Warning: Permanently added '172.25.83.131' (ECDSA) to the list of known hosts.
Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 974971 --chroot fedora-rawhide-i386 --detached default
Version: 0.29
Task:
{'build_id': 974971,
'buildroot_pkgs': [],
'chroot': 'fedora-rawhide-i386',
'enable_net': False,
'fetch_sources_only': True,
'git_hash': '931913fe7c6973ecd0270698f58a9aea40bd79e3',
'git_repo': 'hhorak/mysql-connector-python-test/python-biopython',
'memory_reqs': 2048,
'package_name': 'python-biopython',
'package_version': '1.73-5.fc31',
'project_dirname': 'mysql-connector-python-test',
'project_name': 'mysql-connector-python-test',
'project_owner': 'hhorak',
'repos': [{'baseurl': 'https://copr-be.cloud.fedoraproject.org/results/hhorak/mysql-connector-python-test/fedora-rawhide-i386/',
'id': 'copr_base',
'name': 'Copr repository'}],
'source_json': {'clone_url': 'https://copr-dist-git.fedorainfracloud.org/git/hhorak/mysql-connector-python-test/python-biopython.git',
'committish': '931913fe7c6973ecd0270698f58a9aea40bd79e3'},
'source_type': 8,
'submitter': 'hhorak',
'task_id': '974971-fedora-rawhide-i386',
'timeout': 75600,
'use_bootstrap_container': False,
'with_opts': [],
'without_opts': []}
Running: git clone https://copr-dist-git.fedorainfracloud.org/git/hhorak/mysql-connector-python-test/python-biopython.git /tmp/tmpldafv_jl/python-biopython --depth 500 --no-single-branch
cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/hhorak/mysql-connector-python-test/python-biopython.git', '/tmp/tmpldafv_jl/python-biopython', '--depth', '500', '--no-single-branch']
cwd: .
rc: 0
stdout:
stderr: Cloning into '/tmp/tmpldafv_jl/python-biopython'...
Running: git checkout 931913fe7c6973ecd0270698f58a9aea40bd79e3
cmd: ['git', 'checkout', '931913fe7c6973ecd0270698f58a9aea40bd79e3']
cwd: /tmp/tmpldafv_jl/python-biopython
rc: 0
stdout:
stderr: Note: checking out '931913fe7c6973ecd0270698f58a9aea40bd79e3'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:
git checkout -b <new-branch-name>
HEAD is now at 931913f automatic import of python-biopython
Running: cp -r . /tmp/tmpq_qr6tvy
cmd: ['cp', '-r', '.', '/tmp/tmpq_qr6tvy']
cwd: /tmp/tmpldafv_jl/python-biopython
rc: 0
stdout:
stderr:
Generated rpkg config:
[rpkg]
preprocess_spec = True
# auto-packing is deprecated:
auto_pack = True
[git]
lookaside = https://copr-dist-git.fedorainfracloud.org/repo/pkgs/%(ns2)s/%(ns1)s/%(name)s/%(filename)s/%(hashtype)s/%(hash)s/%(filename)s
anongiturl = https://copr-dist-git.fedorainfracloud.org/git/%(module)s
Writing config into /tmp/tmpldafv_jl/.config/rpkg.conf
Running: rpkg -C /tmp/tmpldafv_jl/.config/rpkg.conf sources --outdir /tmp/tmpq_qr6tvy
cmd: ['rpkg', '-C', '/tmp/tmpldafv_jl/.config/rpkg.conf', 'sources', '--outdir', '/tmp/tmpq_qr6tvy']
cwd: /tmp/tmpldafv_jl/python-biopython
rc: 0
stdout: Downloading biopython-1.73.tar.gz from lookaside cache at copr-dist-git.fedorainfracloud.org
stderr:
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
Running (timeout=75600): unbuffer mock --buildsrpm --spec /tmp/tmpq_qr6tvy/python-biopython.spec --sources /tmp/tmpq_qr6tvy --configdir /var/lib/copr-rpmbuild/results/configs --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1563453563.556255 -r child
WARNING: Could not find required logging config file: /var/lib/copr-rpmbuild/results/configs/logging.ini. Using default...
INFO: mock.py version 1.4.16 starting (python version = 3.7.3)...
Start: init plugins
INFO: tmpfs initialized
INFO: selinux disabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
Start: run
INFO: Start(/tmp/tmpq_qr6tvy/python-biopython.spec) Config(974971-fedora-rawhide-i386)
Start: clean chroot
Finish: clean chroot
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/974971-fedora-rawhide-i386-1563453563.556255/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled dnf cache
Start: cleaning dnf metadata
Finish: cleaning dnf metadata
INFO: enabled HW Info plugin
Mock Version: 1.4.16
INFO: Mock Version: 1.4.16
Start: dnf install
Copr repository 21 kB/s | 3.8 kB 00:00
fedora 14 MB/s | 69 MB 00:04
Dependencies resolved.
================================================================================
Package Arch Version Repo Size
================================================================================
Installing group/module packages:
bash i686 5.0.7-1.fc31 fedora 1.7 M
bzip2 i686 1.0.6-29.fc30 fedora 50 k
coreutils i686 8.31-3.fc31 fedora 1.3 M
cpio i686 2.12-10.fc30 fedora 255 k
diffutils i686 3.7-2.fc30 fedora 395 k
fedora-release-common noarch 31-0.7 fedora 19 k
findutils i686 1:4.6.0-23.fc31 fedora 524 k
gawk i686 5.0.1-2.fc31 fedora 1.2 M
glibc-minimal-langpack i686 2.29.9000-31.fc31 fedora 66 k
grep i686 3.3-2.fc31 fedora 253 k
gzip i686 1.9-9.fc31 fedora 153 k
info i686 6.6-1.fc30 fedora 220 k
make i686 1:4.2.1-13.fc30 fedora 490 k
patch i686 2.7.6-9.fc31 fedora 138 k
redhat-rpm-config noarch 137-1.fc31 fedora 63 k
rpm-build i686 4.15.0-0.beta.1.fc31 fedora 118 k
sed i686 4.5-3.fc30 fedora 289 k
shadow-utils i686 2:4.6-14.fc31 fedora 1.2 M
tar i686 2:1.32-1.fc31 fedora 889 k
unzip i686 6.0-43.fc30 fedora 175 k
util-linux i686 2.34-1.fc31 fedora 2.7 M
which i686 2.21-14.fc30 fedora 41 k
xz i686 5.2.4-5.fc30 fedora 148 k
Installing dependencies:
alternatives i686 1.11-4.fc31 fedora 34 k
audit-libs i686 3.0-0.10.20190507gitf58ec40.fc31 fedora 120 k
basesystem noarch 11-7.fc30 fedora 6.9 k
binutils i686 2.32-17.fc31 fedora 5.4 M
binutils-gold i686 2.32-17.fc31 fedora 937 k
brotli i686 1.0.7-3.fc30 fedora 313 k
bzip2-libs i686 1.0.6-29.fc30 fedora 38 k
ca-certificates noarch 2019.2.32-2.fc31 fedora 394 k
coreutils-common i686 8.31-3.fc31 fedora 1.9 M
cracklib i686 2.9.6-19.fc30 fedora 77 k
crypto-policies noarch 20190527-1.git0b3add8.fc31 fedora 47 k
curl i686 7.65.1-1.fc31 fedora 304 k
cyrus-sasl-lib i686 2.1.27-1.fc31 fedora 104 k
dwz i686 0.12-10.fc30 fedora 105 k
efi-srpm-macros noarch 4-2.fc30 fedora 23 k
elfutils i686 0.176-4.fc31 fedora 336 k
elfutils-default-yama-scope
noarch 0.176-4.fc31 fedora 16 k
elfutils-libelf i686 0.176-4.fc31 fedora 197 k
elfutils-libs i686 0.176-4.fc31 fedora 329 k
expat i686 2.2.7-1.fc31 fedora 99 k
fedora-gpg-keys noarch 31-0.2 fedora 102 k
fedora-release noarch 31-0.7 fedora 11 k
fedora-repos noarch 31-0.2 fedora 9.2 k
fedora-repos-rawhide noarch 31-0.2 fedora 8.4 k
file i686 5.37-2.fc31 fedora 51 k
file-libs i686 5.37-2.fc31 fedora 572 k
filesystem i686 3.12-1.fc31 fedora 1.1 M
