Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c119' (ED25519) to the list of known hosts. INFO: Downloading rxode2_3.0.2.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o rxode2_3.0.2.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/iucar/cran/R-CRAN-rxode2/rxode2_3.0.2.tar.gz/md5/eccc205418f16be42f7ebae784e54bc9/rxode2_3.0.2.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 3955k 100 3955k 0 0 27.3M 0 --:--:-- --:--:-- --:--:-- 27.5M INFO: Reading stdout from command: md5sum rxode2_3.0.2.tar.gz Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-uo7sbc0c/R-CRAN-rxode2/R-CRAN-rxode2.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-uo7sbc0c/R-CRAN-rxode2 --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1730339452.741906 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.9 starting (python version = 3.12.1, NVR = mock-5.9-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-uo7sbc0c/R-CRAN-rxode2/R-CRAN-rxode2.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-uo7sbc0c/R-CRAN-rxode2 --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1730339452.741906 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-uo7sbc0c/R-CRAN-rxode2/R-CRAN-rxode2.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.9 INFO: Mock Version: 5.9 Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1730339452.741906/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf5 detected and used (fallback) INFO: Buildroot is handled by package management from host and used with --installroot: rpm-4.19.1.1-1.fc39.x86_64 rpm-sequoia-1.6.0-1.fc39.x86_64 python3-dnf-4.21.1-1.fc39.noarch python3-dnf-plugins-core-4.9.0-1.fc39.noarch yum-4.21.1-1.fc39.noarch dnf5-5.1.17-2.fc39.x86_64 dnf5-plugins-5.1.17-2.fc39.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: fedora 100% | 736.1 KiB/s | 23.6 KiB | 00m00s Copr repository 100% | 26.1 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 20.5 MiB/s | 12.3 MiB | 00m01s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 5.2.32-2.fc42 fedora 8.2 MiB bzip2 x86_64 1.0.8-19.fc41 fedora 95.7 KiB coreutils x86_64 9.5-10.fc42 fedora 5.7 MiB cpio x86_64 2.15-2.fc41 fedora 1.1 MiB diffutils x86_64 3.10-8.fc41 fedora 1.6 MiB fedora-release-common noarch 42-0.6 fedora 19.5 KiB findutils x86_64 1:4.10.0-4.fc41 fedora 1.8 MiB gawk x86_64 5.3.0-4.fc41 fedora 1.7 MiB glibc-minimal-langpack x86_64 2.40.9000-15.fc42 fedora 0.0 B grep x86_64 3.11-9.fc41 fedora 1.0 MiB gzip x86_64 1.13-2.fc41 fedora 389.0 KiB info x86_64 7.1.1-2.fc42 fedora 361.8 KiB patch x86_64 2.7.6-25.fc41 fedora 266.7 KiB redhat-rpm-config noarch 296-1.fc42 fedora 186.6 KiB rpm-build x86_64 4.20.0-1.fc42 fedora 194.3 KiB sed x86_64 4.9-3.fc41 fedora 861.5 KiB shadow-utils x86_64 2:4.16.0-6.fc42 fedora 4.1 MiB tar x86_64 2:1.35-4.fc41 fedora 2.9 MiB unzip x86_64 6.0-64.fc41 fedora 386.8 KiB util-linux x86_64 2.40.2-8.fc42 fedora 3.7 MiB which x86_64 2.21-42.fc41 fedora 80.2 KiB xz x86_64 1:5.6.3-2.fc42 fedora 1.2 MiB Installing dependencies: add-determinism x86_64 0.4.3-1.fc42 fedora 2.4 MiB alternatives x86_64 1.30-1.fc41 fedora 66.3 KiB ansible-srpm-macros noarch 1-16.fc41 fedora 35.7 KiB audit-libs x86_64 4.0.2-1.fc41 fedora 331.3 KiB authselect x86_64 1.5.0-8.fc42 fedora 157.5 KiB authselect-libs x86_64 1.5.0-8.fc42 fedora 822.2 KiB basesystem noarch 11-21.fc41 fedora 0.0 B binutils x86_64 2.43.50-5.fc42 fedora 27.6 MiB build-reproducibility-srpm-macros noarch 0.4.3-1.fc42 fedora 735.0 B bzip2-libs x86_64 1.0.8-19.fc41 fedora 80.7 KiB ca-certificates noarch 2024.2.69_v8.0.401-2.fc42 fedora 2.6 MiB coreutils-common x86_64 9.5-10.fc42 fedora 11.2 MiB cracklib x86_64 2.9.11-6.fc41 fedora 238.9 KiB crypto-policies noarch 20241018-1.gitce922cb.fc42 fedora 137.0 KiB curl x86_64 8.10.1-2.fc42 fedora 453.3 KiB cyrus-sasl-lib x86_64 2.1.28-27.fc41 fedora 2.3 MiB debugedit x86_64 5.1-1.fc42 fedora 192.7 KiB dwz x86_64 0.15-8.fc42 fedora 299.2 KiB ed x86_64 1.20.2-2.fc41 fedora 146.9 KiB efi-srpm-macros noarch 5-12.fc41 fedora 40.1 KiB elfutils x86_64 0.192-3.fc42 fedora 2.7 MiB elfutils-debuginfod-client x86_64 0.192-3.fc42 fedora 76.0 KiB elfutils-default-yama-scope noarch 0.192-3.fc42 fedora 1.8 KiB elfutils-libelf x86_64 0.192-3.fc42 fedora 1.2 MiB elfutils-libs x86_64 0.192-3.fc42 fedora 675.1 KiB fedora-gpg-keys noarch 42-0.3 fedora 126.4 KiB fedora-release noarch 42-0.6 fedora 0.0 B fedora-release-identity-basic noarch 42-0.6 fedora 719.0 B fedora-repos noarch 42-0.3 fedora 4.9 KiB fedora-repos-rawhide noarch 42-0.3 fedora 2.2 KiB file x86_64 5.45-7.fc41 fedora 103.5 KiB file-libs x86_64 5.45-7.fc41 fedora 9.9 MiB filesystem x86_64 3.18-29.fc42 fedora 106.0 B fonts-srpm-macros noarch 1:2.0.5-17.fc41 fedora 55.8 KiB forge-srpm-macros noarch 0.4.0-1.fc42 fedora 38.9 KiB fpc-srpm-macros noarch 1.3-13.fc41 fedora 144.0 B gdb-minimal x86_64 15.2-1.fc42 fedora 13.0 MiB gdbm x86_64 1:1.23-7.fc41 fedora 460.9 KiB gdbm-libs x86_64 1:1.23-7.fc41 fedora 121.9 KiB ghc-srpm-macros noarch 1.9.2-1.fc42 fedora 779.0 B glibc x86_64 2.40.9000-15.fc42 fedora 6.6 MiB glibc-common x86_64 2.40.9000-15.fc42 fedora 1.0 MiB glibc-gconv-extra x86_64 2.40.9000-15.fc42 fedora 7.1 MiB gmp x86_64 1:6.3.0-2.fc41 fedora 811.4 KiB gnat-srpm-macros noarch 6-6.fc41 fedora 1.0 KiB go-srpm-macros noarch 3.6.0-3.fc41 fedora 60.8 KiB jansson x86_64 2.14-1.fc42 fedora 93.1 KiB json-c x86_64 0.17-4.fc41 fedora 82.4 KiB kernel-srpm-macros noarch 1.0-24.fc41 fedora 1.9 KiB keyutils-libs x86_64 1.6.3-4.fc41 fedora 54.4 KiB krb5-libs x86_64 1.21.3-2.fc41 fedora 2.3 MiB libacl x86_64 2.3.2-2.fc41 fedora 40.0 KiB libarchive x86_64 3.7.6-1.fc42 fedora 934.8 KiB libattr x86_64 2.5.2-4.fc41 fedora 28.5 KiB libblkid x86_64 2.40.2-8.fc42 fedora 262.5 KiB libbrotli x86_64 1.1.0-5.fc41 fedora 837.6 KiB libcap x86_64 2.71-1.fc42 fedora 210.8 KiB libcap-ng x86_64 0.8.5-3.fc41 fedora 69.2 KiB libcom_err x86_64 1.47.1-6.fc42 fedora 67.2 KiB libcurl x86_64 8.10.1-2.fc42 fedora 838.4 KiB libeconf x86_64 0.7.4-2.fc42 fedora 68.3 KiB libevent x86_64 2.1.12-14.fc41 fedora 895.7 KiB libfdisk x86_64 2.40.2-8.fc42 fedora 362.9 KiB libffi x86_64 3.4.6-3.fc42 fedora 86.4 KiB libgcc x86_64 14.2.1-4.fc42 fedora 274.6 KiB libgomp x86_64 14.2.1-4.fc42 fedora 523.8 KiB libidn2 x86_64 2.3.7-2.fc41 fedora 329.1 KiB libmount x86_64 2.40.2-8.fc42 fedora 355.8 KiB libnghttp2 x86_64 1.64.0-1.fc42 fedora 174.5 KiB libnsl2 x86_64 2.0.1-2.fc41 fedora 57.9 KiB libpkgconf x86_64 2.3.0-1.fc42 fedora 78.2 KiB libpsl x86_64 0.21.5-4.fc41 fedora 80.5 KiB libpwquality x86_64 1.4.5-11.fc41 fedora 417.8 KiB libselinux x86_64 3.7-6.fc42 fedora 181.1 KiB libsemanage x86_64 3.7-3.fc42 fedora 298.0 KiB libsepol x86_64 3.7-3.fc42 fedora 818.0 KiB libsmartcols x86_64 2.40.2-8.fc42 fedora 180.4 KiB libssh x86_64 0.11.1-1.fc42 fedora 569.6 KiB libssh-config noarch 0.11.1-1.fc42 fedora 277.0 B libstdc++ x86_64 14.2.1-4.fc42 fedora 2.8 MiB libtasn1 x86_64 4.19.0-9.fc41 fedora 175.7 KiB libtirpc x86_64 1.3.6-0.fc42 fedora 203.0 KiB libtool-ltdl x86_64 2.4.7-12.fc41 fedora 66.2 KiB libunistring x86_64 1.1-8.fc41 fedora 1.7 MiB libuuid x86_64 2.40.2-8.fc42 fedora 41.4 KiB libverto x86_64 0.3.2-9.fc41 fedora 29.5 KiB libxcrypt x86_64 4.4.36-7.fc41 fedora 266.8 KiB libxml2 x86_64 2.12.8-2.fc41 fedora 1.7 MiB libzstd x86_64 1.5.6-2.fc41 fedora 795.9 KiB lua-libs x86_64 5.4.7-1.fc42 fedora 285.0 KiB lua-srpm-macros noarch 1-14.fc41 fedora 1.3 KiB lz4-libs x86_64 1.10.0-1.fc41 fedora 145.5 KiB mpfr x86_64 4.2.1-5.fc41 fedora 832.1 KiB ncurses-base noarch 6.5-2.20240629.fc41 fedora 326.3 KiB ncurses-libs x86_64 6.5-2.20240629.fc41 fedora 975.2 KiB ocaml-srpm-macros noarch 10-3.fc41 fedora 1.9 KiB openblas-srpm-macros noarch 2-18.fc41 fedora 112.0 B openldap x86_64 2.6.8-5.fc41 fedora 644.2 KiB openssl-libs x86_64 1:3.2.2-8.fc42 fedora 7.8 MiB p11-kit x86_64 0.25.5-4.fc42 fedora 2.2 MiB p11-kit-trust x86_64 0.25.5-4.fc42 fedora 403.8 KiB package-notes-srpm-macros noarch 0.5-12.fc41 fedora 1.6 KiB pam x86_64 1.6.1-8.fc42 fedora 1.6 MiB pam-libs x86_64 1.6.1-8.fc42 fedora 127.7 KiB pcre2 x86_64 10.44-1.fc41.1 fedora 653.5 KiB pcre2-syntax noarch 10.44-1.fc41.1 fedora 251.6 KiB perl-srpm-macros noarch 1-56.fc41 fedora 861.0 B pkgconf x86_64 2.3.0-1.fc42 fedora 88.6 KiB pkgconf-m4 noarch 2.3.0-1.fc42 fedora 14.4 KiB pkgconf-pkg-config x86_64 2.3.0-1.fc42 fedora 989.0 B popt x86_64 1.19-7.fc41 fedora 136.9 KiB publicsuffix-list-dafsa noarch 20240107-4.fc41 fedora 67.5 KiB pyproject-srpm-macros noarch 1.15.1-1.fc42 fedora 1.9 KiB python-srpm-macros noarch 3.13-3.fc41 fedora 51.0 KiB qt5-srpm-macros noarch 5.15.15-1.fc42 fedora 500.0 B qt6-srpm-macros noarch 6.8.0-1.fc42 fedora 456.0 B readline x86_64 8.2-11.fc42 fedora 493.1 KiB rpm x86_64 4.20.0-1.fc42 fedora 3.1 MiB rpm-build-libs x86_64 4.20.0-1.fc42 fedora 206.7 KiB rpm-libs x86_64 4.20.0-1.fc42 fedora 726.1 KiB rpm-sequoia x86_64 1.7.0-2.fc41 fedora 2.4 MiB rust-srpm-macros noarch 26.3-3.fc42 fedora 4.8 KiB setup noarch 2.15.0-5.fc41 fedora 720.7 KiB sqlite-libs x86_64 3.46.1-1.fc42 fedora 1.4 MiB systemd-libs x86_64 256.7-1.fc42 fedora 2.0 MiB util-linux-core x86_64 2.40.2-8.fc42 fedora 1.5 MiB xxhash-libs x86_64 0.8.2-4.fc42 fedora 88.4 KiB xz-libs x86_64 1:5.6.3-2.fc42 fedora 218.4 KiB zig-srpm-macros noarch 1-3.fc41 fedora 1.1 KiB zip x86_64 3.0-41.fc41 fedora 703.2 KiB zlib-ng-compat x86_64 2.1.7-3.fc42 fedora 138.0 KiB zstd x86_64 1.5.6-2.fc41 fedora 1.7 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 154 packages Total size of inbound packages is 53 MiB. Need to download 0 B. After this operation 180 MiB will be used (install 180 MiB, remove 0 B). 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Importing PGP key 0x105EF944: Userid : "Fedora (42) " Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary The key was successfully imported. Importing PGP key 0xE99D6AD1: Userid : "Fedora (41) " Fingerprint: 466CF2D8B60BC3057AA9453ED0622462E99D6AD1 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-41-primary The key was successfully imported. Importing PGP key 0x31645531: Userid : "Fedora (43) " Fingerprint: C6E7F081CF80E13146676E88829B606631645531 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary The key was successfully imported. 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KiB | 00m00s [ 47/156] Installing pcre2-0:10.44-1.fc 100% | 213.2 MiB/s | 654.9 KiB | 00m00s [ 48/156] Installing grep-0:3.11-9.fc41 100% | 111.5 MiB/s | 1.0 MiB | 00m00s [ 49/156] Installing xz-1:5.6.3-2.fc42. 