582 Installing : texlive-cmextra-6:svn32831.0-35.fc27.1.noarch 374/582 Installing : texlive-ec-6:svn25033.1 [ ] 375/582 Installing : texlive-ec-6:svn25033.1 [= ] 375/582 Installing : texlive-ec-6:svn25033.1 [== ] 375/582 Installing : texlive-ec-6:svn25033.1 [=== ] 375/582 Installing : texlive-ec-6:svn25033.1 [==== ] 375/582 Installing : texlive-ec-6:svn25033.1 [===== ] 375/582 Installing : texlive-ec-6:svn25033.1 [====== ] 375/582 Installing : texlive-ec-6:svn25033.1 [======= ] 375/582 Installing : texlive-ec-6:svn25033.1 [======== ] 375/582 Installing : texlive-ec-6:svn25033.1 [========= ] 375/582 Installing : texlive-ec-6:svn25033.1 [========== ] 375/582 Installing : texlive-ec-6:svn25033.1 [=========== ] 375/582 Installing : texlive-ec-6:svn25033.1 [============ ] 375/582 Installing : texlive-ec-6:svn25033.1 [============= ] 375/582 Installing : texlive-ec-6:svn25033.1 [============== ] 375/582 Installing : texlive-ec-6:svn25033.1 [=============== ] 375/582 Installing : texlive-ec-6:svn25033.1 [================ ] 375/582 Installing : texlive-ec-6:svn25033.1 [================= ] 375/582 Installing : texlive-ec-6:svn25033.1 [================== ] 375/582 Installing : texlive-ec-6:svn25033.1 [=================== ] 375/582 Installing : texlive-ec-6:svn25033.1 [==================== ] 375/582 Installing : texlive-ec-6:svn25033.1 [===================== ] 375/582 Installing : texlive-ec-6:svn25033.1 [====================== ] 375/582 Installing : texlive-ec-6:svn25033.1 [======================= ] 375/582 Installing : texlive-ec-6:svn25033.1.0-35.fc27.1.noarch 375/582 Installing : texlive-fpl-6:svn15878. [ ] 376/582 Installing : texlive-fpl-6:svn15878. [= ] 376/582 Installing : texlive-fpl-6:svn15878. [== ] 376/582 Installing : texlive-fpl-6:svn15878. [==== ] 376/582 Installing : texlive-fpl-6:svn15878. [===== ] 376/582 Installing : texlive-fpl-6:svn15878. [====== ] 376/582 Installing : texlive-fpl-6:svn15878. [======= ] 376/582 Installing : texlive-fpl-6:svn15878. [========= ] 376/582 Installing : texlive-fpl-6:svn15878. [========== ] 376/582 Installing : texlive-fpl-6:svn15878. [=========== ] 376/582 Installing : texlive-fpl-6:svn15878. [============ ] 376/582 Installing : texlive-fpl-6:svn15878. [============= ] 376/582 Installing : texlive-fpl-6:svn15878. [=============== ] 376/582 Installing : texlive-fpl-6:svn15878. [================ ] 376/582 Installing : texlive-fpl-6:svn15878. [================== ] 376/582 Installing : texlive-fpl-6:svn15878. [=================== ] 376/582 Installing : texlive-fpl-6:svn15878. [==================== ] 376/582 Installing : texlive-fpl-6:svn15878. [===================== ] 376/582 Installing : texlive-fpl-6:svn15878. [====================== ] 376/582 Installing : texlive-fpl-6:svn15878. [======================= ] 376/582 Installing : texlive-fpl-6:svn15878.1.002-35.fc27.1.noarch 376/582 Installing : texlive-lm-math-6:svn36 [ ] 377/582 Installing : texlive-lm-math-6:svn36 [== ] 377/582 Installing : texlive-lm-math-6:svn36 [=== ] 377/582 Installing : texlive-lm-math-6:svn36 [==== ] 377/582 Installing : texlive-lm-math-6:svn36 [===== ] 377/582 Installing : texlive-lm-math-6:svn36 [====== ] 377/582 Installing : texlive-lm-math-6:svn36 [======= ] 377/582 Installing : texlive-lm-math-6:svn36 [======== ] 377/582 Installing : texlive-lm-math-6:svn36 [========= ] 377/582 Installing : texlive-lm-math-6:svn36 [========== ] 377/582 Installing : texlive-lm-math-6:svn36 [=========== ] 377/582 Installing : texlive-lm-math-6:svn36 [============ ] 377/582 Installing : texlive-lm-math-6:svn36 [============= ] 377/582 Installing : texlive-lm-math-6:svn36 [============== ] 377/582 Installing : texlive-lm-math-6:svn36 [================ ] 377/582 Installing : texlive-lm-math-6:svn36 [================= ] 377/582 Installing : texlive-lm-math-6:svn36 [================== ] 377/582 Installing : texlive-lm-math-6:svn36 [=================== ] 377/582 Installing : texlive-lm-math-6:svn36 [==================== ] 377/582 Installing : texlive-lm-math-6:svn36 [===================== ] 377/582 Installing : texlive-lm-math-6:svn36 [====================== ] 377/582 Installing : texlive-lm-math-6:svn36 [======================= ] 377/582 Installing : texlive-lm-math-6:svn36915.1.959-35.fc27.1.noarc 377/582 Installing : texlive-mathpazo-6:svn1 [ ] 378/582 Installing : texlive-mathpazo-6:svn1 [= ] 378/582 Installing : texlive-mathpazo-6:svn1 [== ] 378/582 Installing : texlive-mathpazo-6:svn1 [=== ] 378/582 Installing : texlive-mathpazo-6:svn1 [==== ] 378/582 Installing : texlive-mathpazo-6:svn1 [===== ] 378/582 Installing : texlive-mathpazo-6:svn1 [====== ] 378/582 Installing : texlive-mathpazo-6:svn1 [======= ] 378/582 Installing : texlive-mathpazo-6:svn1 [========= ] 378/582 Installing : texlive-mathpazo-6:svn1 [============ ] 378/582 Installing : texlive-mathpazo-6:svn1 [=============== ] 378/582 Installing : texlive-mathpazo-6:svn1 [================= ] 378/582 Installing : texlive-mathpazo-6:svn1 [===================== ] 378/582 Installing : texlive-mathpazo-6:svn1 [====================== ] 378/582 Installing : texlive-mathpazo-6:svn1 [======================= ] 378/582 Installing : texlive-mathpazo-6:svn15878.1.003-35.fc27.1.noar 378/582 Installing : texlive-tex-gyre-math-6 [ ] 379/582 Installing : texlive-tex-gyre-math-6 [= ] 379/582 Installing : texlive-tex-gyre-math-6 [== ] 379/582 Installing : texlive-tex-gyre-math-6 [=== ] 379/582 Installing : texlive-tex-gyre-math-6 [==== ] 379/582 Installing : texlive-tex-gyre-math-6 [===== ] 379/582 Installing : texlive-tex-gyre-math-6 [====== ] 379/582 Installing : texlive-tex-gyre-math-6 [======= ] 379/582 Installing : texlive-tex-gyre-math-6 [======== ] 379/582 Installing : texlive-tex-gyre-math-6 [========= ] 379/582 Installing : texlive-tex-gyre-math-6 [========== ] 379/582 Installing : texlive-tex-gyre-math-6 [=========== ] 379/582 Installing : texlive-tex-gyre-math-6 [============ ] 379/582 Installing : texlive-tex-gyre-math-6 [============= ] 379/582 Installing : texlive-tex-gyre-math-6 [============== ] 379/582 Installing : texlive-tex-gyre-math-6 [=============== ] 379/582 Installing : texlive-tex-gyre-math-6 [================ ] 379/582 Installing : texlive-tex-gyre-math-6 [================= ] 379/582 Installing : texlive-tex-gyre-math-6 [================== ] 379/582 Installing : texlive-tex-gyre-math-6 [=================== ] 379/582 Installing : texlive-tex-gyre-math-6 [==================== ] 379/582 Installing : texlive-tex-gyre-math-6 [===================== ] 379/582 Installing : texlive-tex-gyre-math-6 [====================== ] 379/582 Installing : texlive-tex-gyre-math-6 [======================= ] 379/582 Installing : texlive-tex-gyre-math-6:svn41264-35.fc27.1.noarc 379/582 Installing : texlive-utopia-6:svn158 [ ] 380/582 Installing : texlive-utopia-6:svn158 [= ] 380/582 Installing : texlive-utopia-6:svn158 [== ] 380/582 Installing : texlive-utopia-6:svn158 [=== ] 380/582 Installing : texlive-utopia-6:svn158 [==== ] 380/582 Installing : texlive-utopia-6:svn158 [===== ] 380/582 Installing : texlive-utopia-6:svn158 [====== ] 380/582 Installing : texlive-utopia-6:svn158 [======= ] 380/582 Installing : texlive-utopia-6:svn158 [======== ] 380/582 Installing : texlive-utopia-6:svn158 [========= ] 380/582 Installing : texlive-utopia-6:svn158 [========== ] 380/582 Installing : texlive-utopia-6:svn158 [=========== ] 380/582 Installing : texlive-utopia-6:svn158 [============ ] 380/582 Installing : texlive-utopia-6:svn158 [============= ] 380/582 Installing : texlive-utopia-6:svn158 [============== ] 380/582 Installing : texlive-utopia-6:svn158 [=============== ] 380/582 Installing : texlive-utopia-6:svn158 [================ ] 380/582 Installing : texlive-utopia-6:svn158 [================== ] 380/582 Installing : texlive-utopia-6:svn158 [=================== ] 380/582 Installing : texlive-utopia-6:svn158 [===================== ] 380/582 Installing : texlive-utopia-6:svn158 [====================== ] 380/582 Installing : texlive-utopia-6:svn158 [======================= ] 380/582 Installing : texlive-utopia-6:svn15878.0-35.fc27.1.noarch 380/582 Installing : texlive-wasysym-6:svn15 [ ] 381/582 Installing : texlive-wasysym-6:svn15 [==== ] 381/582 Installing : texlive-wasysym-6:svn15 [======= ] 381/582 Installing : texlive-wasysym-6:svn15 [======================= ] 381/582 Installing : texlive-wasysym-6:svn15878.2.0-35.fc27.1.noarch 381/582 Installing : texlive-babel-english-6 [ ] 382/582 Installing : texlive-babel-english-6 [= ] 382/582 Installing : texlive-babel-english-6 [======================= ] 382/582 Installing : texlive-babel-english-6:svn30264.3.3p-35.fc27.1. 382/582 Installing : texlive-dvisvgm-def-6:s [ ] 383/582 Installing 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386/582 Installing : texlive-mfnfss-6:svn194 [=============== ] 386/582 Installing : texlive-mfnfss-6:svn194 [================== ] 386/582 Installing : texlive-mfnfss-6:svn194 [==================== ] 386/582 Installing : texlive-mfnfss-6:svn194 [======================= ] 386/582 Installing : texlive-mfnfss-6:svn19410.0-35.fc27.1.noarch 386/582 Installing : texlive-pslatex-6:svn16 [ ] 387/582 Installing : texlive-pslatex-6:svn16 [= ] 387/582 Installing : texlive-pslatex-6:svn16 [== ] 387/582 Installing : texlive-pslatex-6:svn16 [==== ] 387/582 Installing : texlive-pslatex-6:svn16 [===== ] 387/582 Installing : texlive-pslatex-6:svn16 [====== ] 387/582 Installing : texlive-pslatex-6:svn16 [======= ] 387/582 Installing : texlive-pslatex-6:svn16 [=========== ] 387/582 Installing : texlive-pslatex-6:svn16 [======================= ] 387/582 Installing : texlive-pslatex-6:svn16416.0-35.fc27.1.noarch 387/582 Installing : texlive-pspicture-6:svn [ ] 388/582 Installing : texlive-pspicture-6:svn [= ] 388/582 Installing : texlive-pspicture-6:svn [=========== ] 388/582 Installing : texlive-pspicture-6:svn [============ ] 388/582 Installing : texlive-pspicture-6:svn [======================= ] 388/582 Installing : texlive-pspicture-6:svn15878.0-35.fc27.1.noarch 388/582 Installing : texlive-iftex-6:svn2965 [ ] 389/582 Installing : texlive-iftex-6:svn2965 [== ] 389/582 Installing : texlive-iftex-6:svn2965 [=== ] 389/582 Installing : texlive-iftex-6:svn2965 [======================= ] 389/582 Installing : texlive-iftex-6:svn29654.0.2-35.fc27.1.noarch 389/582 Installing : texlive-kastrup-6:svn15 [ ] 390/582 Installing : texlive-kastrup-6:svn15 [== ] 390/582 Installing : texlive-kastrup-6:svn15 [=== ] 390/582 Installing : texlive-kastrup-6:svn15 [======================= ] 390/582 Installing : texlive-kastrup-6:svn15878.0-35.fc27.1.noarch 390/582 Installing : texlive-marginnote-6:sv [ ] 391/582 Installing : texlive-marginnote-6:sv [======================= ] 391/582 Installing : 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454/582 Installing : texlive-pdftex-6:svn411 [ ] 455/582 Installing : texlive-pdftex-6:svn411 [== ] 455/582 Installing : texlive-pdftex-6:svn411 [===== ] 455/582 Installing : texlive-pdftex-6:svn411 [======== ] 455/582 Installing : texlive-pdftex-6:svn411 [============ ] 455/582 Installing : texlive-pdftex-6:svn411 [=============== ] 455/582 Installing : texlive-pdftex-6:svn411 [================== ] 455/582 Installing : texlive-pdftex-6:svn411 [===================== ] 455/582 Installing : texlive-pdftex-6:svn411 [======================= ] 455/582 Installing : texlive-pdftex-6:svn41149-35.fc27.1.noarch 455/582 Running scriptlet: texlive-pdftex-6:svn41149-35.fc27.1.noarch 455/582 Installing : texlive-xunicode-6:svn3 [ ] 456/582 Installing : texlive-xunicode-6:svn3 [=== ] 456/582 Installing : texlive-xunicode-6:svn3 [======= ] 456/582 Installing : texlive-xunicode-6:svn3 [=========== ] 456/582 Installing : texlive-xunicode-6:svn3 [=============== ] 456/582 Installing : texlive-xunicode-6:svn3 [================== ] 456/582 Installing : texlive-xunicode-6:svn3 [====================== ] 456/582 Installing : texlive-xunicode-6:svn3 [======================= ] 456/582 Installing : texlive-xunicode-6:svn30466.0.981-35.fc27.1.noar 456/582 Installing : texlive-tipa-6:svn29349 [ ] 457/582 Installing : texlive-tipa-6:svn29349 [= ] 457/582 Installing : texlive-tipa-6:svn29349 [== ] 457/582 Installing : texlive-tipa-6:svn29349 [=== ] 457/582 Installing : texlive-tipa-6:svn29349 [==== ] 457/582 Installing : texlive-tipa-6:svn29349 [===== ] 457/582 Installing : texlive-tipa-6:svn29349 [====== ] 457/582 Installing : texlive-tipa-6:svn29349 [======= ] 457/582 Installing : texlive-tipa-6:svn29349 [======== ] 457/582 Installing : texlive-tipa-6:svn29349 [========= ] 457/582 Installing : texlive-tipa-6:svn29349 [========== ] 457/582 Installing : texlive-tipa-6:svn29349 [=========== ] 457/582 Installing : texlive-tipa-6:svn29349 [============ ] 457/582 Installing : texlive-tipa-6:svn29349 [============= ] 457/582 Installing : texlive-tipa-6:svn29349 [============== ] 457/582 Installing : texlive-tipa-6:svn29349 [=============== ] 457/582 Installing : texlive-tipa-6:svn29349 [================ ] 457/582 Installing : texlive-tipa-6:svn29349 [================= ] 457/582 Installing : texlive-tipa-6:svn29349 [================== ] 457/582 Installing : texlive-tipa-6:svn29349 [=================== ] 457/582 Installing : texlive-tipa-6:svn29349 [==================== ] 457/582 Installing : texlive-tipa-6:svn29349 [===================== ] 457/582 Installing : texlive-tipa-6:svn29349 [====================== ] 457/582 Installing : texlive-tipa-6:svn29349 [======================= ] 457/582 Installing : texlive-tipa-6:svn29349.1.3-35.fc27.1.noarch 457/582 Installing : texlive-algorithms-6:sv [ ] 458/582 Installing : texlive-algorithms-6:sv [====== ] 458/582 Installing : texlive-algorithms-6:sv [======================= ] 458/582 Installing : texlive-algorithms-6:svn38085.0.1-35.fc27.1.noar 458/582 Installing : texlive-bera-6:svn20031 [ ] 459/582 Installing : texlive-bera-6:svn20031 [= ] 459/582 Installing : texlive-bera-6:svn20031 [== ] 459/582 Installing : texlive-bera-6:svn20031 [=== ] 459/582 Installing : texlive-bera-6:svn20031 [==== ] 459/582 Installing : texlive-bera-6:svn20031 [===== ] 459/582 Installing : texlive-bera-6:svn20031 [====== ] 459/582 Installing : texlive-bera-6:svn20031 [======= ] 459/582 Installing : texlive-bera-6:svn20031 [======== ] 459/582 Installing : texlive-bera-6:svn20031 [========= ] 459/582 Installing : texlive-bera-6:svn20031 [========== ] 459/582 Installing : texlive-bera-6:svn20031 [=========== ] 459/582 Installing : texlive-bera-6:svn20031 [============ ] 459/582 Installing : texlive-bera-6:svn20031 [============= ] 459/582 Installing : texlive-bera-6:svn20031 [============== ] 459/582 Installing : texlive-bera-6:svn20031 [=============== ] 459/582 Installing : texlive-bera-6:svn20031 [================ ] 459/582 Installing : texlive-bera-6:svn20031 [================= ] 459/582 Installing : texlive-bera-6:svn20031 [================== ] 459/582 Installing : texlive-bera-6:svn20031 [=================== ] 459/582 Installing : texlive-bera-6:svn20031 [==================== ] 459/582 Installing : texlive-bera-6:svn20031 [===================== ] 459/582 Installing : texlive-bera-6:svn20031 [====================== ] 459/582 Installing : texlive-bera-6:svn20031 [======================= ] 459/582 Installing : texlive-bera-6:svn20031.0-35.fc27.1.noarch 459/582 Installing : texlive-l3packages-6:sv [ ] 460/582 Installing : texlive-l3packages-6:sv [=== ] 460/582 Installing : texlive-l3packages-6:sv [========= ] 460/582 Installing : texlive-l3packages-6:sv [============== ] 460/582 Installing : texlive-l3packages-6:sv [==================== ] 460/582 Installing : texlive-l3packages-6:sv [======================= ] 460/582 Installing : texlive-l3packages-6:svn41246-35.fc27.1.noarch 460/582 Installing : texlive-l3kernel-6:svn4 [ ] 461/582 Installing : texlive-l3kernel-6:svn4 [= ] 461/582 Installing : texlive-l3kernel-6:svn4 [== ] 461/582 Installing : texlive-l3kernel-6:svn4 [=== ] 461/582 Installing : texlive-l3kernel-6:svn4 [==== ] 461/582 Installing : texlive-l3kernel-6:svn4 [===== ] 461/582 Installing : texlive-l3kernel-6:svn4 [====== ] 461/582 Installing : texlive-l3kernel-6:svn4 [======= ] 461/582 Installing : texlive-l3kernel-6:svn4 [======== ] 461/582 Installing : texlive-l3kernel-6:svn4 [========= ] 461/582 Installing : texlive-l3kernel-6:svn4 [========== ] 461/582 Installing : texlive-l3kernel-6:svn4 [=========== ] 461/582 Installing : texlive-l3kernel-6:svn4 [============ ] 461/582 Installing : texlive-l3kernel-6:svn4 [============= ] 461/582 Installing : texlive-l3kernel-6:svn4 [============== ] 461/582 Installing : texlive-l3kernel-6:svn4 [=============== ] 461/582 Installing : texlive-l3kernel-6:svn4 [================ ] 461/582 Installing : texlive-l3kernel-6:svn4 [================= ] 461/582 Installing : texlive-l3kernel-6:svn4 [================== ] 461/582 Installing : texlive-l3kernel-6:svn4 [=================== ] 461/582 Installing : texlive-l3kernel-6:svn4 [==================== ] 461/582 Installing : texlive-l3kernel-6:svn4 [===================== ] 461/582 Installing : texlive-l3kernel-6:svn4 [====================== ] 461/582 Installing : texlive-l3kernel-6:svn4 [======================= ] 461/582 Installing : texlive-l3kernel-6:svn41246-35.fc27.1.noarch 461/582 Installing : texlive-memoir-6:svn412 [ ] 462/582 Installing : texlive-memoir-6:svn412 [= ] 462/582 Installing : texlive-memoir-6:svn412 [== ] 462/582 Installing : texlive-memoir-6:svn412 [=== ] 462/582 Installing : texlive-memoir-6:svn412 [==== ] 462/582 Installing : texlive-memoir-6:svn412 [====== ] 462/582 Installing : texlive-memoir-6:svn412 [======== ] 462/582 Installing : texlive-memoir-6:svn412 [========= ] 462/582 Installing : texlive-memoir-6:svn412 [=========== ] 462/582 Installing : texlive-memoir-6:svn412 [============= ] 462/582 Installing : texlive-memoir-6:svn412 [============== ] 462/582 Installing : texlive-memoir-6:svn412 [================ ] 462/582 Installing : texlive-memoir-6:svn412 [================== ] 462/582 Installing : texlive-memoir-6:svn412 [=================== ] 462/582 Installing : texlive-memoir-6:svn412 [===================== ] 462/582 Installing : texlive-memoir-6:svn412 [======================= ] 462/582 Installing : texlive-memoir-6:svn41203-35.fc27.1.noarch 462/582 Installing : texlive-eso-pic-6:svn37 [ ] 463/582 Installing : texlive-eso-pic-6:svn37 [=================== ] 463/582 Installing : texlive-eso-pic-6:svn37 [======================= ] 463/582 Installing : texlive-eso-pic-6:svn37925.2.0g-35.fc27.1.noarch 463/582 Installing : texlive-pgf-6:svn40966- [ ] 464/582 Installing : texlive-pgf-6:svn40966- [= ] 464/582 Installing : texlive-pgf-6:svn40966- [== ] 464/582 Installing : texlive-pgf-6:svn40966- [=== ] 464/582 Installing : texlive-pgf-6:svn40966- [==== ] 464/582 Installing : texlive-pgf-6:svn40966- [===== ] 464/582 Installing : texlive-pgf-6:svn40966- [====== ] 464/582 Installing : texlive-pgf-6:svn40966- [======= ] 464/582 Installing : texlive-pgf-6:svn40966- [======== ] 464/582 Installing : texlive-pgf-6:svn40966- [========= ] 464/582 Installing : texlive-pgf-6:svn40966- [========== ] 464/582 Installing : texlive-pgf-6:svn40966- [=========== ] 464/582 Installing : texlive-pgf-6:svn40966- [============ ] 464/582 Installing : texlive-pgf-6:svn40966- [============= ] 464/582 Installing : texlive-pgf-6:svn40966- [============== ] 464/582 Installing : texlive-pgf-6:svn40966- [=============== ] 464/582 Installing : texlive-pgf-6:svn40966- [================ ] 464/582 Installing : texlive-pgf-6:svn40966- [================= ] 464/582 Installing : texlive-pgf-6:svn40966- [================== ] 464/582 Installing : texlive-pgf-6:svn40966- [=================== ] 464/582 Installing : texlive-pgf-6:svn40966- [==================== ] 464/582 Installing : texlive-pgf-6:svn40966- [===================== ] 464/582 Installing : texlive-pgf-6:svn40966- [====================== ] 464/582 Installing : texlive-pgf-6:svn40966- [======================= ] 464/582 Installing : texlive-pgf-6:svn40966-35.fc27.1.noarch 464/582 Installing : texlive-xcolor-6:svn410 [ ] 465/582 Installing : texlive-xcolor-6:svn410 [== ] 465/582 Installing : texlive-xcolor-6:svn410 [===== ] 465/582 Installing : texlive-xcolor-6:svn410 [================ ] 465/582 Installing : texlive-xcolor-6:svn410 [======================= ] 465/582 Installing : texlive-xcolor-6:svn41044-35.fc27.1.noarch 465/582 Installing : texlive-geometry-6:svn1 [ ] 466/582 Installing : texlive-geometry-6:svn1 [=================== ] 466/582 Installing : texlive-geometry-6:svn1 [======================= ] 466/582 Installing : texlive-geometry-6:svn19716.5.6-35.fc27.1.noarch 466/582 Installing : texlive-ms-6:svn29849.0 [ ] 467/582 Installing : texlive-ms-6:svn29849.0 [==== ] 467/582 Installing : texlive-ms-6:svn29849.0 [======= ] 467/582 Installing : texlive-ms-6:svn29849.0 [========== ] 467/582 Installing : texlive-ms-6:svn29849.0 [============= ] 467/582 Installing : texlive-ms-6:svn29849.0 [================ ] 467/582 Installing : texlive-ms-6:svn29849.0 [======================= ] 467/582 Installing : texlive-ms-6:svn29849.0-35.fc27.1.noarch 467/582 Installing : texlive-koma-script-6:s [ ] 468/582 Installing : texlive-koma-script-6:s [= ] 468/582 Installing : texlive-koma-script-6:s [== ] 468/582 Installing : texlive-koma-script-6:s [=== ] 468/582 Installing : texlive-koma-script-6:s [==== ] 468/582 Installing : texlive-koma-script-6:s [===== ] 468/582 Installing : texlive-koma-script-6:s [====== ] 468/582 Installing : texlive-koma-script-6:s [======= ] 468/582 Installing : texlive-koma-script-6:s [======== ] 468/582 Installing : texlive-koma-script-6:s [========= ] 468/582 Installing : texlive-koma-script-6:s [========== ] 468/582 Installing : texlive-koma-script-6:s [=========== ] 468/582 Installing : texlive-koma-script-6:s [============ ] 468/582 Installing : texlive-koma-script-6:s [============= ] 468/582 Installing : texlive-koma-script-6:s [============== ] 468/582 Installing : texlive-koma-script-6:s [=============== ] 468/582 Installing : texlive-koma-script-6:s [================ ] 468/582 Installing : texlive-koma-script-6:s [================= ] 468/582 Installing : texlive-koma-script-6:s [================== ] 468/582 Installing : texlive-koma-script-6:s [=================== ] 468/582 Installing : texlive-koma-script-6:s [==================== ] 468/582 Installing : texlive-koma-script-6:s [===================== ] 468/582 Installing : texlive-koma-script-6:s [====================== ] 468/582 Installing : texlive-koma-script-6:s [======================= ] 468/582 Installing : texlive-koma-script-6:svn41508-35.fc27.1.noarch 468/582 Installing : texlive-hyperref-6:svn4 [ ] 469/582 Installing : texlive-hyperref-6:svn4 [= ] 469/582 Installing : texlive-hyperref-6:svn4 [== ] 469/582 Installing : texlive-hyperref-6:svn4 [=== ] 469/582 Installing : texlive-hyperref-6:svn4 [==== ] 469/582 Installing : texlive-hyperref-6:svn4 [===== ] 469/582 Installing : texlive-hyperref-6:svn4 [====== ] 469/582 Installing : texlive-hyperref-6:svn4 [======= ] 469/582 Installing : texlive-hyperref-6:svn4 [======== ] 469/582 Installing : texlive-hyperref-6:svn4 [========= ] 469/582 Installing : texlive-hyperref-6:svn4 [========== ] 469/582 Installing : texlive-hyperref-6:svn4 [=========== ] 469/582 Installing : texlive-hyperref-6:svn4 [============ ] 469/582 Installing : texlive-hyperref-6:svn4 [============= ] 469/582 Installing : texlive-hyperref-6:svn4 [============== ] 469/582 Installing : texlive-hyperref-6:svn4 [=============== ] 469/582 Installing : texlive-hyperref-6:svn4 [================ ] 469/582 Installing : texlive-hyperref-6:svn4 [================= ] 469/582 Installing : texlive-hyperref-6:svn4 [================== ] 469/582 Installing : texlive-hyperref-6:svn4 [=================== ] 469/582 Installing : texlive-hyperref-6:svn4 [==================== ] 469/582 Installing : texlive-hyperref-6:svn4 [===================== ] 469/582 Installing : texlive-hyperref-6:svn4 [====================== ] 469/582 Installing : texlive-hyperref-6:svn4 [======================= ] 469/582 Installing : texlive-hyperref-6:svn41396-35.fc27.1.noarch 469/582 Installing : texlive-latex-6:svn4021 [ ] 470/582 Installing : texlive-latex-6:svn4021 [= ] 470/582 Installing : texlive-latex-6:svn4021 [== ] 470/582 Installing : texlive-latex-6:svn4021 [=== ] 470/582 Installing : texlive-latex-6:svn4021 [==== ] 470/582 Installing : texlive-latex-6:svn4021 [===== ] 470/582 Installing : texlive-latex-6:svn4021 [====== ] 470/582 Installing : texlive-latex-6:svn4021 [======= ] 470/582 Installing : texlive-latex-6:svn4021 [======== ] 470/582 Installing : texlive-latex-6:svn4021 [========= ] 470/582 Installing : texlive-latex-6:svn4021 [========== ] 470/582 Installing : texlive-latex-6:svn4021 [=========== ] 470/582 Installing : texlive-latex-6:svn4021 [============ ] 470/582 Installing : texlive-latex-6:svn4021 [============= ] 470/582 Installing : texlive-latex-6:svn4021 [============== ] 470/582 Installing : texlive-latex-6:svn4021 [=============== ] 470/582 Installing : texlive-latex-6:svn4021 [================ ] 470/582 Installing : texlive-latex-6:svn4021 [================= ] 470/582 Installing : texlive-latex-6:svn4021 [================== ] 470/582 Installing : texlive-latex-6:svn4021 [=================== ] 470/582 Installing : texlive-latex-6:svn4021 [==================== ] 470/582 Installing : texlive-latex-6:svn4021 [===================== ] 470/582 Installing : texlive-latex-6:svn4021 [====================== ] 470/582 Installing : texlive-latex-6:svn4021 [======================= ] 470/582 Installing : texlive-latex-6:svn40218-35.fc27.1.noarch 470/582 Installing : texlive-breakurl-6:svn2 [ ] 471/582 Installing : texlive-breakurl-6:svn2 [= ] 471/582 Installing : texlive-breakurl-6:svn2 [======================= ] 471/582 Installing : texlive-breakurl-6:svn29901.1.40-35.fc27.1.noarc 471/582 Installing : texlive-fontspec-6:svn4 [ ] 472/582 Installing : texlive-fontspec-6:svn4 [=== ] 472/582 Installing : texlive-fontspec-6:svn4 [====== ] 472/582 Installing : texlive-fontspec-6:svn4 [========= ] 472/582 Installing : texlive-fontspec-6:svn4 [========== ] 472/582 Installing : texlive-fontspec-6:svn4 [============= ] 472/582 Installing : texlive-fontspec-6:svn4 [================ ] 472/582 Installing : texlive-fontspec-6:svn4 [==================== ] 472/582 Installing : texlive-fontspec-6:svn4 [===================== ] 472/582 Installing : texlive-fontspec-6:svn4 [====================== ] 472/582 Installing : texlive-fontspec-6:svn4 [======================= ] 472/582 Installing : texlive-fontspec-6:svn41262-35.fc27.1.noarch 472/582 Installing : texlive-luaotfload-bin- [ ] 473/582 Installing : texlive-luaotfload-bin- [====== ] 473/582 Installing : texlive-luaotfload-bin- [============ ] 473/582 Installing : texlive-luaotfload-bin- [=================== ] 473/582 Installing : texlive-luaotfload-bin-6:svn34647.0-35.20160520. 473/582 Installing : texlive-luaotfload-6:sv [ ] 474/582 Installing : texlive-luaotfload-6:sv [= ] 474/582 Installing : texlive-luaotfload-6:sv [== ] 474/582 Installing : texlive-luaotfload-6:sv [=== ] 474/582 Installing : texlive-luaotfload-6:sv [==== ] 474/582 Installing : texlive-luaotfload-6:sv [===== ] 474/582 Installing : texlive-luaotfload-6:sv [====== ] 474/582 Installing : texlive-luaotfload-6:sv [======= ] 474/582 Installing : texlive-luaotfload-6:sv [======== ] 474/582 Installing : texlive-luaotfload-6:sv [========= ] 474/582 Installing : texlive-luaotfload-6:sv [========== ] 474/582 Installing : texlive-luaotfload-6:sv [=========== ] 474/582 Installing : texlive-luaotfload-6:sv [============ ] 474/582 Installing : texlive-luaotfload-6:sv [============= ] 474/582 Installing : texlive-luaotfload-6:sv [============== ] 474/582 Installing : texlive-luaotfload-6:sv [=============== ] 474/582 Installing : texlive-luaotfload-6:sv [================ ] 474/582 Installing : texlive-luaotfload-6:sv [================= ] 474/582 Installing : texlive-luaotfload-6:sv [================== ] 474/582 Installing : texlive-luaotfload-6:sv [=================== ] 474/582 Installing : texlive-luaotfload-6:sv [==================== ] 474/582 Installing : texlive-luaotfload-6:sv [===================== ] 474/582 Installing : texlive-luaotfload-6:sv [====================== ] 474/582 Installing : texlive-luaotfload-6:sv [======================= ] 474/582 Installing : texlive-luaotfload-6:svn40902-35.fc27.1.noarch 474/582 Installing : texlive-luatexbase-6:sv [ ] 475/582 Installing : texlive-luatexbase-6:sv [= ] 475/582 Installing : texlive-luatexbase-6:sv [== ] 475/582 Installing : texlive-luatexbase-6:sv [=== ] 475/582 Installing : texlive-luatexbase-6:sv [==== ] 475/582 Installing : texlive-luatexbase-6:sv [===== ] 475/582 Installing : texlive-luatexbase-6:sv [====== ] 475/582 Installing : texlive-luatexbase-6:sv [======================= ] 475/582 Installing : texlive-luatexbase-6:svn38550-35.fc27.1.noarch 475/582 Installing : texlive-unicode-math-6: [ ] 476/582 Installing : texlive-unicode-math-6: [= ] 476/582 Installing : texlive-unicode-math-6: [=== ] 476/582 Installing : texlive-unicode-math-6: [===== ] 476/582 Installing : texlive-unicode-math-6: [======= ] 476/582 Installing : texlive-unicode-math-6: [========= ] 476/582 Installing : texlive-unicode-math-6: [=========== ] 476/582 Installing : texlive-unicode-math-6: [============ ] 476/582 Installing : texlive-unicode-math-6: [============== ] 476/582 Installing : texlive-unicode-math-6: [================ ] 476/582 Installing : texlive-unicode-math-6: [================= ] 476/582 Installing : texlive-unicode-math-6: [=================== ] 476/582 Installing : texlive-unicode-math-6: [==================== ] 476/582 Installing : texlive-unicode-math-6: [===================== ] 476/582 Installing : texlive-unicode-math-6: [======================= ] 476/582 Installing : texlive-unicode-math-6:svn38462-35.fc27.1.noarch 476/582 Installing : texlive-lualatex-math-6 [ ] 477/582 Installing : texlive-lualatex-math-6 [= ] 477/582 Installing : texlive-lualatex-math-6 [===== ] 477/582 Installing : texlive-lualatex-math-6 [======================= ] 477/582 Installing : texlive-lualatex-math-6:svn40621-35.fc27.1.noarc 477/582 Installing : texlive-filehook-6:svn2 [ ] 478/582 Installing : texlive-filehook-6:svn2 [== ] 478/582 Installing : texlive-filehook-6:svn2 [==== ] 478/582 Installing : texlive-filehook-6:svn2 [====== ] 478/582 Installing : texlive-filehook-6:svn2 [========== ] 478/582 Installing : texlive-filehook-6:svn2 [==================== ] 478/582 Installing : texlive-filehook-6:svn2 [======================= ] 478/582 Installing : texlive-filehook-6:svn24280.0.5d-35.fc27.1.noarc 478/582 Installing : texlive-currfile-6:svn4 [ ] 479/582 Installing : texlive-currfile-6:svn4 [======== ] 479/582 Installing : texlive-currfile-6:svn4 [======================= ] 479/582 Installing : texlive-currfile-6:svn40725-35.fc27.1.noarch 479/582 Installing : texlive-ifplatform-6:sv [ ] 480/582 Installing : texlive-ifplatform-6:sv [= ] 480/582 Installing : texlive-ifplatform-6:sv [== ] 480/582 Installing : texlive-ifplatform-6:sv [======================= ] 480/582 Installing : texlive-ifplatform-6:svn21156.0.4-35.fc27.1.noar 480/582 Installing : texlive-attachfile-6:sv [ ] 481/582 Installing : texlive-attachfile-6:sv [======================= ] 481/582 Installing : texlive-attachfile-6:svn38830-35.fc27.1.noarch 481/582 Installing : texlive-oberdiek-6:svn4 [ ] 482/582 Installing : texlive-oberdiek-6:svn4 [= ] 482/582 Installing : texlive-oberdiek-6:svn4 [== ] 482/582 Installing : texlive-oberdiek-6:svn4 [=== ] 482/582 Installing : texlive-oberdiek-6:svn4 [==== ] 482/582 Installing : texlive-oberdiek-6:svn4 [===== ] 482/582 Installing : texlive-oberdiek-6:svn4 [====== ] 482/582 Installing : texlive-oberdiek-6:svn4 [======= ] 482/582 Installing : texlive-oberdiek-6:svn4 [======== ] 482/582 Installing : texlive-oberdiek-6:svn4 [========= ] 482/582 Installing : texlive-oberdiek-6:svn4 [========== ] 482/582 Installing : texlive-oberdiek-6:svn4 [=========== ] 482/582 Installing : texlive-oberdiek-6:svn4 [============ ] 482/582 Installing : texlive-oberdiek-6:svn4 [============= ] 482/582 Installing : texlive-oberdiek-6:svn4 [============== ] 482/582 Installing : texlive-oberdiek-6:svn4 [=============== ] 482/582 Installing : texlive-oberdiek-6:svn4 [================ ] 482/582 Installing : texlive-oberdiek-6:svn4 [================= ] 482/582 Installing : texlive-oberdiek-6:svn4 [================== ] 482/582 Installing : texlive-oberdiek-6:svn4 [=================== ] 482/582 Installing : texlive-oberdiek-6:svn4 [==================== ] 482/582 Installing : texlive-oberdiek-6:svn4 [===================== ] 482/582 Installing : texlive-oberdiek-6:svn4 [====================== ] 482/582 Installing : texlive-oberdiek-6:svn4 [======================= ] 482/582 Installing : texlive-oberdiek-6:svn41346-35.fc27.1.noarch 482/582 Installing : texlive-listings-6:svn3 [ ] 483/582 Installing : texlive-listings-6:svn3 [== ] 483/582 Installing : texlive-listings-6:svn3 [==== ] 483/582 Installing : texlive-listings-6:svn3 [===== ] 483/582 Installing : texlive-listings-6:svn3 [======= ] 483/582 Installing : texlive-listings-6:svn3 [========= ] 483/582 Installing : texlive-listings-6:svn3 [========== ] 483/582 Installing : texlive-listings-6:svn3 [============ ] 483/582 Installing : texlive-listings-6:svn3 [============= ] 483/582 Installing : texlive-listings-6:svn3 [=============== ] 483/582 Installing : texlive-listings-6:svn3 [================= ] 483/582 Installing : texlive-listings-6:svn3 [================== ] 483/582 Installing : texlive-listings-6:svn3 [=================== ] 483/582 Installing : texlive-listings-6:svn3 [===================== ] 483/582 Installing : texlive-listings-6:svn3 [======================= ] 483/582 Installing : texlive-listings-6:svn37534.1.6-35.fc27.1.noarch 483/582 Installing : texlive-showexpl-6:svn3 [ ] 484/582 Installing : texlive-showexpl-6:svn3 [======================= ] 484/582 Installing : texlive-showexpl-6:svn32737.v0.3l-35.fc27.1.noar 484/582 Installing : texlive-fancyvrb-6:svn1 [ ] 485/582 Installing : texlive-fancyvrb-6:svn1 [============ ] 485/582 Installing : texlive-fancyvrb-6:svn1 [================= ] 485/582 Installing : texlive-fancyvrb-6:svn1 [=================== ] 485/582 Installing : texlive-fancyvrb-6:svn1 [===================== ] 485/582 Installing : texlive-fancyvrb-6:svn1 [======================= ] 485/582 Installing : texlive-fancyvrb-6:svn18492.2.8-35.fc27.1.noarch 485/582 Installing : texlive-pst-grad-6:svn1 [ ] 486/582 Installing : texlive-pst-grad-6:svn1 [============= ] 486/582 Installing : texlive-pst-grad-6:svn1 [====================== ] 486/582 Installing : texlive-pst-grad-6:svn1 [======================= ] 486/582 Installing : texlive-pst-grad-6:svn15878.1.06-35.fc27.1.noarc 486/582 Installing : texlive-pst-text-6:svn1 [ ] 487/582 Installing : texlive-pst-text-6:svn1 [= ] 487/582 Installing : texlive-pst-text-6:svn1 [======= ] 487/582 Installing : texlive-pst-text-6:svn1 [======== ] 487/582 Installing : texlive-pst-text-6:svn1 [==================== ] 487/582 Installing : texlive-pst-text-6:svn1 [====================== ] 487/582 Installing : texlive-pst-text-6:svn1 [======================= ] 487/582 Installing : texlive-pst-text-6:svn15878.1.00-35.fc27.1.noarc 487/582 Installing : texlive-pst-3d-6:svn172 [ ] 488/582 Installing : texlive-pst-3d-6:svn172 [==== ] 488/582 Installing : texlive-pst-3d-6:svn172 [===== ] 488/582 Installing : texlive-pst-3d-6:svn172 [====================== ] 488/582 Installing : texlive-pst-3d-6:svn172 [======================= ] 488/582 Installing : texlive-pst-3d-6:svn17257.1.10-35.fc27.1.noarch 488/582 Installing : texlive-pst-coil-6:svn3 [ ] 489/582 Installing : texlive-pst-coil-6:svn3 [========= ] 489/582 Installing : texlive-pst-coil-6:svn3 [====================== ] 489/582 Installing : texlive-pst-coil-6:svn3 [======================= ] 489/582 Installing : texlive-pst-coil-6:svn37377.1.07-35.fc27.1.noarc 489/582 Installing : texlive-pst-eps-6:svn15 [ ] 490/582 Installing : texlive-pst-eps-6:svn15 [= ] 490/582 Installing : texlive-pst-eps-6:svn15 [===================== ] 490/582 Installing : texlive-pst-eps-6:svn15 [====================== ] 490/582 Installing : texlive-pst-eps-6:svn15 [======================= ] 490/582 Installing : texlive-pst-eps-6:svn15878.1.0-35.fc27.1.noarch 490/582 Installing : texlive-pst-fill-6:svn1 [ ] 491/582 Installing : texlive-pst-fill-6:svn1 [==================== ] 491/582 Installing : texlive-pst-fill-6:svn1 [======================= ] 491/582 Installing : texlive-pst-fill-6:svn15878.1.01-35.fc27.1.noarc 491/582 Installing : texlive-pst-node-6:svn4 [ ] 492/582 Installing : texlive-pst-node-6:svn4 [=== ] 492/582 Installing : texlive-pst-node-6:svn4 [===== ] 492/582 Installing : texlive-pst-node-6:svn4 [============ ] 492/582 Installing : texlive-pst-node-6:svn4 [=================== ] 492/582 Installing : texlive-pst-node-6:svn4 [==================== ] 492/582 Installing : texlive-pst-node-6:svn4 [======================= ] 492/582 Installing : texlive-pst-node-6:svn40743-35.fc27.1.noarch 492/582 Installing : texlive-pst-plot-6:svn4 [ ] 493/582 Installing : texlive-pst-plot-6:svn4 [====== ] 493/582 Installing : texlive-pst-plot-6:svn4 [============ ] 493/582 Installing : texlive-pst-plot-6:svn4 [=================== ] 493/582 Installing : texlive-pst-plot-6:svn4 [==================== ] 493/582 Installing : texlive-pst-plot-6:svn4 [======================= ] 493/582 Installing : texlive-pst-plot-6:svn41242-35.fc27.1.noarch 493/582 Installing : texlive-pst-tools-6:svn [ ] 494/582 Installing : texlive-pst-tools-6:svn [============= ] 494/582 Installing : texlive-pst-tools-6:svn [====================== ] 494/582 Installing : texlive-pst-tools-6:svn [======================= ] 494/582 Installing : texlive-pst-tools-6:svn34067.0.05-35.fc27.1.noar 494/582 Installing : texlive-pst-tree-6:svn2 [ ] 495/582 Installing : texlive-pst-tree-6:svn2 [====================== ] 495/582 Installing : texlive-pst-tree-6:svn2 [======================= ] 495/582 Installing : texlive-pst-tree-6:svn24142.1.12-35.fc27.1.noarc 495/582 Installing : texlive-pstricks-add-6: [ ] 496/582 Installing : texlive-pstricks-add-6: [= ] 496/582 Installing : texlive-pstricks-add-6: [======== ] 496/582 Installing : texlive-pstricks-add-6: [================ ] 496/582 Installing : texlive-pstricks-add-6: [======================= ] 496/582 Installing : texlive-pstricks-add-6:svn40744-35.fc27.1.noarch 496/582 Installing : texlive-auto-pst-pdf-6: [ ] 497/582 Installing : texlive-auto-pst-pdf-6: [= ] 497/582 Installing : texlive-auto-pst-pdf-6: [======================= ] 497/582 Installing : texlive-auto-pst-pdf-6:svn23723.0.6-35.fc27.1.no 497/582 Installing : texlive-pstricks-6:svn4 [ ] 498/582 Installing : texlive-pstricks-6:svn4 [= ] 498/582 Installing : texlive-pstricks-6:svn4 [== ] 498/582 Installing : texlive-pstricks-6:svn4 [==== ] 498/582 Installing : texlive-pstricks-6:svn4 [===== ] 498/582 Installing : texlive-pstricks-6:svn4 [====== ] 498/582 Installing : texlive-pstricks-6:svn4 [======= ] 498/582 Installing : texlive-pstricks-6:svn4 [========= ] 498/582 Installing : texlive-pstricks-6:svn4 [========== ] 498/582 Installing : texlive-pstricks-6:svn4 [============ ] 498/582 Installing : texlive-pstricks-6:svn4 [============== ] 498/582 Installing : texlive-pstricks-6:svn4 [=============== ] 498/582 Installing : texlive-pstricks-6:svn4 [================= ] 498/582 Installing : texlive-pstricks-6:svn4 [================== ] 498/582 Installing : texlive-pstricks-6:svn4 [=================== ] 498/582 Installing : texlive-pstricks-6:svn4 [===================== ] 498/582 Installing : texlive-pstricks-6:svn4 [====================== ] 498/582 Installing : texlive-pstricks-6:svn4 [======================= ] 498/582 Installing : texlive-pstricks-6:svn41321-35.fc27.1.noarch 498/582 Installing : texlive-pst-pdf-bin-6:s [ ] 499/582 Installing : texlive-pst-pdf-bin-6:s [====== ] 499/582 Installing : texlive-pst-pdf-bin-6:s [============ ] 499/582 Installing : texlive-pst-pdf-bin-6:s [=================== ] 499/582 Installing : texlive-pst-pdf-bin-6:svn7838.0-35.20160520.fc27 499/582 Installing : texlive-pst-pdf-6:svn31 [ ] 500/582 Installing : texlive-pst-pdf-6:svn31 [==== ] 500/582 Installing : texlive-pst-pdf-6:svn31 [====== ] 500/582 Installing : texlive-pst-pdf-6:svn31 [======== ] 500/582 Installing : texlive-pst-pdf-6:svn31 [========= ] 500/582 Installing : texlive-pst-pdf-6:svn31 [======================= ] 500/582 Installing : texlive-pst-pdf-6:svn31660.1.1v-35.fc27.1.noarch 500/582 Installing : texlive-collection-basi [ ] 501/582 Installing : texlive-collection-basic-6:svn41149-35.20160520. 501/582 Installing : texlive-rotating-6:svn1 [ ] 502/582 Installing : texlive-rotating-6:svn1 [= ] 502/582 Installing : texlive-rotating-6:svn1 [======================= ] 502/582 Installing : texlive-rotating-6:svn16832.2.16b-35.fc27.1.noar 502/582 Installing : texlive-amscls-6:svn368 [ ] 503/582 Installing : texlive-amscls-6:svn368 [== ] 503/582 Installing : texlive-amscls-6:svn368 [==== ] 503/582 Installing : texlive-amscls-6:svn368 [======= ] 503/582 Installing : texlive-amscls-6:svn368 [========= ] 503/582 Installing : texlive-amscls-6:svn368 [============ ] 503/582 Installing : texlive-amscls-6:svn368 [============== ] 503/582 Installing : texlive-amscls-6:svn368 [================ ] 503/582 Installing : texlive-amscls-6:svn368 [================= ] 503/582 Installing : texlive-amscls-6:svn368 [================== ] 503/582 Installing : texlive-amscls-6:svn368 [==================== ] 503/582 Installing : texlive-amscls-6:svn368 [====================== ] 503/582 Installing : texlive-amscls-6:svn368 [======================= ] 503/582 Installing : texlive-amscls-6:svn36804.0-35.fc27.1.noarch 503/582 Installing : texlive-latex-bin-bin-6 [ ] 504/582 Installing : texlive-latex-bin-bin-6 [=== ] 504/582 Installing : texlive-latex-bin-bin-6 [====== ] 504/582 Installing : texlive-latex-bin-bin-6 [========= ] 504/582 Installing : texlive-latex-bin-bin-6 [============ ] 504/582 Installing : texlive-latex-bin-bin-6 [================ ] 504/582 Installing : texlive-latex-bin-bin-6 [==================== ] 504/582 Installing : texlive-latex-bin-bin-6:svn14050.0-35.20160520.f 504/582 Installing : texlive-latex-bin-6:svn [ ] 505/582 Installing : texlive-latex-bin-6:svn [=================== ] 505/582 Installing : texlive-latex-bin-6:svn [====================== ] 505/582 Installing : texlive-latex-bin-6:svn41438-35.fc27.1.noarch 505/582 Running scriptlet: texlive-latex-bin-6:svn41438-35.fc27.1.noarch 505/582 Installing : texlive-ctable-6:svn386 [ ] 506/582 Installing : texlive-ctable-6:svn386 [======================= ] 506/582 Installing : texlive-ctable-6:svn38672-35.fc27.1.noarch 506/582 Installing : texlive-pst-blur-6:svn1 [ ] 507/582 Installing : texlive-pst-blur-6:svn1 [= ] 507/582 Installing : texlive-pst-blur-6:svn1 [======== ] 507/582 Installing : texlive-pst-blur-6:svn1 [================== ] 507/582 Installing : texlive-pst-blur-6:svn1 [=================== ] 507/582 Installing : texlive-pst-blur-6:svn1 [======================= ] 507/582 Installing : texlive-pst-blur-6:svn15878.2.0-35.fc27.1.noarch 507/582 Installing : texlive-pst-slpe-6:svn2 [ ] 508/582 Installing : texlive-pst-slpe-6:svn2 [========== ] 508/582 Installing : texlive-pst-slpe-6:svn2 [==================== ] 508/582 Installing : texlive-pst-slpe-6:svn2 [======================= ] 508/582 Installing : texlive-pst-slpe-6:svn24391.1.31-35.fc27.1.noarc 508/582 Installing : texlive-powerdot-6:svn3 [ ] 509/582 Installing : texlive-powerdot-6:svn3 [= ] 509/582 Installing : texlive-powerdot-6:svn3 [== ] 509/582 Installing : texlive-powerdot-6:svn3 [=== ] 509/582 Installing : texlive-powerdot-6:svn3 [==== ] 509/582 Installing : texlive-powerdot-6:svn3 [====== ] 509/582 Installing : texlive-powerdot-6:svn3 [======= ] 509/582 Installing : texlive-powerdot-6:svn3 [======== ] 509/582 Installing : texlive-powerdot-6:svn3 [========= ] 509/582 Installing : texlive-powerdot-6:svn3 [========== ] 509/582 Installing : texlive-powerdot-6:svn3 [=========== ] 509/582 Installing : texlive-powerdot-6:svn3 [============ ] 509/582 Installing : texlive-powerdot-6:svn3 [============== ] 509/582 Installing : texlive-powerdot-6:svn3 [=============== ] 509/582 Installing : texlive-powerdot-6:svn3 [================ ] 509/582 Installing : texlive-powerdot-6:svn3 [===================== ] 509/582 Installing : texlive-powerdot-6:svn3 [======================= ] 509/582 Installing : texlive-powerdot-6:svn38984-35.fc27.1.noarch 509/582 Installing : texlive-pdfpages-6:svn4 [ ] 510/582 Installing : texlive-pdfpages-6:svn4 [======== ] 510/582 Installing : texlive-pdfpages-6:svn4 [============== ] 510/582 Installing : texlive-pdfpages-6:svn4 [================ ] 510/582 Installing : texlive-pdfpages-6:svn4 [================= ] 510/582 Installing : texlive-pdfpages-6:svn4 [================== ] 510/582 Installing : texlive-pdfpages-6:svn4 [=================== ] 510/582 Installing : texlive-pdfpages-6:svn4 [===================== ] 510/582 Installing : texlive-pdfpages-6:svn4 [====================== ] 510/582 Installing : texlive-pdfpages-6:svn4 [======================= ] 510/582 Installing : texlive-pdfpages-6:svn40638-35.fc27.1.noarch 510/582 Installing : texlive-tex-gyre-6:svn1 [ ] 511/582 Installing : texlive-tex-gyre-6:svn1 [= ] 511/582 Installing : texlive-tex-gyre-6:svn1 [== ] 511/582 Installing : texlive-tex-gyre-6:svn1 [=== ] 511/582 Installing : texlive-tex-gyre-6:svn1 [==== ] 511/582 Installing : texlive-tex-gyre-6:svn1 [===== ] 511/582 Installing : texlive-tex-gyre-6:svn1 [====== ] 511/582 Installing : texlive-tex-gyre-6:svn1 [======= ] 511/582 Installing : texlive-tex-gyre-6:svn1 [======== ] 511/582 Installing : texlive-tex-gyre-6:svn1 [========= ] 511/582 Installing : texlive-tex-gyre-6:svn1 [========== ] 511/582 Installing : texlive-tex-gyre-6:svn1 [=========== ] 511/582 Installing : texlive-tex-gyre-6:svn1 [============ ] 511/582 Installing : texlive-tex-gyre-6:svn1 [============= ] 511/582 Installing : texlive-tex-gyre-6:svn1 [============== ] 511/582 Installing : texlive-tex-gyre-6:svn1 [=============== ] 511/582 Installing : texlive-tex-gyre-6:svn1 [================ ] 511/582 Installing : texlive-tex-gyre-6:svn1 [================= ] 511/582 Installing : texlive-tex-gyre-6:svn1 [================== ] 511/582 Installing : texlive-tex-gyre-6:svn1 [=================== ] 511/582 Installing : texlive-tex-gyre-6:svn1 [==================== ] 511/582 Installing : texlive-tex-gyre-6:svn1 [===================== ] 511/582 Installing : texlive-tex-gyre-6:svn1 [====================== ] 511/582 Installing : texlive-tex-gyre-6:svn1 [======================= ] 511/582 Installing : texlive-tex-gyre-6:svn18651.2.004-35.fc27.1.noar 511/582 Installing : texlive-sansmathaccent- [ ] 512/582 Installing : texlive-sansmathaccent- [= ] 512/582 Installing : texlive-sansmathaccent- [== ] 512/582 Installing : texlive-sansmathaccent- [==== ] 512/582 Installing : texlive-sansmathaccent- [===== ] 512/582 Installing : texlive-sansmathaccent- [====== ] 512/582 Installing : texlive-sansmathaccent- [======== ] 512/582 Installing : texlive-sansmathaccent- [========== ] 512/582 Installing : texlive-sansmathaccent- [============ ] 512/582 Installing : texlive-sansmathaccent- [============== ] 512/582 Installing : texlive-sansmathaccent- [================ ] 512/582 Installing : texlive-sansmathaccent- [================= ] 512/582 Installing : texlive-sansmathaccent- [================== ] 512/582 Installing : texlive-sansmathaccent- [=================== ] 512/582 Installing : texlive-sansmathaccent- [==================== ] 512/582 Installing : texlive-sansmathaccent- [===================== ] 512/582 Installing : texlive-sansmathaccent- [======================= ] 512/582 Installing : texlive-sansmathaccent-6:svn30187.0-35.fc27.1.no 512/582 Installing : texlive-metalogo-6:svn1 [ ] 513/582 Installing : texlive-metalogo-6:svn1 [= ] 513/582 Installing : texlive-metalogo-6:svn1 [======================= ] 513/582 Installing : texlive-metalogo-6:svn18611.0.12-35.fc27.1.noarc 513/582 Installing : texlive-extsizes-6:svn1 [ ] 514/582 Installing : texlive-extsizes-6:svn1 [==== ] 514/582 Installing : texlive-extsizes-6:svn1 [========= ] 514/582 Installing : texlive-extsizes-6:svn1 [=========== ] 514/582 Installing : texlive-extsizes-6:svn1 [============ ] 514/582 Installing : texlive-extsizes-6:svn1 [================= ] 514/582 Installing : texlive-extsizes-6:svn1 [================== ] 514/582 