fpc-srpm-macros noarch 1.2-1.fc31 fedora 7.5 k
gc i686 7.6.4-5.fc30 fedora 97 k
gdb-minimal i686 8.3.50.20190702-19.fc31 fedora 3.6 M
ghc-srpm-macros noarch 1.4.2-9.fc30 fedora 7.6 k
glibc i686 2.29.9000-31.fc31 fedora 3.4 M
glibc-common i686 2.29.9000-31.fc31 fedora 688 k
gmp i686 1:6.1.2-10.fc31 fedora 259 k
gnat-srpm-macros noarch 4-9.fc30 fedora 8.5 k
go-srpm-macros noarch 3.0.8-3.fc31 fedora 25 k
guile22 i686 2.2.6-1.fc31 fedora 6.7 M
keyutils-libs i686 1.6-2.fc30 fedora 30 k
krb5-libs i686 1.17-35.fc31 fedora 814 k
libacl i686 2.2.53-3.fc30 fedora 25 k
libarchive i686 3.3.3-7.fc31 fedora 381 k
libatomic_ops i686 7.6.10-1.fc31 fedora 34 k
libattr i686 2.4.48-6.fc31 fedora 19 k
libblkid i686 2.34-1.fc31 fedora 171 k
libcap i686 2.26-5.fc30 fedora 47 k
libcap-ng i686 0.7.9-7.fc31 fedora 27 k
libcom_err i686 1.45.2-1.fc31 fedora 28 k
libcurl i686 7.65.1-1.fc31 fedora 293 k
libdb i686 5.3.28-37.fc30 fedora 809 k
libdb-utils i686 5.3.28-37.fc30 fedora 135 k
libfdisk i686 2.34-1.fc31 fedora 224 k
libffi i686 3.1-22.fc31 fedora 32 k
libgcc i686 9.1.1-2.fc31 fedora 99 k
libgcrypt i686 1.8.4-3.fc30 fedora 416 k
libgomp i686 9.1.1-2.fc31 fedora 231 k
libgpg-error i686 1.33-2.fc30 fedora 244 k
libidn2 i686 2.2.0-1.fc31 fedora 91 k
libmetalink i686 0.1.3-8.fc30 fedora 30 k
libmount i686 2.34-1.fc31 fedora 192 k
libnghttp2 i686 1.39.1-1.fc31 fedora 82 k
libnsl2 i686 1.2.0-4.20180605git4a062cf.fc30 fedora 57 k
libpkgconf i686 1.6.3-1.fc31 fedora 40 k
libpsl i686 0.21.0-1.fc31 fedora 59 k
libpwquality i686 1.4.0-12.fc30 fedora 97 k
libselinux i686 2.9-3.fc31 fedora 90 k
libsemanage i686 2.9-1.fc31 fedora 122 k
libsepol i686 2.9-1.fc31 fedora 308 k
libsigsegv i686 2.11-7.fc30 fedora 25 k
libsmartcols i686 2.34-1.fc31 fedora 131 k
libssh i686 0.9.0-5.fc31 fedora 268 k
libssh-config noarch 0.9.0-5.fc31 fedora 11 k
libstdc++ i686 9.1.1-2.fc31 fedora 636 k
libtasn1 i686 4.13-7.fc30 fedora 71 k
libtirpc i686 1.1.4-2.rc2.fc30.1 fedora 105 k
libtool-ltdl i686 2.4.6-30.fc31 fedora 37 k
libunistring i686 0.9.10-5.fc30 fedora 423 k
libutempter i686 1.1.6-16.fc30 fedora 24 k
libuuid i686 2.34-1.fc31 fedora 29 k
libverto i686 0.3.0-7.fc30 fedora 21 k
libxcrypt i686 4.4.6-2.fc31 fedora 129 k
libxml2 i686 2.9.9-2.fc30 fedora 696 k
libzstd i686 1.4.0-1.fc31 fedora 259 k
lua-libs i686 5.3.5-5.fc30 fedora 119 k
lz4-libs i686 1.8.3-2.fc30 fedora 61 k
mpfr i686 3.1.6-4.fc30 fedora 220 k
ncurses i686 6.1-10.20180923.fc30 fedora 363 k
ncurses-base noarch 6.1-10.20180923.fc30 fedora 59 k
ncurses-libs i686 6.1-10.20180923.fc30 fedora 308 k
nim-srpm-macros noarch 2-1.fc31 fedora 8.2 k
ocaml-srpm-macros noarch 5-5.fc30 fedora 7.7 k
openblas-srpm-macros noarch 2-5.fc30 fedora 7.3 k
openldap i686 2.4.47-2.fc31 fedora 314 k
openssl-libs i686 1:1.1.1c-4.fc31 fedora 1.4 M
p11-kit i686 0.23.16.1-1.fc31 fedora 266 k
p11-kit-trust i686 0.23.16.1-1.fc31 fedora 138 k
pam i686 1.3.1-17.fc30 fedora 643 k
pcre i686 8.43-2.fc31 fedora 189 k
pcre2 i686 10.33-7.fc31 fedora 258 k
perl-srpm-macros noarch 1-32.fc31 fedora 8.3 k
pkgconf i686 1.6.3-1.fc31 fedora 42 k
pkgconf-m4 noarch 1.6.3-1.fc31 fedora 15 k
pkgconf-pkg-config i686 1.6.3-1.fc31 fedora 10 k
popt i686 1.16-17.fc30 fedora 57 k
publicsuffix-list-dafsa noarch 20190417-1.fc31 fedora 54 k
python-srpm-macros noarch 3-46.fc31 fedora 16 k
qt5-srpm-macros noarch 5.12.4-1.fc31 fedora 9.0 k
readline i686 8.0-2.fc30 fedora 198 k
rpm i686 4.15.0-0.beta.1.fc31 fedora 500 k
rpm-build-libs i686 4.15.0-0.beta.1.fc31 fedora 105 k
rpm-libs i686 4.15.0-0.beta.1.fc31 fedora 318 k
rust-srpm-macros noarch 10-1.fc31 fedora 9.5 k
setup noarch 2.13.3-1.fc31 fedora 149 k
systemd-libs i686 242-5.git7a6d834.fc31 fedora 549 k
tzdata noarch 2019b-1.fc31 fedora 427 k
xz-libs i686 5.2.4-5.fc30 fedora 92 k
zip i686 3.0-24.fc30 fedora 271 k
zlib i686 1.2.11-15.fc30 fedora 91 k
zstd i686 1.4.0-1.fc31 fedora 390 k
Installing Groups:
Buildsystem building group
Transaction Summary
================================================================================
Install 141 Packages
Total download size: 55 M
Installed size: 231 M
Downloading Packages:
(1/141): basesystem-11-7.fc30.noarch.rpm 116 kB/s | 6.9 kB 00:00
(2/141): alternatives-1.11-4.fc31.i686.rpm 469 kB/s | 34 kB 00:00
(3/141): audit-libs-3.0-0.10.20190507gitf58ec40 1.5 MB/s | 120 kB 00:00
(4/141): binutils-gold-2.32-17.fc31.i686.rpm 24 MB/s | 937 kB 00:00
(5/141): bash-5.0.7-1.fc31.i686.rpm 25 MB/s | 1.7 MB 00:00
(6/141): bzip2-1.0.6-29.fc30.i686.rpm 8.9 MB/s | 50 kB 00:00
(7/141): brotli-1.0.7-3.fc30.i686.rpm 12 MB/s | 313 kB 00:00
(8/141): bzip2-libs-1.0.6-29.fc30.i686.rpm 6.1 MB/s | 38 kB 00:00
(9/141): ca-certificates-2019.2.32-2.fc31.noarc 21 MB/s | 394 kB 00:00
(10/141): coreutils-8.31-3.fc31.i686.rpm 26 MB/s | 1.3 MB 00:00
(11/141): cpio-2.12-10.fc30.i686.rpm 18 MB/s | 255 kB 00:00
(12/141): cracklib-2.9.6-19.fc30.i686.rpm 10 MB/s | 77 kB 00:00
(13/141): crypto-policies-20190527-1.git0b3add8 9.0 MB/s | 47 kB 00:00
(14/141): coreutils-common-8.31-3.fc31.i686.rpm 23 MB/s | 1.9 MB 00:00
(15/141): curl-7.65.1-1.fc31.i686.rpm 8.3 MB/s | 304 kB 00:00
(16/141): cyrus-sasl-lib-2.1.27-1.fc31.i686.rpm 5.5 MB/s | 104 kB 00:00
(17/141): dwz-0.12-10.fc30.i686.rpm 15 MB/s | 105 kB 00:00
(18/141): binutils-2.32-17.fc31.i686.rpm 24 MB/s | 5.4 MB 00:00
(19/141): efi-srpm-macros-4-2.fc30.noarch.rpm 735 kB/s | 23 kB 00:00
(20/141): diffutils-3.7-2.fc30.i686.rpm 7.4 MB/s | 395 kB 00:00
(21/141): elfutils-0.176-4.fc31.i686.rpm 20 MB/s | 336 kB 00:00
(22/141): elfutils-default-yama-scope-0.176-4.f 665 kB/s | 16 kB 00:00
(23/141): elfutils-libs-0.176-4.fc31.i686.rpm 26 MB/s | 329 kB 00:00
(24/141): expat-2.2.7-1.fc31.i686.rpm 16 MB/s | 99 kB 00:00
(25/141): elfutils-libelf-0.176-4.fc31.i686.rpm 8.3 MB/s | 197 kB 00:00
(26/141): fedora-gpg-keys-31-0.2.noarch.rpm 14 MB/s | 102 kB 00:00
(27/141): fedora-repos-31-0.2.noarch.rpm 1.4 MB/s | 9.2 kB 00:00
(28/141): fedora-release-common-31-0.7.noarch.r 2.0 MB/s | 19 kB 00:00
(29/141): fedora-release-31-0.7.noarch.rpm 825 kB/s | 11 kB 00:00
(30/141): fedora-repos-rawhide-31-0.2.noarch.rp 2.4 MB/s | 8.4 kB 00:00
(31/141): file-5.37-2.fc31.i686.rpm 3.2 MB/s | 51 kB 00:00
(32/141): file-libs-5.37-2.fc31.i686.rpm 21 MB/s | 572 kB 00:00
(33/141): fpc-srpm-macros-1.2-1.fc31.noarch.rpm 1.8 MB/s | 7.5 kB 00:00
(34/141): findutils-4.6.0-23.fc31.i686.rpm 24 MB/s | 524 kB 00:00
(35/141): gc-7.6.4-5.fc30.i686.rpm 13 MB/s | 97 kB 00:00