100% | 123.7 MiB/s | 1.2 MiB | 00m00s [ 50/156] Installing libcap-ng-0:0.8.5- 100% | 69.4 MiB/s | 71.0 KiB | 00m00s [ 51/156] Installing audit-libs-0:4.0.2 100% | 162.8 MiB/s | 333.4 KiB | 00m00s [ 52/156] Installing pam-libs-0:1.6.1-8 100% | 63.3 MiB/s | 129.7 KiB | 00m00s [ 53/156] Installing libcap-0:2.71-1.fc 100% | 35.1 MiB/s | 215.8 KiB | 00m00s [ 54/156] Installing systemd-libs-0:256 100% | 185.2 MiB/s | 2.0 MiB | 00m00s [ 55/156] Installing libsmartcols-0:2.4 100% | 177.1 MiB/s | 181.4 KiB | 00m00s [ 56/156] Installing libsepol-0:3.7-3.f 100% | 266.6 MiB/s | 819.0 KiB | 00m00s [ 57/156] Installing libselinux-0:3.7-6 100% | 89.0 MiB/s | 182.3 KiB | 00m00s [ 58/156] Installing sed-0:4.9-3.fc41.x 100% | 106.2 MiB/s | 869.7 KiB | 00m00s [ 59/156] Installing findutils-1:4.10.0 100% | 168.9 MiB/s | 1.9 MiB | 00m00s [ 60/156] Installing libmount-0:2.40.2- 100% | 174.3 MiB/s | 356.9 KiB | 00m00s [ 61/156] Installing lz4-libs-0:1.10.0- 100% | 71.6 MiB/s | 146.6 KiB | 00m00s [ 62/156] Installing lua-libs-0:5.4.7-1 100% | 139.7 MiB/s | 286.2 KiB | 00m00s [ 63/156] Installing libcom_err-0:1.47. 100% | 66.7 MiB/s | 68.3 KiB | 00m00s [ 64/156] Installing alternatives-0:1.3 100% | 66.3 MiB/s | 67.9 KiB | 00m00s [ 65/156] Installing libffi-0:3.4.6-3.f 100% | 85.7 MiB/s | 87.8 KiB | 00m00s [ 66/156] Installing libtasn1-0:4.19.0- 100% | 86.7 MiB/s | 177.5 KiB | 00m00s [ 67/156] Installing p11-kit-0:0.25.5-4 100% | 147.7 MiB/s | 2.2 MiB | 00m00s [ 68/156] Installing libunistring-0:1.1 100% | 288.5 MiB/s | 1.7 MiB | 00m00s [ 69/156] Installing libidn2-0:2.3.7-2. 100% | 81.8 MiB/s | 335.1 KiB | 00m00s [ 70/156] Installing libpsl-0:0.21.5-4. 100% | 79.7 MiB/s | 81.7 KiB | 00m00s [ 71/156] Installing p11-kit-trust-0:0. 100% | 26.4 MiB/s | 405.5 KiB | 00m00s >>> Running post-install scriptlet: p11-kit-trust-0:0.25.5-4.fc42.x86_64 >>> Stop post-install scriptlet: p11-kit-trust-0:0.25.5-4.fc42.x86_64 [ 72/156] Installing zstd-0:1.5.6-2.fc4 100% | 241.6 MiB/s | 1.7 MiB | 00m00s [ 73/156] Installing util-linux-core-0: 100% | 127.3 MiB/s | 1.5 MiB | 00m00s [ 74/156] Installing tar-2:1.35-4.fc41. 100% | 227.6 MiB/s | 3.0 MiB | 00m00s [ 75/156] Installing libsemanage-0:3.7- 100% | 97.6 MiB/s | 299.8 KiB | 00m00s [ 76/156] Installing shadow-utils-2:4.1 100% | 125.6 MiB/s | 4.1 MiB | 00m00s [ 77/156] Installing zip-0:3.0-41.fc41. 100% | 172.6 MiB/s | 707.1 KiB | 00m00s [ 78/156] Installing gdbm-1:1.23-7.fc41 100% | 113.7 MiB/s | 465.8 KiB | 00m00s [ 79/156] Installing cyrus-sasl-lib-0:2 100% | 256.2 MiB/s | 2.3 MiB | 00m00s [ 80/156] Installing libfdisk-0:2.40.2- 100% | 177.7 MiB/s | 364.0 KiB | 00m00s [ 81/156] Installing libxml2-0:2.12.8-2 100% | 244.6 MiB/s | 1.7 MiB | 00m00s [ 82/156] Installing bzip2-0:1.0.8-19.f 100% | 48.9 MiB/s | 100.2 KiB | 00m00s [ 83/156] Installing add-determinism-0: 100% | 270.1 MiB/s | 2.4 MiB | 00m00s [ 84/156] Installing build-reproducibil 100% | 0.0 B/s | 1.0 KiB | 00m00s [ 85/156] Installing sqlite-libs-0:3.46 100% | 238.8 MiB/s | 1.4 MiB | 00m00s [ 86/156] Installing ed-0:1.20.2-2.fc41 100% | 72.8 MiB/s | 149.2 KiB | 00m00s [ 87/156] Installing patch-0:2.7.6-25.f 100% | 131.0 MiB/s | 268.2 KiB | 00m00s [ 88/156] Installing elfutils-default-y 100% | 204.3 KiB/s | 2.0 KiB | 00m00s >>> Running post-install scriptlet: elfutils-default-yama-scope-0:0.192-3.fc42.n >>> Stop post-install scriptlet: elfutils-default-yama-scope-0:0.192-3.fc42.noar [ 89/156] Installing cpio-0:2.15-2.fc41 100% | 137.5 MiB/s | 1.1 MiB | 00m00s [ 90/156] Installing diffutils-0:3.10-8 100% | 159.0 MiB/s | 1.6 MiB | 00m00s [ 91/156] Installing libgomp-0:14.2.1-4 100% | 256.4 MiB/s | 525.2 KiB | 00m00s [ 92/156] Installing json-c-0:0.17-4.fc 100% | 81.7 MiB/s | 83.6 KiB | 00m00s [ 93/156] Installing keyutils-libs-0:1. 100% | 54.5 MiB/s | 55.8 KiB | 00m00s [ 94/156] Installing libverto-0:0.3.2-9 100% | 30.5 MiB/s | 31.3 KiB | 00m00s [ 95/156] Installing jansson-0:2.14-1.f 100% | 92.3 MiB/s | 94.5 KiB | 00m00s [ 96/156] Installing libpkgconf-0:2.3.0 100% | 77.5 MiB/s | 79.3 KiB | 00m00s [ 97/156] Installing pkgconf-0:2.3.0-1. 100% | 44.5 MiB/s | 91.1 KiB | 00m00s [ 98/156] Installing pkgconf-pkg-config 100% | 1.7 MiB/s | 1.8 KiB | 00m00s [ 99/156] Installing xxhash-libs-0:0.8. 100% | 87.7 MiB/s | 89.8 KiB | 00m00s [100/156] Installing libbrotli-0:1.1.0- 100% | 205.0 MiB/s | 839.9 KiB | 00m00s [101/156] Installing libnghttp2-0:1.64. 100% | 171.5 MiB/s | 175.6 KiB | 00m00s [102/156] Installing libtool-ltdl-0:2.4 100% | 65.7 MiB/s | 67.3 KiB | 00m00s [103/156] Installing coreutils-common-0 100% | 254.3 MiB/s | 11.2 MiB | 00m00s [104/156] Installing openssl-libs-1:3.2 100% | 313.1 MiB/s | 7.8 MiB | 00m00s [105/156] Installing coreutils-0:9.5-10 100% | 146.8 MiB/s | 5.7 MiB | 00m00s >>> Running pre-install scriptlet: ca-certificates-0:2024.2.69_v8.0.401-2.fc42.n >>> Stop pre-install scriptlet: ca-certificates-0:2024.2.69_v8.0.401-2.fc42.noar [106/156] Installing ca-certificates-0: 100% | 1.1 MiB/s | 2.4 MiB | 00m02s >>> Running post-install scriptlet: ca-certificates-0:2024.2.69_v8.0.401-2.fc42. >>> Stop post-install scriptlet: ca-certificates-0:2024.2.69_v8.0.401-2.fc42.noa [107/156] Installing krb5-libs-0:1.21.3 100% | 176.9 MiB/s | 2.3 MiB | 00m00s [108/156] Installing libarchive-0:3.7.6 100% | 183.0 MiB/s | 936.7 KiB | 00m00s [109/156] Installing libtirpc-0:1.3.6-0 100% | 100.0 MiB/s | 204.8 KiB | 00m00s [110/156] Installing gzip-0:1.13-2.fc41 100% | 96.3 MiB/s | 394.6 KiB | 00m00s [111/156] Installing authselect-libs-0: 100% | 81.8 MiB/s | 837.2 KiB | 00m00s [112/156] Installing cracklib-0:2.9.11- 100% | 30.6 MiB/s | 250.3 KiB | 00m00s [113/156] Installing libpwquality-0:1.4 100% | 46.7 MiB/s | 430.1 KiB | 00m00s [114/156] Installing libnsl2-0:2.0.1-2. 100% | 28.8 MiB/s | 59.1 KiB | 00m00s [115/156] Installing pam-0:1.6.1-8.fc42 100% | 69.9 MiB/s | 1.7 MiB | 00m00s [116/156] Installing libssh-0:0.11.1-1. 100% | 139.6 MiB/s | 571.7 KiB | 00m00s [117/156] Installing rpm-sequoia-0:1.7. 100% | 295.9 MiB/s | 2.4 MiB | 00m00s [118/156] Installing rpm-libs-0:4.20.0- 100% | 177.7 MiB/s | 727.7 KiB | 00m00s [119/156] Installing libevent-0:2.1.12- 100% | 175.7 MiB/s | 899.5 KiB | 00m00s [120/156] Installing openldap-0:2.6.8-5 100% | 126.6 MiB/s | 648.0 KiB | 00m00s [121/156] Installing libcurl-0:8.10.1-2 100% | 205.0 MiB/s | 839.5 KiB | 00m00s [122/156] Installing elfutils-libs-0:0. 100% | 165.3 MiB/s | 677.0 KiB | 00m00s [123/156] Installing elfutils-debuginfo 100% | 38.2 MiB/s | 78.2 KiB | 00m00s [124/156] Installing elfutils-0:0.192-3 100% | 242.3 MiB/s | 2.7 MiB | 00m00s [125/156] Installing binutils-0:2.43.50 100% | 276.2 MiB/s | 27.6 MiB | 00m00s >>> Running post-install scriptlet: binutils-0:2.43.50-5.fc42.x86_64 >>> Stop post-install scriptlet: binutils-0:2.43.50-5.fc42.x86_64 [126/156] Installing gdb-minimal-0:15.2 100% | 317.0 MiB/s | 13.0 MiB | 00m00s [127/156] Installing debugedit-0:5.1-1. 100% | 95.4 MiB/s | 195.4 KiB | 00m00s [128/156] Installing rpm-build-libs-0:4 100% | 101.3 MiB/s | 207.5 KiB | 00m00s [129/156] Installing curl-0:8.10.1-2.fc 100% | 17.8 MiB/s | 455.8 KiB | 00m00s >>> Running pre-install scriptlet: rpm-0:4.20.0-1.fc42.x86_64 >>> Stop pre-install scriptlet: rpm-0:4.20.0-1.fc42.x86_64 [130/156] Installing rpm-0:4.20.0-1.fc4 100% | 86.4 MiB/s | 2.5 MiB | 00m00s [131/156] Installing efi-srpm-macros-0: 100% | 40.2 MiB/s | 41.2 KiB | 00m00s [132/156] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [133/156] Installing zig-srpm-macros-0: 100% | 1.6 MiB/s | 1.7 KiB | 00m00s [134/156] Installing rust-srpm-macros-0 100% | 5.4 MiB/s | 5.6 KiB | 00m00s [135/156] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 732.0 B | 00m00s [136/156] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [137/156] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [138/156] Installing package-notes-srpm 100% | 0.0 B/s | 2.0 KiB | 00m00s [139/156] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [140/156] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.2 KiB | 00m00s [141/156] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [142/156] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [143/156] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [144/156] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [145/156] Installing ansible-srpm-macro 100% | 35.4 MiB/s | 36.2 KiB | 00m00s [146/156] Installing fonts-srpm-macros- 100% | 55.7 MiB/s | 57.0 KiB | 00m00s [147/156] Installing forge-srpm-macros- 100% | 39.3 MiB/s | 40.3 KiB | 00m00s [148/156] Installing go-srpm-macros-0:3 100% | 60.5 MiB/s | 62.0 KiB | 00m00s [149/156] Installing python-srpm-macros 100% | 50.9 MiB/s | 52.2 KiB | 00m00s [150/156] Installing redhat-rpm-config- 100% | 47.2 MiB/s | 193.2 KiB | 00m00s [151/156] Installing rpm-build-0:4.20.0 100% | 39.6 MiB/s | 202.9 KiB | 00m00s [152/156] Installing pyproject-srpm-mac 100% | 1.2 MiB/s | 2.5 KiB | 00m00s [153/156] Installing util-linux-0:2.40. 100% | 84.4 MiB/s | 3.7 MiB | 00m00s >>> Running post-install scriptlet: util-linux-0:2.40.2-8.fc42.x86_64 >>> Stop post-install scriptlet: util-linux-0:2.40.2-8.fc42.x86_64 [154/156] Installing authselect-0:1.5.0 100% | 52.7 MiB/s | 161.9 KiB | 00m00s [155/156] Installing which-0:2.21-42.fc 100% | 40.2 MiB/s | 82.4 KiB | 00m00s [156/156] Installing info-0:7.1.1-2.fc4 100% | 125.6 KiB/s | 362.2 KiB | 00m03s >>> Running post-transaction scriptlet: filesystem-0:3.18-29.fc42.x86_64 >>> Stop post-transaction scriptlet: filesystem-0:3.18-29.fc42.x86_64 >>> Running post-transaction scriptlet: ca-certificates-0:2024.2.69_v8.0.401-2.f >>> Stop post-transaction scriptlet: ca-certificates-0:2024.2.69_v8.0.401-2.fc42 >>> Running post-transaction scriptlet: authselect-libs-0:1.5.0-8.fc42.x86_64 >>> Stop post-transaction scriptlet: authselect-libs-0:1.5.0-8.fc42.x86_64 >>> Running post-transaction scriptlet: rpm-0:4.20.0-1.fc42.x86_64 >>> Stop post-transaction scriptlet: rpm-0:4.20.0-1.fc42.x86_64 >>> Running trigger-install scriptlet: glibc-common-0:2.40.9000-15.fc42.x86_64 >>> Stop trigger-install scriptlet: glibc-common-0:2.40.9000-15.fc42.x86_64 >>> Running trigger-install scriptlet: info-0:7.1.1-2.fc42.x86_64 >>> Stop trigger-install scriptlet: info-0:7.1.1-2.fc42.x86_64 Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.4.3-1.fc42.x86_64 alternatives-1.30-1.fc41.x86_64 ansible-srpm-macros-1-16.fc41.noarch audit-libs-4.0.2-1.fc41.x86_64 authselect-1.5.0-8.fc42.x86_64 authselect-libs-1.5.0-8.fc42.x86_64 basesystem-11-21.fc41.noarch bash-5.2.32-2.fc42.x86_64 binutils-2.43.50-5.fc42.x86_64 build-reproducibility-srpm-macros-0.4.3-1.fc42.noarch bzip2-1.0.8-19.fc41.x86_64 bzip2-libs-1.0.8-19.fc41.x86_64 ca-certificates-2024.2.69_v8.0.401-2.fc42.noarch coreutils-9.5-10.fc42.x86_64 coreutils-common-9.5-10.fc42.x86_64 cpio-2.15-2.fc41.x86_64 cracklib-2.9.11-6.fc41.x86_64 crypto-policies-20241018-1.gitce922cb.fc42.noarch curl-8.10.1-2.fc42.x86_64 cyrus-sasl-lib-2.1.28-27.fc41.x86_64 debugedit-5.1-1.fc42.x86_64 diffutils-3.10-8.fc41.x86_64 dwz-0.15-8.fc42.x86_64 ed-1.20.2-2.fc41.x86_64 efi-srpm-macros-5-12.fc41.noarch elfutils-0.192-3.fc42.x86_64 elfutils-debuginfod-client-0.192-3.fc42.x86_64 elfutils-default-yama-scope-0.192-3.fc42.noarch elfutils-libelf-0.192-3.fc42.x86_64 elfutils-libs-0.192-3.fc42.x86_64 fedora-gpg-keys-42-0.3.noarch fedora-release-42-0.6.noarch fedora-release-common-42-0.6.noarch