Installing : texlive-extsizes-6:svn1 [==================== ] 514/582 Installing : texlive-extsizes-6:svn1 [===================== ] 514/582 Installing : texlive-extsizes-6:svn1 [====================== ] 514/582 Installing : texlive-extsizes-6:svn1 [======================= ] 514/582 Installing : texlive-extsizes-6:svn17263.1.4a-35.fc27.1.noarc 514/582 Installing : texlive-jknapltx-6:svn1 [ ] 515/582 Installing : texlive-jknapltx-6:svn1 [= ] 515/582 Installing : texlive-jknapltx-6:svn1 [== ] 515/582 Installing : texlive-jknapltx-6:svn1 [===== ] 515/582 Installing : texlive-jknapltx-6:svn1 [======== ] 515/582 Installing : texlive-jknapltx-6:svn1 [============ ] 515/582 Installing : texlive-jknapltx-6:svn1 [============= ] 515/582 Installing : texlive-jknapltx-6:svn1 [============== ] 515/582 Installing : texlive-jknapltx-6:svn1 [=============== ] 515/582 Installing : texlive-jknapltx-6:svn1 [================ ] 515/582 Installing : texlive-jknapltx-6:svn1 [================= ] 515/582 Installing : texlive-jknapltx-6:svn1 [================== ] 515/582 Installing : texlive-jknapltx-6:svn1 [==================== ] 515/582 Installing : texlive-jknapltx-6:svn1 [===================== ] 515/582 Installing : texlive-jknapltx-6:svn1 [====================== ] 515/582 Installing : texlive-jknapltx-6:svn1 [======================= ] 515/582 Installing : texlive-jknapltx-6:svn19440.0-35.fc27.1.noarch 515/582 Installing : texlive-seminar-6:svn34 [ ] 516/582 Installing : texlive-seminar-6:svn34 [= ] 516/582 Installing : texlive-seminar-6:svn34 [== ] 516/582 Installing : texlive-seminar-6:svn34 [=== ] 516/582 Installing : texlive-seminar-6:svn34 [====== ] 516/582 Installing : texlive-seminar-6:svn34 [======= ] 516/582 Installing : texlive-seminar-6:svn34 [=========== ] 516/582 Installing : texlive-seminar-6:svn34 [============ ] 516/582 Installing : texlive-seminar-6:svn34 [================= ] 516/582 Installing : texlive-seminar-6:svn34 [================== ] 516/582 Installing : texlive-seminar-6:svn34 [=================== ] 516/582 Installing : texlive-seminar-6:svn34 [==================== ] 516/582 Installing : texlive-seminar-6:svn34 [====================== ] 516/582 Installing : texlive-seminar-6:svn34 [======================= ] 516/582 Installing : texlive-seminar-6:svn34011.1.62-35.fc27.1.noarch 516/582 Installing : texlive-typehtml-6:svn1 [ ] 517/582 Installing : texlive-typehtml-6:svn1 [======================= ] 517/582 Installing : texlive-typehtml-6:svn17134.0-35.fc27.1.noarch 517/582 Installing : texlive-ucs-6:svn35853. [ ] 518/582 Installing : texlive-ucs-6:svn35853. [= ] 518/582 Installing : texlive-ucs-6:svn35853. [== ] 518/582 Installing : texlive-ucs-6:svn35853. [=== ] 518/582 Installing : texlive-ucs-6:svn35853. [==== ] 518/582 Installing : texlive-ucs-6:svn35853. [===== ] 518/582 Installing : texlive-ucs-6:svn35853. [====== ] 518/582 Installing : texlive-ucs-6:svn35853. [======= ] 518/582 Installing : texlive-ucs-6:svn35853. [======== ] 518/582 Installing : texlive-ucs-6:svn35853. [========= ] 518/582 Installing : texlive-ucs-6:svn35853. [========== ] 518/582 Installing : texlive-ucs-6:svn35853. [=========== ] 518/582 Installing : texlive-ucs-6:svn35853. [============ ] 518/582 Installing : texlive-ucs-6:svn35853. [============= ] 518/582 Installing : texlive-ucs-6:svn35853. [============== ] 518/582 Installing : texlive-ucs-6:svn35853. [=============== ] 518/582 Installing : texlive-ucs-6:svn35853. [================ ] 518/582 Installing : texlive-ucs-6:svn35853. [================= ] 518/582 Installing : texlive-ucs-6:svn35853. [================== ] 518/582 Installing : texlive-ucs-6:svn35853. [=================== ] 518/582 Installing : texlive-ucs-6:svn35853. [==================== ] 518/582 Installing : texlive-ucs-6:svn35853. [===================== ] 518/582 Installing : texlive-ucs-6:svn35853. [====================== ] 518/582 Installing : texlive-ucs-6:svn35853. [======================= ] 518/582 Installing : texlive-ucs-6:svn35853.2.2-35.fc27.1.noarch 518/582 Installing : texlive-beamer-6:svn364 [ ] 519/582 Installing : texlive-beamer-6:svn364 [= ] 519/582 Installing : texlive-beamer-6:svn364 [== ] 519/582 Installing : texlive-beamer-6:svn364 [=== ] 519/582 Installing : texlive-beamer-6:svn364 [==== ] 519/582 Installing : texlive-beamer-6:svn364 [===== ] 519/582 Installing : texlive-beamer-6:svn364 [====== ] 519/582 Installing : texlive-beamer-6:svn364 [======= ] 519/582 Installing : texlive-beamer-6:svn364 [======== ] 519/582 Installing : texlive-beamer-6:svn364 [========= ] 519/582 Installing : texlive-beamer-6:svn364 [========== ] 519/582 Installing : texlive-beamer-6:svn364 [=========== ] 519/582 Installing : texlive-beamer-6:svn364 [============ ] 519/582 Installing : texlive-beamer-6:svn364 [============= ] 519/582 Installing : texlive-beamer-6:svn364 [============== ] 519/582 Installing : texlive-beamer-6:svn364 [=============== ] 519/582 Installing : texlive-beamer-6:svn364 [================ ] 519/582 Installing : texlive-beamer-6:svn364 [================= ] 519/582 Installing : texlive-beamer-6:svn364 [================== ] 519/582 Installing : texlive-beamer-6:svn364 [=================== ] 519/582 Installing : texlive-beamer-6:svn364 [==================== ] 519/582 Installing : texlive-beamer-6:svn364 [===================== ] 519/582 Installing : texlive-beamer-6:svn364 [====================== ] 519/582 Installing : texlive-beamer-6:svn364 [======================= ] 519/582 Installing : texlive-beamer-6:svn36461.3.36-35.fc27.1.noarch 519/582 Installing : texlive-cm-super-6:svn1 [ ] 520/582 Installing : texlive-cm-super-6:svn1 [= ] 520/582 Installing : texlive-cm-super-6:svn1 [== ] 520/582 Installing : texlive-cm-super-6:svn1 [=== ] 520/582 Installing : texlive-cm-super-6:svn1 [==== ] 520/582 Installing : texlive-cm-super-6:svn1 [===== ] 520/582 Installing : texlive-cm-super-6:svn1 [====== ] 520/582 Installing : texlive-cm-super-6:svn1 [======= ] 520/582 Installing : texlive-cm-super-6:svn1 [======== ] 520/582 Installing : texlive-cm-super-6:svn1 [========= ] 520/582 Installing : texlive-cm-super-6:svn1 [========== ] 520/582 Installing : texlive-cm-super-6:svn1 [=========== ] 520/582 Installing : texlive-cm-super-6:svn1 [============ ] 520/582 Installing : texlive-cm-super-6:svn1 [============= ] 520/582 Installing : texlive-cm-super-6:svn1 [============== ] 520/582 Installing : texlive-cm-super-6:svn1 [=============== ] 520/582 Installing : texlive-cm-super-6:svn1 [================ ] 520/582 Installing : texlive-cm-super-6:svn1 [================= ] 520/582 Installing : texlive-cm-super-6:svn1 [================== ] 520/582 Installing : texlive-cm-super-6:svn1 [=================== ] 520/582 Installing : texlive-cm-super-6:svn1 [==================== ] 520/582 Installing : texlive-cm-super-6:svn1 [===================== ] 520/582 Installing : texlive-cm-super-6:svn1 [====================== ] 520/582 Installing : texlive-cm-super-6:svn1 [======================= ] 520/582 Installing : texlive-cm-super-6:svn15878.0-35.fc27.1.noarch 520/582 Installing : texlive-collection-font [ ] 521/582 Installing : texlive-collection-fontsrecommended-6:svn35830.0 521/582 Installing : texlive-ae-6:svn15878.1 [ ] 522/582 Installing : texlive-ae-6:svn15878.1 [= ] 522/582 Installing : texlive-ae-6:svn15878.1 [== ] 522/582 Installing : texlive-ae-6:svn15878.1 [=== ] 522/582 Installing : texlive-ae-6:svn15878.1 [==== ] 522/582 Installing : texlive-ae-6:svn15878.1 [===== ] 522/582 Installing : texlive-ae-6:svn15878.1 [====== ] 522/582 Installing : texlive-ae-6:svn15878.1 [======= ] 522/582 Installing : texlive-ae-6:svn15878.1 [======== ] 522/582 Installing : texlive-ae-6:svn15878.1 [========= ] 522/582 Installing : texlive-ae-6:svn15878.1 [========== ] 522/582 Installing : texlive-ae-6:svn15878.1 [=========== ] 522/582 Installing : texlive-ae-6:svn15878.1 [============ ] 522/582 Installing : texlive-ae-6:svn15878.1 [============= ] 522/582 Installing : texlive-ae-6:svn15878.1 [============== ] 522/582 Installing : texlive-ae-6:svn15878.1 [=============== ] 522/582 Installing : texlive-ae-6:svn15878.1 [================ ] 522/582 Installing : texlive-ae-6:svn15878.1 [================= ] 522/582 Installing : texlive-ae-6:svn15878.1 [================== ] 522/582 Installing : texlive-ae-6:svn15878.1 [=================== ] 522/582 Installing : texlive-ae-6:svn15878.1 [==================== ] 522/582 Installing : texlive-ae-6:svn15878.1 [===================== ] 522/582 Installing : texlive-ae-6:svn15878.1 [====================== ] 522/582 Installing : texlive-ae-6:svn15878.1 [======================= ] 522/582 Installing : texlive-ae-6:svn15878.1.4-35.fc27.1.noarch 522/582 Installing : texlive-ltxmisc-6:svn21 [ ] 523/582 Installing : texlive-ltxmisc-6:svn21 [===== ] 523/582 Installing : texlive-ltxmisc-6:svn21 [====== ] 523/582 Installing : texlive-ltxmisc-6:svn21 [======= ] 523/582 Installing : texlive-ltxmisc-6:svn21 [======== ] 523/582 Installing : texlive-ltxmisc-6:svn21 [============ ] 523/582 Installing : texlive-ltxmisc-6:svn21 [================ ] 523/582 Installing : texlive-ltxmisc-6:svn21 [================= ] 523/582 Installing : texlive-ltxmisc-6:svn21 [===================== ] 523/582 Installing : texlive-ltxmisc-6:svn21 [====================== ] 523/582 Installing : texlive-ltxmisc-6:svn21 [======================= ] 523/582 Installing : texlive-ltxmisc-6:svn21927.0-35.fc27.1.noarch 523/582 Installing : texlive-collection-late [ ] 524/582 Installing : texlive-collection-latex-6:svn41011-35.20160520. 524/582 Installing : texlive-breqn-6:svn3809 [ ] 525/582 Installing : texlive-breqn-6:svn3809 [===== ] 525/582 Installing : texlive-breqn-6:svn3809 [========= ] 525/582 Installing : texlive-breqn-6:svn3809 [============ ] 525/582 Installing : texlive-breqn-6:svn3809 [=============== ] 525/582 Installing : texlive-breqn-6:svn3809 [================== ] 525/582 Installing : texlive-breqn-6:svn3809 [==================== ] 525/582 Installing : texlive-breqn-6:svn3809 [===================== ] 525/582 Installing : texlive-breqn-6:svn3809 [======================= ] 525/582 Installing : texlive-breqn-6:svn38099.0.98d-35.fc27.1.noarch 525/582 Installing : texlive-l3experimental- [ ] 526/582 Installing : texlive-l3experimental- [== ] 526/582 Installing : texlive-l3experimental- [==== ] 526/582 Installing : texlive-l3experimental- [====== ] 526/582 Installing : texlive-l3experimental- [======== ] 526/582 Installing : texlive-l3experimental- [========== ] 526/582 Installing : texlive-l3experimental- [============ ] 526/582 Installing : texlive-l3experimental- [============= ] 526/582 Installing : texlive-l3experimental- [============== ] 526/582 Installing : texlive-l3experimental- [=============== ] 526/582 Installing : texlive-l3experimental- [================ ] 526/582 Installing : texlive-l3experimental- [================= ] 526/582 Installing : texlive-l3experimental- [================== ] 526/582 Installing : texlive-l3experimental- [=================== ] 526/582 Installing : texlive-l3experimental- [==================== ] 526/582 Installing : texlive-l3experimental- [====================== ] 526/582 Installing : texlive-l3experimental- [======================= ] 526/582 Installing : texlive-l3experimental-6:svn41163-35.fc27.1.noar 526/582 Installing : ghostscript-core-9.20-1 [ ] 527/582 Installing : ghostscript-core-9.20-1 [= ] 527/582 Installing : ghostscript-core-9.20-1 [== ] 527/582 Installing : ghostscript-core-9.20-1 [=== ] 527/582 Installing : ghostscript-core-9.20-1 [==== ] 527/582 Installing : ghostscript-core-9.20-1 [===== ] 527/582 Installing : ghostscript-core-9.20-1 [====== ] 527/582 Installing : ghostscript-core-9.20-1 [======= ] 527/582 Installing : ghostscript-core-9.20-1 [======== ] 527/582 Installing : ghostscript-core-9.20-1 [========= ] 527/582 Installing : ghostscript-core-9.20-1 [========== ] 527/582 Installing : ghostscript-core-9.20-1 [=========== ] 527/582 Installing : ghostscript-core-9.20-1 [============ ] 527/582 Installing : ghostscript-core-9.20-1 [============= ] 527/582 Installing : ghostscript-core-9.20-1 [============== ] 527/582 Installing : ghostscript-core-9.20-1 [=============== ] 527/582 Installing : ghostscript-core-9.20-1 [================ ] 527/582 Installing : ghostscript-core-9.20-1 [================= ] 527/582 Installing : ghostscript-core-9.20-1 [================== ] 527/582 Installing : ghostscript-core-9.20-1 [=================== ] 527/582 Installing : ghostscript-core-9.20-1 [==================== ] 527/582 Installing : ghostscript-core-9.20-1 [===================== ] 527/582 Installing : ghostscript-core-9.20-1 [====================== ] 527/582 Installing : ghostscript-core-9.20-1 [======================= ] 527/582 Installing : ghostscript-core-9.20-10.fc27.i686 527/582 Running scriptlet: ghostscript-core-9.20-10.fc27.i686 527/582 Installing : ghostscript-x11-9.20-10 [ ] 528/582 Installing : ghostscript-x11-9.20-10 [========= ] 528/582 Installing : ghostscript-x11-9.20-10 [================== ] 528/582 Installing : ghostscript-x11-9.20-10 [======================= ] 528/582 Installing : ghostscript-x11-9.20-10.fc27.i686 528/582 Installing : ghostscript-9.20-10.fc2 [ ] 529/582 Installing : ghostscript-9.20-10.fc27.i686 529/582 Installing : imlib-1:1.9.15-29.fc26. [ ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [= ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [== ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [=== ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [==== ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [===== ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [====== ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [======= ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [======== ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [========= ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [========== ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [=========== ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [============ ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [============= ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [============== ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [=============== ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [================ ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [================= ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [================== ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [=================== ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [==================== ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [===================== ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [====================== ] 530/582 Installing : imlib-1:1.9.15-29.fc26. [======================= ] 530/582 Installing : imlib-1:1.9.15-29.fc26.i686 530/582 Running scriptlet: imlib-1:1.9.15-29.fc26.i686 530/582 Installing : boost-container-1.63.0- [ ] 531/582 Installing : boost-container-1.63.0- [========= ] 531/582 Installing : boost-container-1.63.0- [================== ] 531/582 Installing : boost-container-1.63.0- [======================= ] 531/582 Installing : boost-container-1.63.0-9.fc27.i686 531/582 Running scriptlet: boost-container-1.63.0-9.fc27.i686 531/582 Installing : boost-devel-1.63.0-9.fc [ ] 532/582 Installing : boost-devel-1.63.0-9.fc [= ] 532/582 Installing : boost-devel-1.63.0-9.fc [== ] 532/582 Installing : boost-devel-1.63.0-9.fc [=== ] 532/582 Installing : boost-devel-1.63.0-9.fc [==== ] 532/582 Installing : boost-devel-1.63.0-9.fc [===== ] 532/582 Installing : boost-devel-1.63.0-9.fc [====== ] 532/582 Installing : boost-devel-1.63.0-9.fc [======= ] 532/582 Installing : boost-devel-1.63.0-9.fc [======== ] 532/582 Installing : boost-devel-1.63.0-9.fc [========= ] 532/582 Installing : boost-devel-1.63.0-9.fc [========== ] 532/582 Installing : boost-devel-1.63.0-9.fc [=========== ] 532/582 Installing : boost-devel-1.63.0-9.fc [============ ] 532/582 Installing : boost-devel-1.63.0-9.fc [============= ] 532/582 Installing : boost-devel-1.63.0-9.fc [============== ] 532/582 Installing : boost-devel-1.63.0-9.fc [=============== ] 532/582 Installing : boost-devel-1.63.0-9.fc [================ ] 532/582 Installing : boost-devel-1.63.0-9.fc [================= ] 532/582 Installing : boost-devel-1.63.0-9.fc [================== ] 532/582 Installing : boost-devel-1.63.0-9.fc [=================== ] 532/582 Installing : boost-devel-1.63.0-9.fc [==================== ] 532/582 Installing : boost-devel-1.63.0-9.fc [===================== ] 532/582 Installing : boost-devel-1.63.0-9.fc [====================== ] 532/582 Installing : boost-devel-1.63.0-9.fc [======================= ] 532/582 Installing : boost-devel-1.63.0-9.fc27.i686 532/582 Installing : inchi-libs-1.0.5-1.fc27 [ ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [= ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [== ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [=== ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [==== ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [===== ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [====== ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [======= ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [======== ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [========= ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [========== ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [=========== ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [============ ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [============= ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [============== ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [=============== ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [================ ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [================= ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [================== ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [=================== ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [==================== ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [===================== ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [====================== ] 533/582 Installing : inchi-libs-1.0.5-1.fc27 [======================= ] 533/582 Installing : inchi-libs-1.0.5-1.fc27.i686 533/582 Running scriptlet: inchi-libs-1.0.5-1.fc27.i686 533/582 Installing : boost-python3-1.63.0-9. [ ] 534/582 Installing : boost-python3-1.63.0-9. [== ] 534/582 Installing : boost-python3-1.63.0-9. [===== ] 534/582 Installing : boost-python3-1.63.0-9. [======== ] 534/582 Installing : boost-python3-1.63.0-9. [=========== ] 534/582 Installing : boost-python3-1.63.0-9. [============== ] 534/582 Installing : boost-python3-1.63.0-9. [================= ] 534/582 Installing : boost-python3-1.63.0-9. [==================== ] 534/582 Installing : boost-python3-1.63.0-9. [======================= ] 534/582 Installing : boost-python3-1.63.0-9.fc27.i686 534/582 Running scriptlet: boost-python3-1.63.0-9.fc27.i686 534/582 Installing : rdkit-2016.09.4-2.fc26. [ ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [= ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [== ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [=== ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [==== ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [===== ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [====== ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [======= ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [======== ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [========= ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [========== ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [=========== ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [============ ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [============= ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [============== ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [=============== ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [================ ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [================= ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [================== ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [=================== ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [==================== ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [===================== ] 535/582 Installing : rdkit-2016.09.4-2.fc26. [====================== ] 535/582 Installing : rdkit-2016.09.4-2.fc26. 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[====================== ] 579/582 Installing : libappstream-glib-0.7.0 [======================= ] 579/582 Installing : libappstream-glib-0.7.0-1.fc27.i686 579/582 Running scriptlet: libappstream-glib-0.7.0-1.fc27.i686 579/582 Installing : python2-rdkit-2016.09.4 [ ] 580/582 Installing : python2-rdkit-2016.09.4 [= ] 580/582 Installing : python2-rdkit-2016.09.4 [== ] 580/582 Installing : python2-rdkit-2016.09.4 [=== ] 580/582 Installing : python2-rdkit-2016.09.4 [==== ] 580/582 Installing : python2-rdkit-2016.09.4 [===== ] 580/582 Installing : python2-rdkit-2016.09.4 [====== ] 580/582 Installing : python2-rdkit-2016.09.4 [======= ] 580/582 Installing : python2-rdkit-2016.09.4 [======== ] 580/582 Installing : python2-rdkit-2016.09.4 [========= ] 580/582 Installing : python2-rdkit-2016.09.4 [========== ] 580/582 Installing : python2-rdkit-2016.09.4 [=========== ] 580/582 Installing : python2-rdkit-2016.09.4 [============ ] 580/582 Installing : python2-rdkit-2016.09.4 [============= ] 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[============ ] 581/582 Installing : desktop-file-utils-0.23 [=============== ] 581/582 Installing : desktop-file-utils-0.23 [================== ] 581/582 Installing : desktop-file-utils-0.23 [==================== ] 581/582 Installing : desktop-file-utils-0.23 [===================== ] 581/582 Installing : desktop-file-utils-0.23 [====================== ] 581/582 Installing : desktop-file-utils-0.23 [======================= ] 581/582 Installing : desktop-file-utils-0.23-3.fc26.i686 581/582 Installing : swig-3.0.12-8.fc27.i686 [ ] 582/582 Installing : swig-3.0.12-8.fc27.i686 [= ] 582/582 Installing : swig-3.0.12-8.fc27.i686 [== ] 582/582 Installing : swig-3.0.12-8.fc27.i686 [=== ] 582/582 Installing : swig-3.0.12-8.fc27.i686 [==== ] 582/582 Installing : swig-3.0.12-8.fc27.i686 [===== ] 582/582 Installing : swig-3.0.12-8.fc27.i686 [====== ] 582/582 Installing : swig-3.0.12-8.fc27.i686 [======= ] 582/582 Installing : swig-3.0.12-8.fc27.i686 [======== ] 582/582 Installing : 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582/582 Running scriptlet: texlive-base-6:2016-35.20160520.fc27.1.noarch 582/582 Running scriptlet: gsettings-desktop-schemas-3.24.0-1.fc27.i686 582/582 Running scriptlet: python3-3.6.1-10.fc27.i686 582/582 Running scriptlet: shared-mime-info-1.8-3.fc27.i686 582/582 Running scriptlet: swig-3.0.12-8.fc27.i686 582/582 Running scriptlet: hicolor-icon-theme-0.15-5.fc27.noarch 582/582 Running scriptlet: fontconfig-2.12.4-1.fc27.i686 582/582 Running scriptlet: systemd-233-6.fc27.i686 582/582 Failed to connect to bus: No such file or directory Running scriptlet: texlive-kpathsea-6:svn41139-35.fc27.1.noarch 582/582 updmap [WARNING]: resetting $HOME value (was /builddir) to root's actual home (/root). Running scriptlet: gdk-pixbuf2-2.36.6-1.fc27.i686 582/582 Running scriptlet: desktop-file-utils-0.23-3.fc26.i686 582/582 Verifying : autoconf-2.69-24.fc26.noarch 1/582 Verifying : automake-1.15-9.fc26.noarch 2/582 Verifying : clipper-devel-2.1-20160709.1.fc26.i686 3/582 Verifying : compat-guile18-devel-1.8.8-16.fc26.i686 4/582 Verifying : desktop-file-utils-0.23-3.fc26.i686 5/582 Verifying : doxygen-1:1.8.13-9.fc27.i686 6/582 Verifying : freeglut-devel-3.0.0-4.fc26.i686 7/582 Verifying : ghostscript-9.20-10.fc27.i686 8/582 Verifying : goocanvas-devel-1.0.0-12.fc26.i686 9/582 Verifying : gtk2-devel-2.24.31-4.fc27.i686 10/582 Verifying : gtkglext-devel-1.2.0-28.fc26.i686 11/582 Verifying : guile-lib-0.2.4-2.fc26.i686 12/582 Verifying : imlib-devel-1:1.9.15-29.fc26.i686 13/582 Verifying : libappstream-glib-0.7.0-1.fc27.i686 14/582 Verifying : libcurl-devel-7.54.1-2.fc27.i686 15/582 Verifying : libgnomecanvas-devel-2.30.3-12.fc26.i686 16/582 Verifying : libtool-2.4.6-18.fc27.i686 17/582 Verifying : mmdb2-devel-2.0.1-7.fc26.i686 18/582 Verifying : pygtk2-devel-2.24.0-16.fc26.i686 19/582 Verifying : python2-devel-2.7.13-12.fc27.i686 20/582 Verifying : python2-rdkit-2016.09.4-2.fc26.i686 21/582 Verifying : rdkit-devel-2016.09.4-2.fc26.i686 22/582 Verifying : refmac-dictionary-5.41-6.fc26.noarch 23/582 Verifying : ssm-devel-1.4-5.fc26.i686 24/582 Verifying : swig-3.0.12-8.fc27.i686 25/582 Verifying : texlive-collection-latexrecommended-6:svn35765.0 26/582 Verifying : texinfo-tex-6.4-2.fc27.i686 27/582 Verifying : gsl-devel-2.4-1.fc27.i686 28/582 Verifying : emacs-filesystem-1:25.2-2.fc27.noarch 29/582 Verifying : m4-1.4.18-3.fc26.i686 30/582 Verifying : perl-4:5.26.0-394.fc27.i686 31/582 Verifying : perl-Carp-1.42-393.fc27.noarch 32/582 Verifying : perl-Data-Dumper-2.167-394.fc27.i686 33/582 Verifying : perl-Errno-1.28-394.fc27.i686 34/582 Verifying : perl-Exporter-5.72-394.fc27.noarch 35/582 Verifying : perl-File-Path-2.14-1.fc27.noarch 36/582 Verifying : perl-Getopt-Long-1:2.50-2.fc27.noarch 37/582 Verifying : perl-IO-1.38-394.fc27.i686 38/582 Verifying : perl-PathTools-3.67-393.fc27.i686 39/582 Verifying : perl-Text-ParseWords-3.30-393.fc27.noarch 40/582 Verifying : perl-constant-1.33-394.fc27.noarch 41/582 Verifying : perl-libs-4:5.26.0-394.fc27.i686 42/582 Verifying : perl-Thread-Queue-3.12-393.fc27.noarch 43/582 Verifying : perl-threads-1:2.16-2.fc27.i686 44/582 Verifying : clipper-2.1-20160709.1.fc26.i686 45/582 Verifying : fftw2-devel-2.1.5-31.fc26.i686 46/582 Verifying : libccp4-devel-6.4.6-4.fc26.i686 47/582 Verifying : compat-guile18-1.8.8-16.fc26.i686 48/582 Verifying : gmp-devel-1:6.1.2-4.fc27.i686 49/582 Verifying : xapian-core-libs-1.4.4-1.fc27.i686 50/582 Verifying : freeglut-3.0.0-4.fc26.i686 51/582 Verifying : mesa-libGL-devel-17.1.4-1.fc27.i686 52/582 Verifying : mesa-libGLU-devel-9.0.0-11.fc26.i686 53/582 Verifying : ghostscript-core-9.20-10.fc27.i686 54/582 Verifying : ghostscript-x11-9.20-10.fc27.i686 55/582 Verifying : cairo-devel-1.14.10-1.fc27.i686 56/582 Verifying : goocanvas-1.0.0-12.fc26.i686 57/582 Verifying : atk-2.25.2-1.fc27.i686 58/582 Verifying : atk-devel-2.25.2-1.fc27.i686 59/582 Verifying : cairo-1.14.10-1.fc27.i686 60/582 Verifying : fontconfig-2.12.4-1.fc27.i686 61/582 Verifying : freetype-2.8-3.fc27.i686 62/582 Verifying : gdk-pixbuf2-2.36.6-1.fc27.i686 63/582 Verifying : gdk-pixbuf2-devel-2.36.6-1.fc27.i686 64/582 Verifying : glib2-devel-2.53.3-1.fc27.i686 65/582 Verifying : gtk2-2.24.31-4.fc27.i686 66/582 Verifying : libX11-1.6.5-2.fc27.i686 67/582 Verifying : libX11-devel-1.6.5-2.fc27.i686 68/582 Verifying : libXcomposite-0.4.4-9.fc26.i686 69/582 Verifying : libXcomposite-devel-0.4.4-9.fc26.i686 70/582 Verifying : libXcursor-1.1.14-8.fc26.i686 71/582 Verifying : libXcursor-devel-1.1.14-8.fc26.i686 72/582 Verifying : libXdamage-1.1.4-9.fc26.i686 73/582 Verifying : libXext-1.3.3-5.fc26.i686 74/582 Verifying : libXext-devel-1.3.3-5.fc26.i686 75/582 Verifying : 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python3-rpm-generators-4.13.0.1-2.fc27.noarch 115/582 Verifying : boost-python-1.63.0-9.fc27.i686 116/582 Verifying : boost-system-1.63.0-9.fc27.i686 117/582 Verifying : boost-thread-1.63.0-9.fc27.i686 118/582 Verifying : pycairo-1.10.0-6.fc26.i686 119/582 Verifying : python2-numpy-1:1.13.1-1.fc27.i686 120/582 Verifying : python2-pillow-4.2.1-2.fc27.i686 121/582 Verifying : rdkit-2016.09.4-2.fc26.i686 122/582 Verifying : xorg-x11-fonts-Type1-7.5-17.fc26.noarch 123/582 Verifying : boost-devel-1.63.0-9.fc27.i686 124/582 Verifying : ssm-1.4-5.fc26.i686 125/582 Verifying : texlive-anysize-6:svn15878.0-35.fc27.1.noarch 126/582 Verifying : texlive-base-6:2016-35.20160520.fc27.1.noarch 127/582 Verifying : texlive-beamer-6:svn36461.3.36-35.fc27.1.noarch 128/582 Verifying : texlive-booktabs-6:svn40846-35.fc27.1.noarch 129/582 Verifying : texlive-breqn-6:svn38099.0.98d-35.fc27.1.noarch 130/582 Verifying : texlive-caption-6:svn41409-35.fc27.1.noarch 131/582 Verifying : 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: texlive-fp-6:svn15878.0-35.fc27.1.noarch 147/582 Verifying : texlive-index-6:svn24099.4.1beta-35.fc27.1.noarc 148/582 Verifying : texlive-jknapltx-6:svn19440.0-35.fc27.1.noarch 149/582 Verifying : texlive-koma-script-6:svn41508-35.fc27.1.noarch 150/582 Verifying : texlive-l3experimental-6:svn41163-35.fc27.1.noar 151/582 Verifying : texlive-l3kernel-6:svn41246-35.fc27.1.noarch 152/582 Verifying : texlive-l3packages-6:svn41246-35.fc27.1.noarch 153/582 Verifying : texlive-lineno-6:svn21442.4.41-35.fc27.1.noarch 154/582 Verifying : texlive-listings-6:svn37534.1.6-35.fc27.1.noarch 155/582 Verifying : texlive-mathtools-6:svn38833-35.fc27.1.noarch 156/582 Verifying : texlive-mdwtools-6:svn15878.1.05.4-35.fc27.1.noa 157/582 Verifying : texlive-memoir-6:svn41203-35.fc27.1.noarch 158/582 Verifying : texlive-metalogo-6:svn18611.0.12-35.fc27.1.noarc 159/582 Verifying : texlive-microtype-6:svn41127-35.fc27.1.noarch 160/582 Verifying : texlive-ms-6:svn29849.0-35.fc27.1.noarch 161/582 Verifying : texlive-ntgclass-6:svn15878.2.1a-35.fc27.1.noarc 162/582 Verifying : texlive-parskip-6:svn19963.2.0-35.fc27.1.noarch 163/582 Verifying : texlive-pdfpages-6:svn40638-35.fc27.1.noarch 164/582 Verifying : texlive-powerdot-6:svn38984-35.fc27.1.noarch 165/582 Verifying : texlive-psfrag-6:svn15878.3.04-35.fc27.1.noarch 166/582 Verifying : texlive-rcs-6:svn15878.0-35.fc27.1.noarch 167/582 Verifying : texlive-rotating-6:svn16832.2.16b-35.fc27.1.noar 168/582 Verifying : texlive-sansmath-6:svn17997.1.1-35.fc27.1.noarch 169/582 Verifying : texlive-section-6:svn20180.0-35.fc27.1.noarch 170/582 Verifying : texlive-seminar-6:svn34011.1.62-35.fc27.1.noarch 171/582 Verifying : texlive-sepnum-6:svn20186.2.0-35.fc27.1.noarch 172/582 Verifying : texlive-setspace-6:svn24881.6.7a-35.fc27.1.noarc 173/582 Verifying : texlive-subfig-6:svn15878.1.3-35.fc27.1.noarch 174/582 Verifying : texlive-textcase-6:svn15878.0-35.fc27.1.noarch 175/582 Verifying : texlive-thumbpdf-6:svn34621.3.16-35.fc27.1.noarc 176/582 Verifying : texlive-typehtml-6:svn17134.0-35.fc27.1.noarch 177/582 Verifying : texlive-underscore-6:svn18261.0-35.fc27.1.noarch 178/582 Verifying : texlive-xcolor-6:svn41044-35.fc27.1.noarch 179/582 Verifying : texlive-xkeyval-6:svn35741.2.7a-35.fc27.1.noarch 180/582 Verifying : texinfo-6.4-2.fc27.i686 181/582 Verifying : texlive-collection-basic-6:svn41149-35.20160520. 182/582 Verifying : texlive-epsf-6:svn21461.2.7.4-35.fc27.1.noarch 183/582 Verifying : texlive-tetex-bin-6:svn36770.0-35.20160520.fc27. 184/582 Verifying : gsl-2.4-1.fc27.i686 185/582 Verifying : perl-Scalar-List-Utils-3:1.48-1.fc27.i686 186/582 Verifying : perl-Text-Tabs+Wrap-2013.0523-393.fc27.noarch 187/582 Verifying : perl-Unicode-Normalize-1.25-393.fc27.i686 188/582 Verifying : perl-macros-4:5.26.0-394.fc27.i686 189/582 Verifying : perl-parent-1:0.236-393.fc27.noarch 190/582 Verifying : perl-threads-shared-1.57-2.fc27.i686 191/582 Verifying : perl-Pod-Usage-4:1.69-393.fc27.noarch 192/582 Verifying : perl-Socket-4:2.024-3.fc27.i686 193/582 Verifying : fftw2-2.1.5-31.fc26.i686 194/582 Verifying : libccp4-6.4.6-4.fc26.i686 195/582 Verifying : gmp-c++-1:6.1.2-4.fc27.i686 196/582 Verifying : libICE-1.0.9-9.fc27.i686 197/582 Verifying : libXxf86vm-1.1.4-4.fc26.i686 198/582 Verifying : libglvnd-glx-1:0.2.999-20.20170620gitd850cdd.fc2 199/582 Verifying : libXdamage-devel-1.1.4-9.fc26.i686 200/582 Verifying : libXxf86vm-devel-1.1.4-4.fc26.i686 201/582 Verifying : libdrm-devel-2.4.81-1.fc27.i686 202/582 Verifying : libglvnd-devel-1:0.2.999-20.20170620gitd850cdd.f 203/582 Verifying : libxcb-devel-1.12-3.fc26.i686 204/582 Verifying : mesa-libGL-17.1.4-1.fc27.i686 205/582 Verifying : mesa-libglapi-17.1.4-1.fc27.i686 206/582 Verifying : gl-manpages-1.1-13.20161227.fc26.noarch 207/582 Verifying : mesa-libGLU-9.0.0-11.fc26.i686 208/582 Verifying : cups-libs-1:2.2.4-1.fc27.i686 209/582 Verifying : ghostscript-fonts-5.50-36.fc26.noarch 210/582 Verifying : lcms2-2.8-3.fc26.i686 211/582 Verifying : libjpeg-turbo-1.5.1-2.fc27.i686 212/582 Verifying : libpng-2:1.6.29-1.fc27.i686 213/582 Verifying : libtiff-4.0.8-1.fc27.i686 214/582 Verifying : openjpeg2-2.1.2-4.fc26.i686 215/582 Verifying : poppler-data-0.4.7-7.fc26.noarch 216/582 Verifying : urw-fonts-3:2.4-23.fc26.noarch 217/582 Verifying : libSM-1.2.2-5.fc26.i686 218/582 Verifying : libXt-1.1.5-4.fc26.i686 219/582 Verifying : fontconfig-devel-2.12.4-1.fc27.i686 220/582 Verifying : freetype-devel-2.8-3.fc27.i686 221/582 Verifying : libXrender-devel-0.9.10-2.fc26.i686 222/582 Verifying : libpng-devel-2:1.6.29-1.fc27.i686 223/582 Verifying : mesa-libEGL-devel-17.1.4-1.fc27.i686 224/582 Verifying : pixman-devel-0.34.0-3.fc26.i686 225/582 Verifying : libglvnd-egl-1:0.2.999-20.20170620gitd850cdd.fc2 226/582 Verifying : libxcb-1.12-3.fc26.i686 227/582 Verifying : pixman-0.34.0-3.fc26.i686 228/582 Verifying : fontpackages-filesystem-1.44-18.fc26.noarch 229/582 Verifying : shared-mime-info-1.8-3.fc27.i686 230/582 Verifying : pcre-devel-8.41-1.fc27.i686 231/582 Verifying : perl-File-Temp-0.230.400-393.fc27.noarch 232/582 Verifying : python3-3.6.1-10.fc27.i686 233/582 Verifying : gdk-pixbuf2-modules-2.36.6-1.fc27.i686 234/582 Verifying : gtk-update-icon-cache-3.22.16-1.fc27.i686 235/582 Verifying : hicolor-icon-theme-0.15-5.fc27.noarch 236/582 Verifying : libX11-common-1.6.5-2.fc27.noarch 237/582 Verifying : xorg-x11-proto-devel-7.7-22.fc27.noarch 238/582 Verifying : harfbuzz-1.4.6-1.fc27.i686 239/582 Verifying : libXft-2.3.2-5.fc26.i686 240/582 Verifying : libthai-0.1.25-2.fc26.i686 241/582 Verifying : harfbuzz-devel-1.4.6-1.fc27.i686 242/582 Verifying : libXft-devel-2.3.2-5.fc26.i686 243/582 Verifying : python2-pip-9.0.1-10.fc27.noarch 244/582 Verifying : python2-setuptools-36.0.1-1.fc27.noarch 245/582 Verifying : libXmu-1.1.2-5.fc26.i686 246/582 Verifying : pangox-compat-0.0.2-8.fc26.i686 247/582 Verifying : giflib-4.1.6-17.fc27.i686 248/582 Verifying : glib-1:1.2.10-48.fc26.i686 249/582 Verifying : gtk+-1:1.2.10-83.fc26.i686 250/582 Verifying : libICE-devel-1.0.9-9.fc27.i686 251/582 Verifying : libSM-devel-1.2.2-5.fc26.i686 252/582 Verifying : glib-networking-2.50.0-2.fc26.i686 253/582 Verifying : docbook-style-xsl-1.79.2-4.fc26.noarch 254/582 Verifying : docbook-utils-0.6.14-42.fc26.noarch 255/582 Verifying : libxslt-1.1.29-2.fc27.i686 256/582 Verifying : openjade-1.3.2-53.fc26.i686 257/582 Verifying : sgml-common-0.6.3-45.fc26.noarch 258/582 Verifying : source-highlight-3.1.8-10.fc26.i686 259/582 Verifying : libart_lgpl-2.3.21-16.fc26.i686 260/582 Verifying : libglade2-2.6.4-15.fc26.i686 261/582 Verifying : libffi-devel-3.1-12.fc27.i686 262/582 Verifying : pygobject2-2.28.6-17.fc26.i686 263/582 Verifying : pygobject2-codegen-2.28.6-17.fc26.i686 264/582 Verifying : pygobject2-doc-2.28.6-17.fc26.i686 265/582 Verifying : python3-setuptools-36.0.1-1.fc27.noarch 266/582 Verifying : python-xpyb-1.3.1-7.fc26.i686 267/582 Verifying : libgfortran-7.1.1-5.fc27.i686 268/582 Verifying : libquadmath-7.1.1-5.fc27.i686 269/582 Verifying : python2-nose-1.3.7-13.fc26.noarch 270/582 Verifying : libimagequant-2.10.1-1.fc27.i686 271/582 Verifying : libwebp-0.6.0-2.fc26.i686 272/582 Verifying : python2-olefile-0.44-2.fc26.noarch 273/582 Verifying : boost-python3-1.63.0-9.fc27.i686 274/582 Verifying : boost-regex-1.63.0-9.fc27.i686 275/582 Verifying : boost-serialization-1.63.0-9.fc27.i686 276/582 Verifying : inchi-libs-1.0.5-1.fc27.i686 277/582 Verifying : ttmkfdir-3.0.9-49.fc26.i686 278/582 Verifying : xorg-x11-font-utils-1:7.5-33.fc26.i686 279/582 Verifying : boost-1.63.0-9.fc27.i686 280/582 Verifying : boost-atomic-1.63.0-9.fc27.i686 281/582 Verifying : boost-chrono-1.63.0-9.fc27.i686 282/582 Verifying : boost-container-1.63.0-9.fc27.i686 283/582 Verifying : boost-context-1.63.0-9.fc27.i686 284/582 Verifying : boost-coroutine-1.63.0-9.fc27.i686 285/582 Verifying : boost-date-time-1.63.0-9.fc27.i686 286/582 Verifying : boost-fiber-1.63.0-9.fc27.i686 287/582 Verifying : boost-filesystem-1.63.0-9.fc27.i686 288/582 Verifying : boost-graph-1.63.0-9.fc27.i686 289/582 Verifying : boost-iostreams-1.63.0-9.fc27.i686 290/582 Verifying : boost-locale-1.63.0-9.fc27.i686 291/582 Verifying : boost-log-1.63.0-9.fc27.i686 292/582 Verifying : boost-math-1.63.0-9.fc27.i686 293/582 Verifying : boost-numpy-1.63.0-9.fc27.i686 294/582 Verifying : boost-program-options-1.63.0-9.fc27.i686 295/582 Verifying : boost-random-1.63.0-9.fc27.i686 296/582 Verifying : boost-signals-1.63.0-9.fc27.i686 297/582 Verifying : boost-test-1.63.0-9.fc27.i686 298/582 Verifying : boost-timer-1.63.0-9.fc27.i686 299/582 Verifying : boost-type_erasure-1.63.0-9.fc27.i686 300/582 Verifying : boost-wave-1.63.0-9.fc27.i686 301/582 Verifying : libicu-devel-57.1-4.fc26.i686 302/582 Verifying : libquadmath-devel-7.1.1-5.fc27.i686 303/582 Verifying : texlive-kpathsea-bin-6:svn40473-35.20160520.fc27 304/582 Verifying : texlive-kpathsea-6:svn41139-35.fc27.1.noarch 305/582 Verifying : texlive-amscls-6:svn36804.0-35.fc27.1.noarch 306/582 Verifying : texlive-amsfonts-6:svn29208.3.04-35.fc27.1.noarc 307/582 Verifying : texlive-amsmath-6:svn41561-35.fc27.1.noarch 308/582 Verifying : texlive-geometry-6:svn19716.5.6-35.fc27.1.noarch 309/582 Verifying : texlive-graphics-6:svn41015-35.fc27.1.noarch 310/582 Verifying : texlive-hyperref-6:svn41396-35.fc27.1.noarch 311/582 Verifying : texlive-latex-6:svn40218-35.fc27.1.noarch 312/582 Verifying : texlive-oberdiek-6:svn41346-35.fc27.1.noarch 313/582 Verifying : texlive-pgf-6:svn40966-35.fc27.1.noarch 314/582 Verifying : texlive-sansmathaccent-6:svn30187.0-35.fc27.1.no 315/582 Verifying : texlive-tools-6:svn40934-35.fc27.1.noarch 316/582 Verifying : texlive-ucs-6:svn35853.2.2-35.fc27.1.noarch 317/582 Verifying : texlive-avantgar-6:svn31835.0-35.fc27.1.noarch 318/582 Verifying : texlive-bookman-6:svn31835.0-35.fc27.1.noarch 319/582 Verifying : texlive-charter-6:svn15878.0-35.fc27.1.noarch 320/582 Verifying : texlive-cm-super-6:svn15878.0-35.fc27.1.noarch 321/582 Verifying : texlive-cmextra-6:svn32831.0-35.fc27.1.noarch 322/582 Verifying : texlive-courier-6:svn35058.0-35.fc27.1.noarch 323/582 Verifying : texlive-ec-6:svn25033.1.0-35.fc27.1.noarch 324/582 Verifying : texlive-euro-6:svn22191.1.1-35.fc27.1.noarch 325/582 Verifying : texlive-eurosym-6:svn17265.1.4_subrfix-35.fc27.1 326/582 Verifying : texlive-fpl-6:svn15878.1.002-35.fc27.1.noarch 327/582 Verifying : texlive-helvetic-6:svn31835.0-35.fc27.1.noarch 328/582 Verifying : texlive-lm-math-6:svn36915.1.959-35.fc27.1.noarc 329/582 Verifying : texlive-lm-6:svn28119.2.004-35.fc27.1.noarch 330/582 Verifying : texlive-manfnt-font-6:svn35799.0-35.fc27.1.noarc 331/582 Verifying : texlive-marvosym-6:svn29349.2.2a-35.fc27.1.noarc 332/582 Verifying : texlive-mathpazo-6:svn15878.1.003-35.fc27.1.noar 333/582 Verifying : texlive-mflogo-font-6:svn36898.1.002-35.fc27.1.n 334/582 Verifying : texlive-ncntrsbk-6:svn31835.0-35.fc27.1.noarch 335/582 Verifying : texlive-palatino-6:svn31835.0-35.fc27.1.noarch 336/582 Verifying : texlive-pxfonts-6:svn15878.0-35.fc27.1.noarch 337/582 Verifying : texlive-rsfs-6:svn15878.0-35.fc27.1.noarch 338/582 Verifying : texlive-symbol-6:svn31835.0-35.fc27.1.noarch 339/582 Verifying : texlive-tex-gyre-math-6:svn41264-35.fc27.1.noarc 340/582 Verifying : texlive-tex-gyre-6:svn18651.2.004-35.fc27.1.noar 341/582 Verifying : texlive-times-6:svn35058.0-35.fc27.1.noarch 342/582 Verifying : texlive-tipa-6:svn29349.1.3-35.fc27.1.noarch 343/582 Verifying : texlive-txfonts-6:svn15878.0-35.fc27.1.noarch 344/582 Verifying : texlive-utopia-6:svn15878.0-35.fc27.1.noarch 345/582 Verifying : texlive-wasy-6:svn35831.0-35.fc27.1.noarch 346/582 Verifying : texlive-wasy2-ps-6:svn35830.0-35.fc27.1.noarch 347/582 Verifying : texlive-wasysym-6:svn15878.2.0-35.fc27.1.noarch 348/582 Verifying : texlive-zapfchan-6:svn31835.0-35.fc27.1.noarch 349/582 Verifying : texlive-zapfding-6:svn31835.0-35.fc27.1.noarch 350/582 Verifying : texlive-ae-6:svn15878.1.4-35.fc27.1.noarch 351/582 Verifying : texlive-babel-english-6:svn30264.3.3p-35.fc27.1. 352/582 Verifying : texlive-babel-6:svn40706-35.fc27.1.noarch 353/582 Verifying : texlive-babelbib-6:svn25245.1.31-35.fc27.1.noarc 354/582 Verifying : texlive-carlisle-6:svn18258.0-35.fc27.1.noarch 355/582 Verifying : texlive-colortbl-6:svn29803.v1.0a-35.fc27.1.noar 356/582 Verifying : texlive-dvisvgm-def-6:svn41011-35.fc27.1.noarch 357/582 Verifying : texlive-fancyhdr-6:svn15878.3.1-35.fc27.1.noarch 358/582 Verifying : texlive-fix2col-6:svn38770-35.fc27.1.noarch 359/582 Verifying : texlive-graphics-cfg-6:svn40269-35.fc27.1.noarch 360/582 Verifying : texlive-latex-bin-6:svn41438-35.fc27.1.noarch 361/582 Verifying : texlive-latex-fonts-6:svn28888.0-35.fc27.1.noarc 362/582 Verifying : texlive-latexconfig-6:svn40274-35.fc27.1.noarch 363/582 Verifying : texlive-ltxmisc-6:svn21927.0-35.fc27.1.noarch 364/582 Verifying : texlive-mfnfss-6:svn19410.0-35.fc27.1.noarch 365/582 Verifying : texlive-mptopdf-6:svn41282-35.fc27.1.noarch 366/582 Verifying : texlive-natbib-6:svn20668.8.31b-35.fc27.1.noarch 367/582 Verifying : texlive-pdftex-def-6:svn22653.0.06d-35.fc27.1.no 368/582 Verifying : texlive-pslatex-6:svn16416.0-35.fc27.1.noarch 369/582 Verifying : texlive-psnfss-6:svn33946.9.2a-35.fc27.1.noarch 370/582 Verifying : texlive-pspicture-6:svn15878.0-35.fc27.1.noarch 371/582 Verifying : texlive-url-6:svn32528.3.4-35.fc27.1.noarch 372/582 Verifying : texlive-etoolbox-6:svn38031.2.2a-35.fc27.1.noarc 373/582 Verifying : texlive-pstricks-6:svn41321-35.fc27.1.noarch 374/582 Verifying : texlive-iftex-6:svn29654.0.2-35.fc27.1.noarch 375/582 Verifying : texlive-kastrup-6:svn15878.0-35.fc27.1.noarch 376/582 Verifying : texlive-luaotfload-6:svn40902-35.fc27.1.noarch 377/582 Verifying : texlive-xunicode-6:svn30466.0.981-35.fc27.1.noar 378/582 Verifying : texlive-marginnote-6:svn41382-35.fc27.1.noarch 379/582 Verifying : texlive-mparhack-6:svn15878.1.4-35.fc27.1.noarch 380/582 Verifying : texlive-csquotes-6:svn39538-35.fc27.1.noarch 381/582 Verifying : texlive-enumitem-6:svn24146.3.5.2-35.fc27.1.noar 382/582 Verifying : texlive-finstrut-6:svn21719.0.5-35.fc27.1.noarch 383/582 Verifying : texlive-ltabptch-6:svn17533.1.74d-35.fc27.1.noar 384/582 Verifying : texlive-algorithms-6:svn38085.0.1-35.fc27.1.noar 385/582 Verifying : texlive-etex-pkg-6:svn39355-35.fc27.1.noarch 386/582 Verifying : texlive-ifetex-6:svn24853.1.2-35.fc27.1.noarch 387/582 Verifying : texlive-ifluatex-6:svn41346-35.fc27.1.noarch 388/582 Verifying : texlive-ifxetex-6:svn19685.0.5-35.fc27.1.noarch 389/582 Verifying : texlive-footmisc-6:svn23330.5.5b-35.fc27.1.noarc 390/582 Verifying : texlive-pst-blur-6:svn15878.2.0-35.fc27.1.noarch 391/582 Verifying : texlive-pst-grad-6:svn15878.1.06-35.fc27.1.noarc 392/582 Verifying : texlive-pst-slpe-6:svn24391.1.31-35.fc27.1.noarc 393/582 Verifying : texlive-pst-text-6:svn15878.1.00-35.fc27.1.noarc 394/582 Verifying : texlive-type1cm-6:svn21820.0-35.fc27.1.noarch 395/582 Verifying : texlive-pst-ovl-6:svn40873-35.fc27.1.noarch 396/582 Verifying : texlive-thumbpdf-bin-6:svn6898.0-35.20160520.fc2 397/582 Verifying : perl-Encode-4:2.91-11.fc27.i686 398/582 Verifying : perl-MIME-Base64-3.15-393.fc27.i686 399/582 Verifying : perl-Pod-Simple-1:3.35-393.fc27.noarch 400/582 Verifying : perl-Storable-1:2.62-393.fc27.i686 401/582 Verifying : perl-Text-Unidecode-1.30-3.fc27.noarch 402/582 Verifying : perl-Unicode-EastAsianWidth-1.33-10.fc27.noarch 403/582 Verifying : perl-libintl-perl-1.26-4.fc27.i686 404/582 Verifying : texlive-bibtex-6:svn40768-35.fc27.1.noarch 405/582 Verifying : texlive-cm-6:svn32865.0-35.fc27.1.noarch 406/582 Verifying : texlive-dvipdfmx-bin-6:svn40273-35.20160520.fc27 407/582 Verifying : texlive-dvipdfmx-def-6:svn40328-35.fc27.1.noarch 408/582 Verifying : texlive-dvipdfmx-6:svn41149-35.fc27.1.noarch 409/582 Verifying : texlive-dvips-6:svn41149-35.fc27.1.noarch 410/582 Verifying : texlive-enctex-6:svn34957.0-35.fc27.1.noarch 411/582 Verifying : texlive-etex-6:svn37057.0-35.fc27.1.noarch 412/582 Verifying : texlive-glyphlist-6:svn28576.0-35.fc27.1.noarch 413/582 Verifying : texlive-gsftopk-6:svn40768-35.fc27.1.noarch 414/582 Verifying : texlive-hyph-utf8-6:svn41189-35.fc27.1.noarch 415/582 Verifying : texlive-hyphen-base-6:svn41138-35.fc27.1.noarch 416/582 Verifying : texlive-knuth-lib-6:svn35820.0-35.fc27.1.noarch 417/582 Verifying : texlive-knuth-local-6:svn38627-35.fc27.1.noarch 418/582 Verifying : texlive-lua-alt-getopt-6:svn29349.0.7.0-35.fc27. 419/582 Verifying : texlive-luatex-6:svn40963-35.fc27.1.noarch 420/582 Verifying : texlive-makeindex-6:svn40768-35.fc27.1.noarch 421/582 Verifying : texlive-metafont-6:svn40793-35.fc27.1.noarch 422/582 Verifying : texlive-mflogo-6:svn38628-35.fc27.1.noarch 423/582 Verifying : texlive-mfware-6:svn40768-35.fc27.1.noarch 424/582 Verifying : texlive-pdftex-6:svn41149-35.fc27.1.noarch 425/582 Verifying : texlive-plain-6:svn40274-35.fc27.1.noarch 426/582 Verifying : texlive-tetex-6:svn41059-35.fc27.1.noarch 427/582 Verifying : texlive-tex-ini-files-6:svn40533-35.fc27.1.noarc 428/582 Verifying : texlive-tex-6:svn40793-35.fc27.1.noarch 429/582 Verifying : texlive-texconfig-6:svn40768-35.fc27.1.noarch 430/582 Verifying : texlive-texlive-common-doc-6:svn40682-35.fc27.1. 431/582 Verifying : texlive-texlive-docindex-6:svn41430-35.fc27.1.no 432/582 Verifying : texlive-texlive-en-6:svn41185-35.fc27.1.noarch 433/582 Verifying : texlive-texlive-msg-translations-6:svn41431-35.f 434/582 Verifying : texlive-texlive-scripts-6:svn41433-35.fc27.1.noa 435/582 Verifying : texlive-texlive.infra-6:svn41280-35.fc27.1.noarc 436/582 Verifying : texlive-unicode-data-6:svn39808-35.fc27.1.noarch 437/582 Verifying : texlive-updmap-map-6:svn41159-35.fc27.1.noarch 438/582 Verifying : texlive-xdvi-bin-6:svn40750-35.20160520.fc27.1.i 439/582 Verifying : texlive-xdvi-6:svn40768-35.fc27.1.noarch 440/582 Verifying : perl-Pod-Perldoc-3.28-394.fc27.noarch 441/582 Verifying : perl-podlators-4.09-393.fc27.noarch 442/582 Verifying : libglvnd-1:0.2.999-20.20170620gitd850cdd.fc27.i6 443/582 Verifying : libdrm-2.4.81-1.fc27.i686 444/582 Verifying : libglvnd-core-devel-1:0.2.999-20.20170620gitd850 445/582 Verifying : libglvnd-gles-1:0.2.999-20.20170620gitd850cdd.fc 446/582 Verifying : libglvnd-opengl-1:0.2.999-20.20170620gitd850cdd. 447/582 Verifying : libXau-devel-1.0.8-7.fc26.i686 448/582 Verifying : libxshmfence-1.2-4.fc26.i686 449/582 Verifying : avahi-libs-0.7-1.fc27.i686 450/582 Verifying : jbigkit-libs-2.1-6.fc26.i686 451/582 Verifying : expat-devel-2.2.1-2.fc27.i686 452/582 Verifying : bzip2-devel-1.0.6-22.fc26.i686 453/582 Verifying : mesa-libEGL-17.1.4-1.fc27.i686 454/582 Verifying : libXau-1.0.8-7.fc26.i686 455/582 Verifying : pcre-cpp-8.41-1.fc27.i686 456/582 Verifying : pcre-utf16-8.41-1.fc27.i686 457/582 Verifying : pcre-utf32-8.41-1.fc27.i686 458/582 Verifying : python3-libs-3.6.1-10.fc27.i686 459/582 Verifying : python3-pip-9.0.1-10.fc27.noarch 460/582 Verifying : jasper-libs-2.0.12-1.fc27.i686 461/582 Verifying : graphite2-1.3.10-1.fc27.i686 462/582 Verifying : libdatrie-0.2.9-4.fc26.i686 463/582 Verifying : graphite2-devel-1.3.10-1.fc27.i686 464/582 Verifying : harfbuzz-icu-1.4.6-1.fc27.i686 465/582 Verifying : gsettings-desktop-schemas-3.24.0-1.fc27.i686 466/582 Verifying : libproxy-0.4.15-1.fc27.i686 467/582 Verifying : docbook-dtds-1.0-66.fc26.noarch 468/582 Verifying : xml-common-0.6.3-45.fc26.noarch 469/582 Verifying : docbook-style-dsssl-1.79-23.fc26.noarch 470/582 Verifying : perl-SGMLSpm-1.03ii-40.fc27.noarch 471/582 Verifying : opensp-1.5.2-24.fc26.i686 472/582 Verifying : ctags-5.8-19.fc26.i686 473/582 Verifying : libicu-57.1-4.fc26.i686 474/582 Verifying : libXfont-1.5.2-2.fc26.i686 475/582 Verifying : libfontenc-1.1.3-4.fc26.i686 476/582 Verifying : texlive-lib-6:2016-35.20160520.fc27.1.i686 477/582 Verifying : texlive-metafont-bin-6:svn40987-35.20160520.fc27 478/582 Verifying : perl-Digest-MD5-2.55-393.fc27.i686 479/582 Verifying : texlive-parallel-6:svn15878.0-35.fc27.1.noarch 480/582 Verifying : texlive-qstest-6:svn15878.0-35.fc27.1.noarch 481/582 Verifying : texlive-sauerj-6:svn15878.0-35.fc27.1.noarch 482/582 Verifying : texlive-soul-6:svn15878.2.4-35.fc27.1.noarch 483/582 Verifying : texlive-unicode-math-6:svn38462-35.fc27.1.noarch 484/582 Verifying : texlive-filehook-6:svn24280.0.5d-35.fc27.1.noarc 485/582 Verifying : texlive-latex-bin-bin-6:svn14050.0-35.20160520.f 486/582 Verifying : texlive-beton-6:svn15878.0-35.fc27.1.noarch 487/582 Verifying : texlive-mptopdf-bin-6:svn18674.0-35.20160520.fc2 488/582 Verifying : texlive-auto-pst-pdf-6:svn23723.0.6-35.fc27.1.no 489/582 Verifying : texlive-bera-6:svn20031.0-35.fc27.1.noarch 490/582 Verifying : texlive-breakurl-6:svn29901.1.40-35.fc27.1.noarc 491/582 Verifying : texlive-chngcntr-6:svn17157.1.0a-35.fc27.1.noarc 492/582 Verifying : texlive-filecontents-6:svn24250.1.3-35.fc27.1.no 493/582 Verifying : texlive-multido-6:svn18302.1.42-35.fc27.1.noarch 494/582 Verifying : texlive-paralist-6:svn39247-35.fc27.1.noarch 495/582 Verifying : texlive-pst-3d-6:svn17257.1.10-35.fc27.1.noarch 496/582 Verifying : texlive-pst-coil-6:svn37377.1.07-35.fc27.1.noarc 497/582 Verifying : texlive-pst-eps-6:svn15878.1.0-35.fc27.1.noarch 498/582 Verifying : texlive-pst-fill-6:svn15878.1.01-35.fc27.1.noarc 499/582 Verifying : texlive-pst-node-6:svn40743-35.fc27.1.noarch 500/582 Verifying : texlive-pst-plot-6:svn41242-35.fc27.1.noarch 501/582 Verifying : texlive-pst-tools-6:svn34067.0.05-35.fc27.1.noar 502/582 Verifying : texlive-pst-tree-6:svn24142.1.12-35.fc27.1.noarc 503/582 Verifying : texlive-pstricks-add-6:svn40744-35.fc27.1.noarch 504/582 Verifying : texlive-showexpl-6:svn32737.v0.3l-35.fc27.1.noar 505/582 Verifying : texlive-lualibs-6:svn40370-35.fc27.1.noarch 506/582 Verifying : texlive-luaotfload-bin-6:svn34647.0-35.20160520. 