(36/141): filesystem-3.12-1.fc31.i686.rpm 17 MB/s | 1.1 MB 00:00
(37/141): ghc-srpm-macros-1.4.2-9.fc30.noarch.r 1.6 MB/s | 7.6 kB 00:00
(38/141): gawk-5.0.1-2.fc31.i686.rpm 25 MB/s | 1.2 MB 00:00
(39/141): glibc-common-2.29.9000-31.fc31.i686.r 19 MB/s | 688 kB 00:00
(40/141): glibc-minimal-langpack-2.29.9000-31.f 7.7 MB/s | 66 kB 00:00
(41/141): gmp-6.1.2-10.fc31.i686.rpm 19 MB/s | 259 kB 00:00
(42/141): gnat-srpm-macros-4-9.fc30.noarch.rpm 2.4 MB/s | 8.5 kB 00:00
(43/141): gdb-minimal-8.3.50.20190702-19.fc31.i 28 MB/s | 3.6 MB 00:00
(44/141): go-srpm-macros-3.0.8-3.fc31.noarch.rp 841 kB/s | 25 kB 00:00
(45/141): glibc-2.29.9000-31.fc31.i686.rpm 26 MB/s | 3.4 MB 00:00
(46/141): grep-3.3-2.fc31.i686.rpm 8.4 MB/s | 253 kB 00:00
(47/141): gzip-1.9-9.fc31.i686.rpm 13 MB/s | 153 kB 00:00
(48/141): info-6.6-1.fc30.i686.rpm 13 MB/s | 220 kB 00:00
(49/141): keyutils-libs-1.6-2.fc30.i686.rpm 2.8 MB/s | 30 kB 00:00
(50/141): libacl-2.2.53-3.fc30.i686.rpm 2.9 MB/s | 25 kB 00:00
(51/141): krb5-libs-1.17-35.fc31.i686.rpm 30 MB/s | 814 kB 00:00
(52/141): libarchive-3.3.3-7.fc31.i686.rpm 15 MB/s | 381 kB 00:00
(53/141): libatomic_ops-7.6.10-1.fc31.i686.rpm 2.2 MB/s | 34 kB 00:00
(54/141): libattr-2.4.48-6.fc31.i686.rpm 2.7 MB/s | 19 kB 00:00
(55/141): libcap-2.26-5.fc30.i686.rpm 5.7 MB/s | 47 kB 00:00
(56/141): libblkid-2.34-1.fc31.i686.rpm 15 MB/s | 171 kB 00:00
(57/141): libcap-ng-0.7.9-7.fc31.i686.rpm 3.8 MB/s | 27 kB 00:00
(58/141): libcurl-7.65.1-1.fc31.i686.rpm 23 MB/s | 293 kB 00:00
(59/141): libcom_err-1.45.2-1.fc31.i686.rpm 1.4 MB/s | 28 kB 00:00
(60/141): libdb-utils-5.3.28-37.fc30.i686.rpm 12 MB/s | 135 kB 00:00
(61/141): libdb-5.3.28-37.fc30.i686.rpm 26 MB/s | 809 kB 00:00
(62/141): libfdisk-2.34-1.fc31.i686.rpm 12 MB/s | 224 kB 00:00
(63/141): libffi-3.1-22.fc31.i686.rpm 2.0 MB/s | 32 kB 00:00
(64/141): libgcc-9.1.1-2.fc31.i686.rpm 5.2 MB/s | 99 kB 00:00
(65/141): libgomp-9.1.1-2.fc31.i686.rpm 17 MB/s | 231 kB 00:00
(66/141): libgcrypt-1.8.4-3.fc30.i686.rpm 20 MB/s | 416 kB 00:00
(67/141): libidn2-2.2.0-1.fc31.i686.rpm 14 MB/s | 91 kB 00:00
(68/141): libmetalink-0.1.3-8.fc30.i686.rpm 5.7 MB/s | 30 kB 00:00
(69/141): libgpg-error-1.33-2.fc30.i686.rpm 11 MB/s | 244 kB 00:00
(70/141): libmount-2.34-1.fc31.i686.rpm 18 MB/s | 192 kB 00:00
(71/141): libnghttp2-1.39.1-1.fc31.i686.rpm 11 MB/s | 82 kB 00:00
(72/141): guile22-2.2.6-1.fc31.i686.rpm 27 MB/s | 6.7 MB 00:00
(73/141): libnsl2-1.2.0-4.20180605git4a062cf.fc 1.5 MB/s | 57 kB 00:00
(74/141): libpkgconf-1.6.3-1.fc31.i686.rpm 1.1 MB/s | 40 kB 00:00
(75/141): libpsl-0.21.0-1.fc31.i686.rpm 3.7 MB/s | 59 kB 00:00
(76/141): libselinux-2.9-3.fc31.i686.rpm 5.4 MB/s | 90 kB 00:00
(77/141): libpwquality-1.4.0-12.fc30.i686.rpm 5.0 MB/s | 97 kB 00:00
(78/141): libsemanage-2.9-1.fc31.i686.rpm 17 MB/s | 122 kB 00:00
(79/141): libsepol-2.9-1.fc31.i686.rpm 29 MB/s | 308 kB 00:00
(80/141): libsigsegv-2.11-7.fc30.i686.rpm 1.6 MB/s | 25 kB 00:00
(81/141): libsmartcols-2.34-1.fc31.i686.rpm 7.8 MB/s | 131 kB 00:00
(82/141): libssh-0.9.0-5.fc31.i686.rpm 21 MB/s | 268 kB 00:00
(83/141): libssh-config-0.9.0-5.fc31.noarch.rpm 1.6 MB/s | 11 kB 00:00
(84/141): libtasn1-4.13-7.fc30.i686.rpm 9.8 MB/s | 71 kB 00:00
(85/141): libtirpc-1.1.4-2.rc2.fc30.1.i686.rpm 10 MB/s | 105 kB 00:00
(86/141): libtool-ltdl-2.4.6-30.fc31.i686.rpm 8.4 MB/s | 37 kB 00:00
(87/141): libstdc++-9.1.1-2.fc31.i686.rpm 26 MB/s | 636 kB 00:00
(88/141): libutempter-1.1.6-16.fc30.i686.rpm 2.8 MB/s | 24 kB 00:00
(89/141): libunistring-0.9.10-5.fc30.i686.rpm 24 MB/s | 423 kB 00:00
(90/141): libuuid-2.34-1.fc31.i686.rpm 4.0 MB/s | 29 kB 00:00
(91/141): libverto-0.3.0-7.fc30.i686.rpm 2.8 MB/s | 21 kB 00:00
(92/141): libxcrypt-4.4.6-2.fc31.i686.rpm 11 MB/s | 129 kB 00:00
(93/141): libzstd-1.4.0-1.fc31.i686.rpm 18 MB/s | 259 kB 00:00
(94/141): lua-libs-5.3.5-5.fc30.i686.rpm 13 MB/s | 119 kB 00:00
(95/141): lz4-libs-1.8.3-2.fc30.i686.rpm 7.5 MB/s | 61 kB 00:00
(96/141): libxml2-2.9.9-2.fc30.i686.rpm 24 MB/s | 696 kB 00:00
(97/141): mpfr-3.1.6-4.fc30.i686.rpm 23 MB/s | 220 kB 00:00
(98/141): ncurses-6.1-10.20180923.fc30.i686.rpm 30 MB/s | 363 kB 00:00
(99/141): ncurses-base-6.1-10.20180923.fc30.noa 601 kB/s | 59 kB 00:00
(100/141): nim-srpm-macros-2-1.fc31.noarch.rpm 80 kB/s | 8.2 kB 00:00
(101/141): ncurses-libs-6.1-10.20180923.fc30.i6 1.5 MB/s | 308 kB 00:00
(102/141): make-4.2.1-13.fc30.i686.rpm 2.1 MB/s | 490 kB 00:00
(103/141): ocaml-srpm-macros-5-5.fc30.noarch.rp 929 kB/s | 7.7 kB 00:00
(104/141): openblas-srpm-macros-2-5.fc30.noarch 1.2 MB/s | 7.3 kB 00:00
(105/141): openldap-2.4.47-2.fc31.i686.rpm 27 MB/s | 314 kB 00:00
(106/141): p11-kit-0.23.16.1-1.fc31.i686.rpm 17 MB/s | 266 kB 00:00
(107/141): p11-kit-trust-0.23.16.1-1.fc31.i686. 15 MB/s | 138 kB 00:00
(108/141): patch-2.7.6-9.fc31.i686.rpm 10 MB/s | 138 kB 00:00
(109/141): openssl-libs-1.1.1c-4.fc31.i686.rpm 26 MB/s | 1.4 MB 00:00
(110/141): pam-1.3.1-17.fc30.i686.rpm 15 MB/s | 643 kB 00:00
(111/141): pcre-8.43-2.fc31.i686.rpm 7.2 MB/s | 189 kB 00:00
(112/141): pcre2-10.33-7.fc31.i686.rpm 20 MB/s | 258 kB 00:00
(113/141): pkgconf-m4-1.6.3-1.fc31.noarch.rpm 597 kB/s | 15 kB 00:00
(114/141): perl-srpm-macros-1-32.fc31.noarch.rp 60 kB/s | 8.3 kB 00:00
(115/141): pkgconf-1.6.3-1.fc31.i686.rpm 302 kB/s | 42 kB 00:00
(116/141): pkgconf-pkg-config-1.6.3-1.fc31.i686 99 kB/s | 10 kB 00:00
(117/141): popt-1.16-17.fc30.i686.rpm 558 kB/s | 57 kB 00:00
(118/141): python-srpm-macros-3-46.fc31.noarch. 160 kB/s | 16 kB 00:00
(119/141): publicsuffix-list-dafsa-20190417-1.f 263 kB/s | 54 kB 00:00
(120/141): qt5-srpm-macros-5.12.4-1.fc31.noarch 86 kB/s | 9.0 kB 00:00
(121/141): readline-8.0-2.fc30.i686.rpm 957 kB/s | 198 kB 00:00
(122/141): redhat-rpm-config-137-1.fc31.noarch. 63 kB/s | 63 kB 00:00
(123/141): rpm-4.15.0-0.beta.1.fc31.i686.rpm 498 kB/s | 500 kB 00:01
(124/141): rpm-build-4.15.0-0.beta.1.fc31.i686. 9.4 MB/s | 118 kB 00:00
(125/141): rust-srpm-macros-10-1.fc31.noarch.rp 3.7 MB/s | 9.5 kB 00:00
(126/141): rpm-build-libs-4.15.0-0.beta.1.fc31. 5.8 MB/s | 105 kB 00:00
(127/141): rpm-libs-4.15.0-0.beta.1.fc31.i686.r 21 MB/s | 318 kB 00:00
(128/141): setup-2.13.3-1.fc31.noarch.rpm 18 MB/s | 149 kB 00:00
(129/141): sed-4.5-3.fc30.i686.rpm 9.2 MB/s | 289 kB 00:00
(130/141): systemd-libs-242-5.git7a6d834.fc31.i 25 MB/s | 549 kB 00:00
(131/141): shadow-utils-4.6-14.fc31.i686.rpm 29 MB/s | 1.2 MB 00:00
(132/141): tzdata-2019b-1.fc31.noarch.rpm 19 MB/s | 427 kB 00:00
(133/141): unzip-6.0-43.fc30.i686.rpm 8.7 MB/s | 175 kB 00:00