fedora-release-identity-basic-42-0.6.noarch fedora-repos-42-0.3.noarch fedora-repos-rawhide-42-0.3.noarch file-5.45-7.fc41.x86_64 file-libs-5.45-7.fc41.x86_64 filesystem-3.18-29.fc42.x86_64 findutils-4.10.0-4.fc41.x86_64 fonts-srpm-macros-2.0.5-17.fc41.noarch forge-srpm-macros-0.4.0-1.fc42.noarch fpc-srpm-macros-1.3-13.fc41.noarch gawk-5.3.0-4.fc41.x86_64 gdb-minimal-15.2-1.fc42.x86_64 gdbm-1.23-7.fc41.x86_64 gdbm-libs-1.23-7.fc41.x86_64 ghc-srpm-macros-1.9.2-1.fc42.noarch glibc-2.40.9000-15.fc42.x86_64 glibc-common-2.40.9000-15.fc42.x86_64 glibc-gconv-extra-2.40.9000-15.fc42.x86_64 glibc-minimal-langpack-2.40.9000-15.fc42.x86_64 gmp-6.3.0-2.fc41.x86_64 gnat-srpm-macros-6-6.fc41.noarch go-srpm-macros-3.6.0-3.fc41.noarch gpg-pubkey-105ef944-65ca83d1 gpg-pubkey-31645531-66b6dccf gpg-pubkey-e99d6ad1-64d2612c grep-3.11-9.fc41.x86_64 gzip-1.13-2.fc41.x86_64 info-7.1.1-2.fc42.x86_64 jansson-2.14-1.fc42.x86_64 json-c-0.17-4.fc41.x86_64 kernel-srpm-macros-1.0-24.fc41.noarch keyutils-libs-1.6.3-4.fc41.x86_64 krb5-libs-1.21.3-2.fc41.x86_64 libacl-2.3.2-2.fc41.x86_64 libarchive-3.7.6-1.fc42.x86_64 libattr-2.5.2-4.fc41.x86_64 libblkid-2.40.2-8.fc42.x86_64 libbrotli-1.1.0-5.fc41.x86_64 libcap-2.71-1.fc42.x86_64 libcap-ng-0.8.5-3.fc41.x86_64 libcom_err-1.47.1-6.fc42.x86_64 libcurl-8.10.1-2.fc42.x86_64 libeconf-0.7.4-2.fc42.x86_64 libevent-2.1.12-14.fc41.x86_64 libfdisk-2.40.2-8.fc42.x86_64 libffi-3.4.6-3.fc42.x86_64 libgcc-14.2.1-4.fc42.x86_64 libgomp-14.2.1-4.fc42.x86_64 libidn2-2.3.7-2.fc41.x86_64 libmount-2.40.2-8.fc42.x86_64 libnghttp2-1.64.0-1.fc42.x86_64 libnsl2-2.0.1-2.fc41.x86_64 libpkgconf-2.3.0-1.fc42.x86_64 libpsl-0.21.5-4.fc41.x86_64 libpwquality-1.4.5-11.fc41.x86_64 libselinux-3.7-6.fc42.x86_64 libsemanage-3.7-3.fc42.x86_64 libsepol-3.7-3.fc42.x86_64 libsmartcols-2.40.2-8.fc42.x86_64 libssh-0.11.1-1.fc42.x86_64 libssh-config-0.11.1-1.fc42.noarch libstdc++-14.2.1-4.fc42.x86_64 libtasn1-4.19.0-9.fc41.x86_64 libtirpc-1.3.6-0.fc42.x86_64 libtool-ltdl-2.4.7-12.fc41.x86_64 libunistring-1.1-8.fc41.x86_64 libuuid-2.40.2-8.fc42.x86_64 libverto-0.3.2-9.fc41.x86_64 libxcrypt-4.4.36-7.fc41.x86_64 libxml2-2.12.8-2.fc41.x86_64 libzstd-1.5.6-2.fc41.x86_64 lua-libs-5.4.7-1.fc42.x86_64 lua-srpm-macros-1-14.fc41.noarch lz4-libs-1.10.0-1.fc41.x86_64 mpfr-4.2.1-5.fc41.x86_64 ncurses-base-6.5-2.20240629.fc41.noarch ncurses-libs-6.5-2.20240629.fc41.x86_64 ocaml-srpm-macros-10-3.fc41.noarch openblas-srpm-macros-2-18.fc41.noarch openldap-2.6.8-5.fc41.x86_64 openssl-libs-3.2.2-8.fc42.x86_64 p11-kit-0.25.5-4.fc42.x86_64 p11-kit-trust-0.25.5-4.fc42.x86_64 package-notes-srpm-macros-0.5-12.fc41.noarch pam-1.6.1-8.fc42.x86_64 pam-libs-1.6.1-8.fc42.x86_64 patch-2.7.6-25.fc41.x86_64 pcre2-10.44-1.fc41.1.x86_64 pcre2-syntax-10.44-1.fc41.1.noarch perl-srpm-macros-1-56.fc41.noarch pkgconf-2.3.0-1.fc42.x86_64 pkgconf-m4-2.3.0-1.fc42.noarch pkgconf-pkg-config-2.3.0-1.fc42.x86_64 popt-1.19-7.fc41.x86_64 publicsuffix-list-dafsa-20240107-4.fc41.noarch pyproject-srpm-macros-1.15.1-1.fc42.noarch python-srpm-macros-3.13-3.fc41.noarch qt5-srpm-macros-5.15.15-1.fc42.noarch qt6-srpm-macros-6.8.0-1.fc42.noarch readline-8.2-11.fc42.x86_64 redhat-rpm-config-296-1.fc42.noarch rpm-4.20.0-1.fc42.x86_64 rpm-build-4.20.0-1.fc42.x86_64 rpm-build-libs-4.20.0-1.fc42.x86_64 rpm-libs-4.20.0-1.fc42.x86_64 rpm-sequoia-1.7.0-2.fc41.x86_64 rust-srpm-macros-26.3-3.fc42.noarch sed-4.9-3.fc41.x86_64 setup-2.15.0-5.fc41.noarch shadow-utils-4.16.0-6.fc42.x86_64 sqlite-libs-3.46.1-1.fc42.x86_64 systemd-libs-256.7-1.fc42.x86_64 tar-1.35-4.fc41.x86_64 unzip-6.0-64.fc41.x86_64 util-linux-2.40.2-8.fc42.x86_64 util-linux-core-2.40.2-8.fc42.x86_64 which-2.21-42.fc41.x86_64 xxhash-libs-0.8.2-4.fc42.x86_64 xz-5.6.3-2.fc42.x86_64 xz-libs-5.6.3-2.fc42.x86_64 zig-srpm-macros-1-3.fc41.noarch zip-3.0-41.fc41.x86_64 zlib-ng-compat-2.1.7-3.fc42.x86_64 zstd-1.5.6-2.fc41.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 warning: %source_date_epoch_from_changelog is set, but %changelog has no entries to take a date from Wrote: /builddir/build/SRPMS/R-CRAN-rxode2-3.0.2-1.fc42.copr8192634.src.rpm RPM build warnings: %source_date_epoch_from_changelog is set, but %changelog has no entries to take a date from Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1730339452.741906/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-uo7sbc0c/R-CRAN-rxode2/R-CRAN-rxode2.spec) Config(child) 0 minutes 18 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 INFO: Start(/var/lib/copr-rpmbuild/results/R-CRAN-rxode2-3.0.2-1.fc42.copr8192634.src.rpm) Config(fedora-rawhide-x86_64) Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1730339452.741906/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management from host and used with --installroot: rpm-4.19.1.1-1.fc39.x86_64 rpm-sequoia-1.6.0-1.fc39.x86_64 python3-dnf-4.21.1-1.fc39.noarch python3-dnf-plugins-core-4.9.0-1.fc39.noarch yum-4.21.1-1.fc39.noarch dnf5-5.1.17-2.fc39.x86_64 dnf5-plugins-5.1.17-2.fc39.x86_64 Finish: chroot init Start: build phase for R-CRAN-rxode2-3.0.2-1.fc42.copr8192634.src.rpm Start: build setup for R-CRAN-rxode2-3.0.2-1.fc42.copr8192634.src.rpm Building target platforms: x86_64 Building for target x86_64 warning: %source_date_epoch_from_changelog is set, but %changelog has no entries to take a date from Wrote: /builddir/build/SRPMS/R-CRAN-rxode2-3.0.2-1.fc42.copr8192634.src.rpm RPM build warnings: %source_date_epoch_from_changelog is set, but %changelog has no entries to take a date from Updating and loading repositories: fedora 100% | 636.7 KiB/s | 23.6 KiB | 00m00s Copr repository 100% | 31.4 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 48.4 MiB/s | 12.3 MiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: R-CRAN-BH noarch 1.84.0.0-1.fc41.copr7349931 copr_base 121.0 MiB R-CRAN-PreciseSums x86_64 0.7-1.fc42.copr8029450 copr_base 78.3 KiB R-CRAN-Rcpp x86_64 1.0.13-1.fc41.copr7745410 copr_base 8.4 MiB R-CRAN-RcppArmadillo x86_64 14.0.2.1-1.fc42.copr8016517 copr_base 6.0 MiB R-CRAN-RcppEigen x86_64 0.3.4.0.2-1.fc42.copr8100507 copr_base 9.0 MiB R-CRAN-RcppParallel x86_64 5.1.9-1.fc42.copr7936852 copr_base 1.5 MiB R-CRAN-StanHeaders x86_64 2.32.10-1.fc41.copr7736967 copr_base 9.7 MiB R-CRAN-backports x86_64 1.5.0-1.fc41.copr7483453 copr_base 211.8 KiB R-CRAN-checkmate x86_64 2.3.2-1.fc41.copr7803006 copr_base 1.4 MiB R-CRAN-cli x86_64 3.6.3-1.fc41.copr7649835 copr_base 2.4 MiB R-CRAN-data.table x86_64 1.16.2-1.fc42.copr8128145 copr_base 4.5 MiB R-CRAN-dparser x86_64 1.3.1.13-1.fc42.copr8168029 copr_base 869.1 KiB R-CRAN-ggplot2 noarch 3.5.1-1.fc41.copr7361224 copr_base 7.1 MiB R-CRAN-inline noarch 0.3.19-1.fc41.copr7349930 copr_base 211.0 KiB R-CRAN-lotri x86_64 1.0.0-1.fc42.copr8032936 copr_base 519.1 KiB R-CRAN-magrittr x86_64 2.0.3-1.fc41.copr7349936 copr_base 417.3 KiB R-CRAN-memoise noarch 2.0.1-1.fc41.copr7356088 copr_base 83.7 KiB R-CRAN-qs x86_64 0.27.2-1.fc42.copr8099906 copr_base 3.0 MiB R-CRAN-rex noarch 1.2.1-1.fc42.copr8100517 copr_base 250.4 KiB R-CRAN-rxode2ll x86_64 2.0.11-1.fc41.copr7480751 copr_base 435.6 KiB R-CRAN-sitmo x86_64 2.0.2-1.fc41.copr7353638 copr_base 883.1 KiB R-CRAN-sys x86_64 3.4.3-1.fc42.copr8109592 copr_base 79.9 KiB R-core x86_64 4.4.1-5.fc41 fedora 101.5 MiB R-devel x86_64 4.4.1-5.fc41 fedora 0.0 B Installing dependencies: R-CRAN-MASS x86_64 7.3.61-1.fc41.copr7613806 copr_base 1.8 MiB R-CRAN-Matrix x86_64 1.7.1-1.fc42.copr8157422 copr_base 8.2 MiB R-CRAN-R6 noarch 2.5.1-1.fc41.copr7349938 copr_base 115.9 KiB R-CRAN-RApiSerialize x86_64 0.1.4-1.fc42.copr8089098 copr_base 36.6 KiB R-CRAN-RColorBrewer noarch 1.1.3-1.fc41.copr7349948 copr_base 63.6 KiB R-CRAN-cachem x86_64 1.1.0-1.fc41.copr7452047 copr_base 104.7 KiB R-CRAN-colorspace x86_64 2.1.1-1.fc41.copr7795131 copr_base 4.0 MiB R-CRAN-crayon noarch 1.5.3-1.fc41.copr7633037 copr_base 235.8 KiB R-CRAN-digest x86_64 0.6.37-1.fc42.copr7936834 copr_base 495.7 KiB R-CRAN-fansi x86_64 1.0.6-1.fc41.copr7349952 copr_base 625.8 KiB R-CRAN-farver x86_64 2.1.2-1.fc41.copr7442181 copr_base 2.1 MiB R-CRAN-fastmap x86_64 1.2.0-1.fc41.copr7447859 copr_base 108.5 KiB R-CRAN-glue x86_64 1.8.0-1.fc42.copr8094211 copr_base 349.1 KiB R-CRAN-gtable noarch 0.3.6-1.fc42.copr8178682 copr_base 337.9 KiB R-CRAN-isoband x86_64 0.2.7-1.fc41.copr7351195 copr_base 1.9 MiB R-CRAN-labeling noarch 0.4.3-1.fc41.copr7349947 copr_base 92.7 KiB R-CRAN-lattice x86_64 0.22.6-1.fc41.copr7352639 copr_base 2.0 MiB R-CRAN-lazyeval x86_64 0.2.2-3.fc41.copr7349927 copr_base 362.3 KiB R-CRAN-lifecycle noarch 1.0.4-1.fc41.copr7354340 copr_base 282.7 KiB R-CRAN-mgcv x86_64 1.9.1-1.fc41.copr7357272 copr_base 4.5 MiB R-CRAN-munsell noarch 0.5.1-1.fc41.copr7353599 copr_base 379.0 KiB R-CRAN-nlme x86_64 3.1.166-1.fc42.copr7936970 copr_base 3.8 MiB R-CRAN-pillar noarch 1.9.0-1.fc41.copr7357931 copr_base 1.4 MiB R-CRAN-pkgconfig noarch 2.0.3-3.fc41.copr7349937 copr_base 34.0 KiB R-CRAN-rlang x86_64 1.1.4-1.fc41.copr7531082 copr_base 2.6 MiB R-CRAN-scales noarch 1.3.0-1.fc41.copr7356067 copr_base 1.1 MiB R-CRAN-stringfish x86_64 0.16.0-1.fc41.copr7355169 copr_base 807.6 KiB R-CRAN-tibble x86_64 3.2.1-1.fc41.copr7359525 copr_base 1.7 MiB R-CRAN-utf8 x86_64 1.2.4-1.fc41.copr7349954 copr_base 470.9 KiB R-CRAN-vctrs x86_64 0.6.5-1.fc41.copr7356070 copr_base 2.3 MiB R-CRAN-viridisLite noarch 0.4.2-1.fc41.copr7349928 copr_base 1.3 MiB R-CRAN-withr noarch 3.0.2-1.fc42.copr8184963 copr_base 396.0 KiB R-core-devel x86_64 4.4.1-5.fc41 fedora 394.7 KiB R-java x86_64 4.4.1-5.fc41 fedora 0.0 B R-java-devel x86_64 4.4.1-5.fc41 fedora 0.0 B R-littler x86_64 0.3.19-5.fc41 fedora 158.1 KiB R-rpm-macros noarch 1.2.1-11.fc41 fedora 5.6 KiB abattis-cantarell-vf-fonts noarch 0.301-13.fc41 fedora 192.7 KiB alsa-lib x86_64 1.2.12-2.fc41 fedora 1.4 MiB annobin-docs noarch 12.70-1.fc42 fedora 97.7 KiB annobin-plugin-gcc x86_64 12.70-1.fc42 fedora 985.6 KiB avahi-libs x86_64 0.8-30.fc42 fedora 174.2 KiB brotli x86_64 1.1.0-5.fc41 fedora 31.8 KiB brotli-devel x86_64 1.1.0-5.fc41 fedora 65.6 KiB bzip2-devel x86_64 1.0.8-19.fc41 fedora 309.8 KiB cairo x86_64 1.18.0-4.fc41 fedora 1.7 MiB cairo-devel x86_64 1.18.0-4.fc41 fedora 2.3 MiB cmake-filesystem x86_64 3.28.3-7.fc41 fedora 0.0 B copy-jdk-configs noarch 4.1-6.fc41 fedora 20.3 KiB cpp x86_64 14.2.1-4.fc42 fedora 35.0 MiB cups-libs x86_64 1:2.4.11-2.fc42 fedora 622.9 KiB dbus-libs x86_64 1:1.14.10-4.fc41 fedora 368.9 KiB default-fonts-core-sans noarch 4.2-1.fc42 fedora 11.9 KiB desktop-file-utils x86_64 0.27-2.fc41 fedora 230.4 KiB emacs-filesystem noarch 1:30.0-3.fc41 fedora 0.0 B expat x86_64 2.6.3-1.fc42 fedora 291.5 KiB flexiblas x86_64 3.4.4-3.fc41 fedora 48.5 KiB flexiblas-devel x86_64 3.4.4-3.fc41 fedora 4.8 MiB flexiblas-netlib x86_64 3.4.4-3.fc41 fedora 10.7 MiB flexiblas-netlib64 x86_64 3.4.4-3.fc41 fedora 10.8 MiB flexiblas-openblas-openmp x86_64 3.4.4-3.fc41 fedora 43.3 KiB flexiblas-openblas-openmp64 x86_64 3.4.4-3.fc41 fedora 43.3 KiB fontconfig x86_64 2.15.0-8.fc41 