507/582 Verifying : texlive-luatexbase-6:svn38550-35.fc27.1.noarch 508/582 Verifying : perl-Pod-Escapes-1:1.07-393.fc27.noarch 509/582 Verifying : texlive-bibtex-bin-6:svn40473-35.20160520.fc27.1 510/582 Verifying : texlive-xetex-bin-6:svn41091-35.20160520.fc27.1. 511/582 Verifying : texlive-dvips-bin-6:svn40987-35.20160520.fc27.1. 512/582 Verifying : texlive-gsftopk-bin-6:svn40473-35.20160520.fc27. 513/582 Verifying : texlive-graphics-def-6:svn41879-35.fc27.1.noarch 514/582 Verifying : texlive-luatex-bin-6:svn41091-35.20160520.fc27.1 515/582 Verifying : texlive-makeindex-bin-6:svn40473-35.20160520.fc2 516/582 Verifying : texlive-mfware-bin-6:svn40473-35.20160520.fc27.1 517/582 Verifying : texlive-pdftex-bin-6:svn40987-35.20160520.fc27.1 518/582 Verifying : texlive-tex-bin-6:svn40987-35.20160520.fc27.1.i6 519/582 Verifying : texlive-texconfig-bin-6:svn29741.0-35.20160520.f 520/582 Verifying : texlive-texlive-scripts-bin-6:svn29741.0-35.2016 521/582 Verifying : perl-XML-Parser-2.44-7.fc27.i686 522/582 Verifying : perl-XML-XPath-1.40-3.fc27.noarch 523/582 Verifying : texlive-texlive.infra-bin-6:svn40312-35.20160520 524/582 Verifying : libXaw-1.0.13-5.fc26.i686 525/582 Verifying : libXpm-3.5.12-2.fc26.i686 526/582 Verifying : groff-base-1.22.3-9.fc26.i686 527/582 Verifying : perl-HTTP-Tiny-0.070-393.fc27.noarch 528/582 Verifying : perl-Term-ANSIColor-4.06-394.fc27.noarch 529/582 Verifying : perl-Term-Cap-1.17-393.fc27.noarch 530/582 Verifying : libpciaccess-0.13.4-4.fc26.i686 531/582 Verifying : systemd-233-6.fc27.i686 532/582 Verifying : dbus-libs-1:1.11.14-1.fc27.i686 533/582 Verifying : libwayland-client-1.13.0-1.fc26.i686 534/582 Verifying : libwayland-server-1.13.0-1.fc26.i686 535/582 Verifying : mesa-libgbm-17.1.4-1.fc27.i686 536/582 Verifying : libmodman-2.0.1-13.fc26.i686 537/582 Verifying : perl-Digest-1.17-393.fc27.noarch 538/582 Verifying : texlive-lualatex-math-6:svn40621-35.fc27.1.noarc 539/582 Verifying : texlive-ucharcat-6:svn38907-35.fc27.1.noarch 540/582 Verifying : texlive-currfile-6:svn40725-35.fc27.1.noarch 541/582 Verifying : texlive-ifplatform-6:svn21156.0.4-35.fc27.1.noar 542/582 Verifying : texlive-pst-pdf-6:svn31660.1.1v-35.fc27.1.noarch 543/582 Verifying : texlive-pst-math-6:svn34786.0.63-35.fc27.1.noarc 544/582 Verifying : texlive-attachfile-6:svn38830-35.fc27.1.noarch 545/582 Verifying : texlive-varwidth-6:svn24104.0.92-35.fc27.1.noarc 546/582 Verifying : libpaper-1.1.24-14.fc26.i686 547/582 Verifying : poppler-0.56.0-2.fc27.i686 548/582 Verifying : teckit-2.5.1-16.fc26.i686 549/582 Verifying : texlive-xetex-6:svn41438-35.fc27.1.noarch 550/582 Verifying : zziplib-0.13.62-8.fc26.i686 551/582 Verifying : texlive-pdftex-doc-6:svn41149-35.fc27.1.noarch 552/582 Verifying : perl-open-1.11-394.fc27.noarch 553/582 Verifying : perl-Time-Local-1:1.250-393.fc27.noarch 554/582 Verifying : hwdata-0.302-1.fc27.noarch 555/582 Verifying : acl-2.2.52-15.fc27.i686 556/582 Verifying : cryptsetup-libs-1.7.5-1.fc27.i686 557/582 Verifying : dbus-1:1.11.14-1.fc27.i686 558/582 Verifying : iptables-libs-1.6.1-2.fc26.i686 559/582 Verifying : kmod-libs-24-1.fc26.i686 560/582 Verifying : libidn-1.33-2.fc26.i686 561/582 Verifying : libseccomp-2.3.2-3.fc27.i686 562/582 Verifying : qrencode-libs-3.4.4-1.fc27.i686 563/582 Verifying : systemd-pam-233-6.fc27.i686 564/582 Verifying : texlive-environ-6:svn33821.0.3-35.fc27.1.noarch 565/582 Verifying : texlive-pst-pdf-bin-6:svn7838.0-35.20160520.fc27 566/582 Verifying : perl-SelfLoader-1.23-394.fc27.noarch 567/582 Verifying : texlive-xetex-def-6:svn40327-35.fc27.1.noarch 568/582 Verifying : texlive-xetexconfig-6:svn41133-35.fc27.1.noarch 569/582 Verifying : texlive-kpathsea-doc-6:svn41139-35.fc27.1.noarch 570/582 Verifying : perl-encoding-4:2.19-11.fc27.i686 571/582 Verifying : device-mapper-libs-1.02.141-1.fc27.i686 572/582 Verifying : libpcap-14:1.8.1-4.fc27.i686 573/582 Verifying : texlive-trimspaces-6:svn15878.1.1-35.fc27.1.noar 574/582 Verifying : perl-Filter-2:1.57-4.fc27.i686 575/582 Verifying : device-mapper-1.02.141-1.fc27.i686 576/582 Verifying : atlas-3.10.2-16.fc26.i686 577/582 Verifying : aajohan-comfortaa-fonts-2.004-7.fc26.noarch 578/582 Verifying : elinks-0.12-0.52.pre6.fc27.i686 579/582 Verifying : gpm-libs-1.20.7-10.fc26.i686 580/582 Verifying : js-1:1.8.5-27.fc27.i686 581/582 Verifying : libedit-3.1-18.20170329cvs.fc27.i686 582/582 Installed: autoconf.noarch 2.69-24.fc26 automake.noarch 1.15-9.fc26 clipper-devel.i686 2.1-20160709.1.fc26 compat-guile18-devel.i686 1.8.8-16.fc26 desktop-file-utils.i686 0.23-3.fc26 doxygen.i686 1:1.8.13-9.fc27 freeglut-devel.i686 3.0.0-4.fc26 ghostscript.i686 9.20-10.fc27 goocanvas-devel.i686 1.0.0-12.fc26 gsl-devel.i686 2.4-1.fc27 gtk2-devel.i686 2.24.31-4.fc27 gtkglext-devel.i686 1.2.0-28.fc26 guile-lib.i686 0.2.4-2.fc26 imlib-devel.i686 1:1.9.15-29.fc26 libappstream-glib.i686 0.7.0-1.fc27 libcurl-devel.i686 7.54.1-2.fc27 libgnomecanvas-devel.i686 2.30.3-12.fc26 libtool.i686 2.4.6-18.fc27 mmdb2-devel.i686 2.0.1-7.fc26 pygtk2-devel.i686 2.24.0-16.fc26 python2-devel.i686 2.7.13-12.fc27 python2-rdkit.i686 2016.09.4-2.fc26 rdkit-devel.i686 2016.09.4-2.fc26 refmac-dictionary.noarch 5.41-6.fc26 ssm-devel.i686 1.4-5.fc26 swig.i686 3.0.12-8.fc27 texinfo-tex.i686 6.4-2.fc27 texlive-collection-latexrecommended.noarch 6:svn35765.0-35.20160520.fc27.1 aajohan-comfortaa-fonts.noarch 2.004-7.fc26 acl.i686 2.2.52-15.fc27 atk.i686 2.25.2-1.fc27 atk-devel.i686 2.25.2-1.fc27 atlas.i686 3.10.2-16.fc26 avahi-libs.i686 0.7-1.fc27 boost.i686 1.63.0-9.fc27 boost-atomic.i686 1.63.0-9.fc27 boost-chrono.i686 1.63.0-9.fc27 boost-container.i686 1.63.0-9.fc27 boost-context.i686 1.63.0-9.fc27 boost-coroutine.i686 1.63.0-9.fc27 boost-date-time.i686 1.63.0-9.fc27 boost-devel.i686 1.63.0-9.fc27 boost-fiber.i686 1.63.0-9.fc27 boost-filesystem.i686 1.63.0-9.fc27 boost-graph.i686 1.63.0-9.fc27 boost-iostreams.i686 1.63.0-9.fc27 boost-locale.i686 1.63.0-9.fc27 boost-log.i686 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texlive-ms.noarch 6:svn29849.0-35.fc27.1 texlive-multido.noarch 6:svn18302.1.42-35.fc27.1 texlive-natbib.noarch 6:svn20668.8.31b-35.fc27.1 texlive-ncntrsbk.noarch 6:svn31835.0-35.fc27.1 texlive-ntgclass.noarch 6:svn15878.2.1a-35.fc27.1 texlive-oberdiek.noarch 6:svn41346-35.fc27.1 texlive-palatino.noarch 6:svn31835.0-35.fc27.1 texlive-paralist.noarch 6:svn39247-35.fc27.1 texlive-parallel.noarch 6:svn15878.0-35.fc27.1 texlive-parskip.noarch 6:svn19963.2.0-35.fc27.1 texlive-pdfpages.noarch 6:svn40638-35.fc27.1 texlive-pdftex.noarch 6:svn41149-35.fc27.1 texlive-pdftex-bin.i686 6:svn40987-35.20160520.fc27.1 texlive-pdftex-def.noarch 6:svn22653.0.06d-35.fc27.1 texlive-pdftex-doc.noarch 6:svn41149-35.fc27.1 texlive-pgf.noarch 6:svn40966-35.fc27.1 texlive-plain.noarch 6:svn40274-35.fc27.1 texlive-powerdot.noarch 6:svn38984-35.fc27.1 texlive-psfrag.noarch 6:svn15878.3.04-35.fc27.1 texlive-pslatex.noarch 6:svn16416.0-35.fc27.1 texlive-psnfss.noarch 6:svn33946.9.2a-35.fc27.1 texlive-pspicture.noarch 6:svn15878.0-35.fc27.1 texlive-pst-3d.noarch 6:svn17257.1.10-35.fc27.1 texlive-pst-blur.noarch 6:svn15878.2.0-35.fc27.1 texlive-pst-coil.noarch 6:svn37377.1.07-35.fc27.1 texlive-pst-eps.noarch 6:svn15878.1.0-35.fc27.1 texlive-pst-fill.noarch 6:svn15878.1.01-35.fc27.1 texlive-pst-grad.noarch 6:svn15878.1.06-35.fc27.1 texlive-pst-math.noarch 6:svn34786.0.63-35.fc27.1 texlive-pst-node.noarch 6:svn40743-35.fc27.1 texlive-pst-ovl.noarch 6:svn40873-35.fc27.1 texlive-pst-pdf.noarch 6:svn31660.1.1v-35.fc27.1 texlive-pst-pdf-bin.noarch 6:svn7838.0-35.20160520.fc27.1 texlive-pst-plot.noarch 6:svn41242-35.fc27.1 texlive-pst-slpe.noarch 6:svn24391.1.31-35.fc27.1 texlive-pst-text.noarch 6:svn15878.1.00-35.fc27.1 texlive-pst-tools.noarch 6:svn34067.0.05-35.fc27.1 texlive-pst-tree.noarch 6:svn24142.1.12-35.fc27.1 texlive-pstricks.noarch 6:svn41321-35.fc27.1 texlive-pstricks-add.noarch 6:svn40744-35.fc27.1 texlive-pxfonts.noarch 6:svn15878.0-35.fc27.1 texlive-qstest.noarch 6:svn15878.0-35.fc27.1 texlive-rcs.noarch 6:svn15878.0-35.fc27.1 texlive-rotating.noarch 6:svn16832.2.16b-35.fc27.1 texlive-rsfs.noarch 6:svn15878.0-35.fc27.1 texlive-sansmath.noarch 6:svn17997.1.1-35.fc27.1 texlive-sansmathaccent.noarch 6:svn30187.0-35.fc27.1 texlive-sauerj.noarch 6:svn15878.0-35.fc27.1 texlive-section.noarch 6:svn20180.0-35.fc27.1 texlive-seminar.noarch 6:svn34011.1.62-35.fc27.1 texlive-sepnum.noarch 6:svn20186.2.0-35.fc27.1 texlive-setspace.noarch 6:svn24881.6.7a-35.fc27.1 texlive-showexpl.noarch 6:svn32737.v0.3l-35.fc27.1 texlive-soul.noarch 6:svn15878.2.4-35.fc27.1 texlive-subfig.noarch 6:svn15878.1.3-35.fc27.1 texlive-symbol.noarch 6:svn31835.0-35.fc27.1 texlive-tetex.noarch 6:svn41059-35.fc27.1 texlive-tetex-bin.noarch 6:svn36770.0-35.20160520.fc27.1 texlive-tex.noarch 6:svn40793-35.fc27.1 texlive-tex-bin.i686 6:svn40987-35.20160520.fc27.1 texlive-tex-gyre.noarch 6:svn18651.2.004-35.fc27.1 texlive-tex-gyre-math.noarch 6:svn41264-35.fc27.1 texlive-tex-ini-files.noarch 6:svn40533-35.fc27.1 texlive-texconfig.noarch 6:svn40768-35.fc27.1 texlive-texconfig-bin.noarch 6:svn29741.0-35.20160520.fc27.1 texlive-texlive-common-doc.noarch 6:svn40682-35.fc27.1 texlive-texlive-docindex.noarch 6:svn41430-35.fc27.1 texlive-texlive-en.noarch 6:svn41185-35.fc27.1 texlive-texlive-msg-translations.noarch 6:svn41431-35.fc27.1 texlive-texlive-scripts.noarch 6:svn41433-35.fc27.1 texlive-texlive-scripts-bin.noarch 6:svn29741.0-35.20160520.fc27.1 texlive-texlive.infra.noarch 6:svn41280-35.fc27.1 texlive-texlive.infra-bin.i686 6:svn40312-35.20160520.fc27.1 texlive-textcase.noarch 6:svn15878.0-35.fc27.1 texlive-thumbpdf.noarch 6:svn34621.3.16-35.fc27.1 texlive-thumbpdf-bin.noarch 6:svn6898.0-35.20160520.fc27.1 texlive-times.noarch 6:svn35058.0-35.fc27.1 texlive-tipa.noarch 6:svn29349.1.3-35.fc27.1 texlive-tools.noarch 6:svn40934-35.fc27.1 texlive-trimspaces.noarch 6:svn15878.1.1-35.fc27.1 texlive-txfonts.noarch 6:svn15878.0-35.fc27.1 texlive-type1cm.noarch 6:svn21820.0-35.fc27.1 texlive-typehtml.noarch 6:svn17134.0-35.fc27.1 texlive-ucharcat.noarch 6:svn38907-35.fc27.1 texlive-ucs.noarch 6:svn35853.2.2-35.fc27.1 texlive-underscore.noarch 6:svn18261.0-35.fc27.1 texlive-unicode-data.noarch 6:svn39808-35.fc27.1 texlive-unicode-math.noarch 6:svn38462-35.fc27.1 texlive-updmap-map.noarch 6:svn41159-35.fc27.1 texlive-url.noarch 6:svn32528.3.4-35.fc27.1 texlive-utopia.noarch 6:svn15878.0-35.fc27.1 texlive-varwidth.noarch 6:svn24104.0.92-35.fc27.1 texlive-wasy.noarch 6:svn35831.0-35.fc27.1 texlive-wasy2-ps.noarch 6:svn35830.0-35.fc27.1 texlive-wasysym.noarch 6:svn15878.2.0-35.fc27.1 texlive-xcolor.noarch 6:svn41044-35.fc27.1 texlive-xdvi.noarch 6:svn40768-35.fc27.1 texlive-xdvi-bin.i686 6:svn40750-35.20160520.fc27.1 texlive-xetex.noarch 6:svn41438-35.fc27.1 texlive-xetex-bin.i686 6:svn41091-35.20160520.fc27.1 texlive-xetex-def.noarch 6:svn40327-35.fc27.1 texlive-xetexconfig.noarch 6:svn41133-35.fc27.1 texlive-xkeyval.noarch 6:svn35741.2.7a-35.fc27.1 texlive-xunicode.noarch 6:svn30466.0.981-35.fc27.1 texlive-zapfchan.noarch 6:svn31835.0-35.fc27.1 texlive-zapfding.noarch 6:svn31835.0-35.fc27.1 ttmkfdir.i686 3.0.9-49.fc26 urw-fonts.noarch 3:2.4-23.fc26 xapian-core-libs.i686 1.4.4-1.fc27 xml-common.noarch 0.6.3-45.fc26 xorg-x11-font-utils.i686 1:7.5-33.fc26 xorg-x11-fonts-Type1.noarch 7.5-17.fc26 xorg-x11-proto-devel.noarch 7.7-22.fc27 zlib-devel.i686 1.2.11-2.fc26 zziplib.i686 0.13.62-8.fc26 Complete! Finish: build setup for coot-0.8.8-2.fc27.src.rpm Start: rpmbuild coot-0.8.8-2.fc27.src.rpm Building target platforms: i686 Building for target i686 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.hQir4w + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf coot-0.8.8 + /usr/bin/gzip -dc /builddir/build/SOURCES/coot-0.8.8.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd coot-0.8.8 + /usr/bin/gzip -dc /builddir/build/SOURCES/reference-structures.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . Patch #0 (coot-configure.ac.patch): + echo 'Patch #0 (coot-configure.ac.patch):' + /usr/bin/patch --no-backup-if-mismatch -p0 --fuzz=0 patching file configure.ac Hunk #2 succeeded at 157 (offset 9 lines). Patch #1 (coot-makefile.patch): + echo 'Patch #1 (coot-makefile.patch):' + /usr/bin/patch --no-backup-if-mismatch -p0 --fuzz=0 patching file src/Makefile.am Hunk #1 succeeded at 460 (offset 3 lines). patching file lbg/Makefile.am Patch #2 (coot-guile.patch): + echo 'Patch #2 (coot-guile.patch):' + /usr/bin/patch --no-backup-if-mismatch -p0 --fuzz=0 patching file macros/guile.m4 Patch #3 (coot-utils.patch): + echo 'Patch #3 (coot-utils.patch):' + /usr/bin/patch --no-backup-if-mismatch -p0 --fuzz=0 patching file coot-utils/coot-shelx.hh patching file coot-utils/coot-hole.hh Patch #4 (coot-rdkit.patch): + echo 'Patch #4 (coot-rdkit.patch):' + /usr/bin/patch --no-backup-if-mismatch -p0 --fuzz=0 patching file lbg/lbg-search.cc Patch #5 (coot-lbg.patch): + echo 'Patch #5 (coot-lbg.patch):' + /usr/bin/patch --no-backup-if-mismatch -p0 --fuzz=0 patching file lbg/lbg.cc Hunk #1 succeeded at 4905 (offset 32 lines). + cp /builddir/build/SOURCES/coot.in ./src/ + cp /builddir/build/SOURCES/coot.desktop . + iconv -f iso8859-1 -t utf-8 README + mv -f README.conv README + rm macros/libtool.m4 + aclocal -I macros + libtoolize --automake --copy + autoconf + automake --copy --add-missing --gnu src/Makefile.am:464: warning: pythondir was already defined in condition TRUE, which includes condition COOT_USE_PYTHON ... configure.ac:215: ... 'pythondir' previously defined here + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.mto0uK '/usr/lib/rpm/redhat/config.sub' -> './config.sub' '/usr/lib/rpm/redhat/config.guess' -> './config.guess' + umask 022 + cd /builddir/build/BUILD + cd coot-0.8.8 + mkdir guile + CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables' + export CFLAGS + CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables' + export CXXFLAGS + FFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -I/usr/lib/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -I/usr/lib/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + export LDFLAGS + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./config.sub ++ basename ./config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./config.guess ++ basename ./config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./config.guess + '[' 1 = 1 ']' + '[' x '!=' x-specs=/usr/lib/rpm/redhat/redhat-hardened-ld ']' ++ find . -name ltmain.sh + for i in $(find . -name ltmain.sh) + /usr/bin/sed -i.backup -e 's~compiler_flags=$~compiler_flags="-specs=/usr/lib/rpm/redhat/redhat-hardened-ld"~' ./ltmain.sh + ./configure --build=i686-redhat-linux-gnu --host=i686-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-guile --with-python --with-pygtk --disable-static 'CXXFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing' --with-enhanced-ligand-tools 'RDKIT_LIBS=-lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7' 'RDKIT_CXXFLAGS=-I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT' checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for style of include used by make... GNU checking for i686-redhat-linux-gnu-gcc... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for library containing strerror... none required checking for i686-redhat-linux-gnu-gcc... gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for i686-redhat-linux-gnu-g++... no checking for i686-redhat-linux-gnu-c++... no checking for i686-redhat-linux-gnu-gpp... no checking for i686-redhat-linux-gnu-aCC... no checking for i686-redhat-linux-gnu-CC... no checking for i686-redhat-linux-gnu-cxx... no checking for i686-redhat-linux-gnu-cc++... no checking for i686-redhat-linux-gnu-cl.exe... no checking for i686-redhat-linux-gnu-FCC... no checking for i686-redhat-linux-gnu-KCC... no checking for i686-redhat-linux-gnu-RCC... no checking for i686-redhat-linux-gnu-xlC_r... no checking for i686-redhat-linux-gnu-xlC... no checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking build system type... i686-redhat-linux-gnu checking host system type... i686-redhat-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert i686-redhat-linux-gnu file names to i686-redhat-linux-gnu format... func_convert_file_noop checking how to convert i686-redhat-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for i686-redhat-linux-gnu-objdump... no checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for i686-redhat-linux-gnu-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for i686-redhat-linux-gnu-ar... no checking for ar... ar checking for archiver @FILE support... @ checking for i686-redhat-linux-gnu-strip... no checking for strip... strip checking for i686-redhat-linux-gnu-ranlib... no checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for i686-redhat-linux-gnu-mt... no checking for mt... no checking if : is a manifest tool... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking what warning flags to pass to the C compiler... -Wall -Wunused checking what language compliance flags to pass to the C compiler... checking what warning flags to pass to the C++ compiler... -Wall -Wno-unused checking what language compliance flags to pass to the C++ compiler... checking sys/stdtypes.h usability... no checking sys/stdtypes.h presence... no checking for sys/stdtypes.h... no checking for OpenMP flag of C compiler... -fopenmp checking for i686-redhat-linux-gnu-pkg-config... /usr/bin/i686-redhat-linux-gnu-pkg-config checking pkg-config is at least version 0.9.0... yes checking for GLIB... yes checking if this is MINGW on Windows... no checking for SQLite3... no checking for mmdb2... yes checking for ssm... yes no checking for prefixed single-precision FFTW2 (sfftw.h)... yes checking for Clipper... yes Congratulations, you are using Guile checking for guile1.8... /usr/bin/guile1.8 checking for guile1.8-config... /usr/bin/guile1.8-config checking for guile1.8-tools... /usr/bin/guile1.8-tools checking libguile compile flags... -pthread checking libguile link flags... -pthread -lguile checking GUILE_VERSION: 1.8 checking for gsl-config... /usr/bin/gsl-config checking for GSL - version >= 1.3... yes checking for GTK... yes checking for GNOME_CANVAS... yes checking for pkg-config... (cached) /usr/bin/i686-redhat-linux-gnu-pkg-config checking for GtkGLExt - version >= 1.0.0... yes (version 1.2.0) checking for glLineWidth in -lGL... yes checking for GLUT... yes checking for Python... checking Python.h usability... yes checking Python.h presence... yes checking for Python.h... yes Cool, using Python checking for PYGTK... yes Good we have pygtk checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.7/site-packages checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages checking for guile-gtk... checking for boostlib >= 1.20.0... yes checking for python2.7... /usr/bin/python2.7 checking for a version of Python >= '2.1.0'... yes checking for the distutils Python package... yes checking for Python include path... -I/usr/include/python2.7 checking for Python library path... -L/usr/lib -lpython2.7 checking for Python site-packages path... /usr/lib/python2.7/site-packages checking python extra libraries... -lpthread -ldl -lutil -lm checking python extra linking flags... -Xlinker -export-dynamic checking consistency of all components of python development environment... yes checking whether the Boost::Python library is available... yes checking for exit in -lboost_python... yes checking libglade... no checking for Goocanvas... yes Not using MySQL database checking for curl >= 7.9.7... ./configure: line 21973: bc: command not found 7.54.1 checking build type... Linux-i386-fedora-27-python-gtk2 checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating macros/Makefile config.status: creating pdb-templates/Makefile config.status: creating scheme/Makefile config.status: creating python/Makefile config.status: creating compat/Makefile config.status: creating utils/Makefile config.status: creating coot-utils/Makefile config.status: creating protein_db/Makefile config.status: creating ccp4mg-utils/Makefile config.status: creating coords/Makefile config.status: creating db-main/Makefile config.status: creating density-contour/Makefile config.status: creating surface/Makefile config.status: creating coot-surface/Makefile config.status: creating angles/Makefile config.status: creating mini-mol/Makefile config.status: creating skeleton/Makefile config.status: creating ligand/Makefile config.status: creating geometry/Makefile config.status: creating ideal/Makefile config.status: creating build/Makefile config.status: creating analysis/Makefile config.status: creating high-res/Makefile config.status: creating tw/Makefile config.status: creating cootaneer/Makefile config.status: creating cootilus/Makefile config.status: creating greg-tests/Makefile config.status: creating python-tests/Makefile config.status: creating lidia-core/Makefile config.status: creating libgtkgraph/Makefile config.status: creating goograph/Makefile config.status: creating lbg/Makefile config.status: creating doc/Makefile config.status: creating src/Makefile config.status: creating src/coot config.status: creating python/coot_load_modules.py config.status: creating data/Makefile config.status: creating pixmaps/Makefile config.status: creating pixmaps/icons/Makefile config.status: creating rama-data/Makefile config.status: creating man/Makefile config.status: creating pyrogen/Makefile config.status: creating pyrogen/pyrogen config.status: creating auxil/Makefile config.status: creating auxil/catcheck/Makefile config.status: creating auxil/rama/Makefile config.status: creating auxil/sec-str/Makefile config.status: creating auxil/strand-analysis/Makefile config.status: creating auxil/vectors/Makefile config.status: creating rcrane/Makefile config.status: executing depfiles commands config.status: executing libtool commands + sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool + sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool + sed -i -e 's! -shared ! -Wl,--as-needed\0!g' libtool + sed -i 's|$(SHELL) ./config.status;; \\|echo "skipping";; \\|' Makefile + cp libtool libtool.tdf + make -j2 CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /builddir/build/BUILD/coot-0.8.8/missing aclocal-1.15 -I macros -I macros CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /builddir/build/BUILD/coot-0.8.8/missing autoconf cd . && /bin/sh /builddir/build/BUILD/coot-0.8.8/missing automake-1.15 --gnu /bin/sh ./config.status --recheck running CONFIG_SHELL=/bin/sh /bin/sh ./configure --build=i686-redhat-linux-gnu --host=i686-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-guile --with-python --with-pygtk --disable-static CXXFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing --with-enhanced-ligand-tools RDKIT_LIBS=-lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 RDKIT_CXXFLAGS=-I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT build_alias=i686-redhat-linux-gnu host_alias=i686-redhat-linux-gnu CFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables LDFLAGS=-Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld PKG_CONFIG_PATH=:/usr/lib/pkgconfig:/usr/share/pkgconfig --no-create --no-recursion checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for style of include used by make... GNU checking for i686-redhat-linux-gnu-gcc... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for library containing strerror... none required checking for i686-redhat-linux-gnu-gcc... gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for i686-redhat-linux-gnu-g++... no checking for i686-redhat-linux-gnu-c++... no checking for i686-redhat-linux-gnu-gpp... no checking for i686-redhat-linux-gnu-aCC... no checking for i686-redhat-linux-gnu-CC... no checking for i686-redhat-linux-gnu-cxx... no checking for i686-redhat-linux-gnu-cc++... no checking for i686-redhat-linux-gnu-cl.exe... no checking for i686-redhat-linux-gnu-FCC... no checking for i686-redhat-linux-gnu-KCC... no checking for i686-redhat-linux-gnu-RCC... no checking for i686-redhat-linux-gnu-xlC_r... no checking for i686-redhat-linux-gnu-xlC... no checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking build system type... i686-redhat-linux-gnu checking host system type... i686-redhat-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert i686-redhat-linux-gnu file names to i686-redhat-linux-gnu format... func_convert_file_noop checking how to convert i686-redhat-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for i686-redhat-linux-gnu-objdump... no checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for i686-redhat-linux-gnu-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for i686-redhat-linux-gnu-ar... no checking for ar... ar checking for archiver @FILE support... @ checking for i686-redhat-linux-gnu-strip... no checking for strip... strip checking for i686-redhat-linux-gnu-ranlib... no checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for i686-redhat-linux-gnu-mt... no checking for mt... no checking if : is a manifest tool... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking what warning flags to pass to the C compiler... -Wall -Wunused checking what language compliance flags to pass to the C compiler... checking what warning flags to pass to the C++ compiler... -Wall -Wno-unused checking what language compliance flags to pass to the C++ compiler... checking sys/stdtypes.h usability... no checking sys/stdtypes.h presence... no checking for sys/stdtypes.h... no checking for OpenMP flag of C compiler... src/Makefile.am:464: warning: pythondir was already defined in condition TRUE, which includes condition COOT_USE_PYTHON ... configure.ac:215: ... 'pythondir' previously defined here -fopenmp checking for i686-redhat-linux-gnu-pkg-config... /usr/bin/i686-redhat-linux-gnu-pkg-config checking pkg-config is at least version 0.9.0... yes checking for GLIB... yes checking if this is MINGW on Windows... no checking for SQLite3... no checking for mmdb2... yes checking for ssm... yes no checking for prefixed single-precision FFTW2 (sfftw.h)... yes checking for Clipper... yes Congratulations, you are using Guile checking for guile1.8... /usr/bin/guile1.8 checking for guile1.8-config... /usr/bin/guile1.8-config checking for guile1.8-tools... /usr/bin/guile1.8-tools checking libguile compile flags... -pthread checking libguile link flags... -pthread -lguile checking GUILE_VERSION: 1.8 checking for gsl-config... /usr/bin/gsl-config checking for GSL - version >= 1.3... yes checking for GTK... yes checking for GNOME_CANVAS... yes checking for pkg-config... (cached) /usr/bin/i686-redhat-linux-gnu-pkg-config checking for GtkGLExt - version >= 1.0.0... yes (version 1.2.0) checking for glLineWidth in -lGL... yes checking for GLUT... yes checking for Python... checking Python.h usability... yes checking Python.h presence... yes checking for Python.h... yes Cool, using Python checking for PYGTK... yes Good we have pygtk checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.7/site-packages checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages checking for guile-gtk... checking for boostlib >= 1.20.0... yes checking for python2.7... /usr/bin/python2.7 checking for a version of Python >= '2.1.0'... yes checking for the distutils Python package... yes checking for Python include path... -I/usr/include/python2.7 checking for Python library path... -L/usr/lib -lpython2.7 checking for Python site-packages path... /usr/lib/python2.7/site-packages checking python extra libraries... -lpthread -ldl -lutil -lm checking python extra linking flags... -Xlinker -export-dynamic checking consistency of all components of python development environment... yes checking whether the Boost::Python library is available... yes checking for exit in -lboost_python... yes checking libglade... no checking for Goocanvas... yes Not using MySQL database checking for curl >= 7.9.7... ./configure: line 21977: bc: command not found 7.54.1 checking build type... Linux-i386-fedora-27-python-gtk2 checking that generated files are newer than configure... done configure: creating ./config.status /bin/sh ./config.status skipping Making all in auxil make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' Making all in catcheck make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil/catcheck' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil/catcheck' Making all in rama make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil/rama' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil/rama' Making all in sec-str make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil/sec-str' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil/sec-str' Making all in strand-analysis make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil/strand-analysis' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil/strand-analysis' Making all in vectors make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil/vectors' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil/vectors' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil' Making all in scheme make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/scheme' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/scheme' Making all in python make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/python' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/python' Making all in pdb-templates make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pdb-templates' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pdb-templates' Making all in macros make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/macros' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/macros' Making all in compat make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/compat' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c -o getopt.lo getopt.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 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.libs/getopt.o libtool: compile: gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c getopt1.c -fPIC -DPIC -o .libs/getopt1.o /bin/sh ../libtool --tag=CC --mode=link gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions 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"-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c win-compat.cc -fPIC -DPIC -o .libs/win-compat.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o threads.lo threads.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c threads.cc -fPIC -DPIC -o .libs/threads.o /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-utils.la -rpath /usr/lib coot-utils.lo coot-fasta.lo atomic-numbers.lo gdk-keysyms.lo hsv-rgb.lo dodec.lo win-compat.lo threads.lo libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/coot-utils.o .libs/coot-fasta.o .libs/atomic-numbers.o .libs/gdk-keysyms.o .libs/hsv-rgb.o .libs/dodec.o .libs/win-compat.o .libs/threads.o -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-utils.so.0 -o .libs/libcoot-utils.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-utils.so.0" && ln -s "libcoot-utils.so.0.0.0" "libcoot-utils.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-utils.so" && ln -s "libcoot-utils.so.0.0.0" "libcoot-utils.so") libtool: link: ( cd ".libs" && rm -f "libcoot-utils.la" && ln -s "../libcoot-utils.la" "libcoot-utils.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/utils' Making all in protein_db make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/protein_db' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches 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-fno-strict-aliasing -Wall -Wno-unused -c -o protein_db_utils.lo protein_db_utils.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c protein_db.cpp -fPIC -DPIC -o .libs/protein_db.o libtool: compile: g++ 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-Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-protein-db.la -rpath /usr/lib protein_db.lo protein_db_utils.lo rna_db.lo -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/protein_db.o .libs/protein_db_utils.o .libs/rna_db.o -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o 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"-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c atom-quads.cc -fPIC -DPIC -o .libs/atom-quads.o /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-mini-mol.la -rpath /usr/lib mini-mol.lo mini-mol-utils.lo atom-quads.lo ../utils/libcoot-utils.la -lmmdb2 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/mini-mol.o .libs/mini-mol-utils.o .libs/atom-quads.o ../utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-mini-mol.so.0 -o .libs/libcoot-mini-mol.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-mini-mol.so.0" && ln -s "libcoot-mini-mol.so.0.0.0" "libcoot-mini-mol.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-mini-mol.so" && ln -s "libcoot-mini-mol.so.0.0.0" "libcoot-mini-mol.so") libtool: link: ( cd ".libs" && rm -f "libcoot-mini-mol.la" && ln -s "../libcoot-mini-mol.la" "libcoot-mini-mol.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/mini-mol' Making all in geometry make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/geometry' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 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-DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o compare-dictionaries.o compare-dictionaries.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o make-shelx-restraints.o make-shelx-restraints.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o available-comp-id.o available-comp-id.cc /bin/sh ../libtool --tag=CXX --mode=link g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-geometry.la -rpath /usr/lib protein-geometry.lo protein-geometry-mmdb.lo read-sbase.lo energy-lib.lo chem_mods.lo srs-interface.lo protein-donor-acceptors.lo lbg-graph.lo dreiding.lo dict-utils.lo cif-parse.lo main-chain.lo residue-and-atom-specs.lo mol-utils-2.lo ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/protein-geometry.o .libs/protein-geometry-mmdb.o .libs/read-sbase.o .libs/energy-lib.o .libs/chem_mods.o .libs/srs-interface.o .libs/protein-donor-acceptors.o .libs/lbg-graph.o .libs/dreiding.o .libs/dict-utils.o .libs/cif-parse.o .libs/main-chain.o .libs/residue-and-atom-specs.o .libs/mol-utils-2.o -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ../mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-geometry.so.0 -o .libs/libcoot-geometry.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-geometry.so.0" && ln -s "libcoot-geometry.so.0.0.0" "libcoot-geometry.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-geometry.so" && ln -s "libcoot-geometry.so.0.0.0" "libcoot-geometry.so") libtool: link: ( cd ".libs" && rm -f "libcoot-geometry.la" && ln -s "../libcoot-geometry.la" "libcoot-geometry.la" ) /bin/sh ../libtool --tag=CXX --mode=link g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o coot-compare-dictionaries compare-dictionaries.o ./libcoot-geometry.la /bin/sh ../libtool --tag=CXX --mode=link g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o coot-available-comp-id available-comp-id.o ./libcoot-geometry.la libtool: link: g++ -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/coot-compare-dictionaries compare-dictionaries.o ./.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 /bin/sh ../libtool --tag=CXX --mode=link g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o coot-make-shelx-restraints make-shelx-restraints.o ./libcoot-geometry.la libtool: link: g++ -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/coot-available-comp-id available-comp-id.o ./.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 libtool: link: g++ -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/coot-make-shelx-restraints make-shelx-restraints.o ./.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/geometry' Making all in coot-utils make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coot-utils' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o coot-coord-utils.lo coot-coord-utils.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o coot-coord-utils-nucleotides.lo coot-coord-utils-nucleotides.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 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-lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-map-heavy.so.0 -o .libs/libcoot-map-heavy.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-map-heavy.so.0" && ln -s "libcoot-map-heavy.so.0.0.0" "libcoot-map-heavy.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-map-heavy.so" && ln -s "libcoot-map-heavy.so.0.0.0" "libcoot-map-heavy.so") libtool: link: ( cd ".libs" && rm -f "libcoot-map-heavy.la" && ln -s "../libcoot-map-heavy.la" "libcoot-map-heavy.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coot-utils' Making all in surface make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/surface' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXSphereElement.lo CXXSphereElement.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXChargeTable.lo CXXChargeTable.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXSphereElement.cpp -fPIC -DPIC -o .libs/CXXSphereElement.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXChargeTable.cpp -fPIC -DPIC -o .libs/CXXChargeTable.o In file included from CXXNewHood.h:22:0, from CXXSphereElement.cpp:19: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXSphereNode.lo CXXSphereNode.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXSphereNode.cpp -fPIC -DPIC -o .libs/CXXSphereNode.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXCircle.lo CXXCircle.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXSphereTriangle.lo CXXSphereTriangle.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXCircle.cpp -fPIC -DPIC -o .libs/CXXCircle.o In file included from CXXNewHood.h:22:0, from CXXCircle.cpp:12: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXSphereTriangle.cpp -fPIC -DPIC -o .libs/CXXSphereTriangle.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXCircleNode.lo CXXCircleNode.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXCircleNode.cpp -fPIC -DPIC -o .libs/CXXCircleNode.o In file included from CXXNewHood.h:22:0, from CXXCircleNode.cpp:13: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXSphereTriangleEdge.lo CXXSphereTriangleEdge.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXSphereTriangleEdge.cpp -fPIC -DPIC -o .libs/CXXSphereTriangleEdge.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXCoord.lo CXXCoord.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXCoord.cpp -fPIC -DPIC -o .libs/CXXCoord.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXSurface.lo CXXSurface.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXCreator.lo CXXCreator.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXSurface.cpp -fPIC -DPIC -o .libs/CXXSurface.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXCreator.cpp -fPIC -DPIC -o .libs/CXXCreator.o In file included from CXXNewHood.h:22:0, from CXXSurface.cpp:17: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) CXXSurface.cpp:593:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(none) shared(nSelAtoms, SelAtom, cout, unitSphereAtOrigin, vdwBallPntrs, contactMap, ContextSelAtom, splitReentrantProbes) schedule(dynamic, 100) //num_threads(2) CXXSurface.cpp:597:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical(cout) CXXSurface.cpp:618:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (mainTriangles) CXXSurface.cpp: In member function 'int CXXSurface::calculateVDWFromAtoms(mmdb::PManager, int, int, double, double, bool)': CXXSurface.cpp:497:45: warning: deleting object of abstract class type 'CXXBall' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] if (vdwBallPntrs[i]) delete vdwBallPntrs[i]; ^ CXXSurface.cpp:502:54: warning: deleting object of abstract class type 'CXXBall' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] if (contextBallPntrs[i]) delete contextBallPntrs[i]; ^ CXXSurface.cpp: In member function 'int CXXSurface::calculateAccessibleFromAtoms(mmdb::PManager, int, int, double, double, bool)': CXXSurface.cpp:549:45: warning: deleting object of abstract class type 'CXXBall' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] if (vdwBallPntrs[i]) delete vdwBallPntrs[i]; ^ CXXSurface.cpp:554:54: warning: deleting object of abstract class type 'CXXBall' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] if (contextBallPntrs[i]) delete contextBallPntrs[i]; ^ CXXSurface.cpp: In member function 'int CXXSurface::calculateFromAtoms(mmdb::PManager, int, int, double, double, bool)': CXXSurface.cpp:634:79: warning: deleting object of polymorphic class type 'CXXAtomBall' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] if (vdwBallPntrs[i]) delete static_cast(vdwBallPntrs[i]); ^ CXXSurface.cpp:637:87: warning: deleting object of polymorphic class type 'CXXAtomBall' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] if (contextBallPntrs[i]) delete static_cast(contextBallPntrs[i]); ^ CXXSurface.cpp:641:76: warning: deleting object of polymorphic class type 'CXXReentrantProbeBall' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete static_cast(reentrantProbes[i]); ^ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXSurfaceVertex.lo CXXSurfaceVertex.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXSurfaceVertex.cpp -fPIC -DPIC -o .libs/CXXSurfaceVertex.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXException.lo CXXException.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXException.cpp -fPIC -DPIC -o .libs/CXXException.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXTorusElement.lo CXXTorusElement.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXTorusElement.cpp -fPIC -DPIC -o .libs/CXXTorusElement.o In file included from CXXNewHood.h:22:0, from CXXTorusElement.cpp:17: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXFFTSolventMap.lo CXXFFTSolventMap.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXFFTSolventMap.cpp -fPIC -DPIC -o .libs/CXXFFTSolventMap.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXTorusNode.lo CXXTorusNode.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXTorusNode.cpp -fPIC -DPIC -o .libs/CXXTorusNode.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXFortranFile.lo CXXFortranFile.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXNewHood.lo CXXNewHood.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXFortranFile.cpp -fPIC -DPIC -o .libs/CXXFortranFile.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXNewHood.cpp -fPIC -DPIC -o .libs/CXXNewHood.o In file included from CXXNewHood.h:22:0, from CXXNewHood.cpp:15: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) CXXNewHood.cpp:345:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (circleNodes) CXXNewHood.cpp:376:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (mainTriangles) CXXNewHood.cpp:409:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (mainTriangles) /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXTriangle.lo CXXTriangle.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXTriangle.cpp -fPIC -DPIC -o .libs/CXXTriangle.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXNode.lo CXXNode.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXNode.cpp -fPIC -DPIC -o .libs/CXXNode.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXQADSurface.lo CXXQADSurface.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXQADSurface.cpp -fPIC -DPIC -o .libs/CXXQADSurface.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXBall.lo CXXBall.cpp In file included from CXXNewHood.h:22:0, from CXXQADSurface.h:11, from CXXQADSurface.cpp:1: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXBall.cpp -fPIC -DPIC -o .libs/CXXBall.o In file included from CXXBall.cpp:10:0: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) CXXBall.cpp:34:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(none) shared(delta, nBalls, contactMap, aSurface, raggedEdges, insideOrOutside, ballPntrs) schedule(dynamic, 10) //num_threads(2) CXXBall.cpp:83:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(none) shared(trimmedBalls, contactMap, insideOrOutside, reformattedEdges, delta, aSurface) schedule(dynamic, 10) //num_threads(2) CXXBall.cpp:197:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(none) shared (binnedballs, ballRadiusX2, limits, binWidth, nBins, balls, contactMap) schedule(dynamic,10) //num_threads(2) /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXQADSurfaceStaticData.lo CXXQADSurfaceStaticData.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXQADSurfaceStaticData.cpp -fPIC -DPIC -o .libs/CXXQADSurfaceStaticData.o In file included from CXXNewHood.h:22:0, from CXXQADSurface.h:11, from CXXQADSurfaceStaticData.cpp:1: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXSpace.lo CXXSpace.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXSpace.cpp -fPIC -DPIC -o .libs/CXXSpace.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o CXXUtils.lo CXXUtils.cpp CXXSpace.cpp: In member function 'int CXXSpace::dumpSpaceSlice(int, int, int)': CXXSpace.cpp:516:8: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (j == (dim[1]-1)) ^~ CXXSpace.cpp:518:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' break; ^~~~~ CXXSpace.cpp:523:8: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (j == (dim[1]-1)) ^~ CXXSpace.cpp:526:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' break; ^~~~~ CXXSpace.cpp:563:8: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (i == (dim[0]-1)) ^~ CXXSpace.cpp:566:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' break; ^~~~~ CXXSpace.cpp:571:8: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (i == (dim[0]-1)) ^~ CXXSpace.cpp:575:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' break; ^~~~~ CXXSpace.cpp:605:8: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (i == (dim[0]-1)) ^~ CXXSpace.cpp:608:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' break; ^~~~~ CXXSpace.cpp:613:8: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (i == (dim[0]-1)) ^~ CXXSpace.cpp:616:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' break; ^~~~~ libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CXXUtils.cpp -fPIC -DPIC -o .libs/CXXUtils.o /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-electrostatics.la -rpath /usr/lib CXXSphereElement.lo CXXChargeTable.lo CXXSphereNode.lo CXXCircle.lo CXXSphereTriangle.lo CXXCircleNode.lo CXXSphereTriangleEdge.lo CXXCoord.lo CXXSurface.lo CXXCreator.lo CXXSurfaceVertex.lo CXXException.lo CXXTorusElement.lo CXXFFTSolventMap.lo CXXTorusNode.lo CXXFortranFile.lo CXXNewHood.lo CXXTriangle.lo CXXNode.lo CXXQADSurface.lo CXXBall.lo CXXQADSurfaceStaticData.lo CXXSpace.lo CXXUtils.lo -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lsrfftw -lsfftw -lmmdb2 libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/CXXSphereElement.o .libs/CXXChargeTable.o .libs/CXXSphereNode.o .libs/CXXCircle.o .libs/CXXSphereTriangle.o .libs/CXXCircleNode.o .libs/CXXSphereTriangleEdge.o .libs/CXXCoord.o .libs/CXXSurface.o .libs/CXXCreator.o .libs/CXXSurfaceVertex.o .libs/CXXException.o .libs/CXXTorusElement.o .libs/CXXFFTSolventMap.o .libs/CXXTorusNode.o .libs/CXXFortranFile.o .libs/CXXNewHood.o .libs/CXXTriangle.o .libs/CXXNode.o .libs/CXXQADSurface.o .libs/CXXBall.o .libs/CXXQADSurfaceStaticData.o .libs/CXXSpace.o .libs/CXXUtils.o -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lpthread -lccp4c -lsrfftw -lsfftw -lmmdb2 -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-electrostatics.so.0 -o .libs/libcoot-electrostatics.