(134/141): which-2.21-14.fc30.i686.rpm 6.6 MB/s | 41 kB 00:00
(135/141): tar-1.32-1.fc31.i686.rpm 14 MB/s | 889 kB 00:00
(136/141): xz-5.2.4-5.fc30.i686.rpm 7.2 MB/s | 148 kB 00:00
(137/141): xz-libs-5.2.4-5.fc30.i686.rpm 8.1 MB/s | 92 kB 00:00
(138/141): zlib-1.2.11-15.fc30.i686.rpm 10 MB/s | 91 kB 00:00
(139/141): zip-3.0-24.fc30.i686.rpm 20 MB/s | 271 kB 00:00
(140/141): util-linux-2.34-1.fc31.i686.rpm 35 MB/s | 2.7 MB 00:00
(141/141): zstd-1.4.0-1.fc31.i686.rpm 14 MB/s | 390 kB 00:00
--------------------------------------------------------------------------------
Total 18 MB/s | 55 MB 00:02
warning: /var/lib/mock/974971-fedora-rawhide-i386-1563453563.556255/root/var/cache/dnf/fedora-6cb74b5c20b9e175/packages/alternatives-1.11-4.fc31.i686.rpm: Header V3 RSA/SHA256 Signature, key ID 3c3359c4: NOKEY
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0x3C3359C4:
Userid : "Fedora (31) <fedora-31-primary@fedoraproject.org>"
Fingerprint: 7D22 D586 7F2A 4236 474B F7B8 50CB 390B 3C33 59C4
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-31-primary
Key imported successfully
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0xCFC659B9:
Userid : "Fedora (30) <fedora-30-primary@fedoraproject.org>"
Fingerprint: F1D8 EC98 F241 AAF2 0DF6 9420 EF3C 111F CFC6 59B9
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-30-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Running scriptlet: filesystem-3.12-1.fc31.i686 1/1
Preparing : 1/1
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Installing : glibc-minimal-langpack-2.29.9000-31.fc31.i686 28/141
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Installing : libsepol-2.9-1.fc31.i686 32/141
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Installing : zlib-1.2.11-15.fc30.i686 33/141
Installing : bzip2-libs-1.0.6-29.fc30.i686 34/141
Installing : xz-libs-5.2.4-5.fc30.i686 35/141
Installing : libstdc++-9.1.1-2.fc31.i686 36/141
Installing : elfutils-libelf-0.176-4.fc31.i686 37/141
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Installing : libxcrypt-4.4.6-2.fc31.i686 39/141
Installing : gmp-1:6.1.2-10.fc31.i686 40/141
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Verifying : libdb-utils-5.3.28-37.fc30.i686 62/141
Verifying : libfdisk-2.34-1.fc31.i686 63/141
Verifying : libffi-3.1-22.fc31.i686 64/141
Verifying : libgcc-9.1.1-2.fc31.i686 65/141
Verifying : libgcrypt-1.8.4-3.fc30.i686 66/141
Verifying : libgomp-9.1.1-2.fc31.i686 67/141
Verifying : libgpg-error-1.33-2.fc30.i686 68/141
Verifying : libidn2-2.2.0-1.fc31.i686 69/141
Verifying : libmetalink-0.1.3-8.fc30.i686 70/141
Verifying : libmount-2.34-1.fc31.i686 71/141
Verifying : libnghttp2-1.39.1-1.fc31.i686 72/141
Verifying : libnsl2-1.2.0-4.20180605git4a062cf.fc30.i686 73/141
Verifying : libpkgconf-1.6.3-1.fc31.i686 74/141
Verifying : libpsl-0.21.0-1.fc31.i686 75/141
Verifying : libpwquality-1.4.0-12.fc30.i686 76/141
Verifying : libselinux-2.9-3.fc31.i686 77/141
Verifying : libsemanage-2.9-1.fc31.i686 78/141
Verifying : libsepol-2.9-1.fc31.i686 79/141
Verifying : libsigsegv-2.11-7.fc30.i686 80/141
Verifying : libsmartcols-2.34-1.fc31.i686 81/141
Verifying : libssh-0.9.0-5.fc31.i686 82/141
Verifying : libssh-config-0.9.0-5.fc31.noarch 83/141
Verifying : libstdc++-9.1.1-2.fc31.i686 84/141
Verifying : libtasn1-4.13-7.fc30.i686 85/141
Verifying : libtirpc-1.1.4-2.rc2.fc30.1.i686 86/141
Verifying : libtool-ltdl-2.4.6-30.fc31.i686 87/141
Verifying : libunistring-0.9.10-5.fc30.i686 88/141
Verifying : libutempter-1.1.6-16.fc30.i686 89/141
Verifying : libuuid-2.34-1.fc31.i686 90/141
Verifying : libverto-0.3.0-7.fc30.i686 91/141
Verifying : libxcrypt-4.4.6-2.fc31.i686 92/141
Verifying : libxml2-2.9.9-2.fc30.i686 93/141
Verifying : libzstd-1.4.0-1.fc31.i686 94/141
Verifying : lua-libs-5.3.5-5.fc30.i686 95/141
Verifying : lz4-libs-1.8.3-2.fc30.i686 96/141
Verifying : make-1:4.2.1-13.fc30.i686 97/141
Verifying : mpfr-3.1.6-4.fc30.i686 98/141
Verifying : ncurses-6.1-10.20180923.fc30.i686 99/141
Verifying : ncurses-base-6.1-10.20180923.fc30.noarch 100/141
Verifying : ncurses-libs-6.1-10.20180923.fc30.i686 101/141
Verifying : nim-srpm-macros-2-1.fc31.noarch 102/141
Verifying : ocaml-srpm-macros-5-5.fc30.noarch 103/141
Verifying : openblas-srpm-macros-2-5.fc30.noarch 104/141
Verifying : openldap-2.4.47-2.fc31.i686 105/141
Verifying : openssl-libs-1:1.1.1c-4.fc31.i686 106/141
Verifying : p11-kit-0.23.16.1-1.fc31.i686 107/141
Verifying : p11-kit-trust-0.23.16.1-1.fc31.i686 108/141
Verifying : pam-1.3.1-17.fc30.i686 109/141
Verifying : patch-2.7.6-9.fc31.i686 110/141
Verifying : pcre-8.43-2.fc31.i686 111/141
Verifying : pcre2-10.33-7.fc31.i686 112/141
Verifying : perl-srpm-macros-1-32.fc31.noarch 113/141
Verifying : pkgconf-1.6.3-1.fc31.i686 114/141
Verifying : pkgconf-m4-1.6.3-1.fc31.noarch 115/141
Verifying : pkgconf-pkg-config-1.6.3-1.fc31.i686 116/141
Verifying : popt-1.16-17.fc30.i686 117/141
Verifying : publicsuffix-list-dafsa-20190417-1.fc31.noarch 118/141
Verifying : python-srpm-macros-3-46.fc31.noarch 119/141
Verifying : qt5-srpm-macros-5.12.4-1.fc31.noarch 120/141
Verifying : readline-8.0-2.fc30.i686 121/141
Verifying : redhat-rpm-config-137-1.fc31.noarch 122/141
Verifying : rpm-4.15.0-0.beta.1.fc31.i686 123/141
Verifying : rpm-build-4.15.0-0.beta.1.fc31.i686 124/141
Verifying : rpm-build-libs-4.15.0-0.beta.1.fc31.i686 125/141
Verifying : rpm-libs-4.15.0-0.beta.1.fc31.i686 126/141
Verifying : rust-srpm-macros-10-1.fc31.noarch 127/141
Verifying : sed-4.5-3.fc30.i686 128/141
Verifying : setup-2.13.3-1.fc31.noarch 129/141
Verifying : shadow-utils-2:4.6-14.fc31.i686 130/141
Verifying : systemd-libs-242-5.git7a6d834.fc31.i686 131/141
Verifying : tar-2:1.32-1.fc31.i686 132/141
Verifying : tzdata-2019b-1.fc31.noarch 133/141
Verifying : unzip-6.0-43.fc30.i686 134/141
Verifying : util-linux-2.34-1.fc31.i686 135/141
Verifying : which-2.21-14.fc30.i686 136/141
Verifying : xz-5.2.4-5.fc30.i686 137/141
Verifying : xz-libs-5.2.4-5.fc30.i686 138/141
Verifying : zip-3.0-24.fc30.i686 139/141
Verifying : zlib-1.2.11-15.fc30.i686 140/141
Verifying : zstd-1.4.0-1.fc31.i686 141/141
Installed:
bash-5.0.7-1.fc31.i686
bzip2-1.0.6-29.fc30.i686
coreutils-8.31-3.fc31.i686
cpio-2.12-10.fc30.i686
diffutils-3.7-2.fc30.i686
fedora-release-common-31-0.7.noarch
findutils-1:4.6.0-23.fc31.i686
gawk-5.0.1-2.fc31.i686
glibc-minimal-langpack-2.29.9000-31.fc31.i686
grep-3.3-2.fc31.i686
gzip-1.9-9.fc31.i686
info-6.6-1.fc30.i686