fedora 791.9 KiB fontconfig-devel x86_64 2.15.0-8.fc41 fedora 117.2 KiB fonts-filesystem noarch 1:2.0.5-17.fc41 fedora 0.0 B freetype x86_64 2.13.3-1.fc42 fedora 850.5 KiB freetype-devel x86_64 2.13.3-1.fc42 fedora 8.5 MiB fribidi x86_64 1.0.16-1.fc42 fedora 194.5 KiB gcc x86_64 14.2.1-4.fc42 fedora 104.4 MiB gcc-c++ x86_64 14.2.1-4.fc42 fedora 38.2 MiB gcc-gfortran x86_64 14.2.1-4.fc42 fedora 37.2 MiB gcc-plugin-annobin x86_64 14.2.1-4.fc42 fedora 61.1 KiB gettext x86_64 0.22.5-6.fc41 fedora 5.2 MiB gettext-envsubst x86_64 0.22.5-6.fc41 fedora 74.9 KiB gettext-libs x86_64 0.22.5-6.fc41 fedora 1.7 MiB gettext-runtime x86_64 0.22.5-6.fc41 fedora 481.3 KiB glib2 x86_64 2.82.2-1.fc42 fedora 14.7 MiB glib2-devel x86_64 2.82.2-1.fc42 fedora 15.7 MiB glibc-devel x86_64 2.40.9000-15.fc42 fedora 2.3 MiB gnutls x86_64 3.8.7-4.fc42 fedora 3.2 MiB google-noto-fonts-common noarch 20240901-1.fc42 fedora 17.5 KiB google-noto-sans-vf-fonts noarch 20240901-1.fc42 fedora 1.2 MiB graphite2 x86_64 1.3.14-16.fc41 fedora 192.0 KiB graphite2-devel x86_64 1.3.14-16.fc41 fedora 49.1 KiB harfbuzz x86_64 10.0.1-1.fc42 fedora 2.7 MiB harfbuzz-cairo x86_64 10.0.1-1.fc42 fedora 52.3 KiB harfbuzz-devel x86_64 10.0.1-1.fc42 fedora 5.1 MiB harfbuzz-icu x86_64 10.0.1-1.fc42 fedora 19.5 KiB hwloc-libs x86_64 2.11.2-1.fc42 fedora 2.9 MiB java-21-openjdk x86_64 1:21.0.5.0.11-1.fc42 fedora 1.1 MiB java-21-openjdk-devel x86_64 1:21.0.5.0.11-1.fc42 fedora 11.2 MiB java-21-openjdk-headless x86_64 1:21.0.5.0.11-1.fc42 fedora 203.9 MiB javapackages-filesystem noarch 6.3.4-1.fc42 fedora 1.9 KiB jbigkit-libs x86_64 2.1-30.fc41 fedora 117.6 KiB kernel-headers x86_64 6.12.0-0.rc5.44.fc42 fedora 6.4 MiB less x86_64 668-1.fc42 fedora 406.4 KiB libICE x86_64 1.1.1-4.fc41 fedora 181.2 KiB libRmath x86_64 4.4.1-5.fc41 fedora 246.8 KiB libRmath-devel x86_64 4.4.1-5.fc41 fedora 17.4 KiB libSM x86_64 1.2.4-4.fc41 fedora 97.3 KiB libX11 x86_64 1.8.10-2.fc42 fedora 1.3 MiB libX11-common noarch 1.8.10-2.fc42 fedora 1.1 MiB libX11-devel x86_64 1.8.10-2.fc42 fedora 1.0 MiB libX11-xcb x86_64 1.8.10-2.fc42 fedora 15.0 KiB libXau x86_64 1.0.11-7.fc41 fedora 66.9 KiB libXau-devel x86_64 1.0.11-7.fc41 fedora 6.4 KiB libXcomposite x86_64 0.4.6-4.fc41 fedora 44.5 KiB libXext x86_64 1.3.6-2.fc41 fedora 90.1 KiB libXext-devel x86_64 1.3.6-2.fc41 fedora 98.9 KiB libXft x86_64 2.3.8-7.fc41 fedora 164.5 KiB libXft-devel x86_64 2.3.8-7.fc41 fedora 31.7 KiB libXi x86_64 1.8.2-1.fc42 fedora 80.7 KiB libXmu x86_64 1.2.1-2.fc41 fedora 191.5 KiB libXrender x86_64 0.9.11-7.fc41 fedora 50.1 KiB libXrender-devel x86_64 0.9.11-7.fc41 fedora 50.1 KiB libXt x86_64 1.3.0-4.fc41 fedora 429.9 KiB libXtst x86_64 1.2.5-1.fc41 fedora 33.6 KiB libb2 x86_64 0.98.1-12.fc41 fedora 42.2 KiB libblkid-devel x86_64 2.40.2-8.fc42 fedora 44.9 KiB libdatrie x86_64 0.2.13-10.fc41 fedora 57.9 KiB libdeflate x86_64 1.22-2.fc42 fedora 118.1 KiB libdeflate-devel x86_64 1.22-2.fc42 fedora 25.7 KiB libffi-devel x86_64 3.4.6-3.fc42 fedora 33.1 KiB libfontenc x86_64 1.1.8-2.fc41 fedora 67.0 KiB libgfortran x86_64 14.2.1-4.fc42 fedora 3.0 MiB libicu x86_64 74.2-2.fc41 fedora 34.9 MiB libicu-devel x86_64 74.2-2.fc41 fedora 5.6 MiB libjpeg-turbo x86_64 3.0.4-1.fc42 fedora 789.1 KiB liblerc x86_64 4.0.0-7.fc41 fedora 607.5 KiB libmount-devel x86_64 2.40.2-8.fc42 fedora 63.5 KiB libmpc x86_64 1.3.1-6.fc41 fedora 164.7 KiB libpng x86_64 2:1.6.44-1.fc42 fedora 245.8 KiB libpng-devel x86_64 2:1.6.44-1.fc42 fedora 886.0 KiB libquadmath x86_64 14.2.1-4.fc42 fedora 325.9 KiB libquadmath-devel x86_64 14.2.1-4.fc42 fedora 21.9 KiB libselinux-devel x86_64 3.7-6.fc42 fedora 126.5 KiB libsepol-devel x86_64 3.7-3.fc42 fedora 120.3 KiB libstdc++-devel x86_64 14.2.1-4.fc42 fedora 15.4 MiB libtextstyle x86_64 0.22.5-6.fc41 fedora 195.6 KiB libthai x86_64 0.1.29-9.fc41 fedora 783.5 KiB libtiff x86_64 4.6.0-6.fc42 fedora 606.0 KiB libtirpc-devel x86_64 1.3.6-0.fc42 fedora 251.6 KiB libwebp x86_64 1.4.0-4.fc41 fedora 822.6 KiB libxcb x86_64 1.17.0-3.fc42 fedora 1.2 MiB libxcb-devel x86_64 1.17.0-3.fc42 fedora 2.7 MiB libxcrypt-devel x86_64 4.4.36-7.fc41 fedora 30.3 KiB libxml2-devel x86_64 2.12.8-2.fc41 fedora 3.4 MiB lksctp-tools x86_64 1.0.19-9.fc41 fedora 275.2 KiB lua x86_64 5.4.7-1.fc42 fedora 610.5 KiB lua-posix x86_64 36.2.1-7.fc41 fedora 599.8 KiB make x86_64 1:4.4.1-9.fc42 fedora 1.8 MiB mkfontscale x86_64 1.2.3-1.fc41 fedora 49.2 KiB mpdecimal x86_64 2.5.1-16.fc41 fedora 204.9 KiB nettle x86_64 3.10-3.fc41 fedora 793.0 KiB nspr x86_64 4.35.0-29.fc42 fedora 320.4 KiB nss x86_64 3.104.0-1.fc42 fedora 1.9 MiB nss-softokn x86_64 3.104.0-1.fc42 fedora 1.9 MiB nss-softokn-freebl x86_64 3.104.0-1.fc42 fedora 783.6 KiB nss-sysinit x86_64 3.104.0-1.fc42 fedora 22.2 KiB nss-util x86_64 3.104.0-1.fc42 fedora 205.1 KiB openblas x86_64 0.3.26-5.fc41 fedora 96.0 KiB openblas-openmp x86_64 0.3.26-5.fc41 fedora 39.4 MiB openblas-openmp64 x86_64 0.3.26-5.fc41 fedora 39.5 MiB pango x86_64 1.54.0-2.fc41 fedora 996.2 KiB pcre2-devel x86_64 10.44-1.fc41.1 fedora 2.0 MiB pcre2-utf16 x86_64 10.44-1.fc41.1 fedora 590.1 KiB pcre2-utf32 x86_64 10.44-1.fc41.1 fedora 562.0 KiB pixman x86_64 0.43.4-2.fc41 fedora 718.1 KiB pixman-devel x86_64 0.43.4-2.fc41 fedora 49.4 KiB python-pip-wheel noarch 24.2-2.fc42 fedora 1.2 MiB python3 x86_64 3.13.0-1.fc42 fedora 31.8 KiB python3-libs x86_64 3.13.0-1.fc42 fedora 40.4 MiB python3-packaging noarch 24.1-2.fc41 fedora 422.3 KiB sysprof-capture-devel x86_64 47.0-1.fc42 fedora 273.2 KiB tbb x86_64 2021.13.0-2.fc41 fedora 440.8 KiB tbb-bind x86_64 2021.13.0-2.fc41 fedora 23.7 KiB tbb-devel x86_64 2021.13.0-2.fc41 fedora 1.3 MiB tcl x86_64 1:8.6.15-2.fc42 fedora 4.2 MiB tcl-devel x86_64 1:8.6.15-2.fc42 fedora 793.3 KiB tk x86_64 1:8.6.15-1.fc42 fedora 3.6 MiB tk-devel x86_64 1:8.6.15-1.fc42 fedora 985.4 KiB tre x86_64 0.8.0-45.20140228gitc2f5d13.fc41 fedora 75.9 KiB tre-common noarch 0.8.0-45.20140228gitc2f5d13.fc41 fedora 81.0 KiB tre-devel x86_64 0.8.0-45.20140228gitc2f5d13.fc41 fedora 10.7 KiB ttmkfdir x86_64 3.0.9-71.fc41 fedora 122.7 KiB tzdata noarch 2024a-9.fc41 fedora 1.7 MiB tzdata-java noarch 2024a-9.fc41 fedora 101.7 KiB xdg-utils noarch 1.2.1-2.fc41 fedora 346.3 KiB xml-common noarch 0.6.3-65.fc41 fedora 78.4 KiB xorg-x11-fonts-Type1 noarch 7.5-39.fc41 fedora 863.3 KiB xorg-x11-proto-devel noarch 2024.1-3.fc41 fedora 1.7 MiB xz-devel x86_64 1:5.6.3-2.fc42 fedora 255.6 KiB zlib-ng-compat-devel x86_64 2.1.7-3.fc42 fedora 106.8 KiB Transaction Summary: Installing: 217 packages Total size of inbound packages is 330 MiB. Need to download 44 MiB. After this operation 1 GiB will be used (install 1 GiB, remove 0 B). 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Finish: build setup for R-CRAN-rxode2-3.0.2-1.fc42.copr8192634.src.rpm Start: rpmbuild R-CRAN-rxode2-3.0.2-1.fc42.copr8192634.src.rpm Building target platforms: x86_64 Building for target x86_64 warning: %source_date_epoch_from_changelog is set, but %changelog has no entries to take a date from Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.u7s7Od + umask 022 + cd /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build + test -d /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build + /usr/bin/rm -rf /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build + /usr/bin/mkdir -p /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build + /usr/bin/mkdir -p /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build/SPECPARTS + RPM_EC=0 ++ jobs -p + exit 0 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.tM9NMS + umask 022 + cd /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build + cd /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build + rm -rf rxode2 + /usr/bin/mkdir -p rxode2 + cd rxode2 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/rxode2_3.0.2.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + find -type f -executable -exec grep -Iq . '{}' ';' -exec sed -i -e '$a\' '{}' ';' + '[' -d rxode2/src ']' + find rxode2/src -type f -exec sed -i s@/usr/bin/strip@/usr/bin/true@g '{}' ';' + '[' -d rxode2/src ']' + find rxode2/src/Makevars.in -type f -exec sed -i s@-g0@@g '{}' ';' + find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' '{}' ';' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.9g6vJ6 + umask 022 + cd /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd rxode2 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.yrXnaS + umask 022 + cd /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build + '[' /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build/BUILDROOT ++ dirname /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build/BUILDROOT + mkdir -p /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build + mkdir /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build/BUILDROOT + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd rxode2 + mkdir -p /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build/BUILDROOT/usr/local/lib/R/library + /usr/bin/R CMD INSTALL -l /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build/BUILDROOT/usr/local/lib/R/library rxode2 * installing *source* package ‘rxode2’ ... ** package ‘rxode2’ successfully unpacked and MD5 sums checked ** using staged installation R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-redhat-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > ## This is only for rxode2 > for (f in c("inst/include/rxode2_RcppExports.h", "src/RcppExports.cpp")) { + l <- readLines(f) + w <- which(regexpr("^[#]include ", l) != -1) + if (length(w) > 0) { + l <- l[-w] + } + w <- which(regexpr("^[#]define R_STRICT_HEADERS", l) != -1) + if (length(w) > 0) { + l <- l[-w] + } + l <- c("#define R_STRICT_HEADERS", + "#include ", + l) + file.out <- file(f, "wb") + writeLines(l, file.out) + close(file.out) + } > > l <- readLines("R/RcppExports.R") > w <- which(regexpr("# Register entry points", l, fixed=TRUE) != -1) > if (length(w) >= 1) { + w <- w[1] + l <- l[seq(1, w-1)] + RcppExports.R <- file("R/RcppExports.R", "wb") + writeLines(l, RcppExports.R) + close(RcppExports.R) + } > > .in <- suppressWarnings(readLines("src/Makevars.in")) > .in <- gsub("@ARMA@", file.path(find.package("RcppArmadillo"),"include"), .in) > .in <- gsub("@BH@", file.path(find.package("BH"),"include"), .in) > .in <- gsub("@RCPP@", file.path(find.package("Rcpp"),"include"), .in) > .in <- gsub("@EG@", file.path(find.package("RcppEigen"),"include"), .in) > > .in <- gsub("@SL@", paste(capture.output(StanHeaders:::LdFlags()), capture.output(RcppParallel:::RcppParallelLibs())), #nolint + .in) > > > .badStan <- "" > .in <- gsub("@SH@", gsub("-I", "-@ISYSTEM@", + paste(capture.output(StanHeaders:::CxxFlags()), # nolint + capture.output(RcppParallel:::CxxFlags()), # nolint + paste0("-@ISYSTEM@'", system.file('include', 'src', package = 'StanHeaders', mustWork = TRUE), "'"), + .badStan)), + .in) > > > > > if (.Platform$OS.type == "windows" && !file.exists("src/Makevars.win")) { + .in <- gsub("@CXX14STD@", "-std=c++1y", .in) + file.out <- file("src/Makevars.win", "wb") + writeLines(gsub("@ISYSTEM@", "I", .in), + file.out) + close(file.out) + } else { + .in <- gsub("@CXX14STD@", "-std=gnu++14", .in) + file.out <- file("src/Makevars", "wb") + writeLines(gsub("@ISYSTEM@", "isystem", .in), + file.out) + close(file.out) + } > > if (file.exists("man/reexports.Rd")) { + l <- readLines("man/reexports.Rd") + if (!any(regexpr("[\\]value", l) != -1)) { + l <- c(l, "\\value{ Inherited from parent routine }") + file.out <- file("man/reexports.Rd", "wb") + writeLines(l, file.out) + close(file.out) + } + } > > > unlink("R/rxode2_md5.R") > > cpp <- list.files("src", pattern = ".