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-electrostatics.so.0" && ln -s "libcoot-electrostatics.so.0.0.0" "libcoot-electrostatics.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-electrostatics.so" && ln -s "libcoot-electrostatics.so.0.0.0" "libcoot-electrostatics.so") libtool: link: ( cd ".libs" && rm -f "libcoot-electrostatics.la" && ln -s "../libcoot-electrostatics.la" "libcoot-electrostatics.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/surface' Making all in coot-surface make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coot-surface' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o coot-surface.lo coot-surface.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o rgbreps.lo rgbreps.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c coot-surface.cc -fPIC -DPIC -o .libs/coot-surface.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c rgbreps.cc -fPIC -DPIC -o .libs/rgbreps.o /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-surface.la -rpath /usr/lib coot-surface.lo rgbreps.lo ../surface/libcoot-electrostatics.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -lglut -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lGL libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/coot-surface.o .libs/rgbreps.o ../surface/.libs/libcoot-electrostatics.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lglut -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lGL -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-surface.so.0 -o .libs/libcoot-surface.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-surface.so.0" && ln -s "libcoot-surface.so.0.0.0" "libcoot-surface.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-surface.so" && ln -s "libcoot-surface.so.0.0.0" "libcoot-surface.so") libtool: link: ( cd ".libs" && rm -f "libcoot-surface.la" && ln -s "../libcoot-surface.la" "libcoot-surface.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coot-surface' Making all in lidia-core make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/lidia-core' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o lbg-shared.lo lbg-shared.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit 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"libcoot-coords.so" && ln -s "libcoot-coords.so.0.0.0" "libcoot-coords.so") libtool: link: ( cd ".libs" && rm -f "libcoot-coords.la" && ln -s "../libcoot-coords.la" "libcoot-coords.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coords' Making all in angles make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/angles' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -g -O1 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o libcoot_AngleInfo_la-AngleInfo.lo `test -f 'AngleInfo.cc' || echo './'`AngleInfo.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ 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-g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c AngleInfo-angle-torsions-autogen.cc -fPIC -DPIC -o .libs/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -g -O1 -O2 -g -pipe -Wall 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"../libcoot-AngleInfo.la" "libcoot-AngleInfo.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/angles' Making all in skeleton make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/skeleton' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -g -pipe -Wall -Werror=format-security 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../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o BuildCas.lo BuildCas.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c BuildCas.cc -fPIC -DPIC -o .libs/BuildCas.o /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-skeleton.la -rpath /usr/lib dm-utils.lo graphical_skel.lo BuildCas.lo ../angles/libcoot-AngleInfo.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/dm-utils.o .libs/graphical_skel.o .libs/BuildCas.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ../angles/.libs/libcoot-AngleInfo.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so -lgsl -lgslcblas /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-skeleton.so.0 -o .libs/libcoot-skeleton.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-skeleton.so.0" && ln -s "libcoot-skeleton.so.0.0.0" "libcoot-skeleton.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-skeleton.so" && ln -s "libcoot-skeleton.so.0.0.0" "libcoot-skeleton.so") libtool: link: ( cd ".libs" && rm -f "libcoot-skeleton.la" && ln -s "../libcoot-skeleton.la" "libcoot-skeleton.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/skeleton' Making all in ccp4mg-utils make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -DUSE_LIBPNG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o geomutil.lo geomutil.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -DUSE_LIBPNG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o mgtree.lo mgtree.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_LIBPNG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c mgtree.cc -fPIC -DPIC -o .libs/mgtree.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_LIBPNG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c geomutil.cc -fPIC -DPIC -o .libs/geomutil.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -DUSE_LIBPNG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o cartesian.lo cartesian.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_LIBPNG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c cartesian.cc -fPIC -DPIC -o .libs/cartesian.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -DUSE_LIBPNG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o matrix.lo matrix.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_LIBPNG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c matrix.cc -fPIC -DPIC -o .libs/matrix.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -DUSE_LIBPNG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o quat.lo quat.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -DUSE_LIBPNG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o ppmutil.lo ppmutil.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_LIBPNG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c quat.cc -fPIC -DPIC -o .libs/quat.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_LIBPNG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c ppmutil.cc -fPIC -DPIC -o .libs/ppmutil.o ppmutil.cc: In member function 'void image_info::readpng(const char*)': ppmutil.cc:2508:79: warning: 'palette' may be used uninitialized in this function [-Wmaybe-uninitialized] pixels[i*width*colourspace+j*colourspace] = palette[row_pointers[i][j]].red; ^ ppmutil.cc:2512:9: warning: 'num_trans' may be used uninitialized in this function [-Wmaybe-uninitialized] if(row_pointers[i][j] >&, const std::vector >&, const std::vector >&) const': mogul-interface.hh:27:10: warning: '.coot::mogul_item::idx_4' may be used uninitialized in this function [-Wmaybe-uninitialized] class mogul_item { ^~~~~~~~~~ mogul-interface.hh:27:10: warning: '.coot::mogul_item::dmin' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+64).coot::mogul_distribution::bin_start' may be used uninitialized in this function [-Wmaybe-uninitialized] class mogul_distribution { ^~~~~~~~~~~~~~~~~~ mogul-interface.hh:16:10: warning: '*((void*)(&)+64).coot::mogul_distribution::bin_end' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+64).coot::mogul_distribution::bin_width' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+64).coot::mogul_distribution::n_bins' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh: In member function 'coot::mogul_item coot::mogul::parse_item_line(const std::vector >&, int) const': mogul-interface.hh:27:10: warning: '.coot::mogul_item::idx_3' may be used uninitialized in this function [-Wmaybe-uninitialized] class mogul_item { ^~~~~~~~~~ mogul-interface.hh:27:10: warning: '.coot::mogul_item::idx_4' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:27:10: warning: '.coot::mogul_item::dmin' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+64).coot::mogul_distribution::bin_start' may be used uninitialized in this function [-Wmaybe-uninitialized] class mogul_distribution { ^~~~~~~~~~~~~~~~~~ mogul-interface.hh:16:10: warning: '*((void*)(&)+64).coot::mogul_distribution::bin_end' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+64).coot::mogul_distribution::bin_width' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+64).coot::mogul_distribution::n_bins' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:27:10: warning: '.coot::mogul_item::idx_4' may be used uninitialized in this function [-Wmaybe-uninitialized] class mogul_item { ^~~~~~~~~~ mogul-interface.hh:27:10: warning: '.coot::mogul_item::dmin' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+64).coot::mogul_distribution::bin_start' may be used uninitialized in this function [-Wmaybe-uninitialized] class mogul_distribution { ^~~~~~~~~~~~~~~~~~ mogul-interface.hh:16:10: warning: '*((void*)(&)+64).coot::mogul_distribution::bin_end' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+64).coot::mogul_distribution::bin_width' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+64).coot::mogul_distribution::n_bins' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:27:10: warning: '.coot::mogul_item::mean' may be used uninitialized in this function [-Wmaybe-uninitialized] class mogul_item { ^~~~~~~~~~ mogul-interface.hh:27:10: warning: '.coot::mogul_item::median' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:27:10: warning: '.coot::mogul_item::std_dev' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:27:10: warning: '.coot::mogul_item::z' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+64).coot::mogul_distribution::bin_start' may be used uninitialized in this function [-Wmaybe-uninitialized] class mogul_distribution { ^~~~~~~~~~~~~~~~~~ mogul-interface.hh:16:10: warning: '*((void*)(&)+64).coot::mogul_distribution::bin_end' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+64).coot::mogul_distribution::bin_width' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+64).coot::mogul_distribution::n_bins' may be used uninitialized in this function [-Wmaybe-uninitialized] /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o stats.lo stats.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c stats.cc -fPIC -DPIC -o .libs/stats.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o cablam.lo cablam.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c cablam.cc -fPIC -DPIC -o .libs/cablam.o g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o bfactan.o bfactan.cc /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-analysis.la -rpath /usr/lib bfkurt.lo mogul.lo kolmogorov.lo stats.lo cablam.lo ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lmmdb2 -lgsl -lgslcblas -lm libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/bfkurt.o .libs/mogul.o .libs/kolmogorov.o .libs/stats.o .libs/cablam.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ../coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so ../geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so ../mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c ../utils/.libs/libcoot-utils.so -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-analysis.so.0 -o .libs/libcoot-analysis.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-analysis.so.0" && ln -s "libcoot-analysis.so.0.0.0" "libcoot-analysis.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-analysis.so" && ln -s "libcoot-analysis.so.0.0.0" "libcoot-analysis.so") libtool: link: ( cd ".libs" && rm -f "libcoot-analysis.la" && ln -s "../libcoot-analysis.la" "libcoot-analysis.la" ) /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o coot-bfactan bfactan.o libcoot-analysis.la ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 libtool: link: g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/coot-bfactan bfactan.o ./.libs/libcoot-analysis.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so -lgsl -lgslcblas ../geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so ../mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/analysis' Making all in ideal make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ideal' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_GSL -I/usr/include -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o simple-restraint.lo simple-restraint.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_GSL -I/usr/include -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o mods.lo mods.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DHAVE_GSL -I/usr/include -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c mods.cc -fPIC -DPIC -o .libs/mods.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 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"libcoot-ideal.so") libtool: link: ( cd ".libs" && rm -f "libcoot-ideal.la" && ln -s "../libcoot-ideal.la" "libcoot-ideal.la" ) /bin/sh ../libtool --tag=CXX --mode=link g++ -DHAVE_GSL -I/usr/include -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -lmmdb2 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o mini-rsr-bin mini-rsr.o ./libcoot-ideal.la ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la ../compat/libcoot-compat.la ../mini-mol/libcoot-mini-mol.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -lgsl -lgslcblas -lm libtool: link: g++ -DHAVE_GSL -I/usr/include -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/mini-rsr-bin mini-rsr.o ./.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-shelx.so ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-coord-utils.so ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so ../utils/.libs/libcoot-utils.so ../compat/.libs/libcoot-compat.so ../mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lm make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ideal' Making all in ligand make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ligand' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_GSL -I/usr/include -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 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-DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_GSL -I/usr/include -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o wiggly-ligand.lo wiggly-ligand.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DHAVE_GSL -I/usr/include -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c wiggly-ligand.cc -fPIC -DPIC -o .libs/wiggly-ligand.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" 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-DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_GSL -I/usr/include -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o trace.lo trace.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DHAVE_GSL -I/usr/include -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c trace.cc -fPIC -DPIC -o .libs/trace.o trace.cc:353:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for shared(scores) trace.cc:1202:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for // currently we write out the fragments, not store them /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_GSL -I/usr/include -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall 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../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_GSL -I/usr/include -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o multi-peptide.lo multi-peptide.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DHAVE_GSL -I/usr/include -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c multi-peptide.cc -fPIC -DPIC -o .libs/multi-peptide.o /bin/sh ../libtool --tag=CXX --mode=compile g++ 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-DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DHAVE_GSL -I/usr/include -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c ligands-db.cc -fPIC -DPIC -o .libs/ligands-db.o g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_GSL -I/usr/include -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o find-ligand.o find-ligand.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_GSL -I/usr/include -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o find-waters.o find-waters.cc /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 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-L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so ../db-main/.libs/libcoot-db-main.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../geometry/.libs/libcoot-geometry.so ../mini-mol/.libs/libcoot-mini-mol.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers 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/usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-ligand.so.0 -o .libs/libcoot-ligand.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-ligand.so.0" && ln -s "libcoot-ligand.so.0.0.0" "libcoot-ligand.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-ligand.so" && ln -s "libcoot-ligand.so.0.0.0" "libcoot-ligand.so") libtool: link: ( cd ".libs" && rm -f "libcoot-ligand.la" && ln -s "../libcoot-ligand.la" "libcoot-ligand.la" ) /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o findligand-bin find-ligand.o ./libcoot-ligand.la ../ideal/libcoot-ideal.la ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../db-main/libcoot-db-main.la ../ccp4mg-utils/libccp4mg-utils.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../lidia-core/libcoot-lidia-core.la ../coot-utils/libcoot-shelx.la ../mini-mol/libcoot-mini-mol.la ../compat/libcoot-compat.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -lgsl -lgslcblas -lm /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o findwaters-bin find-waters.o ./libcoot-ligand.la ../ideal/libcoot-ideal.la ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../ccp4mg-utils/libccp4mg-utils.la ../db-main/libcoot-db-main.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../lidia-core/libcoot-lidia-core.la ../coot-utils/libcoot-shelx.la ../mini-mol/libcoot-mini-mol.la ../compat/libcoot-compat.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -lgsl -lgslcblas -lm libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/findligand-bin find-ligand.o ./.libs/libcoot-ligand.so /builddir/build/BUILD/coot-0.8.8/ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/db-main/.libs/libcoot-db-main.so /builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/.libs/libccp4mg-utils.so /builddir/build/BUILD/coot-0.8.8/analysis/.libs/libcoot-analysis.so ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so ../db-main/.libs/libcoot-db-main.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-coord-utils.so ../utils/.libs/libcoot-utils.so ../lidia-core/.libs/libcoot-lidia-core.so ../coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so ../mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so ../compat/.libs/libcoot-compat.so -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lm libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/findwaters-bin find-waters.o ./.libs/libcoot-ligand.so /builddir/build/BUILD/coot-0.8.8/ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/db-main/.libs/libcoot-db-main.so /builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/.libs/libccp4mg-utils.so /builddir/build/BUILD/coot-0.8.8/analysis/.libs/libcoot-analysis.so ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../db-main/.libs/libcoot-db-main.so ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-coord-utils.so ../utils/.libs/libcoot-utils.so ../lidia-core/.libs/libcoot-lidia-core.so ../coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so ../mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so ../compat/.libs/libcoot-compat.so -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lm make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ligand' Making all in high-res make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/high-res' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" 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-DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o sequence-assignment.lo sequence-assignment.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c sequence-assignment.cc -fPIC -DPIC -o .libs/sequence-assignment.o /bin/sh ../libtool --tag=CXX --mode=link g++ -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-high-res.la -rpath /usr/lib high-res.lo coot-atom-graph.lo residue-distortions.lo sequence-assignment.lo ../mini-mol/libcoot-mini-mol.la ../ligand/libcoot-ligand.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/high-res.o .libs/coot-atom-graph.o .libs/residue-distortions.o .libs/sequence-assignment.o -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/ideal/.libs -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/db-main/.libs -L/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/analysis/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ../mini-mol/.libs/libcoot-mini-mol.so ../ligand/.libs/libcoot-ligand.so 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libtool: link: (cd ".libs" && rm -f "libcoot-high-res.so" && ln -s "libcoot-high-res.so.0.0.0" "libcoot-high-res.so") libtool: link: ( cd ".libs" && rm -f "libcoot-high-res.la" && ln -s "../libcoot-high-res.la" "libcoot-high-res.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/high-res' Making all in build make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/build' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 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"-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c CalphaBuild.cc -fPIC -DPIC -o .libs/CalphaBuild.o /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-cabuild.la -rpath /usr/lib CalphaBuild.lo ../angles/libcoot-AngleInfo.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw 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"libcoot-tw.so") libtool: link: ( cd ".libs" && rm -f "libcoot-tw.la" && ln -s "../libcoot-tw.la" "libcoot-tw.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/tw' Making all in libgtkgraph make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/libgtkgraph' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" 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-DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c annotation.c -fPIC -DPIC -o .libs/annotation.o libtool: compile: gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c polar_util.c -fPIC -DPIC -o .libs/polar_util.o /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c -o trace.lo trace.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c -o axis.lo axis.c libtool: compile: gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c trace.c -fPIC -DPIC -o .libs/trace.o libtool: compile: gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c axis.c -fPIC -DPIC -o .libs/axis.o trace.c: In function 'gtk_graph_trace_set_data': trace.c:147:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (xd[i] > xmax_store) ^~ trace.c:149:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (xd[i] < xmin_store ) ^~ trace.c: In function 'gtk_graph_trace_format_marker': trace.c:259:12: warning: this 'else' clause does not guard... [-Wmisleading-indentation] else ^~~~ trace.c:261:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' break; ^~~~~ /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c -o gtkgraph.lo gtkgraph.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c -o polar.lo polar.c libtool: compile: gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c gtkgraph.c -fPIC -DPIC -o .libs/gtkgraph.o libtool: compile: gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c polar.c -fPIC -DPIC -o .libs/polar.o /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c -o smith.lo smith.c libtool: compile: gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c smith.c -fPIC -DPIC -o .libs/smith.o /bin/sh ../libtool --tag=CC --mode=link gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-gtkgraph.la -rpath /usr/lib annotation.lo polar_util.lo trace.lo axis.lo gtkgraph.lo polar.lo smith.lo -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lm libtool: link: gcc -Wl,--as-needed -shared -fPIC -DPIC .libs/annotation.o .libs/polar_util.o .libs/trace.o .libs/axis.o .libs/gtkgraph.o .libs/polar.o .libs/smith.o -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lm -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-gtkgraph.so.0 -o .libs/libcoot-gtkgraph.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-gtkgraph.so.0" && ln -s "libcoot-gtkgraph.so.0.0.0" "libcoot-gtkgraph.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-gtkgraph.so" && ln -s "libcoot-gtkgraph.so.0.0.0" "libcoot-gtkgraph.so") libtool: link: ( cd ".libs" && rm -f "libcoot-gtkgraph.la" && ln -s "../libcoot-gtkgraph.la" "libcoot-gtkgraph.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/libgtkgraph' Making all in lbg make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/lbg' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o lbg.lo lbg.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o lbg-flev.lo lbg-flev.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c lbg.cc -fPIC -DPIC -o .libs/lbg.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c lbg-flev.cc -fPIC -DPIC -o .libs/lbg-flev.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o wmolecule.lo wmolecule.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK 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-I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o lbg-search.lo lbg-search.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c lbg-search.cc -fPIC -DPIC -o .libs/lbg-search.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 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../lidia-core/libcoot-lidia-core.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -lgsl -lgslcblas -lm -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lcairo -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil libtool: link: g++ 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-lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lpython2.7 -lpthread -ldl -lm -lutil make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/lbg' Making all in cootaneer make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/cootaneer' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o buccaneer-lib.lo buccaneer-lib.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o buccaneer-prot.lo buccaneer-prot.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c buccaneer-prot.cpp -fPIC -DPIC -o .libs/buccaneer-prot.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c buccaneer-lib.cpp -fPIC -DPIC -o .libs/buccaneer-lib.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o buccaneer-sequence.lo buccaneer-sequence.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c buccaneer-sequence.cpp -fPIC -DPIC -o .libs/buccaneer-sequence.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o cootaneer-sequence.lo cootaneer-sequence.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c cootaneer-sequence.cpp -fPIC -DPIC -o .libs/cootaneer-sequence.o /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcootaneer.la -rpath /usr/lib buccaneer-lib.lo buccaneer-prot.lo buccaneer-sequence.lo cootaneer-sequence.lo -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 libtool: link: g++ -fPIC -DPIC 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"libcootaneer.so.0.0.0" "libcootaneer.so") libtool: link: ( cd ".libs" && rm -f "libcootaneer.la" && ln -s "../libcootaneer.la" "libcootaneer.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/cootaneer' Making all in cootilus make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/cootilus' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ 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-Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o nautilus-tools.lo nautilus-tools.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 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-DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c nautilus-ss-find.cpp -fPIC -DPIC -o .libs/nautilus-ss-find.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" 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-DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c cootilus-build.cpp -fPIC -DPIC -o .libs/cootilus-build.o /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcootilus.la -rpath /usr/lib nucleicacid_db.lo nautilus-tools.lo nautilus-ss-find.lo nautilus-join.lo nautilus-target.lo cootilus-build.lo -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/nucleicacid_db.o .libs/nautilus-tools.o .libs/nautilus-ss-find.o .libs/nautilus-join.o .libs/nautilus-target.o .libs/cootilus-build.o -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcootilus.so.0 -o .libs/libcootilus.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcootilus.so.0" && ln -s "libcootilus.so.0.0.0" "libcootilus.so.0") libtool: link: (cd ".libs" && rm -f "libcootilus.so" && ln -s "libcootilus.so.0.0.0" "libcootilus.so") libtool: link: ( cd ".libs" && rm -f "libcootilus.la" && ln -s "../libcootilus.la" "libcootilus.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/cootilus' Making all in goograph make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/goograph' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 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-lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/goograph.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField 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"libcoot-goograph.so" && ln -s "libcoot-goograph.so.0.0.0" "libcoot-goograph.so") libtool: link: ( cd ".libs" && rm -f "libcoot-goograph.la" && ln -s "../libcoot-goograph.la" "libcoot-goograph.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/goograph' Making all in pyrogen make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pyrogen' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I.. -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o mmff-restraints.lo mmff-restraints.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 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-DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c mmff-restraints.cc -fPIC -DPIC -o .libs/mmff-restraints.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" 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-DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I.. -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o pyrogen-swig.lo pyrogen-swig.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c pyrogen-swig.cc -fPIC -DPIC -o .libs/pyrogen-swig.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I.. -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o restraints.lo restraints.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c restraints.cc -fPIC -DPIC -o .libs/restraints.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I.. -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o restraints-boost.lo restraints-boost.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c restraints-boost.cc -fPIC -DPIC -o .libs/restraints-boost.o cd .. && /bin/sh ./config.status pyrogen/pyrogen config.status: creating pyrogen/pyrogen /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot_py_restraints.la -rpath /usr/lib mmff-restraints.lo py-restraints.lo ../geometry/libcoot-geometry.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/mmff-restraints.o .libs/py-restraints.o -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ../geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lmmdb2 -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lpthread -ldl -lutil -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-export-dynamic -Wl,-soname -Wl,libcoot_py_restraints.so.0 -o .libs/libcoot_py_restraints.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot_py_restraints.so.0" && ln -s "libcoot_py_restraints.so.0.0.0" "libcoot_py_restraints.so.0") libtool: link: (cd ".libs" && rm -f "libcoot_py_restraints.so" && ln -s "libcoot_py_restraints.so.0.0.0" "libcoot_py_restraints.so") libtool: link: ( cd ".libs" && rm -f "libcoot_py_restraints.la" && ln -s "../libcoot_py_restraints.la" "libcoot_py_restraints.la" ) /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -module -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o _pyrogen_swig.la -rpath /usr/lib/python2.7/site-packages pyrogen-swig.lo restraints.lo libcoot_py_restraints.la ../ideal/libcoot-ideal.la ../analysis/libcoot-analysis.la ../geometry/libcoot-geometry.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/pyrogen-swig.o .libs/restraints.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ./.libs/libcoot_py_restraints.so ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so ../analysis/.libs/libcoot-analysis.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so -lgsl -lgslcblas ../geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lmmdb2 -lpython2.7 -lpthread -ldl -lutil -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-export-dynamic -Wl,-soname -Wl,_pyrogen_swig.so.0 -o .libs/_pyrogen_swig.so.0.0.0 libtool: link: (cd ".libs" && rm -f "_pyrogen_swig.so.0" && ln -s "_pyrogen_swig.so.0.0.0" "_pyrogen_swig.so.0") libtool: link: (cd ".libs" && rm -f "_pyrogen_swig.so" && ln -s "_pyrogen_swig.so.0.0.0" "_pyrogen_swig.so") libtool: link: ( cd ".libs" && rm -f "_pyrogen_swig.la" && ln -s "../_pyrogen_swig.la" "_pyrogen_swig.la" ) /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -module -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o pyrogen_boost.la -rpath /usr/lib/python2.7/site-packages restraints-boost.lo libcoot_py_restraints.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../lidia-core/libcoot-lidia-core.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/restraints-boost.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ./.libs/libcoot_py_restraints.so -ldl -lutil ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lpython2.7 -lboost_python -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,pyrogen_boost.so.0 -o .libs/pyrogen_boost.so.0.0.0 libtool: link: (cd ".libs" && rm -f "pyrogen_boost.so.0" && ln -s "pyrogen_boost.so.0.0.0" "pyrogen_boost.so.0") libtool: link: (cd ".libs" && rm -f "pyrogen_boost.so" && ln -s "pyrogen_boost.so.0.0.0" "pyrogen_boost.so") libtool: link: ( cd ".libs" && rm -f "pyrogen_boost.la" && ln -s "../pyrogen_boost.la" "pyrogen_boost.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pyrogen' Making all in src make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/src' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o fix-nomenclature.o fix-nomenclature.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o coot-nomenclature.o coot-nomenclature.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o main.o main.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o boot-python.o boot-python.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o atom-overlaps.o atom-overlaps.cc main.cc: In function 'int main(int, char**)': main.cc:208:19: warning: 'void g_type_init()' is deprecated [-Wdeprecated-declarations] g_type_init(); // for lbg command-line mode, so that ^ In file included from /usr/include/glib-2.0/gobject/gobject.h:24:0, from /usr/include/glib-2.0/gobject/gbinding.h:29, from /usr/include/glib-2.0/glib-object.h:23, from /usr/include/glib-2.0/gio/gioenums.h:28, from /usr/include/glib-2.0/gio/giotypes.h:28, from /usr/include/glib-2.0/gio/gio.h:26, from /usr/include/gtk-2.0/gdk/gdkapplaunchcontext.h:30, from /usr/include/gtk-2.0/gdk/gdk.h:32, from /usr/include/gtk-2.0/gtk/gtk.h:32, from main.cc:49: /usr/include/glib-2.0/gobject/gtype.h:686:23: note: declared here void g_type_init (void); ^~~~~~~~~~~ g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o git-revision-count.o git-revision-count.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o scm-boot-guile.o scm-boot-guile.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-analysis.o c-interface-analysis.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-build.o c-interface-build.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-build-morph.o c-interface-build-morph.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-build-main-chain.o c-interface-build-main-chain.cc In file included from molecule-class-info.h:115:0, from graphics-info.h:75, from c-interface-build.cc:70: atom-attribute.hh: In function 'int set_atom_attributes(SCM)': atom-attribute.hh:25:10: warning: '.coot::atom_attribute_setting_help_t::i' may be used uninitialized in this function [-Wmaybe-uninitialized] class atom_attribute_setting_help_t { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ atom-attribute.hh: In function 'int set_atom_attributes_py(PyObject*)': atom-attribute.hh:25:10: warning: '.coot::atom_attribute_setting_help_t::i' may be used uninitialized in this function [-Wmaybe-uninitialized] class atom_attribute_setting_help_t { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-build-side-chain.o c-interface-build-side-chain.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-build-symmetry.o c-interface-build-symmetry.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 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-DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE 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-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread 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-I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-mogul.o c-interface-mogul.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 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-I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-mogul-scripting.o c-interface-mogul-scripting.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 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-I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-mutate.o c-interface-mutate.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm 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-I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-ncs.o c-interface-ncs.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 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c-interface-network.o c-interface-network.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 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-Wno-unused -c -o c-interface-nucleotides.o c-interface-nucleotides.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 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-fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-python.o c-interface-python.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 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-fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-pisa.o c-interface-pisa.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 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-fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-pisa-gui.o c-interface-pisa-gui.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo 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-Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-sharpen.o c-interface-sharpen.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS 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-Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-superpose.o c-interface-superpose.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS 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-I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-validate.o c-interface-validate.cc c-interface-validate.cc: In function 'int probe_available_p()': c-interface-validate.cc:943:30: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] if (scm_is_true(scm_thunk) == 1) { ^~ In file included from /usr/include/libguile.h:34:0, from graphics-info.h:116, from c-interface-validate.cc:54: c-interface-validate.cc:943:7: note: add parentheses around left hand side expression to silence this warning if (scm_is_true(scm_thunk) == 1) { ^ g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" 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-DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-test.o c-interface-test.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o cc-interface-user-defined-atom-colours.o cc-interface-user-defined-atom-colours.cc gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c -o callbacks.o callbacks.c callbacks.c: In function 'on_phs_cell_choice_ok_button_clicked': callbacks.c:1790:26: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=] snprintf(tmp_name, 3, "%-d", i); ^~~ callbacks.c:1790:25: note: directive argument in the range [0, 2147483647] snprintf(tmp_name, 3, "%-d", i); ^~~~~ In file included from /usr/include/stdio.h:862:0, from callbacks.c:26: /usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o cfc.o cfc.cc In file included from /usr/include/python2.7/pyconfig.h:4:0, from /usr/include/python2.7/Python.h:8, from cfc.hh:28, from cfc.cc:43: /usr/include/python2.7/pyconfig-32.h:1199:0: warning: "_POSIX_C_SOURCE" redefined #define _POSIX_C_SOURCE 200112L In file included from /usr/include/c++/7/i686-redhat-linux/bits/os_defines.h:39:0, from /usr/include/c++/7/i686-redhat-linux/bits/c++config.h:533, from /usr/include/c++/7/cstddef:49, from cfc.cc:27: /usr/include/features.h:260:0: note: this is the location of the previous definition # define _POSIX_C_SOURCE 200809L In file included from /usr/include/python2.7/pyconfig.h:4:0, from /usr/include/python2.7/Python.h:8, from cfc.hh:28, from cfc.cc:43: /usr/include/python2.7/pyconfig-32.h:1221:0: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/c++/7/i686-redhat-linux/bits/os_defines.h:39:0, from /usr/include/c++/7/i686-redhat-linux/bits/c++config.h:533, from /usr/include/c++/7/cstddef:49, from cfc.cc:27: /usr/include/features.h:201:0: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o change-dir.o change-dir.cc change-dir.cc: In function 'void change_directory_maybe()': change-dir.cc:58:14: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(s); ~~~~~^~~ change-dir.cc:63:10: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(s); ~~~~~^~~ g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o cmtz-interface.o cmtz-interface.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o command-line.o command-line.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o command-line-extern.o command-line-extern.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o coot-colour.o coot-colour.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o coot-align.o coot-align.cc gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c -o coot-glue-gtk2.o coot-glue-gtk2.c g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o coot-glue-gtk2-python.o coot-glue-gtk2-python.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 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-I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o coot-hydrogens.o coot-hydrogens.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o coot_pythonmodule.o coot_pythonmodule.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o coot-setup-python.o coot-setup-python.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o coot_wrap_guile.o coot_wrap_guile.cc In file included from /usr/include/python2.7/pyconfig.h:4:0, from /usr/include/python2.7/Python.h:8, from coot_wrap_guile.cc:4: /usr/include/python2.7/pyconfig-32.h:1199:0: warning: "_POSIX_C_SOURCE" redefined #define _POSIX_C_SOURCE 200112L In file included from /usr/include/c++/7/i686-redhat-linux/bits/os_defines.h:39:0, from /usr/include/c++/7/i686-redhat-linux/bits/c++config.h:533, from /usr/include/c++/7/cstddef:49, from coot_wrap_guile.cc:2: /usr/include/features.h:260:0: note: this is the location of the previous definition # define _POSIX_C_SOURCE 200809L In file included from /usr/include/python2.7/pyconfig.h:4:0, from /usr/include/python2.7/Python.h:8, from coot_wrap_guile.cc:4: /usr/include/python2.7/pyconfig-32.h:1221:0: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/c++/7/i686-redhat-linux/bits/os_defines.h:39:0, from /usr/include/c++/7/i686-redhat-linux/bits/c++config.h:533, from /usr/include/c++/7/cstddef:49, from coot_wrap_guile.cc:2: /usr/include/features.h:201:0: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o drag-and-drop.o drag-and-drop.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o draw-generic-display-objects.o draw-generic-display-objects.cc coot_wrap_guile.cc: In function 'scm_unused_struct* _wrap_IntVector_popN___(SCM)': coot_wrap_guile.cc:2680:18: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] gswig_result = scm_from_long(result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ coot_wrap_guile.cc: In function 'scm_unused_struct* _wrap_IntVector_ref(SCM, SCM)': coot_wrap_guile.cc:2718:18: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] gswig_result = scm_from_long(result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o flev.o flev.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 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-DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info.o graphics-info.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 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-DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info-defines.o graphics-info-defines.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 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-DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info-graphs.o graphics-info-graphs.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 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-DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info-gui.o graphics-info-gui.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 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-I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info-modelling.o graphics-info-modelling.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 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-I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info-navigation.o graphics-info-navigation.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 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-I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info-navigation-gtk1.o graphics-info-navigation-gtk1.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread 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-I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info-navigation-gtk2.o graphics-info-navigation-gtk2.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info-preferences.o graphics-info-preferences.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info-network.o graphics-info-network.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info-mutate.o graphics-info-mutate.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info-lsq.o graphics-info-lsq.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info-pick.o graphics-info-pick.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info-refmac.o graphics-info-refmac.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info-render.o graphics-info-render.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 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-I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info-superpose.o graphics-info-superpose.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-ligand-view.o graphics-ligand-view.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o gl-matrix.o gl-matrix.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o gtk-manual.o gtk-manual.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o gtk-widget-conversion-utils.o gtk-widget-conversion-utils.cc gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c -o gtk2-interface.o gtk2-interface.c gtk2-interface.c: In function 'create_coot_references_dialog': gtk2-interface.c:30439:15: warning: variable 'tmp_toolbar_icon_size' set but not used [-Wunused-but-set-variable] GtkIconSize tmp_toolbar_icon_size; ^~~~~~~~~~~~~~~~~~~~~ gtk2-interface.c: In function 'create_multi_residue_torsion_dialog': gtk2-interface.c:31783:7: warning: 'gdk_pixbuf_unref' is deprecated: Use 'g_object_unref' instead [-Wdeprecated-declarations] gdk_pixbuf_unref (multi_residue_torsion_dialog_icon_pixbuf); ^~~~~~~~~~~~~~~~ In file included from /usr/include/gdk-pixbuf-2.0/gdk-pixbuf/gdk-pixbuf.h:34:0, from /usr/include/gtk-2.0/gdk/gdkpixbuf.h:37, from /usr/include/gtk-2.0/gdk/gdkcairo.h:28, from /usr/include/gtk-2.0/gdk/gdk.h:33, from /usr/include/gtk-2.0/gtk/gtk.h:32, from gtk2-interface.c:18: /usr/include/gdk-pixbuf-2.0/gdk-pixbuf/gdk-pixbuf-core.h:232:12: note: declared here void gdk_pixbuf_unref (GdkPixbuf *pixbuf); ^~~~~~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c -o interface.o interface.c g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o lbg-callbacks-outer.o lbg-callbacks-outer.