make-1:4.2.1-13.fc30.i686
patch-2.7.6-9.fc31.i686
redhat-rpm-config-137-1.fc31.noarch
rpm-build-4.15.0-0.beta.1.fc31.i686
sed-4.5-3.fc30.i686
shadow-utils-2:4.6-14.fc31.i686
tar-2:1.32-1.fc31.i686
unzip-6.0-43.fc30.i686
util-linux-2.34-1.fc31.i686
which-2.21-14.fc30.i686
xz-5.2.4-5.fc30.i686
alternatives-1.11-4.fc31.i686
audit-libs-3.0-0.10.20190507gitf58ec40.fc31.i686
basesystem-11-7.fc30.noarch
binutils-2.32-17.fc31.i686
binutils-gold-2.32-17.fc31.i686
brotli-1.0.7-3.fc30.i686
bzip2-libs-1.0.6-29.fc30.i686
ca-certificates-2019.2.32-2.fc31.noarch
coreutils-common-8.31-3.fc31.i686
cracklib-2.9.6-19.fc30.i686
crypto-policies-20190527-1.git0b3add8.fc31.noarch
curl-7.65.1-1.fc31.i686
cyrus-sasl-lib-2.1.27-1.fc31.i686
dwz-0.12-10.fc30.i686
efi-srpm-macros-4-2.fc30.noarch
elfutils-0.176-4.fc31.i686
elfutils-default-yama-scope-0.176-4.fc31.noarch
elfutils-libelf-0.176-4.fc31.i686
elfutils-libs-0.176-4.fc31.i686
expat-2.2.7-1.fc31.i686
fedora-gpg-keys-31-0.2.noarch
fedora-release-31-0.7.noarch
fedora-repos-31-0.2.noarch
fedora-repos-rawhide-31-0.2.noarch
file-5.37-2.fc31.i686
file-libs-5.37-2.fc31.i686
filesystem-3.12-1.fc31.i686
fpc-srpm-macros-1.2-1.fc31.noarch
gc-7.6.4-5.fc30.i686
gdb-minimal-8.3.50.20190702-19.fc31.i686
ghc-srpm-macros-1.4.2-9.fc30.noarch
glibc-2.29.9000-31.fc31.i686
glibc-common-2.29.9000-31.fc31.i686
gmp-1:6.1.2-10.fc31.i686
gnat-srpm-macros-4-9.fc30.noarch
go-srpm-macros-3.0.8-3.fc31.noarch
guile22-2.2.6-1.fc31.i686
keyutils-libs-1.6-2.fc30.i686
krb5-libs-1.17-35.fc31.i686
libacl-2.2.53-3.fc30.i686
libarchive-3.3.3-7.fc31.i686
libatomic_ops-7.6.10-1.fc31.i686
libattr-2.4.48-6.fc31.i686
libblkid-2.34-1.fc31.i686
libcap-2.26-5.fc30.i686
libcap-ng-0.7.9-7.fc31.i686
libcom_err-1.45.2-1.fc31.i686
libcurl-7.65.1-1.fc31.i686
libdb-5.3.28-37.fc30.i686
libdb-utils-5.3.28-37.fc30.i686
libfdisk-2.34-1.fc31.i686
libffi-3.1-22.fc31.i686
libgcc-9.1.1-2.fc31.i686
libgcrypt-1.8.4-3.fc30.i686
libgomp-9.1.1-2.fc31.i686
libgpg-error-1.33-2.fc30.i686
libidn2-2.2.0-1.fc31.i686
libmetalink-0.1.3-8.fc30.i686
libmount-2.34-1.fc31.i686
libnghttp2-1.39.1-1.fc31.i686
libnsl2-1.2.0-4.20180605git4a062cf.fc30.i686
libpkgconf-1.6.3-1.fc31.i686
libpsl-0.21.0-1.fc31.i686
libpwquality-1.4.0-12.fc30.i686
libselinux-2.9-3.fc31.i686
libsemanage-2.9-1.fc31.i686
libsepol-2.9-1.fc31.i686
libsigsegv-2.11-7.fc30.i686
libsmartcols-2.34-1.fc31.i686
libssh-0.9.0-5.fc31.i686
libssh-config-0.9.0-5.fc31.noarch
libstdc++-9.1.1-2.fc31.i686
libtasn1-4.13-7.fc30.i686
libtirpc-1.1.4-2.rc2.fc30.1.i686
libtool-ltdl-2.4.6-30.fc31.i686
libunistring-0.9.10-5.fc30.i686
libutempter-1.1.6-16.fc30.i686
libuuid-2.34-1.fc31.i686
libverto-0.3.0-7.fc30.i686
libxcrypt-4.4.6-2.fc31.i686
libxml2-2.9.9-2.fc30.i686
libzstd-1.4.0-1.fc31.i686
lua-libs-5.3.5-5.fc30.i686
lz4-libs-1.8.3-2.fc30.i686
mpfr-3.1.6-4.fc30.i686
ncurses-6.1-10.20180923.fc30.i686
ncurses-base-6.1-10.20180923.fc30.noarch
ncurses-libs-6.1-10.20180923.fc30.i686
nim-srpm-macros-2-1.fc31.noarch
ocaml-srpm-macros-5-5.fc30.noarch
openblas-srpm-macros-2-5.fc30.noarch
openldap-2.4.47-2.fc31.i686
openssl-libs-1:1.1.1c-4.fc31.i686
p11-kit-0.23.16.1-1.fc31.i686
p11-kit-trust-0.23.16.1-1.fc31.i686
pam-1.3.1-17.fc30.i686
pcre-8.43-2.fc31.i686
pcre2-10.33-7.fc31.i686
perl-srpm-macros-1-32.fc31.noarch
pkgconf-1.6.3-1.fc31.i686
pkgconf-m4-1.6.3-1.fc31.noarch
pkgconf-pkg-config-1.6.3-1.fc31.i686
popt-1.16-17.fc30.i686
publicsuffix-list-dafsa-20190417-1.fc31.noarch
python-srpm-macros-3-46.fc31.noarch
qt5-srpm-macros-5.12.4-1.fc31.noarch
readline-8.0-2.fc30.i686
rpm-4.15.0-0.beta.1.fc31.i686
rpm-build-libs-4.15.0-0.beta.1.fc31.i686
rpm-libs-4.15.0-0.beta.1.fc31.i686
rust-srpm-macros-10-1.fc31.noarch
setup-2.13.3-1.fc31.noarch
systemd-libs-242-5.git7a6d834.fc31.i686
tzdata-2019b-1.fc31.noarch
xz-libs-5.2.4-5.fc30.i686
zip-3.0-24.fc30.i686
zlib-1.2.11-15.fc30.i686
zstd-1.4.0-1.fc31.i686
Complete!
Finish: dnf install
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
Start: buildsrpm
Start: rpmbuild -bs
warning: line 25: It's not recommended to have unversioned Obsoletes: Obsoletes: python2-biopython
Building target platforms: i686
Building for target i686
setting SOURCE_DATE_EPOCH=1563148800
Wrote: /builddir/build/SRPMS/python-biopython-1.73-5.fc31.src.rpm
Finish: rpmbuild -bs
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/974971-fedora-rawhide-i386-1563453563.556255/root/var/log/dnf.rpm.log
/var/lib/mock/974971-fedora-rawhide-i386-1563453563.556255/root/var/log/dnf.librepo.log
/var/lib/mock/974971-fedora-rawhide-i386-1563453563.556255/root/var/log/dnf.log
Finish: buildsrpm
INFO: Done(/tmp/tmpq_qr6tvy/python-biopython.spec) Config(child) 1 minutes 3 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 (timeout=75600): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/python-biopython-1.73-5.fc31.src.rpm --configdir /var/lib/copr-rpmbuild/results/configs --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1563453628.674863 -r child
WARNING: Could not find required logging config file: /var/lib/copr-rpmbuild/results/configs/logging.ini. Using default...
INFO: mock.py version 1.4.16 starting (python version = 3.7.3)...
Start: init plugins
INFO: tmpfs initialized
INFO: selinux disabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
Start: run
INFO: Start(/var/lib/copr-rpmbuild/results/python-biopython-1.73-5.fc31.src.rpm) Config(974971-fedora-rawhide-i386)
Start: clean chroot
Finish: clean chroot
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/974971-fedora-rawhide-i386-1563453628.674863/root.
INFO: calling preinit hooks
INFO: enabled root cache
Start: unpacking root cache
Finish: unpacking root cache
INFO: enabled dnf cache
Start: cleaning dnf metadata
Finish: cleaning dnf metadata
INFO: enabled HW Info plugin
Mock Version: 1.4.16
INFO: Mock Version: 1.4.16
Start: dnf update
Copr repository 33 kB/s | 3.3 kB 00:00
fedora 35 kB/s | 5.3 kB 00:00
Dependencies resolved.
Nothing to do.
Complete!
Finish: dnf update
Finish: chroot init
Start: build phase for python-biopython-1.73-5.fc31.src.rpm
Start: build setup for python-biopython-1.73-5.fc31.src.rpm
warning: line 25: It's not recommended to have unversioned Obsoletes: Obsoletes: python2-biopython
Building target platforms: i686
Building for target i686
setting SOURCE_DATE_EPOCH=1563148800
Wrote: /builddir/build/SRPMS/python-biopython-1.73-5.fc31.src.rpm
Copr repository 41 kB/s | 3.3 kB 00:00
fedora 38 kB/s | 5.3 kB 00:00
Dependencies resolved.