(c|h|cpp|f)$") > include <- list.files("inst/include") > #Rfiles <- list.files("R/", pattern = ".R") > > cmd <- file.path(R.home("bin"), "R") > args <- c("CMD", "config") > > md5 <- digest::digest(c(lapply(c(paste0("src/", cpp), + paste0("inst/include/", include)#, + #paste0("R/", Rfiles) + ), digest::digest, file = TRUE), + ## vapply(c("BLAS_LIBS", "CC", "CFLAGS", "CPICFLAGS", + ## "CXX", "CXXFLAGS", "CXXPICFLAGS", + ## "CXX11", "CXX11STD", "CXX11FLAGS", "CXX11PICFLAGS", + ## "CXX14", "CXX14STD", "CXX14FLAGS", "CXX14PICFLAGS", + ## "CXX17", "CXX17STD", "CXX17FLAGS", "CXX17PICFLAGS", + ## "CXX20", "CXX20STD", "CXX20FLAGS", "CXX20PICFLAGS", + ## "FC", "FFLAGS", "FCFLAGS", "FPICFLAGS"), + ## function(cfg) { + ## rawToChar(sys::exec_internal(cmd, c(args, cfg))$stdout) + ## }, character(1) + ## ), + "" + )) > unlink("R/rxode2_md5.R") > md5file <- file("R/rxode2_md5.R", "wb") > writeLines(sprintf("rxode2.md5 <- \"%s\"\n", md5), md5file) > close(md5file) > > l <- readLines("DESCRIPTION") > w <- which(regexpr("Version[:] *(.*)$", l) != -1) > v <- gsub("Version[:] *(.*)$", "\\1", l[w]) > > unlink("inst/include/rxode2parseVer.h") > ode.h <- file("inst/include/rxode2parseVer.h", "wb") > writeLines(c(sprintf("#define __VER_md5__ \"%s\"", md5), + "#define __VER_repo__ \"https://github.com/nlmixr2/rxode2\"", + sprintf("#define __VER_ver__ \"%s\"", v)), + ode.h) > close(ode.h) > > unlink("src/sbuf.c") > l <- readLines("inst/include/sbuf.c") > sbuf.c <- file("src/sbuf.c", "wb") > writeLines(l, sbuf.c) > close(sbuf.c) > > > unlink("src/codegen2.h") > l <- readLines("inst/include/rxode2_model_shared.c") > > l <- l[l != ""] > l <- gsub(" *= *NULL;", "=NULL;", l) > > def <- l > w <- which(regexpr("double _prod", def) != -1) - 1 > def <- def[1:w] > def <- gsub("=NULL", "", def) > def <- gsub("[^ ]* *[*]?([^;]*);", "\\1", def) > > def <- unique(c(def, c("_sum", "_udf", "_sign", "_prod", "_max", "_min", "_transit4P", "_transit3P", "_assignFuns0", "_assignFuns", "_getRxSolve_", "_solveData", "_rxord", "__assignFuns2"))) > > w0 <- which(grepl("double +_prod", l))[1] > r <- 1:(w0 - 1) > l0 <- l[r] > l <- l[-r] > > > w1 <- which(regexpr("dynamic start", l) != -1) > l1 <- l[1:w1] > > > > w2 <- which(regexpr("dynamic stop", l) != -1) > l2 <- l[seq(w2, length(l))] > > w3 <- which(regexpr("assign start", l2) != -1) > > l3 <- l2[seq(w3, length(l2))] > l2 <- l2[1:w3] > > w4 <- which(regexpr("assign stop", l3) != -1) > l3 <- l3[seq(w4, length(l3))] > > dfP <- l[seq(w1+1, w2-1)] > > dfP <- dfP[regexpr("^ *$", dfP)==-1] > df <- setNames(do.call("rbind",lapply(seq_along(dfP), + function(i) { + .r <- sub("^ *", "", dfP[[i]]) + .r <- sub("^([^ ]*) *= *[(]", "\\1,", .r) + .r <- sub("^([^ ]*) *[)] *R_GetCCallable *[(] *\"", "\\1,", .r, perl=TRUE) + .r <- sub("^([^ ]*) *\" *, *\"", "\\1,", .r, perl=TRUE) + .r <- sub("^([^ ]*)\" *[)] *; *", "\\1",.r, perl=TRUE) + data.frame(t(strsplit(.r, ",")[[1]]),stringsAsFactors = FALSE) + })), c("fun", "type", "package", "packageFun")) > > df$rxFun <- df$fun > df$argMax <- df$argMin <- NA_integer_ > df$threadSafe <- 1L > df <- df[,c("rxFun", "fun", "type", "package", "packageFun", "argMin", "argMax", "threadSafe")] > df$rxFun <- gsub("_llik", "llik", df$rxFun) > > def <- def[!(def %in% df$rxFun)] > def <- def[!(def %in% df$fun)] > > .parseEnv <- new.env(parent=emptyenv()) > source("R/parseFuns.R") > > df$argMin <- vapply(df$rxFun, function(f) { + .n <- .parseEnv$.parseNum[f] + if (is.na(.n)) return(NA_integer_) + .n <-setNames(.n, NULL) + as.integer(.n) + }, integer(1), USE.NAMES=TRUE) > > df$argMax <- df$argMin > > dfStr <- deparse(df) > dfStr[1] <- paste(".parseEnv$.rxode2parseDf <- ", dfStr[1]) > > dfIni.R <- file("R/dfIni.R", "wb") > writeLines(dfStr, + dfIni.R) > close(dfIni.R) > > ## deparse1 came from R 4.0, use deparse2 > deparse2 <- function(expr, collapse = " ", width.cutoff = 500L, ...) { + paste(deparse(expr, width.cutoff, ...), collapse = collapse) + } > > final <- c("#include ", + "#include ", + "unsigned long int __timeId=0;", + "void writeHeader(const char *md5, const char *extra) {", + paste0("sAppend(&sbOut, \"#define ", def, " _rx%s%s%ld\\n\", extra, md5, __timeId++);"), + "}", + "void writeBody0(void) {", + paste0("sAppendN(&sbOut, ", vapply(paste0(l0, "\n"), deparse2, character(1)), ", ", nchar(l0) + 1, ");"), + "}", + "void writeBody1(void) {", + paste0("sAppendN(&sbOut, ", vapply(paste0(l1, "\n"), deparse2, character(1)), ", ", nchar(l1) + 1, ");"), + "}", + "void writeBody2(void) {", + paste0("sAppendN(&sbOut, ", vapply(paste0(l2, "\n"), deparse2, character(1)), ", ", nchar(l2) + 1, ");"), + "}", + "void writeBody3(void) {", + paste0("sAppendN(&sbOut, ", vapply(paste0(l3, "\n"), deparse2, character(1)), ", ", nchar(l3) + 1, ");"), + "}", + "void writeFooter(void) {", + paste0("sAppendN(&sbOut, \"#undef ", def, "\\n\", ", nchar(def) + 8, ");"), + "}" + ) > > codegen2.h <- file("src/codegen2.h", "wb") > writeLines(final, + codegen2.h) > close(codegen2.h) > > proc.time() user system elapsed 0.225 0.087 0.290 --------[begin src/Makevars]-------- # -*- mode: makefile-gmake -*- BH=/usr/local/lib/R/library/BH/include RCPP=/usr/local/lib/R/library/Rcpp/include EG=/usr/local/lib/R/library/RcppEigen/include SH=-isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' CXX_STD = CXX17 ################################################################################ ## Package library flags. PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) -L'/usr/local/lib/R/library/RcppParallel/lib/' -Wl,-rpath,'/usr/local/lib/R/library/RcppParallel/lib/' -ltbb -ltbbmalloc -L/usr/lib64 -Wl,-rpath,/usr/lib64 -ltbb -ltbbmalloc # Release options PKG_CFLAGS = -D_isrxode2_ PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"$(BH)" -isystem"$(EG)" $(SH) -isystem"$(RCPP)" --------[end src/Makevars]-------- --------[begin R/RxODE_md5.R]-------- rxode2.md5 <- "81d3f05c9cb380efff615aa6e88cf4c4" --------[end R/RxODE_md5.R]-------- ** libs using C compiler: ‘gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-4)’ using Fortran compiler: ‘GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-4)’ using C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-4)’ using C++17 g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c RcppExports.cpp -o RcppExports.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c approx.c -o approx.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c boost.cpp -o boost.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c box.c -o box.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c call_dvode.c -o call_dvode.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c cbindThetaOmega.cpp -o cbindThetaOmega.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c cfode.c -o cfode.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c cfode_static.c -o cfode_static.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c checkmate.cpp -o checkmate.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c checkmate_stub.c -o checkmate_stub.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c codegen.c -o codegen.o codegen.c: In function ‘codegen’: codegen.c:344:19: warning: unused variable ‘assignOne’ [-Wunused-variable] 344 | int assignOne = 0; | ^~~~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c common.c -o common.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c corfailure.c -o corfailure.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c correction.c -o correction.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c cvPost.cpp -o cvPost.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c daxpy.c -o daxpy.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c ddot.c -o ddot.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c dgefa.c -o dgefa.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c dgesl.c -o dgesl.o gfortran -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules -c dgpadm.f -o dgpadm.o gfortran -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules -c dlsoda.f -o dlsoda.o dlsoda.f: In function ‘dlsoda_’: dlsoda.f:2536:72: warning: ‘ml’ may be used uninitialized [-Wmaybe-uninitialized] 2536 | IF (JT .GE. 4) LENWM = (2*ML + MU + 1)*N + 2 | ^ dlsoda.f:2407:32: note: ‘ml’ was declared here 2407 | 1 LENIW, LENRW, LENWM, ML, MORD, MU, MXHNL0, MXSTP0 | ^ dlsoda.f:2536:72: warning: ‘mu’ may be used uninitialized [-Wmaybe-uninitialized] 2536 | IF (JT .GE. 4) LENWM = (2*ML + MU + 1)*N + 2 | ^ dlsoda.f:2407:42: note: ‘mu’ was declared here 2407 | 1 LENIW, LENRW, LENWM, ML, MORD, MU, MXHNL0, MXSTP0 | ^ dlsoda.f:2615:29: warning: ‘h0’ may be used uninitialized [-Wmaybe-uninitialized] 2615 | IF (H0 .NE. 0.0D0 .AND. (T + H0 - TCRIT)*H0 .GT. 0.0D0) | ^ dlsoda.f:2412:48: note: ‘h0’ was declared here 2412 | DOUBLE PRECISION ATOLI, AYI, BIG, EWTI, H0, HMAX, HMX, RH, RTOLI, | ^ dlsoda.f:2851:72: warning: ‘tcrit’ may be used uninitialized [-Wmaybe-uninitialized] 2851 | IHIT = ABS(TN - TCRIT) .LE. 100.0D0*UROUND*HMX | ^ dlsoda.f:2413:14: note: ‘tcrit’ was declared here 2413 | 1 TCRIT, TDIST, TNEXT, TOL, TOLSF, TP, SIZE, SUM, W0 | ^ dlsoda.f:2874:10: warning: ‘ihit’ may be used uninitialized [-Wmaybe-uninitialized] 2874 | IF (IHIT) T = TCRIT | ^ dlsoda.f:2415:18: note: ‘ihit’ was declared here 2415 | LOGICAL IHIT | ^ gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c dop853.c -o dop853.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c dscal.c -o dscal.o gfortran -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules -c dsphiv.f -o dsphiv.o dsphiv.f: In function ‘dsphiv_’: dsphiv.f:270:72: warning: ‘hj1j’ may be used uninitialized [-Wmaybe-uninitialized] 270 | wsp(iphih+mbrkdwn+1) = hj1j*wsp(iphih+2*mx+mbrkdwn-1) | ^ dsphiv.f:125:35: note: ‘hj1j’ was declared here 125 | . avnorm, hj1j, hjj, SQR1 | ^ g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c et.cpp -o et.