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o lbg-interface.o lbg-interface.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o molecule-class-info.o molecule-class-info.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o molecule-class-info-bonds.o molecule-class-info-bonds.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o molecule-class-info-maps.o molecule-class-info-maps.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o molecule-class-info-maps-2.o molecule-class-info-maps-2.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o molecule-class-info-kdc.o molecule-class-info-kdc.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o molecule-class-info-dots.o molecule-class-info-dots.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo 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-DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c -o read-phs.o read-phs.c read-phs.c: In function 'phs_pdb_cell_symm': read-phs.c:239:8: warning: variable 'imol' set but not used [-Wunused-but-set-variable] int imol; ^~~~ read-phs.c: In function 'do_phs_cell_choice_window': read-phs.c:146:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=] snprintf(tmp_name, 3, "%-d", i); ^~~ read-phs.c:146:29: note: directive argument in the range [0, 2147483647] snprintf(tmp_name, 3, "%-d", i); ^~~~~ In file included from /usr/include/stdio.h:862:0, from read-phs.c:27: /usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read-phs.c:154:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=] snprintf(tmp_name, 3, "%-d", i); ^~~ read-phs.c:154:29: note: directive argument in the range [0, 2147483647] snprintf(tmp_name, 3, "%-d", i); ^~~~~ In file included from /usr/include/stdio.h:862:0, from read-phs.c:27: /usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read-phs.c:162:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=] snprintf(tmp_name, 3, "%-d", i); ^~~ read-phs.c:162:29: note: directive argument in the range [0, 2147483647] snprintf(tmp_name, 3, "%-d", i); ^~~~~ In file included from /usr/include/stdio.h:862:0, from read-phs.c:27: /usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read-phs.c:170:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=] snprintf(tmp_name, 3, "%-d", i); ^~~ read-phs.c:170:29: note: directive argument in the range [0, 2147483647] snprintf(tmp_name, 3, "%-d", i); ^~~~~ In file included from /usr/include/stdio.h:862:0, from read-phs.c:27: /usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read-phs.c:178:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=] snprintf(tmp_name, 3, "%-d", i); ^~~ read-phs.c:178:29: note: directive argument in the range [0, 2147483647] snprintf(tmp_name, 3, "%-d", i); ^~~~~ In file included from /usr/include/stdio.h:862:0, from read-phs.c:27: /usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read-phs.c:186:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=] snprintf(tmp_name, 3, "%-d", i); ^~~ read-phs.c:186:29: note: directive argument in the range [0, 2147483647] snprintf(tmp_name, 3, "%-d", i); ^~~~~ In file included from /usr/include/stdio.h:862:0, from read-phs.c:27: /usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read-phs.c:194:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=] snprintf(tmp_name, 3, "%-d", i); ^~~ read-phs.c:194:29: note: directive argument in the range [0, 2147483647] snprintf(tmp_name, 3, "%-d", i); ^~~~~ In file included from /usr/include/stdio.h:862:0, from read-phs.c:27: /usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -Wall -Wunused -c -o read-cif.o read-cif.c g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o rama_mousey.o rama_mousey.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o rama_plot.o rama_plot.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include 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-I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include 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-DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm 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-I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall 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-I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o coot_wrap_python.o coot_wrap_python.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -c -o density-score-by-residue-src.o density-score-by-residue-src.cc cd .. && /bin/sh ./config.status src/coot config.status: creating src/coot /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o coot-fix-nomenclature-errors fix-nomenclature.o coot-nomenclature.o ../ligand/libcoot-ligand.la ../db-main/libcoot-db-main.la ../ideal/libcoot-ideal.la ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../ccp4mg-utils/libccp4mg-utils.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-shelx.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la -lgsl -lgslcblas -lm -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DPKGPYTHONDIR=\"/usr/lib/python2.7/site-packages/coot\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-i386-fedora-27-python-gtk2\" -DCOOT_BUILD_INFO_STRING=\"\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/coot-fix-nomenclature-errors fix-nomenclature.o coot-nomenclature.o ../ligand/.libs/libcoot-ligand.so /builddir/build/BUILD/coot-0.8.8/ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/db-main/.libs/libcoot-db-main.so /builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/.libs/libccp4mg-utils.so /builddir/build/BUILD/coot-0.8.8/analysis/.libs/libcoot-analysis.so ../db-main/.libs/libcoot-db-main.so ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-shelx.so ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 ../utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lgsl -lgslcblas -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -pthread /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o coot-density-score-by-residue-bin density-score-by-residue-src.o ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-shelx.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la ../compat/libcoot-compat.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -lgsl -lgslcblas -lm libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DPKGPYTHONDIR=\"/usr/lib/python2.7/site-packages/coot\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-i386-fedora-27-python-gtk2\" -DCOOT_BUILD_INFO_STRING=\"\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/coot-density-score-by-residue-bin density-score-by-residue-src.o ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so ../mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-shelx.so ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so ../compat/.libs/libcoot-compat.so -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lm -pthread /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-i386-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o coot-bin main.o boot-python.o atom-overlaps.o git-revision-count.o scm-boot-guile.o c-interface-analysis.o c-interface-build.o c-interface-build-morph.o c-interface-build-main-chain.o c-interface-build-side-chain.o c-interface-build-symmetry.o c-interface-build-gui.o c-interface-database.o c-interface-gui.o c-interface-gtk2.o c-interface-info.o c-interface-kk.o c-interface-ligands.o c-interface-ligands-gui.o c-interface-maps.o c-interface-mmdb.o c-interface-mogul.o c-interface-mogul-scripting.o c-interface-mutate.o c-interface-ncs.o c-interface-network.o c-interface-nucleotides.o c-interface-python.o c-interface-pisa.o c-interface-pisa-gui.o c-interface-preferences.o c-interface-refine.o c-interface-residues.o c-interface-refmac.o c-interface-scm.o c-interface-sequence.o c-interface-sfs.o c-interface-sharpen.o c-interface-superpose.o c-interface-validate.o c-interface-view.o c-interface-widgets.o c-interface-waters.o c-interface-waters-gui.o c-interface.o c-interface-test.o cc-interface-user-defined-atom-colours.o callbacks.o cfc.o change-dir.o cmtz-interface.o command-line.o command-line-extern.o coot-colour.o coot-align.o coot-nomenclature.o coot-glue-gtk2.o coot-glue-gtk2-python.o coot-hydrogens.o coot_pythonmodule.o coot-setup-python.o coot_wrap_guile.o drag-and-drop.o draw-generic-display-objects.o flev.o generic-objects.o geometry-graphs.o get-residue.o get-monomer.o globjects.o globularize.o graphics-info.o graphics-info-defines.o graphics-info-graphs.o graphics-info-gui.o graphics-info-modelling.o graphics-info-navigation.o graphics-info-navigation-gtk1.o graphics-info-navigation-gtk2.o graphics-info-preferences.o graphics-info-network.o graphics-info-mutate.o graphics-info-lsq.o graphics-info-pick.o graphics-info-refmac.o graphics-info-render.o graphics-info-residues.o graphics-info-scripting.o graphics-info-state.o graphics-info-superpose.o graphics-ligand-view.o gl-matrix.o gtk-manual.o gtk-widget-conversion-utils.o gtk2-interface.o interface.o lbg-callbacks-outer.o lbg-interface.o molecule-class-info.o molecule-class-info-bonds.o molecule-class-info-maps.o molecule-class-info-maps-2.o molecule-class-info-kdc.o molecule-class-info-dots.o molecule-class-info-dots-internal.o molecule-class-info-other.o molecule-class-info-build.o molecule-class-info-mutate.o molecule-class-info-residues.o molecule-class-info-refine.o molecule-class-info-kk.o molecule-class-info-surface.o molecule-class-info-patterson.o molecule-class-info-ncs.o molecule-class-info-widget-work.o nsv.o pick.o probe-clash-score.o protein_db-interface.o read-phs.o read-cif.o rama_mousey.o rama_plot.o restraints-editor.o sdf-interface.o support.o support-gtk2-extras.o testing.o testing-2.o trackball.o sequence-view.o seq-view-interface.o user-mods.o xmap-utils.o view.o coot_wrap_python.o ../lbg/libcoot-lidia.la ../ligand/libcoot-ligand.la ../lidia-core/libcoot-lidia-core.la ../goograph/libcoot-goograph.la ../libgtkgraph/libcoot-gtkgraph.la ../density-contour/libcoot-isosurface.la ../build/libcoot-cabuild.la ../skeleton/libcoot-skeleton.la ../angles/libcoot-AngleInfo.la ../db-main/libcoot-db-main.la ../high-res/libcoot-high-res.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-surface/libcoot-surface.la ../surface/libcoot-electrostatics.la ../ccp4mg-utils/libccp4mg-utils.la ../coot-utils/libcoot-map-heavy.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-shelx.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la ../analysis/libcoot-analysis.la ../protein_db/libcoot-protein-db.la ../cootilus/libcootilus.la ../cootaneer/libcootaneer.la ../compat/libcoot-compat.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lssm -lmmdb2 -lmmdb2 -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil -pthread -lguile -lgtkglext-x11-1.0 -lgdkglext-x11-1.0 -lGLU -lGL -lXmu -lXt -lSM -lICE -lpangox-1.0 -lX11 -Wl,--export-dynamic -lgmodule-2.0 -pthread -lglib-2.0 -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lglut -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lgnomecanvas-2 -lart_lgpl_2 -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lgsl -lgslcblas -lm -lcurl -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lcairo -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DPKGPYTHONDIR=\"/usr/lib/python2.7/site-packages/coot\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-i386-fedora-27-python-gtk2\" -DCOOT_BUILD_INFO_STRING=\"\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/coot-bin main.o boot-python.o atom-overlaps.o git-revision-count.o scm-boot-guile.o c-interface-analysis.o c-interface-build.o c-interface-build-morph.o c-interface-build-main-chain.o c-interface-build-side-chain.o c-interface-build-symmetry.o c-interface-build-gui.o c-interface-database.o c-interface-gui.o c-interface-gtk2.o c-interface-info.o c-interface-kk.o c-interface-ligands.o c-interface-ligands-gui.o c-interface-maps.o c-interface-mmdb.o c-interface-mogul.o c-interface-mogul-scripting.o c-interface-mutate.o c-interface-ncs.o c-interface-network.o c-interface-nucleotides.o c-interface-python.o c-interface-pisa.o c-interface-pisa-gui.o c-interface-preferences.o c-interface-refine.o c-interface-residues.o c-interface-refmac.o c-interface-scm.o c-interface-sequence.o c-interface-sfs.o c-interface-sharpen.o c-interface-superpose.o c-interface-validate.o c-interface-view.o c-interface-widgets.o c-interface-waters.o c-interface-waters-gui.o c-interface.o c-interface-test.o cc-interface-user-defined-atom-colours.o callbacks.o cfc.o change-dir.o cmtz-interface.o command-line.o command-line-extern.o coot-colour.o coot-align.o coot-nomenclature.o coot-glue-gtk2.o coot-glue-gtk2-python.o coot-hydrogens.o coot_pythonmodule.o coot-setup-python.o coot_wrap_guile.o drag-and-drop.o draw-generic-display-objects.o flev.o generic-objects.o geometry-graphs.o get-residue.o get-monomer.o globjects.o globularize.o graphics-info.o graphics-info-defines.o graphics-info-graphs.o graphics-info-gui.o graphics-info-modelling.o graphics-info-navigation.o graphics-info-navigation-gtk1.o graphics-info-navigation-gtk2.o graphics-info-preferences.o graphics-info-network.o graphics-info-mutate.o graphics-info-lsq.o graphics-info-pick.o graphics-info-refmac.o graphics-info-render.o graphics-info-residues.o graphics-info-scripting.o graphics-info-state.o graphics-info-superpose.o graphics-ligand-view.o gl-matrix.o gtk-manual.o gtk-widget-conversion-utils.o gtk2-interface.o interface.o lbg-callbacks-outer.o lbg-interface.o molecule-class-info.o molecule-class-info-bonds.o molecule-class-info-maps.o molecule-class-info-maps-2.o molecule-class-info-kdc.o molecule-class-info-dots.o molecule-class-info-dots-internal.o molecule-class-info-other.o molecule-class-info-build.o molecule-class-info-mutate.o molecule-class-info-residues.o molecule-class-info-refine.o molecule-class-info-kk.o molecule-class-info-surface.o molecule-class-info-patterson.o molecule-class-info-ncs.o molecule-class-info-widget-work.o nsv.o pick.o probe-clash-score.o protein_db-interface.o read-phs.o read-cif.o rama_mousey.o rama_plot.o restraints-editor.o sdf-interface.o support.o support-gtk2-extras.o testing.o testing-2.o trackball.o sequence-view.o seq-view-interface.o user-mods.o xmap-utils.o view.o coot_wrap_python.o -Wl,-export-dynamic -pthread -Wl,--export-dynamic -pthread ../lbg/.libs/libcoot-lidia.so ../ligand/.libs/libcoot-ligand.so ../lidia-core/.libs/libcoot-lidia-core.so ../goograph/.libs/libcoot-goograph.so ../libgtkgraph/.libs/libcoot-gtkgraph.so ../density-contour/.libs/libcoot-isosurface.so ../build/.libs/libcoot-cabuild.so ../skeleton/.libs/libcoot-skeleton.so /builddir/build/BUILD/coot-0.8.8/angles/.libs/libcoot-AngleInfo.so ../angles/.libs/libcoot-AngleInfo.so ../db-main/.libs/libcoot-db-main.so ../high-res/.libs/libcoot-high-res.so /builddir/build/BUILD/coot-0.8.8/ligand/.libs/libcoot-ligand.so /builddir/build/BUILD/coot-0.8.8/ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/db-main/.libs/libcoot-db-main.so /builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/.libs/libccp4mg-utils.so /builddir/build/BUILD/coot-0.8.8/analysis/.libs/libcoot-analysis.so ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so ../coot-surface/.libs/libcoot-surface.so /builddir/build/BUILD/coot-0.8.8/surface/.libs/libcoot-electrostatics.so ../surface/.libs/libcoot-electrostatics.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-shelx.so ../utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../analysis/.libs/libcoot-analysis.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so ../protein_db/.libs/libcoot-protein-db.so ../cootilus/.libs/libcootilus.so ../cootaneer/.libs/libcootaneer.so ../compat/.libs/libcoot-compat.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lssm -lmmdb2 -lpthread -ldl -lutil -lguile -lgtkglext-x11-1.0 -lgdkglext-x11-1.0 -lGLU -lGL -lXt -lSM -lICE -lpangox-1.0 -lX11 -lgmodule-2.0 -lglut -lXmu -lgnomecanvas-2 -lart_lgpl_2 -lgsl -lgslcblas -lm -lcurl -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lpython2.7 -lboost_python -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -pthread make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/src' Making all in data make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/data' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/data' Making all in man make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/man' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/man' Making all in rama-data make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/rama-data' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/rama-data' Making all in doc make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/doc' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/doc' Making all in rcrane make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/rcrane' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/rcrane' Making all in pixmaps make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' Making all in icons make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps/icons' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps/icons' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping sed -e 's/#GTK2 //' ./cootrc.template > cootrc make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' + pushd src ~/build/BUILD/coot-0.8.8/src ~/build/BUILD/coot-0.8.8 + doxygen coot-dox.cfg /builddir/build/BUILD/coot-0.8.8/src/cc-interface.hh:59: warning: Compound coot::pisa_interface_bond_info_t is not documented. /builddir/build/BUILD/coot-0.8.8/src/cc-interface.hh:299: warning: Compound coot::file_attribs_info_t is not documented. /builddir/build/BUILD/coot-0.8.8/src/cc-interface.hh:45: warning: Compound coot::alias_path_t is not documented. /builddir/build/BUILD/coot-0.8.8/src/cc-interface.hh:287: warning: Compound coot::str_mtime is not documented. Notice: Output directory `doxygen' does not exist. I have created it for you. Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching INPUT for files to process... Reading and parsing tag files Parsing files Preprocessing /builddir/build/BUILD/coot-0.8.8/src/c-interface.h... Parsing file /builddir/build/BUILD/coot-0.8.8/src/c-interface.h... Preprocessing /builddir/build/BUILD/coot-0.8.8/src/cc-interface.hh... Parsing file /builddir/build/BUILD/coot-0.8.8/src/cc-interface.hh... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Associating documentation with classes... Computing nesting relations for classes... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Freeing entry tree Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Computing dependencies between directories... Generating citations page... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file c-interface.h... Generating code for file cc-interface.hh... Generating file documentation... Generating docs for file c-interface.h... Generating page documentation... Generating group documentation... Generating class documentation... Generating namespace index... Generating docs for compound coot::alias_path_t... Generating docs for compound coot::file_attribs_info_t... Generating docs for compound coot::pisa_interface_bond_info_t... Generating docs for compound coot::str_mtime... Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Generating XML output... Generating XML output for class coot::alias_path_t Generating XML output for class coot::file_attribs_info_t Generating XML output for class coot::pisa_interface_bond_info_t Generating XML output for class coot::str_mtime Generating XML output for namespace coot Generating XML output for file c-interface.h Generating XML output for file cc-interface.hh lookup cache used 844/65536 hits=1882 misses=845 finished... ~/build/BUILD/coot-0.8.8 ~/build/BUILD/coot-0.8.8/doc ~/build/BUILD/coot-0.8.8 + popd + pushd doc + make coot-user-manual.pdf make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' xsltproc ../doc/xml2texi.xsl ../src/doxygen/xml/c-interface_8h.xml > c-interface_8h.texi xsltproc ../doc/xml2texi.xsl ../src/doxygen/xml/cc-interface_8hh.xml > cc-interface_8hh.texi guile -s ../scheme/snarf-coot-docs.scm ../scheme /usr/bin/guile-tools ;;; note: auto-compilation is enabled, set GUILE_AUTO_COMPILE=0 ;;; or pass the --no-auto-compile argument to disable. ;;; compiling /usr/bin/guile-tools ;;; compiled /builddir/.cache/guile/ccache/2.0-LE-4-2.0/usr/bin/guild.go /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "ncs.texi.tmp" "../scheme/ncs.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "ncs.texi.tmp" "../scheme/ncs.scm") returns status 0 making "ncs.texi" by greping... "ncs.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "bit.texi.tmp" "../scheme/bit.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "bit.texi.tmp" "../scheme/bit.scm") returns status 0 making "bit.texi" by greping... "bit.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "extra-top-level.texi.tmp" "../scheme/extra-top-level.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "extra-top-level.texi.tmp" "../scheme/extra-top-level.scm") returns status 0 making "extra-top-level.texi" by greping... "extra-top-level.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "get-ebi.save.texi.tmp" "../scheme/get-ebi.save.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "get-ebi.save.texi.tmp" "../scheme/get-ebi.save.scm") returns status 0 making "get-ebi.save.texi" by greping... "get-ebi.save.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "clear-backup.texi.tmp" "../scheme/clear-backup.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "clear-backup.texi.tmp" "../scheme/clear-backup.scm") returns status 0 making "clear-backup.texi" by greping... "clear-backup.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "gui-add-linked-cho.texi.tmp" "../scheme/gui-add-linked-cho.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "gui-add-linked-cho.texi.tmp" "../scheme/gui-add-linked-cho.scm") returns status 0 making "gui-add-linked-cho.texi" by greping... "gui-add-linked-cho.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "coot-gui.texi.tmp" "../scheme/coot-gui.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "coot-gui.texi.tmp" "../scheme/coot-gui.scm") returns status 0 making "coot-gui.texi" by greping... "coot-gui.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "gui-hole.texi.tmp" "../scheme/gui-hole.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "gui-hole.texi.tmp" "../scheme/gui-hole.scm") returns status 0 making "gui-hole.texi" by greping... "gui-hole.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "extensions.texi.tmp" "../scheme/extensions.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "extensions.texi.tmp" "../scheme/extensions.scm") returns status 0 making "extensions.texi" by greping... "extensions.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "shelx-extensions.texi.tmp" "../scheme/shelx-extensions.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "shelx-extensions.texi.tmp" "../scheme/shelx-extensions.scm") returns status 0 making "shelx-extensions.texi" by greping... "shelx-extensions.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "redefine-functions.texi.tmp" "../scheme/redefine-functions.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "redefine-functions.texi.tmp" "../scheme/redefine-functions.scm") returns status 0 making "redefine-functions.texi" by greping... "redefine-functions.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "coot-utils.texi.tmp" "../scheme/coot-utils.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "coot-utils.texi.tmp" "../scheme/coot-utils.scm") returns status 0 making "coot-utils.texi" by greping... "coot-utils.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "raster3d.texi.tmp" "../scheme/raster3d.scm/usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools ") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "raster3d.texi.tmp" "../scheme/raster3d.scm") returns status 0 making "raster3d.texi" by greping... "raster3d.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "3d-generator-import.texi.tmp" "../scheme/3d-generator-import.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "3d-generator-import.texi.tmp" "../scheme/3d-generator-import.scm") returns status 0 making "3d-generator-import.texi" by greping... "3d-generator-import.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "generic-objects.texi.tmp" "../scheme/generic-objects.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "generic-objects.texi.tmp" "../scheme/generic-objects.scm") returns status 0 making "generic-objects.texi" by greping... "generic-objects.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "refmac.texi.tmp" "../scheme/refmac.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "refmac.texi.tmp" "../scheme/refmac.scm") returns status 0 making "refmac.texi" by greping... "refmac.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "libcheck.texi.tmp" "../scheme/libcheck.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "libcheck.texi.tmp" "../scheme/libcheck.scm") returns status 0 making "libcheck.texi" by greping... "libcheck.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "my-readline.texi.tmp" "../scheme/my-readline.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "my-readline.texi.tmp" "../scheme/my-readline.scm") returns status 0 making "my-readline.texi" by greping... "my-readline.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "get-ebi.texi.tmp" "../scheme/get-ebi.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "get-ebi.texi.tmp" "../scheme/get-ebi.scm") returns status 0 making "get-ebi.texi" by greping... "get-ebi.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "dictionary-generators.texi.tmp" "../scheme/dictionary-generators.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "dictionary-generators.texi.tmp" "../scheme/dictionary-generators.scm") returns status 0 making "dictionary-generators.texi" by greping... "dictionary-generators.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "0-auto-rot.texi.tmp" "../scheme/0-auto-rot.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "0-auto-rot.texi.tmp" "../scheme/0-auto-rot.scm") returns status 0 making "0-auto-rot.texi" by greping... "0-auto-rot.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "local-code.texi.tmp" "../scheme/local-code.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "local-code.texi.tmp" "../scheme/local-code.scm") returns status 0 making "local-code.texi" by greping... "local-code.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "matrices.texi.tmp" "../scheme/matrices.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "matrices.texi.tmp" "../scheme/matrices.scm") returns status 0 making "matrices.texi" by greping... "matrices.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "fitting.texi.tmp" "../scheme/fitting.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "fitting.texi.tmp" "../scheme/fitting.scm") returns status 0 making "fitting.texi" by greping... "fitting.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "coot-crash-catcher.texi.tmp" "../scheme/coot-crash-catcher.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "coot-crash-catcher.texi.tmp" "./usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep ./scheme/coot-crash-catcher.scm") returns status 0 making "coot-crash-catcher.texi" by greping... "coot-crash-catcher.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "povray.texi.tmp" "../scheme/povray.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "povray.texi.tmp" "../scheme/povray.scm") returns status 0 making "povray.texi" by greping... "povray.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "file-utils.texi.tmp" "../scheme/file-utils.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "file-utils.texi.tmp" "../scheme/file-utils.scm") returns status 0 making "file-utils.texi" by greping... "file-utils.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "junk.texi.tmp" "../scheme/junk.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "junk.texi.tmp" "../scheme/junk.scm") returns status 0 making "junk.texi" by greping... "junk.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "gui-ligand-sliders.texi.tmp" "../scheme/gui-ligand-sliders.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "gui-ligand-sliders.texi.tmp" "../scheme/gui-ligand-sliders.scm") returns status 0 making "gui-ligand-sliders.texi" by greping... "gui-ligand-sliders.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "coot-lsq.texi.tmp" "../scheme/coot-lsq.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "coot-lsq.texi.tmp" "../scheme/coot-lsq.scm") returns status 0 making "coot-lsq.texi" by greping... "coot-lsq.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "mutate.texi.tmp" "../scheme/mutate.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "mutate.texi.tmp" "../scheme/mutate.scm") returns status 0 making "mutate.texi" by greping... "mutate.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "filter.texi.tmp" "../scheme/filter.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "filter.texi.tmp" "../scheme/filter.scm") returns status 0 making "filter.texi" by greping... "filter.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "enhanced-ligand.texi.tmp" "../scheme/enhanced-ligand.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "enhanced-ligand.texi.tmp" "../scheme/enhanced-ligand.scm") returns status 0 making "enhanced-ligand.texi" by greping... "enhanced-ligand.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "gui-prosmart.texi.tmp" "../scheme/gui-prosmart.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "gui-prosmart.texi.tmp" "../scheme/gui-prosmart.scm") returns status 0 making "gui-prosmart.texi" by greping... "gui-prosmart.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "americanisms.texi.tmp" "../scheme/americanisms.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "americanisms.texi.tmp" "../scheme/americanisms.scm") returns status 0 making "americanisms.texi" by greping... "americanisms.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "tips-gui.texi.tmp" "../scheme/tips-gui.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "tips-gui.texi.tmp" "../scheme/tips-gui.scm") returns status 0 making "tips-gui.texi" by greping... "tips-gui.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "demo-script.texi.tmp" "../scheme/demo-script.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "demo-script.texi.tmp" "../scheme/demo-script.scm") returns status 0 making "demo-script.texi" by greping... "demo-script.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "/usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools brute-lsqman.texi.tmp" "../scheme/brute-lsqman.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "brute-lsqman.texi.tmp" "../scheme/brute-lsqman.scm") returns status 0 making "brute-lsqman.texi" by greping... "brute-lsqman.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "group-settings.texi.tmp" "../scheme/group-settings.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "group-settings.texi.tmp" "../scheme/group-settings.scm") returns status 0 making "group-settings.texi" by greping... "group-settings.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "bones-reader.texi.tmp" "../scheme/bones-reader.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "bones-reader.texi.tmp" "../scheme/bones-reader.scm") returns status 0 making "bones-reader.texi" by greping... "bones-reader.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "parse-pisa-xml.texi.tmp" "../scheme/parse-pisa-xml.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "parse-pisa-xml.texi.tmp" "../scheme/parse-pisa-xml.scm") returns status 0 making "parse-pisa-xml.texi" by greping... "parse-pisa-xml.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "template-key-bindings.texi.tmp" "../scheme/template-key-bindings.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "template-key-bindings.texi.tmp" "../scheme/template-key-bindings.scm") returns status 0 making "template-key-bindings.texi" by greping... "template-key-bindings.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "contact-score-isolated-ligand.texi.tmp" "../scheme/contact-score-isolated-ligand.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "contact-score-isolated-ligand.texi.tmp" "../scheme/contact-score-isolated-ligand.scm") returns status 0 making "contact-score-isolated-ligand.texi" by greping... "contact-score-isolated-ligand.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "tips.texi.tmp" "../scheme/tips.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "tips.texi.tmp" "../scheme/tips.scm") returns status 0 making "tips.texi" by greping... "tips.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "background-demo.texi.tmp" "../scheme/background-demo.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "background-demo.texi.tmp" "../scheme/background-demo.scm") returns status 0 making "background-demo.texi" by greping... "background-demo.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "trivial.texi.tmp" "../scheme/trivial.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "trivial.texi.tmp" "../scheme/trivial.scm") returns status 0 making "trivial.texi" by greping... "trivial.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "coot.texi.tmp" "../scheme/coot.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "coot.texi.tmp" "../scheme/coot.scm") returns status 0 making "coot.texi" by greping... "coot.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "user-define-restraints.texi.tmp" "../scheme/user-define-restraints.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "user-define-restraints.texi.tmp" "../scheme/user-define-restraints.scm") returns status 0 making "user-define-restraints.texi" by greping... "user-define-restraints.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "fascinating-things.texi.tmp" "../scheme/fascinating-things.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "fascinating-things.texi.tmp" "../scheme/fascinating-things.scm") returns status 0 making "fascinating-things.te/usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools xi" by greping... "fascinating-things.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "run-mogul.texi.tmp" "../scheme/run-mogul.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "run-mogul.texi.tmp" "../scheme/run-mogul.scm") returns status 0 making "run-mogul.texi" by greping... "run-mogul.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "remote-control.texi.tmp" "../scheme/remote-control.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "remote-control.texi.tmp" "../scheme/remote-control.scm") returns status 0 making "remote-control.texi" by greping... "remote-control.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "json-reader.texi.tmp" "../scheme/json-reader.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "json-reader.texi.tmp" "../scheme/json-reader.scm") returns status 0 making "json-reader.texi" by greping... "json-reader.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "ligand-check.texi.tmp" "../scheme/ligand-check.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "ligand-check.texi.tmp" "../scheme/ligand-check.scm") returns status 0 making "ligand-check.texi" by greping... "ligand-check.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "simple.texi.tmp" "../scheme/simple.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "simple.texi.tmp" "../scheme/simple.scm") returns status 0 making "simple.texi" by greping... "simple.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "gtkin.texi.tmp" "../scheme/gtkin.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "gtkin.texi.tmp" "../scheme/gtkin.scm") returns status 0 making "gtkin.texi" by greping... "gtkin.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "jligand.texi.tmp" "../scheme/jligand.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "jligand.texi.tmp" "../scheme/jligand.scm") returns status 0 making "jligand.texi" by greping... "jligand.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "check-for-updates.texi.tmp" "../scheme/check-for-updates.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "check-for-updates.texi.tmp" "../scheme/check-for-updates.scm") returns status 0 making "check-for-updates.texi" by greping... "check-for-updates.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "shelx.texi.tmp" "../scheme/shelx.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "shelx.texi.tmp" "../scheme/shelx.scm") returns status 0 making "shelx.texi" by greping... "shelx.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "cns2coot.texi.tmp" "../scheme/cns2coot.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "cns2coot.texi.tmp" "../scheme/cns2coot.scm") returns status 0 making "cns2coot.texi" by greping... "cns2coot.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "jligand-gui.texi.tmp" "../scheme/jligand-gui.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "jligand-gui.texi.tmp" "../scheme/jligand-gui.scm") returns status 0 making "jligand-gui.texi" by greping... "jligand-gui.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "snarf-coot-docs.texi.tmp" "../scheme/snarf-coot-docs.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "snarf-coot-docs.texi.tmp" "../scheme/snarf-coot-docs.scm") returns status 0 making "snarf-coot-docs.texi" by greping... "snarf-coot-docs.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "hello.texi.tmp" "../scheme/hello.scm") > snarf.log exit /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "hello.texi.tmp" "../scheme/hello.scm") returns status 0 making "hello.texi" by greping... "hello.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "get-recent-pdbe.texi.tmp" "../scheme/get-recent-pdbe.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "get-recent-pdbe.texi.tmp" "../scheme/get-recent-pdbe.scm") returns status 0 making "get-recent-pdbe.texi" by greping... "get-recent-pdbe.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "gap.texi.tmp" "../scheme/gap.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "gap.texi.tmp" "../scheme/gap.scm") returns status 0 making "gap.texi" by greping... "gap.texi.tmp" exit status: 1 menu section processing "c-interface_8h.texi" menu section processing "cc-interface_8hh.texi" menu section processing "ncs.texi" menu section processing "extra-top-level.texi" menu section processing "clear-backup.texi" menu section processing "gui-add-linked-cho.texi" menu section processing "coot-gui.texi" menu section processing "redefine-functions.texi" menu section processing "coot-utils.texi" menu section processing "raster3d.texi" menu section processing "3d-generator-import.texi" menu section processing "generic-objects.texi" menu section processing "refmac.texi" menu section processing "libcheck.texi" menu section processing "get-ebi.texi" menu section processing "dictionary-generators.texi" menu section processing "fitting.texi" menu section processing "coot-crash-catcher.texi" menu section processing "povray.texi" menu section processing "gui-ligand-sliders.texi" menu section processing "coot-lsq.texi" menu section processing "mutate.texi" menu section processing "filter.texi" menu section processing "americanisms.texi" menu section processing "tips-gui.texi" menu section processing "brute-lsqman.texi" menu section processing "group-settings.texi" menu section processing "parse-pisa-xml.texi" menu section processing "contact-score-isolated-ligand.texi" menu section processing "tips.texi" menu section processing "background-demo.texi" menu section processing "coot.texi" menu section processing "user-define-restraints.texi" menu section processing "fascinating-things.texi" menu section processing "run-mogul.texi" menu section processing "remote-control.texi" menu section processing "ligand-check.texi" menu section processing "jligand.texi" menu section processing "check-for-updates.texi" menu section processing "shelx.texi" menu section processing "cns2coot.texi" menu section processing "jligand-gui.texi" menu section processing "snarf-coot-docs.texi" menu section processing "hello.texi" menu section processing "get-recent-pdbe.texi" all-useful-texis: ("menu-section.texi" "c-interface_8h-section.texi" "c-interface_8h.texi" "cc-interface_8hh-section.texi" "cc-interface_8hh.texi" "ncs-section.texi" "ncs.texi" "extra-top-level-section.texi" "extra-top-level.texi" "clear-backup-section.texi" "clear-backup.texi" "gui-add-linked-cho-section.texi" "gui-add-linked-cho.texi" "coot-gui-section.texi" "coot-gui.texi" "redefine-functions-section.texi" "redefine-functions.texi" "coot-utils-section.texi" "coot-utils.texi" "raster3d-section.texi" "raster3d.texi" "3d-generator-import-section.texi" "3d-generator-import.texi" "generic-objects-section.texi" "generic-objects.texi" "refmac-section.texi" "refmac.texi" "libcheck-section.texi" "libcheck.texi" "get-ebi-section.texi" "get-ebi.texi" "dictionary-generators-section.texi" "dictionary-generators.texi" "fitting-section.texi" "fitting.texi" "coot-crash-catcher-section.texi" "coot-crash-catcher.texi" "povray-section.texi" "povray.texi" "gui-ligand-sliders-section.texi" "gui-ligand-sliders.texi" "coot-lsq-section.texi" "coot-lsq.texi" "mutate-section.texi" "mutate.texi" "filter-section.texi" "filter.texi" "americanisms-section.texi" "americanisms.texi" "tips-gui-section.texi" "tips-gui.texi" "brute-lsqman-section.texi" "brute-lsqman.texi" "group-settings-section.texi" "group-setti/usr/bin/cat ngs.texi" "parse-pisa-xml-section.texi" "parse-pisa-xml.texi" "contact-score-isolated-ligand-section.texi" "contact-score-isolated-ligand.texi" "tips-section.texi" "tips.texi" "background-demo-section.texi" "background-demo.texi" "coot-section.texi" "coot.texi" "user-define-restraints-section.texi" "user-define-restraints.texi" "fascinating-things-section.texi" "fascinating-things.texi" "run-mogul-section.texi" "run-mogul.texi" "remote-control-section.texi" "remote-control.texi" "ligand-check-section.texi" "ligand-check.texi" "jligand-section.texi" "jligand.texi" "check-for-updates-section.texi" "check-for-updates.texi" "shelx-section.texi" "shelx.texi" "cns2coot-section.texi" "cns2coot.texi" "jligand-gui-section.texi" "jligand-gui.texi" "snarf-coot-docs-section.texi" "snarf-coot-docs.texi" "hello-section.texi" "hello.texi" "get-recent-pdbe-section.texi" "get-recent-pdbe.texi") exit status: 0 ;;; note: auto-compilation is enabled, set GUILE_AUTO_COMPILE=0 ;;; or pass the --no-auto-compile argument to disable. ;;; compiling /builddir/build/BUILD/coot-0.8.8/doc/../scheme/snarf-coot-docs.scm ;;; compiled /builddir/.cache/guile/ccache/2.0-LE-4-2.0/builddir/build/BUILD/coot-0.8.8/scheme/snarf-coot-docs.scm.go ;;; compiling /builddir/build/BUILD/coot-0.8.8/doc/../scheme/filter.scm ;;; compiled /builddir/.cache/guile/ccache/2.0-LE-4-2.0/builddir/build/BUILD/coot-0.8.8/scheme/filter.scm.go if [ ! -e coot-plain-2.eps ] ; then cp ../doc/coot-plain-2.ps coot-plain-2.eps ; fi texi2dvi ../doc/coot-user-manual.texi This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=etex) restricted \write18 enabled. entering extended mode (./../doc/coot-user-manual.texi (/builddir/build/BUILD/coot-0.8.8/doc/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/share/texlive/texmf-dist/tex/generic/epsf/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (coot-plain-2.eps ) [1] [2] [-1] Chapter 1 Underfull \hbox (badness 2556) in paragraph at lines 368--371 @texttt "@textrm The Up-p-sala Electron-Density Server@texttt "@textrm , @text it Acta Crys-tal-lo-graph-ica Sec-tion [1] [2] Cross reference values unknown; you must run TeX again. [3] Chapter 2 [4] [5] [6] Chapter 3 [7] [8] [9] [10] [11] [12] Underfull \hbox (badness 10000) in paragraph at lines 1221--1222 []@texttt (add-key-binding "Refine Active Residue with Auto-accept" "x" refine- [13] [14] Underfull \hbox (badness 3039) in paragraph at lines 1393--1398 []@textrm If you don't want smooth re-cen-tring (slid-ing) []@texttt Edit -> Pr eferences -> Smooth [15] [16] Chapter 4 [17] [18] [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 1813--1814 []@texttt (add-strict-ncs-matrix @textttsl imol ncs-chain-id ncs-target-chain-i d m11 m12 m13 [21] [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 2031--2032 []@texttt (make-ball-and-stick @textttsl imol atom-selection bond-thickness sph ere-size Underfull \hbox (badness 10000) in paragraph at lines 2073--2074 []@texttt (superpose-with-atom-selection @textttsl imol1 imol2 mmdb-atom-select ion-string-1 [24] Underfull \hbox (badness 10000) in paragraph at lines 2104--2105 []@texttt (simple-lsq-match @textttsl ref-start-resno ref-end-resno ref-chain-i d imol-ref Underfull \hbox (badness 10000) in paragraph at lines 2165--2166 []@texttt (overlay-my-ligands @textttsl imol-mov chain-id-mov resno-mov imol-re f chain-id-ref [25] Underfull \hbox (badness 10000) in paragraph at lines 2188--2189 []@texttt (write-residue-range-to-pdb-file @textttsl imol chain-id start-resno en-dresno Chapter 5 [26] [27] [28] Overfull \hbox (32.02371pt too wide) in paragraph at lines 2415--2415 [][][] | [29] [30] Underfull \hbox (badness 10000) in paragraph at lines 2574--2575 []@texttt (fit-residue-range-to-map-by-simplex @textttsl start-resno end-resno alt-loc [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2801--2810 @textrm Sec-ondly @texttt Extensions -> Dock Sequence -> Dock Sequence on this fragment[][]@textrm . Underfull \hbox (badness 10000) in paragraph at lines 2849--2850 []@texttt (auto-fit-best-rotamer @textttsl resno alt-loc ins-code chain-id imol -coords imol-map [34] [35] [36] Underfull \hbox (badness 2073) in paragraph at lines 3048--3051 []@textrm Mutation of DNA or RNA can be per-formed us-ing ``Sim-ple Mu-tate'' f rom the [37] Underfull \hbox (badness 3954) in paragraph at lines 3120--3123 []@textrm The GUI for this can be found un-der @texttt Extensions -> Modelling -> Replace Underfull \hbox (badness 4467) in paragraph at lines 3164--3167 []@textrm This pro-ce-dure cre-ates a pdb file `@texttt monomer-XXX.pdb[]@textr m '[] and a dic-tio-nary file [38] [39] [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3514--3515 []@texttt (copy-residue-range-from-ncs-master-to-others @textttsl imol master-c hain-id [43] [44] [45] [46] Chapter 6 [47] Underfull \hbox (badness 10000) in paragraph at lines 3924--3926 []@texttt (set-auto-read-column-labels "2FOFCWT" "PHIWT" 0)[] (set-auto-read-co lumn- [48] Underfull \hbox (badness 10000) in paragraph at lines 3953--3954 []@texttt (read-phs-and-make-map-using-cell-symm @textttsl phs-file-name space- group-name a b Underfull \hbox (badness 10000) in paragraph at lines 3955--3956 []@texttt (read-pdb-and-make-map-with-reso-limits @textttsl imol-previous phs-f ile-name [49] [50] Underfull \hbox (badness 4328) in paragraph at lines 4147--4155 []@textrm If ac-ti-vated (@texttt Edit -> Map Parameters -> Dynamic Map Samplin g[]@textrm ) the map will be [51] [52] [53] Underfull \hbox (badness 10000) in paragraph at lines 4338--4339 []@texttt (transform-map 3 (list 0.9707 0.2351 0.05033 -0.04676 0.39 -0.9196 -0 .2358 Underfull \hbox (badness 10000) in paragraph at lines 4353--4354 []@texttt (transform-map-using-lsq-matrix @textttsl imol-ref ref-chain ref-resn o-start Underfull \hbox (badness 10000) in paragraph at lines 4353--4354 @textttsl ref-resno-end imol-mov mov-chain mov-resno-start mov-resno-end imol-m ap Chapter 7 [54] [55] [56] [57] Chapter 8 [58] Underfull \hbox (badness 2662) in paragraph at lines 4721--4725 []@textrm Coot uses the par-tial charges of the atoms (the @textsl par-tial[]ch arge @textrm field in the Chapter 9 [59] [60] [61] Chapter 10 [62] Chapter 11 [63] (/builddir/build/BUILD/coot-0.8.8/doc/c-interface_8h.texi [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] Underfull \hbox (badness 3803) in paragraph at lines 5458--5459 []@textrm set the heuris-tic fen-ce-post for the max-i-mum num-ber of residues in the [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189]) Chapter 12 [190] (/builddir/build/BUILD/coot-0.8.8/doc/cc-interface_8hh.texi [191] [192] [193] [194] [195] [196] [197] [198] [199] [200]) Chapter 13 [201] (/builddir/build/BUILD/coot-0.8.8/doc/coot-scheme-functions.texi [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255] [256] [257] [258] [259] [260] [261] [262] [263] [264] [265] [266] [267] Underfull \hbox (badness 3803) in paragraph at lines 5507--5508 []@textrm set the heuris-tic fen-ce-post for the max-i-mum num-ber of residues in the [268] [269] [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] [363] Underfull \hbox (badness 2073) in paragraph at lines 13241--13286 []@textrm pisa[]results name sta-tus to-tal[]asm asm[]set ser[]no as-sem-bly i d size mm-size [364] [365] [366] Underfull \hbox (badness 2393) in paragraph at lines 13596--13605 @textrm sta-tus difference-map-stats: the out-put of map-to-model-correlation- stats-scm Underfull \hbox (badness 10000) in paragraph at lines 13596--13605 @textrm SCM[]UNDEFINED) and b-factor-info list of (median-ratio median-ligand Underfull \hbox (badness 2951) in paragraph at lines 13625--13627 []@textrm JLigand sends Coot a file that con-tains file-names for the link and new [367] [368] [369] Overfull \hbox (6.6734pt too wide) in paragraph at lines 13863--13865 []@textrm Sameer Ve-lankar says to get this file for the lat-est re-leases @te xttt "@textrm http://www.ebi.ac.uk/pdbe-| ) (Concept Index) [370] (Function Index) [371] [372] ) (see the transcript file for additional information) Output written on coot-user-manual.dvi (375 pages, 920544 bytes). Transcript written on coot-user-manual.