================================================================================
Package Arch Version Repository Size
================================================================================
Installing:
mysql-connector-python3 noarch 8.0.16-0.fc31 copr_base 414 k
flex-devel i686 2.6.4-2.fc30 fedora 11 k
gcc i686 9.1.1-2.fc31 fedora 21 M
python3-devel i686 3.7.4-3.fc31 fedora 203 k
python3-mysql i686 1.3.13-2.fc30 fedora 107 k
python3-numpy i686 1:1.16.4-2.fc31 fedora 3.6 M
python3-psycopg2 i686 2.7.7-2.fc31 fedora 169 k
python3-rdflib noarch 4.2.1-9.fc30 fedora 570 k
python3-reportlab i686 3.5.23-2.fc31 fedora 3.0 M
Installing dependencies:
annobin i686 8.77-1.fc31 fedora 108 k
bitstream-vera-fonts-common noarch 1.10-33.fc30 fedora 14 k
bitstream-vera-sans-fonts noarch 1.10-33.fc30 fedora 117 k
cpp i686 9.1.1-2.fc31 fedora 9.7 M
dejavu-fonts-common noarch 2.37-1.fc30 fedora 67 k
dejavu-sans-fonts noarch 2.37-1.fc30 fedora 1.5 M
fontpackages-filesystem noarch 1.44-24.fc30 fedora 8.2 k
freetype i686 2.10.0-2.fc31 fedora 391 k
gdbm-libs i686 1:1.18-4.fc30 fedora 53 k
glibc-devel i686 2.29.9000-31.fc31 fedora 1.0 M
glibc-headers i686 2.29.9000-31.fc31 fedora 464 k
isl i686 0.16.1-8.fc30 fedora 971 k
jbigkit-libs i686 2.1-16.fc30 fedora 50 k
kernel-headers i686 5.3.0-0.rc0.git5.1.fc31 fedora 1.1 M
lcms2 i686 2.9-5.fc30 fedora 167 k
libart_lgpl i686 2.3.21-21.fc30 fedora 70 k
libasan i686 9.1.1-2.fc31 fedora 474 k
libatomic i686 9.1.1-2.fc31 fedora 35 k
libgfortran i686 9.1.1-2.fc31 fedora 652 k
libimagequant i686 2.12.3-1.fc31 fedora 66 k
libjpeg-turbo i686 2.0.2-3.fc31 fedora 174 k
libmpc i686 1.1.0-3.fc30 fedora 62 k
libpng i686 2:1.6.37-1.fc31 fedora 121 k
libpq i686 11.4-1.fc31 fedora 211 k
libquadmath i686 9.1.1-2.fc31 fedora 243 k
libtiff i686 4.0.10-5.fc31 fedora 188 k
libubsan i686 9.1.1-2.fc31 fedora 190 k
libwebp i686 1.0.3-1.fc31 fedora 297 k
libxcrypt-devel i686 4.4.6-2.fc31 fedora 35 k
mariadb-connector-c i686 3.1.2-1.fc31 fedora 167 k
mariadb-connector-c-config noarch 3.1.2-1.fc31 fedora 12 k
openblas i686 0.3.6-2.fc31 fedora 29 k
openblas-threads i686 0.3.6-2.fc31 fedora 3.8 M
openjpeg2 i686 2.3.1-1.fc31 fedora 158 k
python-pip-wheel noarch 19.1.1-1.fc31 fedora 1.1 M
python-rpm-macros noarch 3-46.fc31 fedora 12 k
python-setuptools-wheel noarch 41.0.1-3.fc31 fedora 276 k
python3 i686 3.7.4-3.fc31 fedora 38 k
python3-html5lib noarch 1:1.0.1-3.fc30 fedora 213 k
python3-isodate noarch 0.6.0-1.fc31 fedora 58 k
python3-libs i686 3.7.4-3.fc31 fedora 7.3 M
python3-olefile noarch 0.46-3.fc31 fedora 4.8 M
python3-pillow i686 6.1.0-1.fc31 fedora 669 k
python3-protobuf noarch 3.6.1-4.fc31 fedora 568 k
python3-pyparsing noarch 2.4.0-1.fc31 fedora 142 k
python3-rpm-generators noarch 9-1.fc31 fedora 24 k
python3-rpm-macros noarch 3-46.fc31 fedora 11 k
python3-setuptools noarch 41.0.1-3.fc31 fedora 578 k
python3-six noarch 1.12.0-1.fc30 fedora 35 k
python3-webencodings noarch 0.5.1-7.fc30 fedora 26 k
sqlite-libs i686 3.29.0-1.fc31 fedora 610 k
Transaction Summary
================================================================================
Install 60 Packages
Total download size: 68 M
Installed size: 221 M
Downloading Packages:
(1/60): annobin-8.77-1.fc31.i686.rpm 1.9 MB/s | 108 kB 00:00
(2/60): bitstream-vera-fonts-common-1.10-33.fc3 240 kB/s | 14 kB 00:00
(3/60): bitstream-vera-sans-fonts-1.10-33.fc30. 16 MB/s | 117 kB 00:00
(4/60): dejavu-fonts-common-2.37-1.fc30.noarch. 13 MB/s | 67 kB 00:00
(5/60): dejavu-sans-fonts-2.37-1.fc30.noarch.rp 32 MB/s | 1.5 MB 00:00
(6/60): flex-devel-2.6.4-2.fc30.i686.rpm 1.7 MB/s | 11 kB 00:00
(7/60): fontpackages-filesystem-1.44-24.fc30.no 2.6 MB/s | 8.2 kB 00:00
(8/60): freetype-2.10.0-2.fc31.i686.rpm 27 MB/s | 391 kB 00:00
(9/60): mysql-connector-python3-8.0.16-0.fc31.n 2.2 MB/s | 414 kB 00:00
(10/60): gdbm-libs-1.18-4.fc30.i686.rpm 749 kB/s | 53 kB 00:00
(11/60): cpp-9.1.1-2.fc31.i686.rpm 38 MB/s | 9.7 MB 00:00
(12/60): glibc-headers-2.29.9000-31.fc31.i686.r 22 MB/s | 464 kB 00:00
(13/60): glibc-devel-2.29.9000-31.fc31.i686.rpm 11 MB/s | 1.0 MB 00:00
(14/60): jbigkit-libs-2.1-16.fc30.i686.rpm 4.9 MB/s | 50 kB 00:00
(15/60): isl-0.16.1-8.fc30.i686.rpm 19 MB/s | 971 kB 00:00
(16/60): kernel-headers-5.3.0-0.rc0.git5.1.fc31 3.4 MB/s | 1.1 MB 00:00
(17/60): lcms2-2.9-5.fc30.i686.rpm 518 kB/s | 167 kB 00:00
(18/60): libasan-9.1.1-2.fc31.i686.rpm 29 MB/s | 474 kB 00:00
(19/60): libatomic-9.1.1-2.fc31.i686.rpm 2.8 MB/s | 35 kB 00:00
(20/60): libart_lgpl-2.3.21-21.fc30.i686.rpm 1.8 MB/s | 70 kB 00:00
(21/60): libimagequant-2.12.3-1.fc31.i686.rpm 12 MB/s | 66 kB 00:00
(22/60): libjpeg-turbo-2.0.2-3.fc31.i686.rpm 20 MB/s | 174 kB 00:00
(23/60): libmpc-1.1.0-3.fc30.i686.rpm 9.4 MB/s | 62 kB 00:00
(24/60): libpng-1.6.37-1.fc31.i686.rpm 14 MB/s | 121 kB 00:00
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(29/60): libquadmath-9.1.1-2.fc31.i686.rpm 7.1 MB/s | 243 kB 00:00
(30/60): libxcrypt-devel-4.4.6-2.fc31.i686.rpm 5.9 MB/s | 35 kB 00:00
(31/60): libwebp-1.0.3-1.fc31.i686.rpm 19 MB/s | 297 kB 00:00
(32/60): mariadb-connector-c-config-3.1.2-1.fc3 2.4 MB/s | 12 kB 00:00
(33/60): openblas-0.3.6-2.fc31.i686.rpm 4.3 MB/s | 29 kB 00:00
(34/60): mariadb-connector-c-3.1.2-1.fc31.i686. 7.5 MB/s | 167 kB 00:00
(35/60): openjpeg2-2.3.1-1.fc31.i686.rpm 10 MB/s | 158 kB 00:00
(36/60): python-pip-wheel-19.1.1-1.fc31.noarch. 25 MB/s | 1.1 MB 00:00
(37/60): python-rpm-macros-3-46.fc31.noarch.rpm 3.7 MB/s | 12 kB 00:00
(38/60): python-setuptools-wheel-41.0.1-3.fc31. 22 MB/s | 276 kB 00:00
(39/60): python3-3.7.4-3.fc31.i686.rpm 5.7 MB/s | 38 kB 00:00
(40/60): python3-devel-3.7.4-3.fc31.i686.rpm 11 MB/s | 203 kB 00:00
(41/60): python3-html5lib-1.0.1-3.fc30.noarch.r 22 MB/s | 213 kB 00:00
(42/60): python3-isodate-0.6.0-1.fc31.noarch.rp 10 MB/s | 58 kB 00:00
(43/60): openblas-threads-0.3.6-2.fc31.i686.rpm 26 MB/s | 3.8 MB 00:00
(44/60): python3-mysql-1.3.13-2.fc30.i686.rpm 11 MB/s | 107 kB 00:00
(45/60): gcc-9.1.1-2.fc31.i686.rpm 20 MB/s | 21 MB 00:01
(46/60): python3-numpy-1.16.4-2.fc31.i686.rpm 16 MB/s | 3.6 MB 00:00
(47/60): python3-pillow-6.1.0-1.fc31.i686.rpm 21 MB/s | 669 kB 00:00
(48/60): python3-protobuf-3.6.1-4.fc31.noarch.r 22 MB/s | 568 kB 00:00
(49/60): python3-psycopg2-2.7.7-2.fc31.i686.rpm 6.8 MB/s | 169 kB 00:00
(50/60): python3-pyparsing-2.4.0-1.fc31.noarch. 13 MB/s | 142 kB 00:00
(51/60): python3-libs-3.7.4-3.fc31.i686.rpm 18 MB/s | 7.3 MB 00:00
(52/60): python3-rdflib-4.2.1-9.fc30.noarch.rpm 8.3 MB/s | 570 kB 00:00
(53/60): python3-rpm-generators-9-1.fc31.noarch 4.4 MB/s | 24 kB 00:00
(54/60): python3-olefile-0.46-3.fc31.noarch.rpm 20 MB/s | 4.8 MB 00:00
(55/60): python3-rpm-macros-3-46.fc31.noarch.rp 322 kB/s | 11 kB 00:00
(56/60): python3-six-1.12.0-1.fc30.noarch.rpm 3.5 MB/s | 35 kB 00:00
(57/60): python3-webencodings-0.5.1-7.fc30.noar 4.3 MB/s | 26 kB 00:00
(58/60): python3-setuptools-41.0.1-3.fc31.noarc 17 MB/s | 578 kB 00:00
(59/60): sqlite-libs-3.29.0-1.fc31.i686.rpm 25 MB/s | 610 kB 00:00
(60/60): python3-reportlab-3.5.23-2.fc31.i686.r 25 MB/s | 3.0 MB 00:00
--------------------------------------------------------------------------------
Total 41 MB/s | 68 MB 00:01
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Preparing : 1/1
Installing : fontpackages-filesystem-1.44-24.fc30.noarch 1/60
Installing : bitstream-vera-fonts-common-1.10-33.fc30.noarch 2/60
Installing : bitstream-vera-sans-fonts-1.10-33.fc30.noarch 3/60
Installing : dejavu-fonts-common-2.37-1.fc30.noarch 4/60
Installing : dejavu-sans-fonts-2.37-1.fc30.noarch 5/60
Installing : python3-rpm-macros-3-46.fc31.noarch 6/60
Installing : python-setuptools-wheel-41.0.1-3.fc31.noarch 7/60
Installing : python-rpm-macros-3-46.fc31.noarch 8/60
Installing : python-pip-wheel-19.1.1-1.fc31.noarch 9/60
Installing : openblas-0.3.6-2.fc31.i686 10/60