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c etTran.cpp -o etTran.o etTran.cpp: In function ‘Rcpp::List etTrans(Rcpp::List, const Rcpp::RObject&, bool, bool, bool, bool, Rcpp::Nullable >, Rcpp::CharacterVector, bool, bool, bool, Rcpp::Nullable >)’: etTran.cpp:784:32: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 784 | if (hasCmt || covColi >= 0 && as(lName[covColi]) != "cmt"){ | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ etTran.cpp:2521:34: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2521 | id.size() > (idxOut = idxOutput[iCur]) && | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ etTran.cpp:2524:40: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2524 | idxInput.size() > idxOut && | ~~~~~~~~~~~~~~~~^~~~~~~~ etTran.cpp:2532:41: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2532 | idxOutput.size() < iCur+1 && | ~~~~~~~~~~~~~~~~~^~~~~~~~ etTran.cpp:2533:34: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2533 | id.size() > (idxOut = idxOutput[iCur+1]) && | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ etTran.cpp:2536:40: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2536 | idxInput.size() > idxOut && | ~~~~~~~~~~~~~~~~^~~~~~~~ g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c expandGrid.cpp -o expandGrid.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c expm.cpp -o expm.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c fast_factor.cpp -o fast_factor.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c fnorm.c -o fnorm.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c forder.cpp -o forder.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c genModelVars.c -o genModelVars.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c getOption.c -o getOption.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c handle_evid.c -o handle_evid.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c idamax.c -o idamax.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c init.c -o init.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c intdy.c -o intdy.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c isEt.c -o isEt.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c itostr.c -o itostr.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c lincmt.c -o lincmt.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c lincmtB.cpp -o lincmtB.o In file included from /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/functor.hpp:13, from /usr/local/lib/R/library/StanHeaders/include/stan/math/rev/fun.hpp:201, from /usr/local/lib/R/library/StanHeaders/include/stan/math/rev.hpp:10, from /usr/local/lib/R/library/StanHeaders/include/stan/math.hpp:19, from lincmtB.cpp:64: /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combination(std::vector&, const int&, const int&, const int&)’: /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:73:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 73 | for (std::size_t i = 0; i < p - 1; i++) { | ~~^~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:79:16: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 79 | } while (k < x); | ~~^~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combos(const int&, const double&, const int&, std::vector > >&)’: /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:102:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 102 | for (std::size_t i = 1; i != choose_dimk + 1; i++) { | ~~^~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:105:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 105 | for (std::size_t j = 0; j != k; j++) { | ~~^~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::increment(std::vector&, const int&, const double&, const std::vector&, std::vector >&)’: /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:126:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 126 | for (std::size_t j = 0; j != k; j++) { | ~~^~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:132:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 132 | while ((first_zero < index.size()) && index[first_zero]) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 135 | if (first_zero == index.size()) { | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:143:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 143 | for (std::size_t i = 0; i != first_zero + 1; i++) { | ~~^~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::signcombos(const int&, const double&, const int&, std::vector > >&)’: /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:168:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 168 | for (std::size_t i = 1; i != choose_dimk + 1; i++) { | ~~^~~~~~~~~~~~~~~~~~ In file included from /usr/local/lib/R/library/BH/include/boost/random.hpp:43, from /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/prob/hmm_hidden_state_prob.hpp:8, from /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/prob.hpp:137, from /usr/local/lib/R/library/StanHeaders/include/stan/math/prim.hpp:16, from /usr/local/lib/R/library/StanHeaders/include/stan/math/rev.hpp:14: /usr/local/lib/R/library/BH/include/boost/random/mersenne_twister.hpp: In function ‘std::basic_istream<_CharT2, _Traits2>& boost::random::operator>>(std::basic_istream<_CharT2, _Traits2>&, mersenne_twister_engine&)’: /usr/local/lib/R/library/BH/include/boost/random/mersenne_twister.hpp:234: note: ‘-Wmisleading-indentation’ is disabled from this point onwards, since column-tracking was disabled due to the size of the code/headers 234 | for(std::size_t j = 0; j < mt.state_size; ++j) /usr/local/lib/R/library/BH/include/boost/random/mersenne_twister.hpp:234: note: adding ‘-flarge-source-files’ will allow for more column-tracking support, at the expense of compilation time and memory In file included from lincmtB.cpp:108: ../inst/include/rxode2parseGetTime.h: In function ‘int handleInfusionStartRm(int*, int*, double*, int*, rx_solve*, rx_solving_options*, rx_solving_options_ind*)’: ../inst/include/rxode2parseGetTime.h:223: warning: unused variable ‘curEvid’ [-Wunused-variable] 223 | int curEvid = getEvid(ind, ind->idose[*endIdx+1]); In file included from /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err.hpp:4, from /usr/local/lib/R/library/StanHeaders/include/stan/math/rev/core/profiling.hpp:9, from /usr/local/lib/R/library/StanHeaders/include/stan/math/rev/core.hpp:53, from /usr/local/lib/R/library/StanHeaders/include/stan/math/rev.hpp:8: /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = check_finite >(const char*, const char*, const Eigen::Matrix&)::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((bool)((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime))>* = 0]’: /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ 29 | elementwise_check([](double x) { return std::isfinite(x); }, function, name, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 30 | y, "finite"); | ~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:35:15: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ 35 | check_finite("hypergeometric_pFq", "a", a_ref); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:125:28: required from ‘auto stan::math::hypergeometric_3F2(const Ta&, const Tb&, const Tz&) [with Ta = std::vector >; Tb = std::vector >; Tz = double; stan::require_all_vector_t* = 0; stan::require_stan_scalar_t* = 0]’ 125 | return hypergeometric_pFq(to_vector(a), to_vector(b), z); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:148:28: required from ‘auto stan::math::hypergeometric_3F2(const std::initializer_list<_Tp>&, const std::initializer_list<_Value>&, const Tz&) [with Ta = double; Tb = double; Tz = double; stan::require_all_stan_scalar_t* = 0]’ 148 | return hypergeometric_3F2(std::vector(a), std::vector(b), z); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/rev/fun/inv_inc_beta.hpp:77:37: required from here 77 | + log(hypergeometric_3F2({a_val, a_val, one_m_b}, {ap1, ap1}, w)) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = check_not_nan >(const char*, const char*, const Eigen::Matrix&)::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((bool)((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime))>* = 0]’: /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ 28 | elementwise_check([](double x) { return !std::isnan(x); }, function, name, y, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 29 | "not nan"); | ~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:39:16: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ 39 | check_not_nan("hypergeometric_pFq", "a", a_ref); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:125:28: required from ‘auto stan::math::hypergeometric_3F2(const Ta&, const Tb&, const Tz&) [with Ta = std::vector >; Tb = std::vector >; Tz = double; stan::require_all_vector_t* = 0; stan::require_stan_scalar_t* = 0]’ 125 | return hypergeometric_pFq(to_vector(a), to_vector(b), z); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:148:28: required from ‘auto stan::math::hypergeometric_3F2(const std::initializer_list<_Tp>&, const std::initializer_list<_Value>&, const Tz&) [with Ta = double; Tb = double; Tz = double; stan::require_all_stan_scalar_t* = 0]’ 148 | return hypergeometric_3F2(std::vector(a), std::vector(b), z); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/rev/fun/inv_inc_beta.hpp:77:37: required from here 77 | + log(hypergeometric_3F2({a_val, a_val, one_m_b}, {ap1, ap1}, w)) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = check_finite >(const char*, const char*, const Eigen::Matrix&)::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((bool)((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime))>* = 0]’: /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ 29 | elementwise_check([](double x) { return std::isfinite(x); }, function, name, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 30 | y, "finite"); | ~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:35:15: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ 35 | check_finite("hypergeometric_pFq", "a", a_ref); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ 189 | return hypergeometric_pFq(a_args, b_args, z); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ 190 | auto hyper1 = hypergeometric_2F1(a1_euler, a2_euler, b1, z_euler); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ 306 | return internal::grad_2F1_impl(a1, a2, b1, z, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 307 | precision, max_steps); | ~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:25: required from here 37 | = grad_2F1(a + b, 1.0, a + 1, z); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = check_finite >(const char*, const char*, const Eigen::Matrix&)::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((bool)((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime))>* = 0]’: /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ 29 | elementwise_check([](double x) { return std::isfinite(x); }, function, name, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 30 | y, "finite"); | ~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:36:15: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ 36 | check_finite("hypergeometric_pFq", "b", b_ref); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ 189 | return