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=etex) restricted \write18 enabled. entering extended mode (./../doc/coot-user-manual.texi (/builddir/build/BUILD/coot-0.8.8/doc/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/share/texlive/texmf-dist/tex/generic/epsf/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.aux) (coot-plain-2.eps ) [1] [2] (/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.toc [-1] [-2] [-3] [-4] [-5] [-6] [-7] [-8] [-9] [-10] [-11] [-12] [-13] [-14] [-15] [-16] [-17] [-18] [-19] [-20] [-21] [-22] [-23] [-24] [-25] [-26] [-27] [-28] [-29] [-30] [-31] [-32] [-33] [-34] [-35] [-36] [-37] [-38] [-39] [-40] [-41] [-42]) [-43] Chapter 1 Underfull \hbox (badness 2556) in paragraph at lines 368--371 @texttt "@textrm The Up-p-sala Electron-Density Server@texttt "@textrm , @text it Acta Crys-tal-lo-graph-ica Sec-tion [1] [2] [3] Chapter 2 [4] [5] [6] Chapter 3 [7] [8] [9] [10] [11] [12] Underfull \hbox (badness 10000) in paragraph at lines 1221--1222 []@texttt (add-key-binding "Refine Active Residue with Auto-accept" "x" refine- [13] [14] Underfull \hbox (badness 3039) in paragraph at lines 1393--1398 []@textrm If you don't want smooth re-cen-tring (slid-ing) []@texttt Edit -> Pr eferences -> Smooth [15] [16] Chapter 4 [17] [18] [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 1813--1814 []@texttt (add-strict-ncs-matrix @textttsl imol ncs-chain-id ncs-target-chain-i d m11 m12 m13 [21] [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 2031--2032 []@texttt (make-ball-and-stick @textttsl imol atom-selection bond-thickness sph ere-size Underfull \hbox (badness 10000) in paragraph at lines 2073--2074 []@texttt (superpose-with-atom-selection @textttsl imol1 imol2 mmdb-atom-select ion-string-1 [24] Underfull \hbox (badness 10000) in paragraph at lines 2104--2105 []@texttt (simple-lsq-match @textttsl ref-start-resno ref-end-resno ref-chain-i d imol-ref Underfull \hbox (badness 10000) in paragraph at lines 2165--2166 []@texttt (overlay-my-ligands @textttsl imol-mov chain-id-mov resno-mov imol-re f chain-id-ref [25] Underfull \hbox (badness 10000) in paragraph at lines 2188--2189 []@texttt (write-residue-range-to-pdb-file @textttsl imol chain-id start-resno en-dresno Chapter 5 [26] [27] [28] Overfull \hbox (32.02371pt too wide) in paragraph at lines 2415--2415 [][][] | [29] [30] Underfull \hbox (badness 10000) in paragraph at lines 2574--2575 []@texttt (fit-residue-range-to-map-by-simplex @textttsl start-resno end-resno alt-loc [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2801--2810 @textrm Sec-ondly @texttt Extensions -> Dock Sequence -> Dock Sequence on this fragment[][]@textrm . Underfull \hbox (badness 10000) in paragraph at lines 2849--2850 []@texttt (auto-fit-best-rotamer @textttsl resno alt-loc ins-code chain-id imol -coords imol-map [34] [35] [36] Underfull \hbox (badness 2073) in paragraph at lines 3048--3051 []@textrm Mutation of DNA or RNA can be per-formed us-ing ``Sim-ple Mu-tate'' f rom the [37] Underfull \hbox (badness 3954) in paragraph at lines 3120--3123 []@textrm The GUI for this can be found un-der @texttt Extensions -> Modelling -> Replace Underfull \hbox (badness 4467) in paragraph at lines 3164--3167 []@textrm This pro-ce-dure cre-ates a pdb file `@texttt monomer-XXX.pdb[]@textr m '[] and a dic-tio-nary file [38] [39] [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3514--3515 []@texttt (copy-residue-range-from-ncs-master-to-others @textttsl imol master-c hain-id [43] [44] [45] [46] Chapter 6 [47] Underfull \hbox (badness 10000) in paragraph at lines 3924--3926 []@texttt (set-auto-read-column-labels "2FOFCWT" "PHIWT" 0)[] (set-auto-read-co lumn- [48] Underfull \hbox (badness 10000) in paragraph at lines 3953--3954 []@texttt (read-phs-and-make-map-using-cell-symm @textttsl phs-file-name space- group-name a b Underfull \hbox (badness 10000) in paragraph at lines 3955--3956 []@texttt (read-pdb-and-make-map-with-reso-limits @textttsl imol-previous phs-f ile-name [49] [50] Underfull \hbox (badness 4328) in paragraph at lines 4147--4155 []@textrm If ac-ti-vated (@texttt Edit -> Map Parameters -> Dynamic Map Samplin g[]@textrm ) the map will be [51] [52] [53] Underfull \hbox (badness 10000) in paragraph at lines 4338--4339 []@texttt (transform-map 3 (list 0.9707 0.2351 0.05033 -0.04676 0.39 -0.9196 -0 .2358 Underfull \hbox (badness 10000) in paragraph at lines 4353--4354 []@texttt (transform-map-using-lsq-matrix @textttsl imol-ref ref-chain ref-resn o-start Underfull \hbox (badness 10000) in paragraph at lines 4353--4354 @textttsl ref-resno-end imol-mov mov-chain mov-resno-start mov-resno-end imol-m ap Chapter 7 [54] [55] [56] [57] Chapter 8 [58] Underfull \hbox (badness 2662) in paragraph at lines 4721--4725 []@textrm Coot uses the par-tial charges of the atoms (the @textsl par-tial[]ch arge @textrm field in the Chapter 9 [59] [60] [61] Chapter 10 [62] Chapter 11 [63] (/builddir/build/BUILD/coot-0.8.8/doc/c-interface_8h.texi [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] Underfull \hbox (badness 3803) in paragraph at lines 5458--5459 []@textrm set the heuris-tic fen-ce-post for the max-i-mum num-ber of residues in the [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189]) Chapter 12 [190] (/builddir/build/BUILD/coot-0.8.8/doc/cc-interface_8hh.texi [191] [192] [193] [194] [195] [196] [197] [198] [199] [200]) Chapter 13 [201] (/builddir/build/BUILD/coot-0.8.8/doc/coot-scheme-functions.texi [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255] [256] [257] [258] [259] [260] [261] [262] [263] [264] [265] [266] [267] Underfull \hbox (badness 3803) in paragraph at lines 5507--5508 []@textrm set the heuris-tic fen-ce-post for the max-i-mum num-ber of residues in the [268] [269] [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] [363] Underfull \hbox (badness 2073) in paragraph at lines 13241--13286 []@textrm pisa[]results name sta-tus to-tal[]asm asm[]set ser[]no as-sem-bly i d size mm-size [364] [365] [366] Underfull \hbox (badness 2393) in paragraph at lines 13596--13605 @textrm sta-tus difference-map-stats: the out-put of map-to-model-correlation- stats-scm Underfull \hbox (badness 10000) in paragraph at lines 13596--13605 @textrm SCM[]UNDEFINED) and b-factor-info list of (median-ratio median-ligand Underfull \hbox (badness 2951) in paragraph at lines 13625--13627 []@textrm JLigand sends Coot a file that con-tains file-names for the link and new [367] [368] [369] Overfull \hbox (6.6734pt too wide) in paragraph at lines 13863--13865 []@textrm Sameer Ve-lankar says to get this file for the lat-est re-leases @te xttt "@textrm http://www.ebi.ac.uk/pdbe-| ) (Concept Index) [370] (/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.cps [371] [372]) (Function Index) [373] (/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.fns [374] [375] [376] [377] [378] [379] [380] [381] [382] [383] [384]) [385] ) (see the transcript file for additional information) Output written on coot-user-manual.dvi (430 pages, 1867792 bytes). Transcript written on coot-user-manual.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=etex) restricted \write18 enabled. entering extended mode (./../doc/coot-user-manual.texi (/builddir/build/BUILD/coot-0.8.8/doc/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/share/texlive/texmf-dist/tex/generic/epsf/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.aux) (coot-plain-2.eps ) [1] [2] (/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.toc [-1] [-2] [-3] [-4] [-5] [-6] [-7] [-8] [-9] [-10] [-11] [-12] [-13] [-14] [-15] [-16] [-17] [-18] [-19] [-20] [-21] [-22] [-23] [-24] [-25] [-26] [-27] [-28] [-29] [-30] [-31] [-32] [-33] [-34] [-35] [-36] [-37] [-38] [-39] [-40] [-41] [-42]) [-43] Chapter 1 Underfull \hbox (badness 2556) in paragraph at lines 368--371 @texttt "@textrm The Up-p-sala Electron-Density Server@texttt "@textrm , @text it Acta Crys-tal-lo-graph-ica Sec-tion [1] [2] [3] Chapter 2 [4] [5] [6] Chapter 3 [7] [8] [9] [10] [11] [12] Underfull \hbox (badness 10000) in paragraph at lines 1221--1222 []@texttt (add-key-binding "Refine Active Residue with Auto-accept" "x" refine- [13] [14] Underfull \hbox (badness 3039) in paragraph at lines 1393--1398 []@textrm If you don't want smooth re-cen-tring (slid-ing) []@texttt Edit -> Pr eferences -> Smooth [15] [16] Chapter 4 [17] [18] [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 1813--1814 []@texttt (add-strict-ncs-matrix @textttsl imol ncs-chain-id ncs-target-chain-i d m11 m12 m13 [21] [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 2031--2032 []@texttt (make-ball-and-stick @textttsl imol atom-selection bond-thickness sph ere-size Underfull \hbox (badness 10000) in paragraph at lines 2073--2074 []@texttt (superpose-with-atom-selection @textttsl imol1 imol2 mmdb-atom-select ion-string-1 [24] Underfull \hbox (badness 10000) in paragraph at lines 2104--2105 []@texttt (simple-lsq-match @textttsl ref-start-resno ref-end-resno ref-chain-i d imol-ref Underfull \hbox (badness 10000) in paragraph at lines 2165--2166 []@texttt (overlay-my-ligands @textttsl imol-mov chain-id-mov resno-mov imol-re f chain-id-ref [25] Underfull \hbox (badness 10000) in paragraph at lines 2188--2189 []@texttt (write-residue-range-to-pdb-file @textttsl imol chain-id start-resno en-dresno Chapter 5 [26] [27] [28] Overfull \hbox (32.02371pt too wide) in paragraph at lines 2415--2415 [][][] | [29] [30] Underfull \hbox (badness 10000) in paragraph at lines 2574--2575 []@texttt (fit-residue-range-to-map-by-simplex @textttsl start-resno end-resno alt-loc [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2801--2810 @textrm Sec-ondly @texttt Extensions -> Dock Sequence -> Dock Sequence on this fragment[][]@textrm . Underfull \hbox (badness 10000) in paragraph at lines 2849--2850 []@texttt (auto-fit-best-rotamer @textttsl resno alt-loc ins-code chain-id imol -coords imol-map [34] [35] [36] Underfull \hbox (badness 2073) in paragraph at lines 3048--3051 []@textrm Mutation of DNA or RNA can be per-formed us-ing ``Sim-ple Mu-tate'' f rom the [37] Underfull \hbox (badness 3954) in paragraph at lines 3120--3123 []@textrm The GUI for this can be found un-der @texttt Extensions -> Modelling -> Replace Underfull \hbox (badness 4467) in paragraph at lines 3164--3167 []@textrm This pro-ce-dure cre-ates a pdb file `@texttt monomer-XXX.pdb[]@textr m '[] and a dic-tio-nary file [38] [39] [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3514--3515 []@texttt (copy-residue-range-from-ncs-master-to-others @textttsl imol master-c hain-id [43] [44] [45] [46] Chapter 6 [47] Underfull \hbox (badness 10000) in paragraph at lines 3924--3926 []@texttt (set-auto-read-column-labels "2FOFCWT" "PHIWT" 0)[] (set-auto-read-co lumn- [48] Underfull \hbox (badness 10000) in paragraph at lines 3953--3954 []@texttt (read-phs-and-make-map-using-cell-symm @textttsl phs-file-name space- group-name a b Underfull \hbox (badness 10000) in paragraph at lines 3955--3956 []@texttt (read-pdb-and-make-map-with-reso-limits @textttsl imol-previous phs-f ile-name [49] [50] Underfull \hbox (badness 4328) in paragraph at lines 4147--4155 []@textrm If ac-ti-vated (@texttt Edit -> Map Parameters -> Dynamic Map Samplin g[]@textrm ) the map will be [51] [52] [53] Underfull \hbox (badness 10000) in paragraph at lines 4338--4339 []@texttt (transform-map 3 (list 0.9707 0.2351 0.05033 -0.04676 0.39 -0.9196 -0 .2358 Underfull \hbox (badness 10000) in paragraph at lines 4353--4354 []@texttt (transform-map-using-lsq-matrix @textttsl imol-ref ref-chain ref-resn o-start Underfull \hbox (badness 10000) in paragraph at lines 4353--4354 @textttsl ref-resno-end imol-mov mov-chain mov-resno-start mov-resno-end imol-m ap Chapter 7 [54] [55] [56] [57] Chapter 8 [58] Underfull \hbox (badness 2662) in paragraph at lines 4721--4725 []@textrm Coot uses the par-tial charges of the atoms (the @textsl par-tial[]ch arge @textrm field in the Chapter 9 [59] [60] [61] Chapter 10 [62] Chapter 11 [63] (/builddir/build/BUILD/coot-0.8.8/doc/c-interface_8h.texi [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] Underfull \hbox (badness 3803) in paragraph at lines 5458--5459 []@textrm set the heuris-tic fen-ce-post for the max-i-mum num-ber of residues in the [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189]) Chapter 12 [190] (/builddir/build/BUILD/coot-0.8.8/doc/cc-interface_8hh.texi [191] [192] [193] [194] [195] [196] [197] [198] [199] [200]) Chapter 13 [201] (/builddir/build/BUILD/coot-0.8.8/doc/coot-scheme-functions.texi [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255] [256] [257] [258] [259] [260] [261] [262] [263] [264] [265] [266] [267] Underfull \hbox (badness 3803) in paragraph at lines 5507--5508 []@textrm set the heuris-tic fen-ce-post for the max-i-mum num-ber of residues in the [268] [269] [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] [363] Underfull \hbox (badness 2073) in paragraph at lines 13241--13286 []@textrm pisa[]results name sta-tus to-tal[]asm asm[]set ser[]no as-sem-bly i d size mm-size [364] [365] [366] Underfull \hbox (badness 2393) in paragraph at lines 13596--13605 @textrm sta-tus difference-map-stats: the out-put of map-to-model-correlation- stats-scm Underfull \hbox (badness 10000) in paragraph at lines 13596--13605 @textrm SCM[]UNDEFINED) and b-factor-info list of (median-ratio median-ligand Underfull \hbox (badness 2951) in paragraph at lines 13625--13627 []@textrm JLigand sends Coot a file that con-tains file-names for the link and new [367] [368] [369] Overfull \hbox (6.6734pt too wide) in paragraph at lines 13863--13865 []@textrm Sameer Ve-lankar says to get this file for the lat-est re-leases @te xttt "@textrm http://www.ebi.ac.uk/pdbe-| ) (Concept Index) [370] (/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.cps [371] [372]) (Function Index) [373] (/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.fns [374] [375] [376] [377] [378] [379] [380] [381] [382] [383] [384]) [385] ) (see the transcript file for additional information) Output written on coot-user-manual.dvi (430 pages, 1867792 bytes). Transcript written on coot-user-manual.log. dvips -o coot-user-manual.ps coot-user-manual.dvi This is dvips(k) 5.996 Copyright 2016 Radical Eye Software (www.radicaleye.com) ' TeX output 2017.07.13:2028' -> coot-user-manual.ps . [1 <./coot-plain-2.eps>] [2] [-1] [-2] [-3] [-4] [-5] [-6] [-7] [-8] [-9] [-10] [-11] [-12] [-13] [-14] [-15] [-16] [-17] [-18] [-19] [-20] [-21] [-22] [-23] [-24] [-25] [-26] [-27] [-28] [-29] [-30] [-31] [-32] [-33] [-34] [-35] [-36] [-37] [-38] [-39] [-40] [-41] [-42] [-43] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255] [256] [257] [258] [259] [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] [373] [374] [375] [376] [377] [378] [379] [380] [381] [382] [383] [384] [385] ps2pdf coot-user-manual.ps + make coot-keys-and-buttons.pdf make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' latex ../doc/crib-sheet.tex This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=latex) restricted \write18 enabled. kpathsea: Running mktexfmt latex.fmt mktexfmt: mktexfmt is using the following fmtutil.cnf files (in precedence order): mktexfmt: /usr/share/texlive/texmf-dist/web2c/fmtutil.cnf mktexfmt: mktexfmt is using the following fmtutil.cnf file for writing changes: mktexfmt: /builddir/.cache/texlive/texmf-config/web2c/fmtutil.cnf mktexfmt [WARNING]: double mention of mf/mf-nowin in /usr/share/texlive/texmf-dist/web2c/fmtutil.cnf mktexfmt [WARNING]: double mention of tex/tex in /usr/share/texlive/texmf-dist/web2c/fmtutil.cnf mktexfmt [INFO]: writing formats under /builddir/.cache/texlive/texmf-var/web2c mktexfmt [INFO]: --- remaking latex with pdftex mktexfmt: running `pdftex -ini -jobname=latex -progname=latex -translate-file=cp227.tcx *latex.ini' ... This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (INITEX) restricted \write18 enabled. (/usr/share/texlive/texmf-dist/web2c/cp227.tcx) entering extended mode (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/latex.ini (/usr/share/texlive/texmf-dist/tex/generic/tex-ini-files/pdftexconfig.tex) (/usr/share/texlive/texmf-dist/tex/latex/base/latex.ltx (/usr/share/texlive/texmf-dist/tex/latex/base/texsys.cfg) ./texsys.aux found \@currdir set to: ./. Assuming \openin and \input have the same search path. 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Transcript written on latex.log. mktexfmt [INFO]: /builddir/.cache/texlive/texmf-var/web2c/pdftex/latex.fmt installed. mktexfmt [INFO]: Disabled formats: 32 mktexfmt [INFO]: Successfully rebuilt formats: 1 mktexfmt [INFO]: Not selected formats: 15 mktexfmt [INFO]: Total formats: 48 mktexfmt [INFO]: exiting with status 0 entering extended mode (../doc/crib-sheet.tex LaTeX2e <2016/03/31> Babel <3.9r> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/palatino.sty) No file crib-sheet.aux. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ppl.fd) LaTeX Warning: No \author given. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1] Overfull \hbox (93.56302pt too wide) in paragraph at lines 130--147 [][] Underfull \hbox (badness 1796) in paragraph at lines 149--151 []\OT1/ppl/m/n/10 Intermediate (white) atoms can be dragged (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsppl.fd) Overfull \hbox (10.86366pt too wide) in paragraph at lines 176--198 [] [2] [3] (./crib-sheet.aux) ) (see the transcript file for additional information) Output written on crib-sheet.dvi (3 pages, 7008 bytes). Transcript written on crib-sheet.log. dvips -o crib-sheet.ps crib-sheet.dvi This is dvips(k) 5.996 Copyright 2016 Radical Eye Software (www.radicaleye.com) ' TeX output 2017.07.13:2028' -> crib-sheet.ps . [1] [2] [3] ps2pdf crib-sheet.ps cp crib-sheet.pdf coot-keys-and-buttons.pdf ~/build/BUILD/coot-0.8.8 + popd + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.imLcwR + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386 ++ dirname /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386 + cd coot-0.8.8 + make install DESTDIR=/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386 'INSTALL=install -p' /bin/sh ./config.status skipping Making install in auxil make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' Making install in catcheck make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil/catcheck' make[3]: 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directory '/builddir/build/BUILD/coot-0.8.8/auxil/sec-str' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil/sec-str' Making install in strand-analysis make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil/strand-analysis' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil/strand-analysis' make[4]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[4]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil/strand-analysis' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil/strand-analysis' Making install in vectors make[2]: Entering directory 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Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[4]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil' Making install in scheme make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/scheme' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/scheme' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot/scheme' install -p -m 644 0-auto-rot.scm coot-utils.scm get-ebi.scm mutate.scm background-demo.scm demo-script.scm gtkin.scm my-readline.scm bit.scm extra-top-level.scm hello.scm raster3d.scm brute-lsqman.scm file-utils.scm junk.scm refmac.scm coot-gui.scm filter.scm libcheck.scm simple.scm coot.scm get-ebi.save.scm local-code.scm trivial.scm gap.scm remote-control.scm povray.scm coot-lsq.scm shelx.scm group-settings.scm fitting.scm americanisms.scm tips.scm tips-gui.scm generic-objects.scm cns2coot.scm extensions.scm ncs.scm create-server.scsh coot-crash-catcher.scm '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot/scheme' install -p -m 644 snarf-coot-docs.scm clear-backup.scm bones-reader.scm matrices.scm fascinating-things.scm shelx-extensions.scm parse-pisa-xml.scm check-for-updates.scm 3d-generator-import.scm gui-hole.scm gui-prosmart.scm get-recent-pdbe.scm json-reader.scm jligand.scm jligand-gui.scm redefine-functions.scm user-define-restraints.scm template-key-bindings.scm gui-add-linked-cho.scm ligand-check.scm run-mogul.scm contact-score-isolated-ligand.scm enhanced-ligand.scm gui-ligand-sliders.scm dictionary-generators.scm '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot/scheme' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/scheme' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/scheme' Making install in python make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/python' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/python' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. cd .. && /bin/sh ./config.status python/coot_load_modules.py config.status: creating python/coot_load_modules.py /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot' install -p -m 644 coot_utils.py get_ebi.py mutate.py background_demo.py hello.py raster3d.py brute_lsqman.py refmac.py coot_gui.py filter.py libcheck.py coot_load_modules.py local_code.py gap.py remote_control.py povray.py coot_lsq.py shelx.py group_settings.py fitting.py americanisms.py tips.py tips_gui.py generic_objects.py cns2coot.py extensions.py ncs.py create_server.py python_coot_docs.py clear_backup.py bones_reader.py shelx_extensions.py parse_pisa_xml.py check_for_updates.py 3d_generator_import.py gui_hole.py gui_prosmart.py get_recent_pdbe.py jligand.py jligand_gui.py '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot' install -p -m 644 redefine_functions.py user_define_restraints.py template_key_bindings.py gui_add_linked_cho.py ligand_check.py run_mogul.py contact_score_isolated_ligand.py gui_contact_score_isolated_ligand.py enhanced_ligand.py gui_ligand_sliders.py dictionary_generators.py coot_toolbuttons.py rcrane_loader.py pdbe_validation_data.py ligand_validation_sliders.py chemical_feature_clusters.py res_spec_utils.py '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot' Byte-compiling python modules... coot_utils.pyget_ebi.pymutate.pybackground_demo.pyhello.pyraster3d.pybrute_lsqman.pyrefmac.pycoot_gui.pyfilter.pylibcheck.pycoot_load_modules.pylocal_code.pygap.pyremote_control.pypovray.pycoot_lsq.pyshelx.pygroup_settings.pyfitting.pyamericanisms.pytips.pytips_gui.pygeneric_objects.pycns2coot.pyextensions.pyncs.pycreate_server.pypython_coot_docs.pyclear_backup.pybones_reader.pyshelx_extensions.pyparse_pisa_xml.pycheck_for_updates.py3d_generator_import.pygui_hole.pygui_prosmart.pyget_recent_pdbe.pyjligand.pyjligand_gui.pyredefine_functions.pyuser_define_restraints.pytemplate_key_bindings.pygui_add_linked_cho.pyligand_check.pyrun_mogul.pycontact_score_isolated_ligand.pygui_contact_score_isolated_ligand.pyenhanced_ligand.pygui_ligand_sliders.pydictionary_generators.pycoot_toolbuttons.pyrcrane_loader.pypdbe_validation_data.pyligand_validation_sliders.pychemical_feature_clusters.pyres_spec_utils.py Byte-compiling python modules (optimized versions) ... coot_utils.pyget_ebi.pymutate.pybackground_demo.pyhello.pyraster3d.pybrute_lsqman.pyrefmac.pycoot_gui.pyfilter.pylibcheck.pycoot_load_modules.pylocal_code.pygap.pyremote_control.pypovray.pycoot_lsq.pyshelx.pygroup_settings.pyfitting.pyamericanisms.pytips.pytips_gui.pygeneric_objects.pycns2coot.pyextensions.pyncs.pycreate_server.pypython_coot_docs.pyclear_backup.pybones_reader.pyshelx_extensions.pyparse_pisa_xml.pycheck_for_updates.py3d_generator_import.pygui_hole.pygui_prosmart.pyget_recent_pdbe.pyjligand.pyjligand_gui.pyredefine_functions.pyuser_define_restraints.pytemplate_key_bindings.pygui_add_linked_cho.pyligand_check.pyrun_mogul.pycontact_score_isolated_ligand.pygui_contact_score_isolated_ligand.pyenhanced_ligand.pygui_ligand_sliders.pydictionary_generators.pycoot_toolbuttons.pyrcrane_loader.pypdbe_validation_data.pyligand_validation_sliders.pychemical_feature_clusters.pyres_spec_utils.py make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/python' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/python' Making install in pdb-templates make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pdb-templates' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pdb-templates' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot' install -p -m 644 ASN-NAG-via-NAG-ASN.pdb pyranose-pyranose-via-BETA1-4.pdb pyranose-pyranose-via-ALPHA1-2.pdb pyranose-pyranose-via-ALPHA1-3.pdb pyranose-pyranose-via-ALPHA1-6.pdb SIA-pyranose-via-ALPHA2-3.pdb link-by-torsion-to-pyranose-core-ALPHA1-2.tab link-by-torsion-to-pyranose-core-ALPHA1-3.tab link-by-torsion-to-FUC-core-ALPHA1-3.tab link-by-torsion-to-pyranose-core-ALPHA1-6.tab link-by-torsion-to-pyranose-core-ALPHA2-3.tab link-by-torsion-to-pyranose-core-BETA1-3.tab link-by-torsion-to-pyranose-core-BETA1-4.tab link-by-torsion-to-pyranose-core-NAG-ASN.tab link-by-torsion-to-pyranose-core-XYP-BMA.tab NAG-decorations.tab BMA-decorations.tab MAN-decorations.tab GLC-decorations.tab GAL-decorations.tab FUC-decorations.tab XYP-decorations.tab theor-helix-70.pdb '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pdb-templates' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pdb-templates' Making install in macros make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/macros' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/macros' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/macros' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/macros' Making install in compat make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/compat' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/compat' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-compat.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: install: install -p .libs/libcoot-compat.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-compat.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-compat.so.0.0.0 libcoot-compat.so.0 || { rm -f libcoot-compat.so.0 && ln -s libcoot-compat.so.0.0.0 libcoot-compat.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-compat.so.0.0.0 libcoot-compat.so || { rm -f libcoot-compat.so && ln -s libcoot-compat.so.0.0.0 libcoot-compat.so; }; }) libtool: install: install -p .libs/libcoot-compat.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-compat.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/compat' install -p -m 644 coot-getopt.h '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/compat' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/compat' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/compat' Making install in utils make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/utils' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/utils' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-utils.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: install: install -p .libs/libcoot-utils.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-utils.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-utils.so.0.0.0 libcoot-utils.so.0 || { rm -f libcoot-utils.so.0 && ln -s libcoot-utils.so.0.0.0 libcoot-utils.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-utils.so.0.0.0 libcoot-utils.so || { rm -f libcoot-utils.so && ln -s libcoot-utils.so.0.0.0 libcoot-utils.so; }; }) libtool: install: install -p .libs/libcoot-utils.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-utils.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/utils' install -p -m 644 coot-utils.hh coot-fasta.hh dodec.hh win-compat.hh ctpl_stl.h '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/utils' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/utils' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/utils' Making install in protein_db make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/protein_db' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/protein_db' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-protein-db.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: install: install -p .libs/libcoot-protein-db.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-protein-db.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-protein-db.so.0.0.0 libcoot-protein-db.so.0 || { rm -f libcoot-protein-db.so.0 && ln -s libcoot-protein-db.so.0.0.0 libcoot-protein-db.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-protein-db.so.0.0.0 libcoot-protein-db.so || { rm -f libcoot-protein-db.so && ln -s libcoot-protein-db.so.0.0.0 libcoot-protein-db.so; }; }) libtool: install: install -p .libs/libcoot-protein-db.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-protein-db.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/protein_db' install -p -m 644 protein_db.h protein_db_utils.h rna_db.h '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/protein_db' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot/protein_db' install -p -m 644 protein.db '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot/protein_db' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/protein_db' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/protein_db' Making install in mini-mol make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/mini-mol' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/mini-mol' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-mini-mol.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: warning: relinking 'libcoot-mini-mol.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/mini-mol; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-mini-mol.la -rpath /usr/lib mini-mol.lo mini-mol-utils.lo atom-quads.lo ../utils/libcoot-utils.la -lmmdb2 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/mini-mol.o .libs/mini-mol-utils.o .libs/atom-quads.o -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-mini-mol.so.0 -o .libs/libcoot-mini-mol.so.0.0.0 libtool: install: install -p .libs/libcoot-mini-mol.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-mini-mol.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so.0 || { rm -f libcoot-mini-mol.so.0 && ln -s libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so || { rm -f libcoot-mini-mol.so && ln -s libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so; }; }) libtool: install: install -p .libs/libcoot-mini-mol.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-mini-mol.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/mini-mol' install -p -m 644 mini-mol.hh mini-mol-utils.hh atom-quads.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/mini-mol' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/mini-mol' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/mini-mol' Making install in geometry make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/geometry' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/geometry' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-geometry.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: warning: relinking 'libcoot-geometry.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/geometry; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-geometry.la -rpath /usr/lib protein-geometry.lo protein-geometry-mmdb.lo read-sbase.lo energy-lib.lo chem_mods.lo srs-interface.lo protein-donor-acceptors.lo lbg-graph.lo dreiding.lo dict-utils.lo cif-parse.lo main-chain.lo residue-and-atom-specs.lo mol-utils-2.lo ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/protein-geometry.o .libs/protein-geometry-mmdb.o .libs/read-sbase.o .libs/energy-lib.o .libs/chem_mods.o .libs/srs-interface.o .libs/protein-donor-acceptors.o .libs/lbg-graph.o .libs/dreiding.o .libs/dict-utils.o .libs/cif-parse.o .libs/main-chain.o .libs/residue-and-atom-specs.o .libs/mol-utils-2.o -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-geometry.so.0 -o .libs/libcoot-geometry.so.0.0.0 libtool: install: install -p .libs/libcoot-geometry.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-geometry.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-geometry.so.0.0.0 libcoot-geometry.so.0 || { rm -f libcoot-geometry.so.0 && ln -s libcoot-geometry.so.0.0.0 libcoot-geometry.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-geometry.so.0.0.0 libcoot-geometry.so || { rm -f libcoot-geometry.so && ln -s libcoot-geometry.so.0.0.0 libcoot-geometry.so; }; }) libtool: install: install -p .libs/libcoot-geometry.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-geometry.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin' /bin/sh ../libtool --mode=install install -p coot-compare-dictionaries coot-make-shelx-restraints coot-available-comp-id '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin' libtool: warning: './libcoot-geometry.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib' libtool: install: install -p .libs/coot-compare-dictionaries /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin/coot-compare-dictionaries libtool: warning: './libcoot-geometry.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib' libtool: install: install -p .libs/coot-make-shelx-restraints /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin/coot-make-shelx-restraints libtool: warning: './libcoot-geometry.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib' libtool: install: install -p .libs/coot-available-comp-id /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin/coot-available-comp-id /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/geometry' install -p -m 644 protein-geometry.hh read-sbase.hh lbg-graph.hh srs-interface.hh dict-utils.hh dict-mismatches.hh energy-lib.hh match-results.hh hb-types.hh main-chain.hh residue-and-atom-specs.hh chem_mods.hh mol-utils-2.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/geometry' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/geometry' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/geometry' Making install in coot-utils make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coot-utils' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coot-utils' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-coord-utils.la libcoot-shelx.la libcoot-coord-extras.la libcoot-map-utils.la libcoot-map-heavy.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: warning: relinking 'libcoot-coord-utils.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coot-utils; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-coord-utils.la -rpath /usr/lib coot-coord-utils.lo coot-coord-utils-nucleotides.lo coot-rama.lo coot-h-bonds.lo hole.lo read-sm-cif.lo bonded-pairs.lo helix-analysis.lo elastic.lo glyco-torsions.lo coot-least-squares.lo atom-overlaps.lo reduce.lo ../geometry/libcoot-geometry.la -lgsl -lgslcblas -lm -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/coot-coord-utils.o .libs/coot-coord-utils-nucleotides.o .libs/coot-rama.o .libs/coot-h-bonds.o .libs/hole.o .libs/read-sm-cif.o .libs/bonded-pairs.o .libs/helix-analysis.o .libs/elastic.o .libs/glyco-torsions.o .libs/coot-least-squares.o .libs/atom-overlaps.o .libs/reduce.o -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-coord-utils.so.0 -o .libs/libcoot-coord-utils.so.0.0.0 libtool: install: install -p .libs/libcoot-coord-utils.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-coord-utils.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so.0 || { rm -f libcoot-coord-utils.so.0 && ln -s libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so || { rm -f libcoot-coord-utils.so && ln -s libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so; }; }) libtool: install: install -p .libs/libcoot-coord-utils.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-coord-utils.la libtool: warning: relinking 'libcoot-shelx.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coot-utils; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-shelx.la -rpath /usr/lib coot-shelx-ins.lo libcoot-coord-utils.la ../utils/libcoot-utils.la -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/coot-shelx-ins.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lcoot-utils -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-shelx.so.0 -o .libs/libcoot-shelx.so.0.0.0 libtool: install: install -p .libs/libcoot-shelx.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-shelx.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-shelx.so.0.0.0 libcoot-shelx.so.0 || { rm -f libcoot-shelx.so.0 && ln -s libcoot-shelx.so.0.0.0 libcoot-shelx.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-shelx.so.0.0.0 libcoot-shelx.so || { rm -f libcoot-shelx.so && ln -s libcoot-shelx.so.0.0.0 libcoot-shelx.so; }; }) libtool: install: install -p .libs/libcoot-shelx.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-shelx.la libtool: warning: relinking 'libcoot-coord-extras.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coot-utils; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-coord-extras.la -rpath /usr/lib coot-coord-extras.lo coot-coord-lsq.lo coot-tree-extras.lo water-coordination.lo lsq-improve.lo coot-coord-utils-glyco.lo libcoot-coord-utils.la -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/coot-coord-extras.o .libs/coot-coord-lsq.o .libs/coot-tree-extras.o .libs/water-coordination.o .libs/lsq-improve.o .libs/coot-coord-utils-glyco.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-coord-extras.so.0 -o .libs/libcoot-coord-extras.so.0.0.0 libtool: install: install -p .libs/libcoot-coord-extras.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-coord-extras.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so.0 || { rm -f libcoot-coord-extras.so.0 && ln -s libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so || { rm -f libcoot-coord-extras.so && ln -s libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so; }; }) libtool: install: install -p .libs/libcoot-coord-extras.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-coord-extras.la libtool: warning: relinking 'libcoot-map-utils.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coot-utils; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-map-utils.la -rpath /usr/lib coot-map-utils.lo peak-search.lo peak-search-from-list.lo trim.lo xmap-stats.lo maps-spherical.lo libcoot-coord-utils.la -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/coot-map-utils.o .libs/peak-search.o .libs/peak-search-from-list.o .libs/trim.o .libs/xmap-stats.o .libs/maps-spherical.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-map-utils.so.0 -o .libs/libcoot-map-utils.so.0.0.0 libtool: install: install -p .libs/libcoot-map-utils.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-map-utils.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-map-utils.so.0.0.0 libcoot-map-utils.so.0 || { rm -f libcoot-map-utils.so.0 && ln -s libcoot-map-utils.so.0.0.0 libcoot-map-utils.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-map-utils.so.0.0.0 libcoot-map-utils.so || { rm -f libcoot-map-utils.so && ln -s libcoot-map-utils.so.0.0.0 libcoot-map-utils.so; }; }) libtool: install: install -p .libs/libcoot-map-utils.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-map-utils.la libtool: warning: relinking 'libcoot-map-heavy.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coot-utils; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-map-heavy.la -rpath /usr/lib coot-map-heavy.lo coot-fffear.lo libcoot-map-utils.la libcoot-coord-utils.la -lgsl -lgslcblas -lm -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/coot-map-heavy.o .libs/coot-fffear.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-map-utils -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-map-heavy.so.0 -o .libs/libcoot-map-heavy.so.0.0.0 libtool: install: install -p .libs/libcoot-map-heavy.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-map-heavy.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so.0 || { rm -f libcoot-map-heavy.so.0 && ln -s libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so || { rm -f libcoot-map-heavy.so && ln -s libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so; }; }) libtool: install: install -p .libs/libcoot-map-heavy.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-map-heavy.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/coot-utils' install -p -m 644 peak-search.hh coot-trim.hh coot-coord-utils.hh coot-map-utils.hh coot-coord-extras.hh coot-map-heavy.hh coot-lsq-types.h coot-shelx.hh coot-rama.hh xmap-stats.hh coot-h-bonds.hh lsq-improve.hh coot-hole.hh read-sm-cif.hh bonded-pairs.hh tree.hh helix-analysis.hh elastic.hh emma.hh glyco-torsions.hh coot-least-squares.hh coot-density-stats.hh atom-overlaps.hh reduce.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/coot-utils' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coot-utils' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coot-utils' Making install in surface make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/surface' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/surface' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-electrostatics.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: install: install -p .libs/libcoot-electrostatics.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-electrostatics.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-electrostatics.so.0.0.0 libcoot-electrostatics.so.0 || { rm -f libcoot-electrostatics.so.0 && ln -s libcoot-electrostatics.so.0.0.0 libcoot-electrostatics.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-electrostatics.so.0.0.0 libcoot-electrostatics.so || { rm -f libcoot-electrostatics.so && ln -s libcoot-electrostatics.so.0.0.0 libcoot-electrostatics.so; }; }) libtool: install: install -p .libs/libcoot-electrostatics.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-electrostatics.la libtool: warning: remember to run 'libtool --finish /usr/lib' make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/surface' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/surface' Making install in coot-surface make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coot-surface' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coot-surface' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-surface.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: warning: relinking 'libcoot-surface.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coot-surface; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-surface.la -rpath /usr/lib coot-surface.lo rgbreps.lo ../surface/libcoot-electrostatics.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -lglut -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lGL -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/coot-surface.o .libs/rgbreps.o -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-electrostatics -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lglut -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lGL -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-surface.so.0 -o .libs/libcoot-surface.so.0.0.0 libtool: install: install -p .libs/libcoot-surface.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-surface.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-surface.so.0.0.0 libcoot-surface.so.0 || { rm -f libcoot-surface.so.0 && ln -s libcoot-surface.so.0.0.0 libcoot-surface.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-surface.so.0.0.0 libcoot-surface.so || { rm -f libcoot-surface.so && ln -s libcoot-surface.so.0.0.0 libcoot-surface.so; }; }) libtool: install: install -p .libs/libcoot-surface.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-surface.la libtool: warning: remember to run 'libtool --finish /usr/lib' make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coot-surface' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coot-surface' Making install in lidia-core make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/lidia-core' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/lidia-core' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-lidia-core.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: warning: relinking 'libcoot-lidia-core.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/lidia-core; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-lidia-core.la -rpath /usr/lib lbg-shared.lo lbg-molfile.lo lig-build.lo rdkit-interface.lo cod-types.lo bond-record-container-t.lo cod-atom-type-t.lo cod-atom-types.lo bond-table-record-t.lo chemical-feature-clusters.lo ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la ../coot-utils/libcoot-coord-utils.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/lbg-shared.o .libs/lbg-molfile.o .libs/lig-build.o .libs/rdkit-interface.o .libs/cod-types.o .libs/bond-record-container-t.o .libs/cod-atom-type-t.o .libs/cod-atom-types.o .libs/bond-table-record-t.o .libs/chemical-feature-clusters.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-lidia-core.so.0 -o .libs/libcoot-lidia-core.so.0.0.0 libtool: install: install -p .libs/libcoot-lidia-core.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-lidia-core.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-lidia-core.so.0.0.0 libcoot-lidia-core.so.0 || { rm -f libcoot-lidia-core.so.0 && ln -s libcoot-lidia-core.so.0.0.0 libcoot-lidia-core.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-lidia-core.so.0.0.0 libcoot-lidia-core.so || { rm -f libcoot-lidia-core.so && ln -s libcoot-lidia-core.so.0.0.0 libcoot-lidia-core.so; }; }) libtool: install: install -p .libs/libcoot-lidia-core.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-lidia-core.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/lidia-core' install -p -m 644 lbg-shared.hh lbg-molfile.hh lig-build.hh rdkit-interface.hh use-rdkit.hh cod-types.hh neighbour-sorter.hh bond-record-container-t.hh bond-table-record-t.hh cod-atom-types.hh cod-atom-type-t.hh primes.hh chemical-feature-clusters.hh third-neighbour-info-t.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/lidia-core' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/lidia-core' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/lidia-core' Making install in coords make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coords' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coords' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-coords.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: warning: relinking 'libcoot-coords.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coords; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-coords.la -rpath /usr/lib Bond_lines.lo Cartesian.lo cos-sin.lo mmdb-extras.lo utils.lo mmdb.lo mmdb-crystal.lo Bond_lines_ext.lo coot-close.lo phenix-geo.lo phenix-geo-bonds.lo ../geometry/libcoot-geometry.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-coord-utils.la ../mini-mol/libcoot-mini-mol.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la -lmmdb2 -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/Bond_lines.o .libs/Cartesian.o .libs/cos-sin.o .libs/mmdb-extras.o .libs/utils.o .libs/mmdb.o .libs/mmdb-crystal.o .libs/Bond_lines_ext.o .libs/coot-close.o .libs/phenix-geo.o .libs/phenix-geo-bonds.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-shelx -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lgsl -lgslcblas -lcoot-utils -lmmdb2 -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-coords.so.0 -o .libs/libcoot-coords.so.0.0.0 libtool: install: install -p .libs/libcoot-coords.