Installing : mariadb-connector-c-config-3.1.2-1.fc31.noarch 11/60
Installing : kernel-headers-5.3.0-0.rc0.git5.1.fc31.i686 12/60
Running scriptlet: glibc-headers-2.29.9000-31.fc31.i686 13/60
Installing : glibc-headers-2.29.9000-31.fc31.i686 13/60
Installing : libxcrypt-devel-4.4.6-2.fc31.i686 14/60
Installing : glibc-devel-2.29.9000-31.fc31.i686 15/60
Installing : flex-devel-2.6.4-2.fc30.i686 16/60
Installing : libmpc-1.1.0-3.fc30.i686 17/60
Installing : libjpeg-turbo-2.0.2-3.fc31.i686 18/60
Installing : cpp-9.1.1-2.fc31.i686 19/60
Installing : mariadb-connector-c-3.1.2-1.fc31.i686 20/60
Installing : sqlite-libs-3.29.0-1.fc31.i686 21/60
Installing : openjpeg2-2.3.1-1.fc31.i686 22/60
Installing : libwebp-1.0.3-1.fc31.i686 23/60
Installing : libubsan-9.1.1-2.fc31.i686 24/60
Installing : libquadmath-9.1.1-2.fc31.i686 25/60
Installing : libgfortran-9.1.1-2.fc31.i686 26/60
Installing : openblas-threads-0.3.6-2.fc31.i686 27/60
Installing : libpq-11.4-1.fc31.i686 28/60
Installing : libpng-2:1.6.37-1.fc31.i686 29/60
Installing : freetype-2.10.0-2.fc31.i686 30/60
Installing : libimagequant-2.12.3-1.fc31.i686 31/60
Installing : libatomic-9.1.1-2.fc31.i686 32/60
Installing : libasan-9.1.1-2.fc31.i686 33/60
Installing : libart_lgpl-2.3.21-21.fc30.i686 34/60
Installing : lcms2-2.9-5.fc30.i686 35/60
Installing : jbigkit-libs-2.1-16.fc30.i686 36/60
Installing : libtiff-4.0.10-5.fc31.i686 37/60
Installing : isl-0.16.1-8.fc30.i686 38/60
Installing : gcc-9.1.1-2.fc31.i686 39/60
Installing : gdbm-libs-1:1.18-4.fc30.i686 40/60
Installing : python3-setuptools-41.0.1-3.fc31.noarch 41/60
Installing : python3-3.7.4-3.fc31.i686 42/60
Installing : python3-libs-3.7.4-3.fc31.i686 43/60
Installing : python3-six-1.12.0-1.fc30.noarch 44/60
Installing : python3-isodate-0.6.0-1.fc31.noarch 45/60
Installing : python3-protobuf-3.6.1-4.fc31.noarch 46/60
Installing : python3-olefile-0.46-3.fc31.noarch 47/60
Installing : python3-pyparsing-2.4.0-1.fc31.noarch 48/60
Installing : python3-rpm-generators-9-1.fc31.noarch 49/60
Installing : python3-webencodings-0.5.1-7.fc30.noarch 50/60
Installing : python3-html5lib-1:1.0.1-3.fc30.noarch 51/60
Installing : python3-rdflib-4.2.1-9.fc30.noarch 52/60
Installing : python3-devel-3.7.4-3.fc31.i686 53/60
Installing : mysql-connector-python3-8.0.16-0.fc31.noarch 54/60
Installing : python3-pillow-6.1.0-1.fc31.i686 55/60
Installing : python3-reportlab-3.5.23-2.fc31.i686 56/60
Installing : python3-mysql-1.3.13-2.fc30.i686 57/60
Installing : python3-numpy-1:1.16.4-2.fc31.i686 58/60
Installing : python3-psycopg2-2.7.7-2.fc31.i686 59/60
Installing : annobin-8.77-1.fc31.i686 60/60
Running scriptlet: annobin-8.77-1.fc31.i686 60/60
Verifying : mysql-connector-python3-8.0.16-0.fc31.noarch 1/60
Verifying : annobin-8.77-1.fc31.i686 2/60
Verifying : bitstream-vera-fonts-common-1.10-33.fc30.noarch 3/60
Verifying : bitstream-vera-sans-fonts-1.10-33.fc30.noarch 4/60
Verifying : cpp-9.1.1-2.fc31.i686 5/60
Verifying : dejavu-fonts-common-2.37-1.fc30.noarch 6/60
Verifying : dejavu-sans-fonts-2.37-1.fc30.noarch 7/60
Verifying : flex-devel-2.6.4-2.fc30.i686 8/60
Verifying : fontpackages-filesystem-1.44-24.fc30.noarch 9/60
Verifying : freetype-2.10.0-2.fc31.i686 10/60
Verifying : gcc-9.1.1-2.fc31.i686 11/60
Verifying : gdbm-libs-1:1.18-4.fc30.i686 12/60
Verifying : glibc-devel-2.29.9000-31.fc31.i686 13/60
Verifying : glibc-headers-2.29.9000-31.fc31.i686 14/60
Verifying : isl-0.16.1-8.fc30.i686 15/60
Verifying : jbigkit-libs-2.1-16.fc30.i686 16/60
Verifying : kernel-headers-5.3.0-0.rc0.git5.1.fc31.i686 17/60
Verifying : lcms2-2.9-5.fc30.i686 18/60
Verifying : libart_lgpl-2.3.21-21.fc30.i686 19/60
Verifying : libasan-9.1.1-2.fc31.i686 20/60
Verifying : libatomic-9.1.1-2.fc31.i686 21/60
Verifying : libgfortran-9.1.1-2.fc31.i686 22/60
Verifying : libimagequant-2.12.3-1.fc31.i686 23/60
Verifying : libjpeg-turbo-2.0.2-3.fc31.i686 24/60
Verifying : libmpc-1.1.0-3.fc30.i686 25/60
Verifying : libpng-2:1.6.37-1.fc31.i686 26/60
Verifying : libpq-11.4-1.fc31.i686 27/60
Verifying : libquadmath-9.1.1-2.fc31.i686 28/60
Verifying : libtiff-4.0.10-5.fc31.i686 29/60
Verifying : libubsan-9.1.1-2.fc31.i686 30/60
Verifying : libwebp-1.0.3-1.fc31.i686 31/60
Verifying : libxcrypt-devel-4.4.6-2.fc31.i686 32/60
Verifying : mariadb-connector-c-3.1.2-1.fc31.i686 33/60
Verifying : mariadb-connector-c-config-3.1.2-1.fc31.noarch 34/60
Verifying : openblas-0.3.6-2.fc31.i686 35/60
Verifying : openblas-threads-0.3.6-2.fc31.i686 36/60
Verifying : openjpeg2-2.3.1-1.fc31.i686 37/60
Verifying : python-pip-wheel-19.1.1-1.fc31.noarch 38/60
Verifying : python-rpm-macros-3-46.fc31.noarch 39/60
Verifying : python-setuptools-wheel-41.0.1-3.fc31.noarch 40/60
Verifying : python3-3.7.4-3.fc31.i686 41/60
Verifying : python3-devel-3.7.4-3.fc31.i686 42/60
Verifying : python3-html5lib-1:1.0.1-3.fc30.noarch 43/60
Verifying : python3-isodate-0.6.0-1.fc31.noarch 44/60
Verifying : python3-libs-3.7.4-3.fc31.i686 45/60
Verifying : python3-mysql-1.3.13-2.fc30.i686 46/60
Verifying : python3-numpy-1:1.16.4-2.fc31.i686 47/60
Verifying : python3-olefile-0.46-3.fc31.noarch 48/60
Verifying : python3-pillow-6.1.0-1.fc31.i686 49/60
Verifying : python3-protobuf-3.6.1-4.fc31.noarch 50/60
Verifying : python3-psycopg2-2.7.7-2.fc31.i686 51/60
Verifying : python3-pyparsing-2.4.0-1.fc31.noarch 52/60
Verifying : python3-rdflib-4.2.1-9.fc30.noarch 53/60
Verifying : python3-reportlab-3.5.23-2.fc31.i686 54/60
Verifying : python3-rpm-generators-9-1.fc31.noarch 55/60
Verifying : python3-rpm-macros-3-46.fc31.noarch 56/60
Verifying : python3-setuptools-41.0.1-3.fc31.noarch 57/60
Verifying : python3-six-1.12.0-1.fc30.noarch 58/60
Verifying : python3-webencodings-0.5.1-7.fc30.noarch 59/60
Verifying : sqlite-libs-3.29.0-1.fc31.i686 60/60
Installed:
mysql-connector-python3-8.0.16-0.fc31.noarch
flex-devel-2.6.4-2.fc30.i686
gcc-9.1.1-2.fc31.i686
python3-devel-3.7.4-3.fc31.i686
python3-mysql-1.3.13-2.fc30.i686
python3-numpy-1:1.16.4-2.fc31.i686
python3-psycopg2-2.7.7-2.fc31.i686
python3-rdflib-4.2.1-9.fc30.noarch
python3-reportlab-3.5.23-2.fc31.i686
annobin-8.77-1.fc31.i686
bitstream-vera-fonts-common-1.10-33.fc30.noarch
bitstream-vera-sans-fonts-1.10-33.fc30.noarch
cpp-9.1.1-2.fc31.i686
dejavu-fonts-common-2.37-1.fc30.noarch
dejavu-sans-fonts-2.37-1.fc30.noarch
fontpackages-filesystem-1.44-24.fc30.noarch
freetype-2.10.0-2.fc31.i686
gdbm-libs-1:1.18-4.fc30.i686
glibc-devel-2.29.9000-31.fc31.i686
glibc-headers-2.29.9000-31.fc31.i686
isl-0.16.1-8.fc30.i686
jbigkit-libs-2.1-16.fc30.i686
kernel-headers-5.3.0-0.rc0.git5.1.fc31.i686
lcms2-2.9-5.fc30.i686
libart_lgpl-2.3.21-21.fc30.i686
libasan-9.1.1-2.fc31.i686
libatomic-9.1.1-2.fc31.i686
libgfortran-9.1.1-2.fc31.i686
libimagequant-2.12.3-1.fc31.i686
libjpeg-turbo-2.0.2-3.fc31.i686
libmpc-1.1.0-3.fc30.i686
libpng-2:1.6.37-1.fc31.i686
libpq-11.4-1.fc31.i686
libquadmath-9.1.1-2.fc31.i686
libtiff-4.0.10-5.fc31.i686
libubsan-9.1.1-2.fc31.i686
libwebp-1.0.3-1.fc31.i686
libxcrypt-devel-4.4.6-2.fc31.i686
mariadb-connector-c-3.1.2-1.fc31.i686
mariadb-connector-c-config-3.1.2-1.fc31.noarch
openblas-0.3.6-2.fc31.i686
openblas-threads-0.3.6-2.fc31.i686
openjpeg2-2.3.1-1.fc31.i686
python-pip-wheel-19.1.1-1.fc31.noarch
python-rpm-macros-3-46.fc31.noarch
python-setuptools-wheel-41.0.1-3.fc31.noarch
python3-3.7.4-3.fc31.i686
python3-html5lib-1:1.0.1-3.fc30.noarch
python3-isodate-0.6.0-1.fc31.noarch
python3-libs-3.7.4-3.fc31.i686
python3-olefile-0.46-3.fc31.noarch
python3-pillow-6.1.0-1.fc31.i686
python3-protobuf-3.6.1-4.fc31.noarch
python3-pyparsing-2.4.0-1.fc31.noarch
python3-rpm-generators-9-1.fc31.noarch
python3-rpm-macros-3-46.fc31.noarch
python3-setuptools-41.0.1-3.fc31.noarch
python3-six-1.12.0-1.fc30.noarch
python3-webencodings-0.5.1-7.fc30.noarch
sqlite-libs-3.29.0-1.fc31.i686
Complete!