hypergeometric_pFq(a_args, b_args, z); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ 190 | auto hyper1 = hypergeometric_2F1(a1_euler, a2_euler, b1, z_euler); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ 306 | return internal::grad_2F1_impl(a1, a2, b1, z, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 307 | precision, max_steps); | ~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:25: required from here 37 | = grad_2F1(a + b, 1.0, a + 1, z); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = check_not_nan >(const char*, const char*, const Eigen::Matrix&)::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((bool)((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime))>* = 0]’: /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ 28 | elementwise_check([](double x) { return !std::isnan(x); }, function, name, y, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 29 | "not nan"); | ~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:39:16: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ 39 | check_not_nan("hypergeometric_pFq", "a", a_ref); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ 189 | return hypergeometric_pFq(a_args, b_args, z); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ 190 | auto hyper1 = hypergeometric_2F1(a1_euler, a2_euler, b1, z_euler); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ 306 | return internal::grad_2F1_impl(a1, a2, b1, z, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 307 | precision, max_steps); | ~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:25: required from here 37 | = grad_2F1(a + b, 1.0, a + 1, z); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = check_not_nan >(const char*, const char*, const Eigen::Matrix&)::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((bool)((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime))>* = 0]’: /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ 28 | elementwise_check([](double x) { return !std::isnan(x); }, function, name, y, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 29 | "not nan"); | ~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:40:16: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ 40 | check_not_nan("hypergeometric_pFq", "b", b_ref); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ 189 | return hypergeometric_pFq(a_args, b_args, z); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ 190 | auto hyper1 = hypergeometric_2F1(a1_euler, a2_euler, b1, z_euler); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ 306 | return internal::grad_2F1_impl(a1, a2, b1, z, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 307 | precision, max_steps); | ~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:25: required from here 37 | = grad_2F1(a + b, 1.0, a + 1, z); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ In function ‘handleInfusionItem(int, rx_solve*, rx_solving_options*, rx_solving_options_ind*)’, inlined from ‘getTime__(int, rx_solving_options_ind*, int) [clone .constprop.0]’ at ../inst/include/rxode2parseGetTime.h:381:0: ../inst/include/rxode2parseGetTime.h:314: warning: ‘infBidx’ may be used uninitialized [-Wmaybe-uninitialized] 314 | if (infBidx == -1) return 0.0; ../inst/include/rxode2parseGetTime.h: In function ‘getTime__(int, rx_solving_options_ind*, int) [clone .constprop.0]’: ../inst/include/rxode2parseGetTime.h:312: note: ‘infBidx’ was declared here 312 | int infBidx; gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c lsoda.c -o lsoda.o gfortran -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules -c matexp.f -o matexp.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c matexp_HM98.c -o matexp_HM98.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c methodswitch.c -o methodswitch.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c nearPD.cpp -o nearPD.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c omegaChol.c -o omegaChol.o gfortran -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules -c opkda2.f -o opkda2.o opkda2.f: In function ‘ixsav_’: opkda2.f:650:28: warning: ‘__result_ixsav’ may be used uninitialized [-Wmaybe-uninitialized] 650 | INTEGER FUNCTION IXSAV (IPAR, IVALUE, ISET) | ^ gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c orderswitch.c -o orderswitch.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c par_solve.cpp -o par_solve.o In file included from par_solve.cpp:15: ../inst/include/rxode2parseGetTime.h: In function ‘int handleInfusionStartRm(int*, int*, double*, int*, rx_solve*, rx_solving_options*, rx_solving_options_ind*)’: ../inst/include/rxode2parseGetTime.h:223:9: warning: unused variable ‘curEvid’ [-Wunused-variable] 223 | int curEvid = getEvid(ind, ind->idose[*endIdx+1]); | ^~~~~~~ par_solve.cpp: In function ‘void handleSS(int*, int*, double*, double*, double*, double, double, int, int*, int, int*, rx_solving_options*, rx_solving_options_ind*, t_update_inis, void*)’: par_solve.cpp:1317:39: warning: variable ‘oldI’ set but not used [-Wunused-but-set-variable] 1317 | ei=0, wh, cmt, wh100, whI, wh0, oldI, | ^~~~ ../inst/include/rxode2parseGetTime.h: In function ‘handleInfusionItem(int, rx_solve*, rx_solving_options*, rx_solving_options_ind*) [clone .constprop.0]’: ../inst/include/rxode2parseGetTime.h:314:5: warning: ‘infBidx’ may be used uninitialized [-Wmaybe-uninitialized] 314 | if (infBidx == -1) return 0.0; | ^~ ../inst/include/rxode2parseGetTime.h:312:9: note: ‘infBidx’ was declared here 312 | int infBidx; | ^~~~~~~ par_solve.cpp: In function ‘solveWith1Pt(int*, int*, double*, double*, double*, double, double, int, int*, int, int*, rx_solving_options*, rx_solving_options_ind*, void (*)(int, double*), void*) [clone .isra.0]’: par_solve.cpp:708:5: warning: ‘idid’ may be used uninitialized [-Wmaybe-uninitialized] 708 | if (idid <= 0) { | ^~ par_solve.cpp:701:7: note: ‘idid’ was declared here 701 | int idid, itol=0; | ^~~~ gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c parseLinCmt.c -o parseLinCmt.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c print_node.c -o print_node.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c prja.c -o prja.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c qs.cpp -o qs.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c rprintf.c -o rprintf.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c rx2api.c -o rx2api.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c rxData.cpp -o rxData.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c rxInv.cpp -o rxInv.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c rxOptRep.cpp -o rxOptRep.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c rxStack.cpp -o rxStack.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c rxode2_df.cpp -o rxode2_df.o In file included from rxode2_df.cpp:36: ../inst/include/rxode2parseGetTime.h: In function ‘int handleInfusionStartRm(int*, int*, double*, int*, rx_solve*, rx_solving_options*, rx_solving_options_ind*)’: ../inst/include/rxode2parseGetTime.h:223:9: warning: unused variable ‘curEvid’ [-Wunused-variable] 223 | int curEvid = getEvid(ind, ind->idose[*endIdx+1]); | ^~~~~~~ In function ‘handleInfusionItem(int, rx_solve*, rx_solving_options*, rx_solving_options_ind*)’, inlined from ‘getTime__(int, rx_solving_options_ind*, int) [clone .constprop.0]’ at ../inst/include/rxode2parseGetTime.h:381:34: ../inst/include/rxode2parseGetTime.h:314:5: warning: ‘infBidx’ may be used uninitialized [-Wmaybe-uninitialized] 314 | if (infBidx == -1) return 0.0; | ^~ ../inst/include/rxode2parseGetTime.h: In function ‘getTime__(int, rx_solving_options_ind*, int) [clone .constprop.0]’: ../inst/include/rxode2parseGetTime.h:312:9: note: ‘infBidx’ was declared here 312 | int infBidx; | ^~~~~~~ g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c rxthreefry.cpp -o rxthreefry.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c sbuf.c -o sbuf.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c scaleh.c -o scaleh.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c seed.cpp -o seed.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c solsy.c -o solsy.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c stoda.c -o stoda.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c strdup_printf.c -o strdup_printf.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c strncmp.c -o strncmp.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c strncmpi.c -o strncmpi.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c tran.c -o tran.o In file included from parseFuns.h:151, from tran.c:151: parseFunsDosing.h: In function ‘handleFunctionTad’: parseFunsDosing.h:86:61: warning: value computed is not used [-Wunused-value] 86 | handleFunctionTadEmptyCcode(tf, v2) || | ^~ In file included from tran.c:155: parseAssignStr.h: In function ‘handleStrAssign’: parseAssignStr.h:129:13: warning: unused variable ‘buf’ [-Wunused-variable] 129 | char *buf = tb.str.line[tb.id]; | ^~~ In file included from tran.c:156: parseLevels.h: In function ‘handleLevelsStr1’: parseLevels.h:94:11: warning: unused variable ‘n’ [-Wunused-variable] 94 | int n = get_str_assign_int(tb.id, v); | ^ g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c udf.cpp -o udf.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c utilc.c -o utilc.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -fopenmp -D_isrxode2_ -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/library/BH/include" -isystem"/usr/local/lib/R/library/RcppEigen/include" -isystem'/usr/local/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include/oneapi -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/library/StanHeaders/include/src' -isystem"/usr/local/lib/R/library/Rcpp/include" -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c utilcpp.cpp -o utilcpp.