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-coords.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-coords.so.0.0.0 libcoot-coords.so.0 || { rm -f libcoot-coords.so.0 && ln -s libcoot-coords.so.0.0.0 libcoot-coords.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-coords.so.0.0.0 libcoot-coords.so || { rm -f libcoot-coords.so && ln -s libcoot-coords.so.0.0.0 libcoot-coords.so; }; }) libtool: install: install -p .libs/libcoot-coords.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-coords.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/coords' install -p -m 644 Bond_lines.h Cartesian.h cos-sin.h mmdb.h mmdb-extras.h utils.h mmdb-crystal.h Bond_lines_ext.h coot-close.hh phenix-geo.hh ramachandran-container.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/coords' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coords' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coords' Making install in angles make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/angles' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/angles' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-AngleInfo.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: install: install -p .libs/libcoot-AngleInfo.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-AngleInfo.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so.0 || { rm -f libcoot-AngleInfo.so.0 && ln -s libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so || { rm -f libcoot-AngleInfo.so && ln -s libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so; }; }) libtool: install: install -p .libs/libcoot-AngleInfo.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-AngleInfo.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/angles' install -p -m 644 AngleInfo.h ncube.h wrapped-ncube.h '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/angles' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/angles' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/angles' Making install in skeleton make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/skeleton' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/skeleton' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-skeleton.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: warning: relinking 'libcoot-skeleton.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/skeleton; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-skeleton.la -rpath /usr/lib dm-utils.lo graphical_skel.lo BuildCas.lo ../angles/libcoot-AngleInfo.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/dm-utils.o .libs/graphical_skel.o .libs/BuildCas.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-AngleInfo -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lgsl -lgslcblas -lcoot-utils -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-skeleton.so.0 -o .libs/libcoot-skeleton.so.0.0.0 libtool: install: install -p .libs/libcoot-skeleton.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-skeleton.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-skeleton.so.0.0.0 libcoot-skeleton.so.0 || { rm -f libcoot-skeleton.so.0 && ln -s libcoot-skeleton.so.0.0.0 libcoot-skeleton.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-skeleton.so.0.0.0 libcoot-skeleton.so || { rm -f libcoot-skeleton.so && ln -s libcoot-skeleton.so.0.0.0 libcoot-skeleton.so; }; }) libtool: install: install -p .libs/libcoot-skeleton.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-skeleton.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/skeleton' install -p -m 644 graphical_skel.h dm-utils.h BuildCas.h '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/skeleton' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/skeleton' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/skeleton' Making install in ccp4mg-utils make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libccp4mg-utils.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: install: install -p .libs/libccp4mg-utils.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libccp4mg-utils.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libccp4mg-utils.so.0.0.0 libccp4mg-utils.so.0 || { rm -f libccp4mg-utils.so.0 && ln -s libccp4mg-utils.so.0.0.0 libccp4mg-utils.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libccp4mg-utils.so.0.0.0 libccp4mg-utils.so || { rm -f libccp4mg-utils.so && ln -s libccp4mg-utils.so.0.0.0 libccp4mg-utils.so; }; }) libtool: install: install -p .libs/libccp4mg-utils.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libccp4mg-utils.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/ccp4mg-utils' install -p -m 644 geomutil.h mgtree.h cartesian.h matrix.h quat.h ppmutil.h '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/ccp4mg-utils' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils' Making install in density-contour make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/density-contour' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/density-contour' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-isosurface.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: warning: relinking 'libcoot-isosurface.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/density-contour; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-isosurface.la -rpath /usr/lib Vectors.lo CIsoSurface.lo density-contour-triangles.lo ../coords/libcoot-coords.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/Vectors.o .libs/CIsoSurface.o .libs/density-contour-triangles.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lgsl -lgslcblas -lcoot-utils -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-isosurface.so.0 -o .libs/libcoot-isosurface.so.0.0.0 libtool: install: install -p .libs/libcoot-isosurface.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-isosurface.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-isosurface.so.0.0.0 libcoot-isosurface.so.0 || { rm -f libcoot-isosurface.so.0 && ln -s libcoot-isosurface.so.0.0.0 libcoot-isosurface.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-isosurface.so.0.0.0 libcoot-isosurface.so || { rm -f libcoot-isosurface.so && ln -s libcoot-isosurface.so.0.0.0 libcoot-isosurface.so; }; }) libtool: install: install -p .libs/libcoot-isosurface.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-isosurface.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/density-contour' install -p -m 644 Vectors.h CIsoSurface.h density-contour-triangles.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/density-contour' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/density-contour' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/density-contour' Making install in db-main make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/db-main' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/db-main' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-db-main.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: warning: relinking 'libcoot-db-main.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/db-main; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-db-main.la -rpath /usr/lib db-main.lo db-strands.lo ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/db-main.o .libs/db-strands.o -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-coord-utils -lgsl -lgslcblas -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-db-main.so.0 -o .libs/libcoot-db-main.so.0.0.0 libtool: install: install -p .libs/libcoot-db-main.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-db-main.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-db-main.so.0.0.0 libcoot-db-main.so.0 || { rm -f libcoot-db-main.so.0 && ln -s libcoot-db-main.so.0.0.0 libcoot-db-main.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-db-main.so.0.0.0 libcoot-db-main.so || { rm -f libcoot-db-main.so && ln -s libcoot-db-main.so.0.0.0 libcoot-db-main.so; }; }) libtool: install: install -p .libs/libcoot-db-main.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-db-main.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/db-main' install -p -m 644 db-main.hh db-strands.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/db-main' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/db-main' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/db-main' Making install in analysis make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/analysis' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/analysis' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-analysis.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: warning: relinking 'libcoot-analysis.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/analysis; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-analysis.la -rpath /usr/lib bfkurt.lo mogul.lo kolmogorov.lo stats.lo cablam.lo ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lmmdb2 -lgsl -lgslcblas -lm -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/bfkurt.o .libs/mogul.o .libs/kolmogorov.o .libs/stats.o .libs/cablam.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lcoot-utils -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-analysis.so.0 -o .libs/libcoot-analysis.so.0.0.0 libtool: install: install -p .libs/libcoot-analysis.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-analysis.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-analysis.so.0.0.0 libcoot-analysis.so.0 || { rm -f libcoot-analysis.so.0 && ln -s libcoot-analysis.so.0.0.0 libcoot-analysis.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-analysis.so.0.0.0 libcoot-analysis.so || { rm -f libcoot-analysis.so && ln -s libcoot-analysis.so.0.0.0 libcoot-analysis.so; }; }) libtool: install: install -p .libs/libcoot-analysis.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-analysis.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin' /bin/sh ../libtool --mode=install install -p coot-bfactan '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin' libtool: warning: 'libcoot-analysis.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib' libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib' libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib' libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib' libtool: install: install -p .libs/coot-bfactan /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin/coot-bfactan /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/analysis' install -p -m 644 bfkurt.hh mogul-interface.hh stats.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/analysis' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/analysis' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/analysis' Making install in ideal make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ideal' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ideal' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin' install -p coot-mini-rsr '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-ideal.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: warning: relinking 'libcoot-ideal.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/ideal; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DHAVE_GSL -I/usr/include -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-ideal.la -rpath /usr/lib simple-restraint.lo mods.lo distortion.lo chirals.lo flanking.lo gradients.lo extra-restraints.lo pepflip.lo regularize-minimol.lo lograma.lo extra-restraints-kk.lo simple-restraint-kk.lo torsion-bonds.lo coot-compare-residues.lo link-restraints.lo parallel-planes.lo trans-peptide.lo model-bond-deltas.lo ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la ../lidia-core/libcoot-lidia-core.la -lmmdb2 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lm -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/simple-restraint.o .libs/mods.o .libs/distortion.o .libs/chirals.o .libs/flanking.o .libs/gradients.o .libs/extra-restraints.o .libs/pepflip.o .libs/regularize-minimol.o .libs/lograma.o .libs/extra-restraints-kk.o .libs/simple-restraint-kk.o .libs/torsion-bonds.o .libs/coot-compare-residues.o .libs/link-restraints.o .libs/parallel-planes.o .libs/trans-peptide.o .libs/model-bond-deltas.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-map-heavy -lcoot-map-utils -lcoot-coords -lcoot-shelx -lcoot-coord-extras -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-ideal.so.0 -o .libs/libcoot-ideal.so.0.0.0 libtool: install: install -p .libs/libcoot-ideal.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-ideal.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-ideal.so.0.0.0 libcoot-ideal.so.0 || { rm -f libcoot-ideal.so.0 && ln -s libcoot-ideal.so.0.0.0 libcoot-ideal.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-ideal.so.0.0.0 libcoot-ideal.so || { rm -f libcoot-ideal.so && ln -s libcoot-ideal.so.0.0.0 libcoot-ideal.so; }; }) libtool: install: install -p .libs/libcoot-ideal.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-ideal.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/libexec' /bin/sh ../libtool --mode=install install -p mini-rsr-bin '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/libexec' libtool: warning: './libcoot-ideal.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coords/libcoot-coords.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib' libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib' libtool: warning: '../coords/libcoot-coords.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib' libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib' libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib' libtool: warning: '../compat/libcoot-compat.la' has not been installed in '/usr/lib' libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib' libtool: install: install -p .libs/mini-rsr-bin /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/libexec/mini-rsr-bin /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/ideal' install -p -m 644 test-indexing.hh simple-restraint.hh pepflip.hh regularize-minimol.hh lograma.h parallel-planes.hh torsion-bonds.hh extra-restraints.hh model-bond-deltas.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/ideal' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ideal' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ideal' Making install in ligand make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ligand' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ligand' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin' install -p findwaters findligand '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-ligand.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: warning: relinking 'libcoot-ligand.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/ligand; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-ligand.la -rpath /usr/lib ligand.lo ligand-extras.lo residue_by_phi_psi.lo wiggly-ligand.lo monomer-utils.lo dunbrack.lo chi-angles-autogen.lo chi-angles.lo helix-placement.lo fast-ss-search.lo rigid-body.lo ideal-rna.lo richardson-rotamers.lo richardson-rotamer.lo rotamer.lo torsion-general.lo rotamer-tables.lo primitive-chi-angles.lo dipole.lo base-pairing.lo backrub-rotamer.lo trace.lo trace-2.lo multi-peptide.lo ligands-db.lo ../ideal/libcoot-ideal.la ../coot-utils/libcoot-map-heavy.la ../db-main/libcoot-db-main.la ../ccp4mg-utils/libccp4mg-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../coords/libcoot-coords.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-map-utils.la ../analysis/libcoot-analysis.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/ligand.o .libs/ligand-extras.o .libs/residue_by_phi_psi.o .libs/wiggly-ligand.o .libs/monomer-utils.o .libs/dunbrack.o .libs/chi-angles-autogen.o .libs/chi-angles.o .libs/helix-placement.o .libs/fast-ss-search.o .libs/rigid-body.o .libs/ideal-rna.o .libs/richardson-rotamers.o .libs/richardson-rotamer.o .libs/rotamer.o .libs/torsion-general.o .libs/rotamer-tables.o .libs/primitive-chi-angles.o .libs/dipole.o .libs/base-pairing.o .libs/backrub-rotamer.o .libs/trace.o .libs/trace-2.o .libs/multi-peptide.o .libs/ligands-db.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-ideal -lcoot-map-heavy -lcoot-db-main -lccp4mg-utils -lpng -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lcoot-coord-extras -lcoot-map-utils -lcoot-analysis -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lgsl -lgslcblas -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-ligand.so.0 -o .libs/libcoot-ligand.so.0.0.0 libtool: install: install -p .libs/libcoot-ligand.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-ligand.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-ligand.so.0.0.0 libcoot-ligand.so.0 || { rm -f libcoot-ligand.so.0 && ln -s libcoot-ligand.so.0.0.0 libcoot-ligand.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-ligand.so.0.0.0 libcoot-ligand.so || { rm -f libcoot-ligand.so && ln -s libcoot-ligand.so.0.0.0 libcoot-ligand.so; }; }) libtool: install: install -p .libs/libcoot-ligand.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-ligand.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/libexec' /bin/sh ../libtool --mode=install install -p findligand-bin findwaters-bin '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/libexec' libtool: warning: './libcoot-ligand.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ideal/libcoot-ideal.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/db-main/libcoot-db-main.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/analysis/libcoot-analysis.la' has not been installed in '/usr/lib' libtool: warning: '../ideal/libcoot-ideal.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coords/libcoot-coords.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib' libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib' libtool: warning: '../coords/libcoot-coords.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib' libtool: warning: '../db-main/libcoot-db-main.la' has not been installed in '/usr/lib' libtool: warning: '../ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib' libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib' libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib' libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib' libtool: warning: '../compat/libcoot-compat.la' has not been installed in '/usr/lib' libtool: install: install -p .libs/findligand-bin /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/libexec/findligand-bin libtool: warning: './libcoot-ligand.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ideal/libcoot-ideal.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/db-main/libcoot-db-main.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/analysis/libcoot-analysis.la' has not been installed in '/usr/lib' libtool: warning: '../ideal/libcoot-ideal.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coords/libcoot-coords.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib' libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib' libtool: warning: '../coords/libcoot-coords.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib' libtool: warning: '../ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib' libtool: warning: '../db-main/libcoot-db-main.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib' libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib' libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib' libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib' libtool: warning: '../compat/libcoot-compat.la' has not been installed in '/usr/lib' libtool: install: install -p .libs/findwaters-bin /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/libexec/findwaters-bin /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot/data' install -p -m 644 ligands-2016.db '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot/data' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/ligand' install -p -m 644 ligand.hh residue_by_phi_psi.hh wligand.hh monomer-utils.hh chi-angles.hh dunbrack.hh helix-placement.hh fast-ss-search.hh rigid-body.hh ideal-rna.hh rotamer.hh richardson-rotamer.hh torsion-general.hh primitive-chi-angles.hh dipole.hh base-pairing.hh backrub-rotamer.hh trace.hh multi-peptide.hh ligands-db.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/ligand' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ligand' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ligand' Making install in high-res make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/high-res' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/high-res' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-high-res.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: warning: relinking 'libcoot-high-res.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/high-res; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-high-res.la -rpath /usr/lib high-res.lo coot-atom-graph.lo residue-distortions.lo sequence-assignment.lo ../mini-mol/libcoot-mini-mol.la ../ligand/libcoot-ligand.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/high-res.o .libs/coot-atom-graph.o .libs/residue-distortions.o .libs/sequence-assignment.o -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/ideal/.libs -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/db-main/.libs -L/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/analysis/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-ligand -lcoot-ideal -lcoot-map-heavy -lcoot-db-main -lccp4mg-utils -lpng -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lcoot-coord-extras -lcoot-map-utils -lcoot-analysis -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lgsl -lgslcblas -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-high-res.so.0 -o .libs/libcoot-high-res.so.0.0.0 libtool: install: install -p .libs/libcoot-high-res.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-high-res.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-high-res.so.0.0.0 libcoot-high-res.so.0 || { rm -f libcoot-high-res.so.0 && ln -s libcoot-high-res.so.0.0.0 libcoot-high-res.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-high-res.so.0.0.0 libcoot-high-res.so || { rm -f libcoot-high-res.so && ln -s libcoot-high-res.so.0.0.0 libcoot-high-res.so; }; }) libtool: install: install -p .libs/libcoot-high-res.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-high-res.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/high-res' install -p -m 644 high-res.hh coot-atom-graph.hh coot-node-info.hh sequence-assignment.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/high-res' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/high-res' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/high-res' Making install in build make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/build' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/build' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-cabuild.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: warning: relinking 'libcoot-cabuild.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/build; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-cabuild.la -rpath /usr/lib CalphaBuild.lo ../angles/libcoot-AngleInfo.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/CalphaBuild.o -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-AngleInfo -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-cabuild.so.0 -o .libs/libcoot-cabuild.so.0.0.0 libtool: install: install -p .libs/libcoot-cabuild.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-cabuild.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-cabuild.so.0.0.0 libcoot-cabuild.so.0 || { rm -f libcoot-cabuild.so.0 && ln -s libcoot-cabuild.so.0.0.0 libcoot-cabuild.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-cabuild.so.0.0.0 libcoot-cabuild.so || { rm -f libcoot-cabuild.so && ln -s libcoot-cabuild.so.0.0.0 libcoot-cabuild.so; }; }) libtool: install: install -p .libs/libcoot-cabuild.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-cabuild.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/build' install -p -m 644 CalphaBuild.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/build' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/build' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/build' Making install in greg-tests make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/greg-tests' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/greg-tests' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/greg-tests' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/greg-tests' Making install in python-tests make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/python-tests' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/python-tests' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/python-tests' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/python-tests' Making install in tw make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/tw' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/tw' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-tw.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: install: install -p .libs/libcoot-tw.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-tw.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-tw.so.0.0.0 libcoot-tw.so.0 || { rm -f libcoot-tw.so.0 && ln -s libcoot-tw.so.0.0.0 libcoot-tw.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-tw.so.0.0.0 libcoot-tw.so || { rm -f libcoot-tw.so && ln -s libcoot-tw.so.0.0.0 libcoot-tw.so; }; }) libtool: install: install -p .libs/libcoot-tw.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-tw.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/tw' install -p -m 644 coot-tw.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/tw' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/tw' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/tw' Making install in libgtkgraph make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/libgtkgraph' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/libgtkgraph' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-gtkgraph.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: install: install -p .libs/libcoot-gtkgraph.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-gtkgraph.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-gtkgraph.so.0.0.0 libcoot-gtkgraph.so.0 || { rm -f libcoot-gtkgraph.so.0 && ln -s libcoot-gtkgraph.so.0.0.0 libcoot-gtkgraph.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-gtkgraph.so.0.0.0 libcoot-gtkgraph.so || { rm -f libcoot-gtkgraph.so && ln -s libcoot-gtkgraph.so.0.0.0 libcoot-gtkgraph.so; }; }) libtool: install: install -p .libs/libcoot-gtkgraph.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-gtkgraph.la libtool: warning: remember to run 'libtool --finish /usr/lib' make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/libgtkgraph' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/libgtkgraph' Making install in lbg make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/lbg' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/lbg' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-lidia.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: warning: relinking 'libcoot-lidia.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/lbg; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-lidia.la -rpath /usr/lib lbg.lo lbg-flev.lo wmolecule.lo lbg-search.lo residue-circles.lo pi-stacking.lo flev-annotations.lo lbg-drag-and-drop.lo qed-interface.lo alerts.lo alerts-list.lo qed-properties.lo ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -lgsl -lgslcblas -lm -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lcairo -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/lbg.o .libs/lbg-flev.o .libs/wmolecule.o .libs/lbg-search.o .libs/residue-circles.o .libs/pi-stacking.o .libs/flev-annotations.o .libs/lbg-drag-and-drop.o .libs/qed-interface.o .libs/alerts.o .libs/alerts-list.o .libs/qed-properties.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lpython2.7 -lpthread -ldl -lutil -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-export-dynamic -Wl,-soname -Wl,libcoot-lidia.so.0 -o .libs/libcoot-lidia.so.0.0.0 libtool: install: install -p .libs/libcoot-lidia.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-lidia.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-lidia.so.0.0.0 libcoot-lidia.so.0 || { rm -f libcoot-lidia.so.0 && ln -s libcoot-lidia.so.0.0.0 libcoot-lidia.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-lidia.so.0.0.0 libcoot-lidia.so || { rm -f libcoot-lidia.so && ln -s libcoot-lidia.so.0.0.0 libcoot-lidia.so; }; }) libtool: install: install -p .libs/libcoot-lidia.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-lidia.la /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin' libtool: warning: remember to run 'libtool --finish /usr/lib' /bin/sh ../libtool --mode=install install -p lidia '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin' libtool: warning: './libcoot-lidia.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib' libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib' libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib' libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib' libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib' libtool: install: install -p .libs/lidia /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin/lidia /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot/pixmaps' install -p -m 644 3-c-new.svg 6-c-shadow-experiment.svg single.svg 3-c-other.svg 6-c.svg sp3.svg 3-c.svg 7-c.svg stereo-out.svg 4-c.svg 8-c.svg TheStructorr_magnifying_glass-32.svg 5-c.svg Anonymous_Architetto_--_Chiave.svg TheStructorr_magnifying_glass.svg 6-c-arom.svg charge.svg triple.svg 6-c-exp-2.svg double.svg Trash-hydrogens-Andy_Trash_Can.svg face-smile.svg 05_Hotel_Icon_Hair_Salon.svg '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot/pixmaps' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/lidia' install -p -m 644 __init__.py fetch.py '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/lidia' Byte-compiling python modules... __init__.pyfetch.py Byte-compiling python modules (optimized versions) ... __init__.pyfetch.py /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/lbg' install -p -m 644 lbg.hh w-atom.hh w-bond.hh wmolecule.hh topological-equivalence.hh flev-annotations.hh graphics-c-interface-functions.hh lbg-drag-and-drop.hh qed-interface.hh alerts.hh pi-stacking.hh solvent-exposure-difference.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot/lbg' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot' install -p -m 644 lbg.glade lbg-callbacks.cc '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/lbg' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/lbg' Making install in cootaneer make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/cootaneer' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/cootaneer' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcootaneer.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: install: install -p .libs/libcootaneer.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcootaneer.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcootaneer.so.0.0.0 libcootaneer.so.0 || { rm -f libcootaneer.so.0 && ln -s libcootaneer.so.0.0.0 libcootaneer.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcootaneer.so.0.0.0 libcootaneer.so || { rm -f libcootaneer.so && ln -s libcootaneer.so.0.0.0 libcootaneer.so; }; }) libtool: install: install -p .libs/libcootaneer.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcootaneer.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot' install -p -m 644 cootaneer-llk-2.40.dat '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/cootaneer' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/cootaneer' Making install in cootilus make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/cootilus' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/cootilus' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcootilus.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: install: install -p .libs/libcootilus.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcootilus.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcootilus.so.0.0.0 libcootilus.so.0 || { rm -f libcootilus.so.0 && ln -s libcootilus.so.0.0.0 libcootilus.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcootilus.so.0.0.0 libcootilus.so || { rm -f libcootilus.so && ln -s libcootilus.so.0.0.0 libcootilus.so; }; }) libtool: install: install -p .libs/libcootilus.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcootilus.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot' install -p -m 644 nautilus_lib.pdb '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/cootilus' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/cootilus' Making install in goograph make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/goograph' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/goograph' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot-goograph.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: warning: relinking 'libcoot-goograph.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/goograph; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-goograph.la -rpath /usr/lib goograph.lo ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lcairo -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/goograph.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lcoot-utils -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-goograph.so.0 -o .libs/libcoot-goograph.so.0.0.0 libtool: install: install -p .libs/libcoot-goograph.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-goograph.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-goograph.so.0.0.0 libcoot-goograph.so.0 || { rm -f libcoot-goograph.so.0 && ln -s libcoot-goograph.so.0.0.0 libcoot-goograph.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot-goograph.so.0.0.0 libcoot-goograph.so || { rm -f libcoot-goograph.so && ln -s libcoot-goograph.so.0.0.0 libcoot-goograph.so; }; }) libtool: install: install -p .libs/libcoot-goograph.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-goograph.la libtool: warning: remember to run 'libtool --finish /usr/lib' make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/goograph' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/goograph' Making install in pyrogen make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pyrogen' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pyrogen' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin' install -p pyrogen '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' /bin/sh ../libtool --mode=install install -p libcoot_py_restraints.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib' libtool: warning: relinking 'libcoot_py_restraints.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/pyrogen; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot_py_restraints.la -rpath /usr/lib mmff-restraints.lo py-restraints.lo ../geometry/libcoot-geometry.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/mmff-restraints.o .libs/py-restraints.o -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lmmdb2 -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lpthread -ldl -lutil -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-export-dynamic -Wl,-soname -Wl,libcoot_py_restraints.so.0 -o .libs/libcoot_py_restraints.so.0.0.0 libtool: install: install -p .libs/libcoot_py_restraints.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot_py_restraints.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot_py_restraints.so.0.0.0 libcoot_py_restraints.so.0 || { rm -f libcoot_py_restraints.so.0 && ln -s libcoot_py_restraints.so.0.0.0 libcoot_py_restraints.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib && { ln -s -f libcoot_py_restraints.so.0.0.0 libcoot_py_restraints.so || { rm -f libcoot_py_restraints.so && ln -s libcoot_py_restraints.so.0.0.0 libcoot_py_restraints.so; }; }) libtool: install: install -p .libs/libcoot_py_restraints.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot_py_restraints.la libtool: warning: remember to run 'libtool --finish /usr/lib' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages' /bin/sh ../libtool --mode=install install -p _pyrogen_swig.la pyrogen_boost.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages' libtool: warning: relinking '_pyrogen_swig.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/pyrogen; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -module -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o _pyrogen_swig.la -rpath /usr/lib/python2.7/site-packages pyrogen-swig.lo restraints.lo libcoot_py_restraints.la ../ideal/libcoot-ideal.la ../analysis/libcoot-analysis.la ../geometry/libcoot-geometry.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/pyrogen-swig.o .libs/restraints.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot_py_restraints -lcoot-ideal -lcoot-map-heavy -lcoot-map-utils -lcoot-coords -lcoot-shelx -lcoot-coord-extras -lcoot-lidia-core -lcoot-analysis -lcoot-coord-utils -lgsl -lgslcblas -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lmmdb2 -lpython2.7 -lpthread -ldl -lutil -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-export-dynamic -Wl,-soname -Wl,_pyrogen_swig.so.0 -o .libs/_pyrogen_swig.so.0.0.0 libtool: install: install -p .libs/_pyrogen_swig.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/_pyrogen_swig.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages && { ln -s -f _pyrogen_swig.so.0.0.0 _pyrogen_swig.so.0 || { rm -f _pyrogen_swig.so.0 && ln -s _pyrogen_swig.so.0.0.0 _pyrogen_swig.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages && { ln -s -f _pyrogen_swig.so.0.0.0 _pyrogen_swig.so || { rm -f _pyrogen_swig.so && ln -s _pyrogen_swig.so.0.0.0 _pyrogen_swig.so; }; }) libtool: install: install -p .libs/_pyrogen_swig.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/_pyrogen_swig.la libtool: warning: relinking 'pyrogen_boost.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/pyrogen; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -fasynchronous-unwind-tables -fno-strict-aliasing -Wall -Wno-unused -module -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o pyrogen_boost.la -rpath /usr/lib/python2.7/site-packages restraints-boost.lo libcoot_py_restraints.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../lidia-core/libcoot-lidia-core.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/i686-redhat-linux/7/../../../crti.o /usr/lib/gcc/i686-redhat-linux/7/crtbeginS.o .libs/restraints-boost.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib -L/usr/lib -lcoot_py_restraints -ldl -lutil -lcoot-ideal -lcoot-map-heavy -lcoot-map-utils -lcoot-coord-extras -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lpython2.7 -lboost_python -L/usr/lib/gcc/i686-redhat-linux/7 -L/usr/lib/gcc/i686-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-redhat-linux/7/crtendS.o /usr/lib/gcc/i686-redhat-linux/7/../../../crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -Wl,-z -Wl,relro -Wl,-soname -Wl,pyrogen_boost.so.0 -o .libs/pyrogen_boost.so.0.0.0 libtool: install: install -p .libs/pyrogen_boost.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/pyrogen_boost.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages && { ln -s -f pyrogen_boost.so.0.0.0 pyrogen_boost.so.0 || { rm -f pyrogen_boost.so.0 && ln -s pyrogen_boost.so.0.0.0 pyrogen_boost.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages && { ln -s -f pyrogen_boost.so.0.0.0 pyrogen_boost.so || { rm -f pyrogen_boost.so && ln -s pyrogen_boost.so.0.0.0 pyrogen_boost.so; }; }) libtool: install: install -p .libs/pyrogen_boost.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/pyrogen_boost.la libtool: warning: remember to run 'libtool --finish /usr/lib/python2.7/site-packages' make install-exec-hook make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pyrogen' make[4]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[4]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Nothing to be done for 'install-exec-hook'. make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pyrogen' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot' install -p -m 644 pyrogen.py atom_types.py jay_util.py tautomer.py pyrogen_swig.py coot_git.py '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot' Byte-compiling python modules... pyrogen.pyatom_types.pyjay_util.pytautomer.pypyrogen_swig.pycoot_git.py Byte-compiling python modules (optimized versions) ... pyrogen.pyatom_types.pyjay_util.pytautomer.pypyrogen_swig.pycoot_git.py make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pyrogen' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pyrogen' Making install in src make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/src' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/src' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin' /bin/sh ../libtool --mode=install install -p coot-fix-nomenclature-errors '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin' libtool: warning: '../ligand/libcoot-ligand.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ideal/libcoot-ideal.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/db-main/libcoot-db-main.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/analysis/libcoot-analysis.la' has not been installed in '/usr/lib' libtool: warning: '../db-main/libcoot-db-main.la' has not been installed in '/usr/lib' libtool: warning: '../ideal/libcoot-ideal.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coords/libcoot-coords.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib' libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib' libtool: warning: '../coords/libcoot-coords.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib' libtool: warning: '../ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib' libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib' libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib' libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib' libtool: install: install -p .libs/coot-fix-nomenclature-errors /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin/coot-fix-nomenclature-errors /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin' install -p coot coot-density-score-by-residue '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/libexec' /bin/sh ../libtool --mode=install install -p coot-bin coot-density-score-by-residue-bin '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/libexec' libtool: warning: '../lbg/libcoot-lidia.la' has not been installed in '/usr/lib' libtool: warning: '../ligand/libcoot-ligand.la' has not been installed in '/usr/lib' libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib' libtool: warning: '../goograph/libcoot-goograph.la' has not been installed in '/usr/lib' libtool: warning: '../libgtkgraph/libcoot-gtkgraph.la' has not been installed in '/usr/lib' libtool: warning: '../density-contour/libcoot-isosurface.la' has not been installed in '/usr/lib' libtool: warning: '../build/libcoot-cabuild.la' has not been installed in '/usr/lib' libtool: warning: '../skeleton/libcoot-skeleton.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/angles/libcoot-AngleInfo.la' has not been installed in '/usr/lib' libtool: warning: '../angles/libcoot-AngleInfo.la' has not been installed in '/usr/lib' libtool: warning: '../db-main/libcoot-db-main.la' has not been installed in '/usr/lib' libtool: warning: '../high-res/libcoot-high-res.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ligand/libcoot-ligand.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ideal/libcoot-ideal.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/db-main/libcoot-db-main.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/analysis/libcoot-analysis.la' has not been installed in '/usr/lib' libtool: warning: '../ideal/libcoot-ideal.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coords/libcoot-coords.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib' libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib' libtool: warning: '../coords/libcoot-coords.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib' libtool: warning: '../coot-surface/libcoot-surface.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/surface/libcoot-electrostatics.la' has not been installed in '/usr/lib' libtool: warning: '../surface/libcoot-electrostatics.la' has not been installed in '/usr/lib' libtool: warning: '../ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib' libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib' libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib' libtool: warning: '../analysis/libcoot-analysis.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib' libtool: warning: '../protein_db/libcoot-protein-db.la' has not been installed in '/usr/lib' libtool: warning: '../cootilus/libcootilus.la' has not been installed in '/usr/lib' libtool: warning: '../cootaneer/libcootaneer.la' has not been installed in '/usr/lib' libtool: warning: '../compat/libcoot-compat.la' has not been installed in '/usr/lib' libtool: install: install -p .libs/coot-bin /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/libexec/coot-bin libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib' libtool: warning: '../coords/libcoot-coords.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib' libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib' libtool: warning: '../coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib' libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib' libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib' libtool: warning: '../compat/libcoot-compat.la' has not been installed in '/usr/lib' libtool: install: install -p .libs/coot-density-score-by-residue-bin /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/libexec/coot-density-score-by-residue-bin /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot' install -p coot.py '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot' install -p -m 644 crunch-model.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/include/coot' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/src' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/src' Making install in data make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/data' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/data' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot/data' install -p -m 644 tutorial-modern.pdb rnasa-1.8-all_refmac1.mtz ligands.db '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot/data' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/data' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/data' Making install in man make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/man' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/man' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/man/man1' install -p -m 644 'coot.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/man/man1/coot.1' install -p -m 644 'coot-density-score-by-residue.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/man/man1/coot-density-score-by-residue.1' install -p -m 644 'coot-compare-dictionaries.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/man/man1/coot-compare-dictionaries.1' install -p -m 644 'coot-available-comp-id.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/man/man1/coot-available-comp-id.1' install -p -m 644 'coot-bfactan.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/man/man1/coot-bfactan.1' install -p -m 644 'coot-fix-nomenclature-errors.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/man/man1/coot-fix-nomenclature-errors.1' install -p -m 644 'coot-make-shelx-restraints.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/man/man1/coot-make-shelx-restraints.1' install -p -m 644 'coot-mini-rsr.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/man/man1/coot-mini-rsr.1' install -p -m 644 'lidia.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/man/man1/lidia.1' install -p -m 644 'findwaters.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/man/man1/findwaters.1' install -p -m 644 'findligand.