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/sitmo/include' -I'/usr/local/lib/R/library/lotri/include' -I'/usr/local/lib/R/library/PreciseSums/include' -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/BH/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I'/usr/local/lib/R/library/StanHeaders/include' -I'/usr/local/lib/R/library/dparser/include' -I/usr/local/include -D_isrxode2_ -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c vmnorm.c -o vmnorm.o g++ -std=gnu++17 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -o rxode2.so RcppExports.o approx.o boost.o box.o call_dvode.o cbindThetaOmega.o cfode.o cfode_static.o checkmate.o checkmate_stub.o codegen.o common.o corfailure.o correction.o cvPost.o daxpy.o ddot.o dgefa.o dgesl.o dgpadm.o dlsoda.o dop853.o dscal.o dsphiv.o et.o etTran.o expandGrid.o expm.o fast_factor.o fnorm.o forder.o genModelVars.o getOption.o handle_evid.o idamax.o init.o intdy.o isEt.o itostr.o lincmt.o lincmtB.o lsoda.o matexp.o matexp_HM98.o methodswitch.o nearPD.o omegaChol.o opkda2.o orderswitch.o par_solve.o parseLinCmt.o print_node.o prja.o qs.o rprintf.o rx2api.o rxData.o rxInv.o rxOptRep.o rxStack.o rxode2_df.o rxthreefry.o sbuf.o scaleh.o seed.o solsy.o stoda.o strdup_printf.o strncmp.o strncmpi.o tran.o udf.o utilc.o utilcpp.o vmnorm.o -lflexiblas -lgfortran -lm -lquadmath -fopenmp -L/usr/local/lib/R/library/RcppParallel/lib/ -Wl,-rpath,/usr/local/lib/R/library/RcppParallel/lib/ -ltbb -ltbbmalloc -L/usr/lib64 -Wl,-rpath,/usr/lib64 -ltbb -ltbbmalloc -lgfortran -lm -lquadmath -L/usr/lib64/R/lib -lR installing via 'install.libs.R' to /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build/BUILDROOT/usr/local/lib/R/library/00LOCK-rxode2/00new/rxode2 ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package ‘rxode2’ finding HTML links ... done add.dosing html add.sampling html as.et html as.ini html as.model html as.rxUi html assertCompartmentExists html assertCompartmentName html assertCompartmentNew html assertRxUi html assertVariableExists html assertVariableNew html binomProbs html boxCox html coef.rxode2 html cvPost html dfWishart html dot-assertRenameErrorModelLine html dot-cbindOme html dot-clearPipe html dot-collectWarnings html dot-convertId html dot-copyUi html dot-expandPars html dot-extraC html dot-extraCnow html dot-getLastIdLvl html dot-getWh html dot-handleSingleErrTypeNormOrTFoceiBase html dot-iniGetAppendArg html dot-iniHandleAppend html dot-iniHandleLine html dot-linCmtSensB html dot-matchesLangTemplate html dot-minfo html dot-modelHandleModelLines html dot-pipeRx html dot-quoteCallInfoLines html dot-rxBlankIni html dot-rxC html dot-rxDocTable html dot-rxGetHiBoundaryPred1AndIni html dot-rxGetLambdaFromPred1AndIni html dot-rxGetLowBoundaryPred1AndIni html dot-rxGetPredictionDVTransform html dot-rxGetPredictionF html dot-rxGetPredictionFTransform html dot-rxGetVarianceForErrorType html dot-rxIsLinCmt html dot-rxJacobian html dot-rxLinCmtGen html dot-rxPrune html dot-rxSEeqUsr html dot-rxSens html dot-rxTransInfo html dot-rxTransform html dot-rxWithOptions html dot-rxWithSink html dot-rxWithWd html dot-rxode2ptrs html dot-s3register html dot-symengineFs html dot-toClassicEvid html dot-udfCallFunArg html dot-udfEnvReset html dot-udfEnvSet html dot-udfEnvSetUdf html dot-udfExists html dot-udfMd5Info html dot-useUtf html dot-vecDf html erf html et html etExpand html etRbind html etRep html etSeq html etTrans html eventTable html findLhs html forderForceBase html gammap html gammapDer html gammapInv html gammaq html gammaqInv html genShinyApp.template html getBaseIniSimModel html getBaseSimModel html getBaseSymengineModel html getRxThreads html guide_none html ini-set html ini html invWR1d html is.rxEt html is.rxSolve html is.rxStackData html linMod html llikBeta html llikBinom html llikCauchy html llikChisq html llikExp html llikF html llikGamma html llikGeom html llikNbinom html llikNbinomMu html llikNorm html llikPois html llikT html llikUnif html llikWeibull html logit html lowergamma html meanProbs html model-set html model html modelExtract html odeMethodToInt html phi html plot.rxSolve html plus-.rxSolve html print.rxCoef html print.rxDll html print.rxModelVars html print.rxode2 html probit html rLKJ1 html reexports html rinvchisq html rxAllowUnload html rxAppendModel html rxAssignControlValue html rxAssignPtr html rxBlockZeros html rxC html rxCat html rxCbindStudyIndividual html rxChain html rxChain2 html rxClean html rxCombineErrorLines html rxCompile html rxCondition html rxControlUpdateSens html rxCreateCache html rxD html rxDelete html rxDemoteAddErr html rxDerived html rxDfdy html rxDll html rxDynLoad html rxDynUnload html rxErrTypeCombine html rxEtDispatchSolve html rxEvid html rxExpandFEta_ html rxExpandGrid html rxExpandGrid_ html rxExpandIfElse html rxExpandSens2_ html rxExpandSens_ html rxFixPop html rxForget html rxFun html rxFunParse html rxGetControl html rxGetDistributionSimulationLines html rxGetLin html rxGetModel html rxGetSeed html rxGetrxode2 html rxHtml html rxIndLinState html rxIndLinStrategy html rxInits html rxIntToBase html rxIntToLetter html rxInv html rxIs html rxIsCurrent html rxIsLoaded html rxLhs html rxLock html rxMd5 html rxModelVars html rxModels_ html rxNorm html rxOptExpr html rxParams html rxParseErr html rxParsePk html rxParsePred html rxParseSetSilentErr html rxParseSuppressMsg html rxPkg html rxPp html rxPreferredDistributionName html rxProgress html rxPrune html rxRateDur html rxReload html rxRemoveControl html rxRename html rxRepR0_ html rxReq html rxReservedKeywords html rxResidualError html rxRmvn html rxS html rxSeedEng html rxSetControl html rxSetCovariateNamesForPiping html rxSetIni0 html rxSetPipingAuto html rxSetProd html rxSetProgressBar html rxSetSeed html rxSetSilentErr html rxSetSum html rxSetupIni html rxSetupScale html rxShiny html rxSimThetaOmega html rxSolve html rxSolveFree html rxSolveSetup html rxSplitPlusQ html rxStack html rxState html rxSumProdModel html rxSupportedFuns html rxSuppressMsg html rxSymInvChol html rxSymInvCholCreate html rxSymInvCholN html rxSyncOptions html rxSyntaxFunctions html rxTempDir html rxTheme html rxToSE html rxTrans html rxUdfUi html rxUdfUiData html rxUdfUiEst html rxUdfUiIniDf html rxUdfUiIniLhs html rxUdfUiMv html rxUdfUiNum html rxUdfUiParsing html rxUdfUiReset html rxUiDecompress html rxUiDeparse html rxUiGet html rxUnloadAll html rxUse html rxValidate html rxVersion html rxWithSeed html rxbeta html rxbinom html rxcauchy html rxchisq html rxexp html rxf html rxgamma html rxgeom html rxnbinom html rxnormV html rxode2-set html rxode2 html rxode2parse html rxode2parseAssignPackagesToLoad html rxode2parseAssignPointerTranslation html rxode2parseAssignTranslation html rxode2parseD html rxode2parseGetPointerAssignment html rxode2parseGetTranslation html rxord html rxpois html rxt html rxunif html rxweibull html stat_amt html stat_cens html summary.rxDll html summary.rxode2 html swapMatListWithCube html testIniDf html testRxLinCmt html testRxUnbounded html toTrialDuration html update.rxUi html uppergamma html zeroRe html *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rxode2) + test -d rxode2/src + cd rxode2/src + rm -f RcppExports.o approx.o boost.o box.o call_dvode.o cbindThetaOmega.o cfode.o cfode_static.o checkmate.o checkmate_stub.o codegen.o common.o corfailure.o correction.o cvPost.o daxpy.o ddot.o dgefa.o dgesl.o dgpadm.o dlsoda.o dop853.o dscal.o dsphiv.o et.o etTran.o expandGrid.o expm.o fast_factor.o fnorm.o forder.o genModelVars.o getOption.o handle_evid.o idamax.o init.o intdy.o isEt.o itostr.o lincmt.o lincmtB.o lsoda.o matexp.o matexp_HM98.o methodswitch.o nearPD.o omegaChol.o opkda2.o orderswitch.o par_solve.o parseLinCmt.o print_node.o prja.o qs.o rprintf.o rx2api.o rxData.o rxInv.o rxOptRep.o rxStack.o rxode2_df.o rxthreefry.o sbuf.o scaleh.o seed.o solsy.o stoda.o strdup_printf.o strncmp.o strncmpi.o tran.o udf.o utilc.o utilcpp.o vmnorm.o rxode2.so + rm -f /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build/BUILDROOT/usr/local/lib/R/library/R.css + find /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build/BUILDROOT/usr/local/lib/R/library -type f -exec sed -i s@/builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build/BUILDROOT@@g '{}' ';' + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 3.0.2-1.fc42.copr8192634 --unique-debug-suffix -3.0.2-1.fc42.copr8192634.x86_64 --unique-debug-src-base R-CRAN-rxode2-3.0.2-1.fc42.copr8192634.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build/rxode2 find-debuginfo: starting Extracting debug info from 1 files DWARF-compressing 1 files sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/R-CRAN-rxode2-3.0.2-1.fc42.copr8192634.x86_64 cpio: rxode2/src/src/tran.g.d_parser.c: Cannot stat: No such file or directory find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-determinism --brp -j2 /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build/BUILDROOT Scanned 42 directories and 1171 files, processed 919 inodes, 0 modified (0 replaced + 0 rewritten), 0 unsupported format, 0 errors Reading /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build/SPECPARTS/rpm-debuginfo.specpart Processing files: R-CRAN-rxode2-3.0.2-1.fc42.copr8192634.x86_64 Provides: R-CRAN-rxode2 = 3.0.2-1.fc42.copr8192634 R-CRAN-rxode2(x86-64) = 3.0.2-1.fc42.copr8192634 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.11)(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libflexiblas.so.3()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libgomp.so.1(OMP_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.5)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.18)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libtbb.so.12()(64bit) rtld(GNU_HASH) Processing files: R-CRAN-rxode2-debugsource-3.0.2-1.fc42.copr8192634.x86_64 Provides: R-CRAN-rxode2-debugsource = 3.0.2-1.fc42.copr8192634 R-CRAN-rxode2-debugsource(x86-64) = 3.0.2-1.fc42.copr8192634 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-CRAN-rxode2-debuginfo-3.0.2-1.fc42.copr8192634.x86_64 Provides: R-CRAN-rxode2-debuginfo = 3.0.2-1.fc42.copr8192634 R-CRAN-rxode2-debuginfo(x86-64) = 3.0.2-1.fc42.copr8192634 debuginfo(build-id) = ef51c6d7405432d0bc85616998b9bddf9e4a6822 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-CRAN-rxode2-debugsource(x86-64) = 3.0.2-1.fc42.copr8192634 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build/BUILDROOT Wrote: /builddir/build/RPMS/R-CRAN-rxode2-3.0.2-1.fc42.copr8192634.x86_64.rpm Wrote: /builddir/build/RPMS/R-CRAN-rxode2-debugsource-3.0.2-1.fc42.copr8192634.x86_64.rpm Wrote: /builddir/build/RPMS/R-CRAN-rxode2-debuginfo-3.0.2-1.fc42.copr8192634.x86_64.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.wkdwoL + umask 022 + cd /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build + test -d /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build + rm -rf /builddir/build/BUILD/R-CRAN-rxode2-3.0.2-build + RPM_EC=0 ++ jobs -p + exit 0 RPM build warnings: %source_date_epoch_from_changelog is set, but %changelog has no entries to take a date from Finish: rpmbuild R-CRAN-rxode2-3.0.2-1.fc42.copr8192634.src.rpm Finish: build phase for R-CRAN-rxode2-3.0.2-1.fc42.copr8192634.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1730339452.741906/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names INFO: Done(/var/lib/copr-rpmbuild/results/R-CRAN-rxode2-3.0.2-1.fc42.copr8192634.src.rpm) Config(child) 6 minutes 8 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 Running RPMResults tool Package info: { "packages": [ { "name": "R-CRAN-rxode2", "epoch": null, "version": "3.0.2", "release": "1.fc42.copr8192634", "arch": "src" }, { "name": "R-CRAN-rxode2", "epoch": null, "version": "3.0.2", "release": "1.fc42.copr8192634", "arch": "x86_64" }, { "name": "R-CRAN-rxode2-debugsource", "epoch": null, "version": "3.0.2", "release": "1.fc42.copr8192634", "arch": "x86_64" }, { "name": "R-CRAN-rxode2-debuginfo", "epoch": null, "version": "3.0.2", "release": "1.fc42.copr8192634", "arch": "x86_64" } ] } RPMResults finished