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/man/man1/findligand.1' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/man' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/man' Making install in rama-data make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/rama-data' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/rama-data' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot/rama-data' install -p -m 644 rota500-arg.data rota500-asn.data rota500-asp.data rota500-cys.data rota500-gln.data rota500-glu.data rota500-his.data rota500-ile.data rota500-leu.data rota500-lys.data rota500-met.data rota500-phetyr.data rota500-pro.data rota500-ser.data rota500-thr.data rota500-trp.data rota500-val.data '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot/rama-data' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/rama-data' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/rama-data' Making install in doc make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/doc' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/doc' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/doc' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/doc' Making install in rcrane make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/rcrane' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/rcrane' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane' install -p -m 644 CHANGELOG.txt buildPhosOxy.py installRCrane.py pseudoMolecule.py selectMapDialog.py LICENSE.txt calcCoords.py launch.py pseudoPredictor.py settings.py chain.py linearInterp.py puckerList.py smoothProb.py NOTICE.txt citationPopup.py logo.svg reviewSuitesGui.py stats.py README.txt coot_gui_adapter.py menu.py revisionNum.py strucCalc.py __init__.py coot_utils_adapter.py nextPhos.py rotData.py suite.py about.py nucleotide.py rotamerSeq.py thetaEtaPredictor.py bondLength.py guiUtils.py phenixRestraints.py rotamerize.py traceGui.py buildInitSugar.py icon.svg '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane' install -p -m 644 preLaunchCheck.py safelog.py extendChain.py reportInputErrors.py '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/data' install -p -m 644 data/bases.pdb data/phosAngleSmoothed.csv data/sugarDists.csv data/c2p.pdb data/phosDistSmoothed.csv data/sugarPhosSugarAngleSmoothed.csv data/c3p.pdb data/pseudoChiSmoothed.csv data/thetaEtaClusts.csv data/dihedData.csv data/smoothedPuckerDist.csv data/endingPDists.csv data/startingPDists.csv '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/data' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/rcrane' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/rcrane' Making install in pixmaps make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' Making install in icons make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps/icons' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps/icons' make[4]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[4]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Nothing to be done for 'install-exec-am'. for icon in hicolor_apps_48x48_coot.png hicolor_apps_64x64_coot.png hicolor_apps_96x96_coot.png hicolor_apps_256x256_coot.png hicolor_apps_scalable_coot.svg; do \ THEME=` echo $icon | cut -d_ -f1`; \ CONTEXT=` echo $icon | cut -d_ -f2`; \ SIZE=` echo $icon | cut -d_ -f3`; \ ICONFILE=`echo $icon | cut -d_ -f4`; \ mkdir -p /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/icons/$THEME/$SIZE/$CONTEXT; \ install -p -m 644 ./$icon /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/icons/$THEME/$SIZE/$CONTEXT/$ICONFILE; \ done; make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps/icons' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps/icons' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[4]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[4]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot/pixmaps' install -p -m 644 coot-0.8.8.png coot-0.8.7.png add-alt-conf.png dna.svg probe-clash.svg add-alt-conf.svg edit-backbone.svg radacina_handcuffs-small.svg add-peptide-1.png edit-chi.png ramachandran.png add-peptide-1.svg edit-chi.svg refine-1.svg add-water.svg emsley.jpg refine.png anchor.svg env-distances.png regularize-1.svg aniso-atom.png env-distances.svg regularize.png aniso-atom.svg eugene.jpg renumber-residues.svg appointment-new.png flip-peptide.png reset-view-32.png atom-at-pointer.png flip-peptide.svg reset-view-32.svg atom-at-pointer.svg generic-display-objects.svg reset-view.png auto-fit-rotamer.png geom.svg reset-view.svg auto-fit-rotamer.svg ghosts.png '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot/pixmaps' install -p -m 644 residue-info.png azerbaijan2.svg ghosts.svg residue-info.svg azerbaijan.svg gln-asn-b-factors.svg rigid-body.png calculate-ghosts.svg gln-asn-b-factorssvg.svg rigid-body.svg cell+symm.png glyco-structures.svg rotamers.png cell+symm.svg gnome-run.png rotamers.svg change-chain-id.svg go-to-atom.svg rtz.png chiral.png go-to-ligand.svg rtz.svg chiral.svg gtk-connect-16.png scroll-wheel.svg connect-to-ccp4.svg gtk-font.png secondary-structure.svg connect-to-oca.svg gtk-open-16.png sequence-view.png connect-to-usf.svg gtk-open-24.png sequence-view.svg connect-to-world.svg gtk-open.png side-chain-180.png kevin.jpg side-chain-180.svg kevin-orig.jpg '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot/pixmaps' install -p -m 644 smiles.png kleywegt.svg smiles.svg map.svg spin-view.png coot-favicon.png merge-molecules.svg spin-view.svg coot-icon.png mutate-auto-fit.svg stereo-view.svg coot-save.png mutate.svg stop.svg coot-save-symm.png panel-screenshot.png temperature.png crosshairs.png peptide-omega.png temperature.svg crosshairs.svg peptide-omega.svg torsion-general.svg delete.png phenixed.svg undo-1.png delete.svg pink-pointer.png undo-1.svg density-fit.svg pink-pointer.svg unknown-blob.png diff-map.png plane-distances.png unknown-blob.svg diff-map.svg plane-distances.svg water-diff-map.svg display-manager.png pointer-distances.png '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot/pixmaps' install -p -m 644 water-drop.svg display-manager.svg pointer-distances.svg koppi-green-tick-64.png rygle-red-cross-64.png forest51690-dwcheckno-incomplete-64.png go-to-ligand.png go-to-atom.png azerbaijan.png add-water.png mutate.png mutate-auto-fit.png edit-backbone.png torsion-general.png anchor.png regularize-1.png refine-1.png '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot/pixmaps' make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/appdata' install -p -m 644 coot.appdata.xml '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/appdata' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/applications' install -p -m 644 coot.desktop '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/applications' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot' install -p -m 644 cootrc standard-residues.pdb colours.def mtrix-to-ncs-matrix.awk syminfo.lib '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' + mv reference-structures /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/coot/ + sed -i 's|COOT_PYTHON_DIR=|COOT_PYTHON_DIR=/usr/lib/python2.7/site-packages/coot|' src/coot + sed -i 's|COOT_REFMAC_LIB_DIR=|COOT_REFMAC_LIB_DIR=/usr/share/refmac-dictionary-5.41|' src/coot + install -p -m 755 src/coot /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin/ + rm -f /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libccp4mg-utils.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-AngleInfo.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-analysis.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-cabuild.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-compat.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-coord-extras.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-coord-utils.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-coords.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-db-main.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-electrostatics.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-geometry.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-goograph.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-gtkgraph.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-high-res.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-ideal.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-isosurface.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-lidia-core.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-lidia.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-ligand.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-map-heavy.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-map-utils.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-mini-mol.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-protein-db.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-shelx.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-skeleton.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-surface.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-tw.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-utils.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot_py_restraints.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcootaneer.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcootilus.la + rm -f /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/_pyrogen_swig.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/pyrogen_boost.la ++ find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name '*.py' + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/about.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/about.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/about.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/about.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/about.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/suite.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/suite.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/suite.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/suite.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/suite.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/menu.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/menu.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/menu.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/menu.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/menu.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/stats.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/stats.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/stats.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/stats.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/stats.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/chain.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/chain.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/chain.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/chain.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/chain.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/settings.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/settings.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/settings.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/settings.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/settings.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/launch.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/launch.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/launch.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/launch.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/launch.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_git.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_git.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_git.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_git.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_git.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/pyrogen_swig.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/pyrogen_swig.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/pyrogen_swig.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/pyrogen_swig.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/pyrogen_swig.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/tautomer.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/tautomer.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/tautomer.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/tautomer.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/tautomer.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/jay_util.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/jay_util.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/jay_util.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/jay_util.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/jay_util.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/atom_types.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/atom_types.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/atom_types.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/atom_types.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/atom_types.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/pyrogen.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/pyrogen.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/pyrogen.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/pyrogen.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/pyrogen.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/lidia/fetch.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/lidia/fetch.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/lidia/fetch.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/lidia/fetch.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/lidia/fetch.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/lidia/__init__.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/lidia/__init__.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/lidia/__init__.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/lidia/__init__.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/lidia/__init__.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/res_spec_utils.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/res_spec_utils.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/res_spec_utils.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/res_spec_utils.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/res_spec_utils.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/chemical_feature_clusters.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/chemical_feature_clusters.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/chemical_feature_clusters.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/chemical_feature_clusters.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/chemical_feature_clusters.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ligand_validation_sliders.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ligand_validation_sliders.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ligand_validation_sliders.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ligand_validation_sliders.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ligand_validation_sliders.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/pdbe_validation_data.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/pdbe_validation_data.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/pdbe_validation_data.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/pdbe_validation_data.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/pdbe_validation_data.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane_loader.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane_loader.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane_loader.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane_loader.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/rcrane_loader.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/dictionary_generators.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/dictionary_generators.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/dictionary_generators.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/dictionary_generators.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/dictionary_generators.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_ligand_sliders.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_ligand_sliders.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_ligand_sliders.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_ligand_sliders.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_ligand_sliders.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/enhanced_ligand.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/enhanced_ligand.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/enhanced_ligand.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/enhanced_ligand.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/enhanced_ligand.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_contact_score_isolated_ligand.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_contact_score_isolated_ligand.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_contact_score_isolated_ligand.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_contact_score_isolated_ligand.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_contact_score_isolated_ligand.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/contact_score_isolated_ligand.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/contact_score_isolated_ligand.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/contact_score_isolated_ligand.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/contact_score_isolated_ligand.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/contact_score_isolated_ligand.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/run_mogul.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/run_mogul.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/run_mogul.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/run_mogul.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/run_mogul.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ligand_check.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ligand_check.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ligand_check.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ligand_check.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ligand_check.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_add_linked_cho.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_add_linked_cho.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_add_linked_cho.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_add_linked_cho.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_add_linked_cho.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/template_key_bindings.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/template_key_bindings.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/template_key_bindings.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/template_key_bindings.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/template_key_bindings.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/user_define_restraints.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/user_define_restraints.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/user_define_restraints.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/user_define_restraints.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/user_define_restraints.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/redefine_functions.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/redefine_functions.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/redefine_functions.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/redefine_functions.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/redefine_functions.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/jligand_gui.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/jligand_gui.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/jligand_gui.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/jligand_gui.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/jligand_gui.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/jligand.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/jligand.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/jligand.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/jligand.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/jligand.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_prosmart.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_prosmart.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_prosmart.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_prosmart.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_prosmart.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_hole.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_hole.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_hole.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_hole.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gui_hole.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/3d_generator_import.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/3d_generator_import.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/3d_generator_import.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/3d_generator_import.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/3d_generator_import.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/check_for_updates.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/check_for_updates.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/check_for_updates.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/check_for_updates.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/check_for_updates.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/shelx_extensions.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/shelx_extensions.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/shelx_extensions.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/shelx_extensions.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/shelx_extensions.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/bones_reader.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/bones_reader.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/bones_reader.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/bones_reader.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/bones_reader.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/clear_backup.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/clear_backup.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/clear_backup.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/clear_backup.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/clear_backup.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/python_coot_docs.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/python_coot_docs.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/python_coot_docs.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/python_coot_docs.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/python_coot_docs.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/create_server.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/create_server.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/create_server.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/create_server.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/create_server.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ncs.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ncs.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ncs.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ncs.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ncs.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/extensions.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/extensions.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/extensions.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/extensions.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/extensions.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/cns2coot.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/cns2coot.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/cns2coot.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/cns2coot.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/cns2coot.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/generic_objects.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/generic_objects.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/generic_objects.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/generic_objects.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/generic_objects.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/tips_gui.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/tips_gui.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/tips_gui.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/tips_gui.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/tips_gui.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/tips.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/tips.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/tips.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/tips.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/tips.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/americanisms.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/americanisms.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/americanisms.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/americanisms.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/americanisms.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/fitting.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/fitting.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/fitting.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/fitting.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/fitting.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/group_settings.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/group_settings.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/group_settings.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/group_settings.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/group_settings.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/shelx.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/shelx.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/shelx.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/shelx.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/shelx.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_lsq.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_lsq.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_lsq.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_lsq.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_lsq.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/povray.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/povray.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/povray.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/povray.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/povray.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/remote_control.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/remote_control.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/remote_control.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/remote_control.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/remote_control.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gap.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gap.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gap.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gap.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/gap.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/local_code.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/local_code.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/local_code.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/local_code.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/local_code.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_load_modules.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_load_modules.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_load_modules.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_load_modules.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_load_modules.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/libcheck.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/libcheck.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/libcheck.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/libcheck.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/libcheck.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/filter.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/filter.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/filter.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/filter.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/filter.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_gui.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_gui.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_gui.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_gui.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_gui.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/refmac.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/refmac.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/refmac.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/refmac.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/refmac.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/brute_lsqman.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/brute_lsqman.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/brute_lsqman.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/brute_lsqman.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/brute_lsqman.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/raster3d.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/raster3d.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/raster3d.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/raster3d.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/raster3d.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/hello.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/hello.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/hello.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/hello.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/hello.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/background_demo.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/background_demo.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/background_demo.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/background_demo.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/background_demo.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/mutate.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/mutate.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/mutate.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/mutate.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/mutate.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/get_ebi.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/get_ebi.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/get_ebi.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/get_ebi.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/get_ebi.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_utils.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_utils.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_utils.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_utils.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot_utils.py + cp /builddir/build/SOURCES/__init__.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/ + chmod 644 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/coot/coot.py + desktop-file-install --vendor= --dir=/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/applications coot.desktop + appstream-util validate-relax --nonet /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386//usr/share/appdata/coot.appdata.xml /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386//usr/share/appdata/coot.appdata.xml: GLib-GIO-Message: Using the 'memory' GSettings backend. Your settings will not be saved or shared with other applications. OK + /usr/lib/rpm/find-debuginfo.sh -j2 --strict-build-id -m --build-id-seed 0.8.8-2.fc27 --unique-debug-suffix -0.8.8-2.fc27.i386 --unique-debug-src-base coot-0.8.8-2.fc27.i386 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 /builddir/build/BUILD/coot-0.8.8 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/libexec/coot-density-score-by-residue-bin extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/libexec/coot-bin extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/libexec/findwaters-bin extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/libexec/findligand-bin extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/libexec/mini-rsr-bin extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin/coot-fix-nomenclature-errors extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin/lidia extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin/coot-bfactan extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin/coot-available-comp-id extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin/coot-make-shelx-restraints extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/bin/coot-compare-dictionaries extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot_py_restraints.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-goograph.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcootilus.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcootaneer.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-lidia.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-gtkgraph.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-tw.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-cabuild.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-high-res.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-ligand.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-ideal.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-analysis.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-db-main.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-isosurface.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libccp4mg-utils.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-skeleton.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-AngleInfo.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-coords.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-lidia-core.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-surface.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-electrostatics.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-map-heavy.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-map-utils.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-coord-extras.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-shelx.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-coord-utils.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-geometry.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-mini-mol.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-protein-db.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-utils.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/libcoot-compat.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/pyrogen_boost.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7/site-packages/_pyrogen_swig.so.0.0.0 /usr/lib/rpm/sepdebugcrcfix: Updated 44 CRC32s, 0 CRC32s did match. 36077 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 Bytecompiling .py files below /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/debug/usr/lib/python2.7 using /usr/bin/python2.7 Bytecompiling .py files below /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/lib/python2.7 using /usr/bin/python2.7 + /usr/lib/rpm/brp-python-hardlink Processing files: coot-0.8.8-2.fc27.i686 Provides: appdata() appdata(coot.appdata.xml) application() application(coot.desktop) coot = 0.8.8-2.fc27 coot(x86-32) = 0.8.8-2.fc27 Requires(interp): /bin/sh /bin/sh /bin/sh Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires(post): /bin/sh Requires(postun): /bin/sh Requires(posttrans): /bin/sh Requires: /bin/sh libAlignment.so.1 libDataStructs.so.1 libDepictor.so.1 libDescriptors.so.1 libDistGeomHelpers.so.1 libDistGeometry.so.1 libEigenSolvers.so.1 libFileParsers.so.1 libForceField.so.1 libForceFieldHelpers.so.1 libGL.so.1 libGLU.so.1 libGraphMol.so.1 libICE.so.6 libMolChemicalFeatures.so.1 libMolDraw2D.so.1 libOptimizer.so.1 libRDGeneral.so.1 libRDGeometryLib.so.1 libSM.so.6 libSmilesParse.so.1 libSubstructMatch.so.1 libX11.so.6 libXmu.so.6 libXt.so.6 libart_lgpl_2.so.2 libatk-1.0.so.0 libboost_python.so.1.63.0 libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.2) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.4) libcairo.so.2 libccp4c.so.0 libccp4mg-utils.so.0 libclipper-ccp4.so.2 libclipper-cif.so.2 libclipper-cns.so.2 libclipper-contrib.so.2 libclipper-core.so.2 libclipper-fortran.so.2 libclipper-minimol.so.2 libclipper-mmdb.so.2 libclipper-phs.so.2 libcoot-AngleInfo.so.0 libcoot-analysis.so.0 libcoot-cabuild.so.0 libcoot-compat.so.0 libcoot-coord-extras.so.0 libcoot-coord-utils.so.0 libcoot-coords.so.0 libcoot-db-main.so.0 libcoot-electrostatics.so.0 libcoot-geometry.so.0 libcoot-goograph.so.0 libcoot-gtkgraph.so.0 libcoot-high-res.so.0 libcoot-ideal.so.0 libcoot-isosurface.so.0 libcoot-lidia-core.so.0 libcoot-lidia.so.0 libcoot-ligand.so.0 libcoot-map-heavy.so.0 libcoot-map-utils.so.0 libcoot-mini-mol.so.0 libcoot-protein-db.so.0 libcoot-shelx.so.0 libcoot-skeleton.so.0 libcoot-surface.so.0 libcoot-utils.so.0 libcootaneer.so.0 libcootilus.so.0 libcurl.so.4 libdl.so.2 libfontconfig.so.1 libfreetype.so.6 libgcc_s.so.1 libgcc_s.so.1(GCC_3.0) libgdk-x11-2.0.so.0 libgdk_pixbuf-2.0.so.0 libgdkglext-x11-1.0.so.0 libgio-2.0.so.0 libglib-2.0.so.0 libglut.so.3 libgmodule-2.0.so.0 libgnomecanvas-2.so.0 libgobject-2.0.so.0 libgoocanvas.so.3 libgsl.so.23 libgslcblas.so.0 libgtk-x11-2.0.so.0 libgtkglext-x11-1.0.so.0 libguile.so.17 libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.1) libmmdb2.so.0 libpango-1.0.so.0 libpangocairo-1.0.so.0 libpangoft2-1.0.so.0 libpangox-1.0.so.0 libpng16.so.16 libpthread.so.0 libpthread.so.0(GLIBC_2.0) libpython2.7.so.1.0 libsfftw.so.2 libsrfftw.so.2 libssm.so.2 libstdc++.so.6 libstdc++.so.6(CXXABI_1.3) libstdc++.so.6(CXXABI_1.3.1) libstdc++.so.6(CXXABI_1.3.8) libstdc++.so.6(CXXABI_1.3.9) libstdc++.so.6(GLIBCXX_3.4) libstdc++.so.6(GLIBCXX_3.4.11) libstdc++.so.6(GLIBCXX_3.4.15) libstdc++.so.6(GLIBCXX_3.4.20) libstdc++.so.6(GLIBCXX_3.4.21) libstdc++.so.6(GLIBCXX_3.4.9) libutil.so.1 rtld(GNU_HASH) Processing files: coot-data-0.8.8-2.fc27.noarch Provides: coot-data = 0.8.8-2.fc27 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: libcoot-0.8.8-2.fc27.i686 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.Sw91DE + umask 022 + cd /builddir/build/BUILD + cd coot-0.8.8 + DOCDIR=/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/doc/libcoot + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/doc/libcoot + cp -pr AUTHORS /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/doc/libcoot + cp -pr README /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/doc/libcoot + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.oFKiNr + umask 022 + cd /builddir/build/BUILD + cd coot-0.8.8 + LICENSEDIR=/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/licenses/libcoot + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/licenses/libcoot + cp -pr COPYING /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/licenses/libcoot + exit 0 Provides: libccp4mg-utils.so.0 libcoot = 0.8.8-2.fc27 libcoot(x86-32) = 0.8.8-2.fc27 libcoot-AngleInfo.so.0 libcoot-analysis.so.0 libcoot-cabuild.so.0 libcoot-compat.so.0 libcoot-coord-extras.so.0 libcoot-coord-utils.so.0 libcoot-coords.so.0 libcoot-db-main.so.0 libcoot-electrostatics.so.0 libcoot-geometry.so.0 libcoot-goograph.so.0 libcoot-gtkgraph.so.0 libcoot-high-res.so.0 libcoot-ideal.so.0 libcoot-isosurface.so.0 libcoot-lidia-core.so.0 libcoot-lidia.so.0 libcoot-ligand.so.0 libcoot-map-heavy.so.0 libcoot-map-utils.so.0 libcoot-mini-mol.so.0 libcoot-protein-db.so.0 libcoot-shelx.so.0 libcoot-skeleton.so.0 libcoot-surface.so.0 libcoot-tw.so.0 libcoot-utils.so.0 libcoot_py_restraints.so.0 libcootaneer.so.0 libcootilus.so.0 Requires(interp): /sbin/ldconfig /sbin/ldconfig Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires(post): /sbin/ldconfig Requires(postun): /sbin/ldconfig Requires: libDepictor.so.1 libDescriptors.so.1 libFileParsers.so.1 libForceField.so.1 libForceFieldHelpers.so.1 libGL.so.1 libGraphMol.so.1 libMolChemicalFeatures.so.1 libRDGeneral.so.1 libRDGeometryLib.so.1 libSmilesParse.so.1 libSubstructMatch.so.1 libboost_python.so.1.63.0 libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.11) libc.so.6(GLIBC_2.2) libc.so.6(GLIBC_2.3) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.4) libcairo.so.2 libccp4mg-utils.so.0 libclipper-ccp4.so.2 libclipper-contrib.so.2 libclipper-core.so.2 libclipper-minimol.so.2 libclipper-mmdb.so.2 libcoot-AngleInfo.so.0 libcoot-analysis.so.0 libcoot-coord-extras.so.0 libcoot-coord-utils.so.0 libcoot-coords.so.0 libcoot-db-main.so.0 libcoot-electrostatics.so.0 libcoot-geometry.so.0 libcoot-ideal.so.0 libcoot-lidia-core.so.0 libcoot-ligand.so.0 libcoot-map-heavy.so.0 libcoot-map-utils.so.0 libcoot-mini-mol.so.0 libcoot-shelx.so.0 libcoot-utils.so.0 libgcc_s.so.1 libgcc_s.so.1(GCC_3.0) libgcc_s.so.1(GCC_4.0.0) libgdk-x11-2.0.so.0 libglib-2.0.so.0 libgobject-2.0.so.0 libgoocanvas.so.3 libgsl.so.23 libgslcblas.so.0 libgtk-x11-2.0.so.0 libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.1) libmmdb2.so.0 libpango-1.0.so.0 libpng16.so.16 libpng16.so.16(PNG16_0) libpython2.7.so.1.0 libsrfftw.so.2 libstdc++.so.6 libstdc++.so.6(CXXABI_1.3) libstdc++.so.6(CXXABI_1.3.1) libstdc++.so.6(CXXABI_1.3.8) libstdc++.so.6(CXXABI_1.3.9) libstdc++.so.6(GLIBCXX_3.4) libstdc++.so.6(GLIBCXX_3.4.11) libstdc++.so.6(GLIBCXX_3.4.15) libstdc++.so.6(GLIBCXX_3.4.20) libstdc++.so.6(GLIBCXX_3.4.21) libstdc++.so.6(GLIBCXX_3.4.9) rtld(GNU_HASH) Processing files: libcoot-devel-0.8.8-2.fc27.i686 Provides: libcoot-devel = 0.8.8-2.fc27 libcoot-devel(x86-32) = 0.8.8-2.fc27 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libccp4mg-utils.so.0 libcoot-AngleInfo.so.0 libcoot-analysis.so.0 libcoot-cabuild.so.0 libcoot-compat.so.0 libcoot-coord-extras.so.0 libcoot-coord-utils.so.0 libcoot-coords.so.0 libcoot-db-main.so.0 libcoot-electrostatics.so.0 libcoot-geometry.so.0 libcoot-goograph.so.0 libcoot-gtkgraph.so.0 libcoot-high-res.so.0 libcoot-ideal.so.0 libcoot-isosurface.so.0 libcoot-lidia-core.so.0 libcoot-lidia.so.0 libcoot-ligand.so.0 libcoot-map-heavy.so.0 libcoot-map-utils.so.0 libcoot-mini-mol.so.0 libcoot-protein-db.so.0 libcoot-shelx.so.0 libcoot-skeleton.so.0 libcoot-surface.so.0 libcoot-tw.so.0 libcoot-utils.so.0 libcoot_py_restraints.so.0 libcootaneer.so.0 libcootilus.so.0 Processing files: python2-coot-0.8.8-2.fc27.i686 Provides: python-coot = 0.8.8-2.fc27 python2-coot = 0.8.8-2.fc27 python2-coot(x86-32) = 0.8.8-2.fc27 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libDepictor.so.1 libGraphMol.so.1 libRDGeneral.so.1 libSmilesParse.so.1 libSubstructMatch.so.1 libboost_python.so.1.63.0 libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.4) libcoot-analysis.so.0 libcoot-coord-utils.so.0 libcoot-geometry.so.0 libcoot-ideal.so.0 libcoot-lidia-core.so.0 libcoot-utils.so.0 libcoot_py_restraints.so.0 libgcc_s.so.1 libgcc_s.so.1(GCC_3.0) libmmdb2.so.0 libpython2.7.so.1.0 libstdc++.so.6 libstdc++.so.6(CXXABI_1.3) libstdc++.so.6(CXXABI_1.3.9) libstdc++.so.6(GLIBCXX_3.4) libstdc++.so.6(GLIBCXX_3.4.11) libstdc++.so.6(GLIBCXX_3.4.21) libstdc++.so.6(GLIBCXX_3.4.9) python(abi) = 2.7 rtld(GNU_HASH) Obsoletes: python-coot < 0.8.8-2.fc27 Processing files: coot-doc-0.8.8-2.fc27.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.loYDxU + umask 022 + cd /builddir/build/BUILD + cd coot-0.8.8 + DOCDIR=/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/doc/coot-doc + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/doc/coot-doc + cp -pr doc/coot-keys-and-buttons.pdf /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/doc/coot-doc + cp -pr doc/coot-user-manual.pdf /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/doc/coot-doc + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.6DhPin + umask 022 + cd /builddir/build/BUILD + cd coot-0.8.8 + LICENSEDIR=/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/licenses/coot-doc + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/licenses/coot-doc + cp -pr COPYING /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386/usr/share/licenses/coot-doc + exit 0 Provides: coot-doc = 0.8.8-2.fc27 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: coot-debuginfo-0.8.8-2.fc27.i686 Provides: coot-debuginfo = 0.8.8-2.fc27 coot-debuginfo(x86-32) = 0.8.8-2.fc27 debuginfo(build-id) = 04e75ec97cee9a7101a73214a560cebe7bf0457c debuginfo(build-id) = 05f6408fe387bc7bb31c94232e01541fb2de4a66 debuginfo(build-id) = 0bcb1550de13b0d3d616a5ffbfdd30cb1bfb6a8b debuginfo(build-id) = 1238b296be128a6040e2d0e06408c20c284207a4 debuginfo(build-id) = 19ab3f7209446b623a3bd7d96f1846e25bc4d991 debuginfo(build-id) = 1b6b3ce958f6172af1f0911ecc70915178280bf9 debuginfo(build-id) = 21a345c3e1bad10c2d817e5ebd0923b25df17fb7 debuginfo(build-id) = 26459f4a0475258da0680b1fa9914c35e101968c debuginfo(build-id) = 2be34b8b88aa557b08e826adb00fd3ae65cfe976 debuginfo(build-id) = 2cae37b43f8f2d49d1b49fa5de2f5058e92326d5 debuginfo(build-id) = 2d43d5807ad6a3655dce0ae040269d48ce7348cd debuginfo(build-id) = 3328ef391cae651af456b9c2a92194d019d7538d debuginfo(build-id) = 391949b6a27374a3a5302bca00259efd35ee6e09 debuginfo(build-id) = 3b21245c5d07984c6ad5a2a9a43eb96d06ffbbb3 debuginfo(build-id) = 41b0a7703d7d85fe3d0cb1cc808274ff15d8b0a0 debuginfo(build-id) = 4462ff6809246c4248df6aeece0a7adeafa3c2d6 debuginfo(build-id) = 44941e1e4c20fbdc53afc46dea3d41438c247f00 debuginfo(build-id) = 4789ac1f2376d1855e8f406643323d754fa6a9bf debuginfo(build-id) = 586adcddccf491dd0f1ee2d7d2ed039cc619f5cf debuginfo(build-id) = 6a65d7a7aaed4982cf071b21f1aad7f4292d511a debuginfo(build-id) = 733bfbbfde86733155a15bae430742cbf0c68898 debuginfo(build-id) = 7ee1c7a5592db4a6ce65fd91f6bc169371bb6020 debuginfo(build-id) = 7fbad4def3f8fb883432654e78a0e9fb21d5945f debuginfo(build-id) = 81af2f65e9333d9ffb5ba09689e0c6ab7af53e17 debuginfo(build-id) = 85ba895d77200be1eb3b11136b182e04dc761aa5 debuginfo(build-id) = 8651f90a0770794d4b7a577e026174088f94d080 debuginfo(build-id) = 8a961530a36985eade0cb4c6507696066bb560e8 debuginfo(build-id) = 8d536d9829259309cdb513e3d83f365c8b463967 debuginfo(build-id) = 8f8f677c042715aae53651d512e3e01ede0c0325 debuginfo(build-id) = 948a2ba665ade9a87192ba1bad905346f922c430 debuginfo(build-id) = 958622ea96303a13ab5feafd55775b1357100093 debuginfo(build-id) = 99182afdba674236aaaaba55c484c50d9240c6ec debuginfo(build-id) = ab80df51e93763c3d5b7079f6326a4ddc3c751cf debuginfo(build-id) = aed70432ab2ebd6853a46ce666fffb1c087a3488 debuginfo(build-id) = af4203881e1a28dc189b9ced83703dcc9c0fd764 debuginfo(build-id) = c174fac061092530cbf3610b818c139beef25bdb debuginfo(build-id) = c84493200921add9c66b206a4838fd67bbb900d5 debuginfo(build-id) = c997ea799c89afd318fa64b92a0c997653aebb0c debuginfo(build-id) = d6235406bab3fa14e16e1988954bd141c8234089 debuginfo(build-id) = d8c5d278e57ed9e358b88d9d3ef4c9c26f3b7d50 debuginfo(build-id) = e6169eb4aba37556cd305945f3e913c228c0dd6c debuginfo(build-id) = eaa3b78de2e41ce4bd5f9e1464ebeadc2d9da8a0 debuginfo(build-id) = ead94a0b91c0e241c7956c073a3c961388741f7d debuginfo(build-id) = fbef621fe6e988f6a34e5a106f0a5cd984dda10e Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386 Wrote: /builddir/build/RPMS/coot-0.8.8-2.fc27.i686.rpm Wrote: /builddir/build/RPMS/coot-data-0.8.8-2.fc27.noarch.rpm Wrote: /builddir/build/RPMS/libcoot-0.8.8-2.fc27.i686.rpm Wrote: /builddir/build/RPMS/libcoot-devel-0.8.8-2.fc27.i686.rpm Wrote: /builddir/build/RPMS/python2-coot-0.8.8-2.fc27.i686.rpm Wrote: /builddir/build/RPMS/coot-doc-0.8.8-2.fc27.noarch.rpm Wrote: /builddir/build/RPMS/coot-debuginfo-0.8.8-2.fc27.i686.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.49oboU + umask 022 + cd /builddir/build/BUILD + cd coot-0.8.8 + /usr/bin/rm -rf /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.i386 + exit 0 Finish: rpmbuild coot-0.8.8-2.fc27.src.rpm Finish: build phase for coot-0.8.8-2.fc27.src.rpm INFO: Done(intermediate-srpm/coot-0.8.8-2.fc27.src.rpm) Config(child) 21 minutes 43 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run