Finish: build setup for python-biopython-1.73-5.fc31.src.rpm
Start: rpmbuild python-biopython-1.73-5.fc31.src.rpm
warning: line 25: It's not recommended to have unversioned Obsoletes: Obsoletes: python2-biopython
Building target platforms: i686
Building for target i686
setting SOURCE_DATE_EPOCH=1563148800
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.rtqZuv
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf python-biopython-1.73
+ /usr/bin/mkdir -p python-biopython-1.73
+ cd python-biopython-1.73
+ /usr/bin/gzip -dc /builddir/build/SOURCES/biopython-1.73.tar.gz
+ /usr/bin/tar -xof -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ pushd biopython-1.73
+ find Scripts -type f -exec chmod -x '{}' ';'
+ find Doc -type f -exec chmod -x '{}' ';'
+ find Doc -type f -exec sed -i 's/\r//' '{}' ';'
+ find Bio -type f -exec chmod -x '{}' ';'
+ find Bio -type f -name '*.py' -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' '{}' ';'
+ popd
+ cp -a biopython-1.73 python3
+ RPM_EC=0
++ jobs -p
+ exit 0
~/build/BUILD/python-biopython-1.73/biopython-1.73 ~/build/BUILD/python-biopython-1.73
~/build/BUILD/python-biopython-1.73
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.Nq5EAu
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.73
+ pushd python3
+ CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld'
+ /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -s'
~/build/BUILD/python-biopython-1.73/python3 ~/build/BUILD/python-biopython-1.73
running build
running build_py
creating build
creating build/lib.linux-i686-3.7
creating build/lib.linux-i686-3.7/Bio
copying Bio/File.py -> build/lib.linux-i686-3.7/Bio
copying Bio/LogisticRegression.py -> build/lib.linux-i686-3.7/Bio
copying Bio/MaxEntropy.py -> build/lib.linux-i686-3.7/Bio
copying Bio/NaiveBayes.py -> build/lib.linux-i686-3.7/Bio
copying Bio/Seq.py -> build/lib.linux-i686-3.7/Bio
copying Bio/SeqFeature.py -> build/lib.linux-i686-3.7/Bio
copying Bio/SeqRecord.py -> build/lib.linux-i686-3.7/Bio
copying Bio/__init__.py -> build/lib.linux-i686-3.7/Bio
copying Bio/_utils.py -> build/lib.linux-i686-3.7/Bio
copying Bio/bgzf.py -> build/lib.linux-i686-3.7/Bio
copying Bio/kNN.py -> build/lib.linux-i686-3.7/Bio
copying Bio/pairwise2.py -> build/lib.linux-i686-3.7/Bio
copying Bio/triefind.py -> build/lib.linux-i686-3.7/Bio
copying Bio/Index.py -> build/lib.linux-i686-3.7/Bio
copying Bio/MarkovModel.py -> build/lib.linux-i686-3.7/Bio
creating build/lib.linux-i686-3.7/Bio/Align
copying Bio/Align/__init__.py -> build/lib.linux-i686-3.7/Bio/Align
copying Bio/Align/AlignInfo.py -> build/lib.linux-i686-3.7/Bio/Align
creating build/lib.linux-i686-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_Clustalw.py -> build/lib.linux-i686-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_MSAProbs.py -> build/lib.linux-i686-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_Muscle.py -> build/lib.linux-i686-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_Probcons.py -> build/lib.linux-i686-3.7/Bio/Align/Applications
copying Bio/Align/Applications/__init__.py -> build/lib.linux-i686-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_ClustalOmega.py -> build/lib.linux-i686-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_Dialign.py -> build/lib.linux-i686-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_Mafft.py -> build/lib.linux-i686-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_Prank.py -> build/lib.linux-i686-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_TCoffee.py -> build/lib.linux-i686-3.7/Bio/Align/Applications
creating build/lib.linux-i686-3.7/Bio/AlignIO
copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-i686-3.7/Bio/AlignIO
copying Bio/AlignIO/Interfaces.py -> build/lib.linux-i686-3.7/Bio/AlignIO
copying Bio/AlignIO/MauveIO.py -> build/lib.linux-i686-3.7/Bio/AlignIO
copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-i686-3.7/Bio/AlignIO
copying Bio/AlignIO/__init__.py -> build/lib.linux-i686-3.7/Bio/AlignIO
copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-i686-3.7/Bio/AlignIO
copying Bio/AlignIO/FastaIO.py -> build/lib.linux-i686-3.7/Bio/AlignIO
copying Bio/AlignIO/MafIO.py -> build/lib.linux-i686-3.7/Bio/AlignIO
copying Bio/AlignIO/NexusIO.py -> build/lib.linux-i686-3.7/Bio/AlignIO
copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-i686-3.7/Bio/AlignIO
creating build/lib.linux-i686-3.7/Bio/Alphabet
copying Bio/Alphabet/Reduced.py -> build/lib.linux-i686-3.7/Bio/Alphabet
copying Bio/Alphabet/IUPAC.py -> build/lib.linux-i686-3.7/Bio/Alphabet
copying Bio/Alphabet/__init__.py -> build/lib.linux-i686-3.7/Bio/Alphabet
creating build/lib.linux-i686-3.7/Bio/Application
copying Bio/Application/__init__.py -> build/lib.linux-i686-3.7/Bio/Application
creating build/lib.linux-i686-3.7/Bio/Blast
copying Bio/Blast/NCBIWWW.py -> build/lib.linux-i686-3.7/Bio/Blast
copying Bio/Blast/ParseBlastTable.py -> build/lib.linux-i686-3.7/Bio/Blast
copying Bio/Blast/Applications.py -> build/lib.linux-i686-3.7/Bio/Blast
copying Bio/Blast/NCBIXML.py -> build/lib.linux-i686-3.7/Bio/Blast
copying Bio/Blast/Record.py -> build/lib.linux-i686-3.7/Bio/Blast
copying Bio/Blast/__init__.py -> build/lib.linux-i686-3.7/Bio/Blast
creating build/lib.linux-i686-3.7/Bio/CAPS
copying Bio/CAPS/__init__.py -> build/lib.linux-i686-3.7/Bio/CAPS
creating build/lib.linux-i686-3.7/Bio/codonalign
copying Bio/codonalign/chisq.py -> build/lib.linux-i686-3.7/Bio/codonalign
copying Bio/codonalign/codonalphabet.py -> build/lib.linux-i686-3.7/Bio/codonalign
copying Bio/codonalign/__init__.py -> build/lib.linux-i686-3.7/Bio/codonalign
copying Bio/codonalign/codonalignment.py -> build/lib.linux-i686-3.7/Bio/codonalign
copying Bio/codonalign/codonseq.py -> build/lib.linux-i686-3.7/Bio/codonalign
creating build/lib.linux-i686-3.7/Bio/Compass
copying Bio/Compass/__init__.py -> build/lib.linux-i686-3.7/Bio/Compass
creating build/lib.linux-i686-3.7/Bio/Crystal
copying Bio/Crystal/__init__.py -> build/lib.linux-i686-3.7/Bio/Crystal
creating build/lib.linux-i686-3.7/Bio/Data
copying Bio/Data/CodonTable.py -> build/lib.linux-i686-3.7/Bio/Data
copying Bio/Data/SCOPData.py -> build/lib.linux-i686-3.7/Bio/Data
copying Bio/Data/__init__.py -> build/lib.linux-i686-3.7/Bio/Data
copying Bio/Data/IUPACData.py -> build/lib.linux-i686-3.7/Bio/Data
creating build/lib.linux-i686-3.7/Bio/Emboss
copying Bio/Emboss/Primer3.py -> build/lib.linux-i686-3.7/Bio/Emboss
copying Bio/Emboss/__init__.py -> build/lib.linux-i686-3.7/Bio/Emboss
copying Bio/Emboss/Applications.py -> build/lib.linux-i686-3.7/Bio/Emboss
copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-i686-3.7/Bio/Emboss
creating build/lib.linux-i686-3.7/Bio/Entrez
copying Bio/Entrez/__init__.py -> build/lib.linux-i686-3.7/Bio/Entrez
copying Bio/Entrez/Parser.py -> build/lib.linux-i686-3.7/Bio/Entrez
creating build/lib.linux-i686-3.7/Bio/ExPASy
copying Bio/ExPASy/Prodoc.py -> build/lib.linux-i686-3.7/Bio/ExPASy
copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-i686-3.7/Bio/ExPASy
copying Bio/ExPASy/cellosaurus.py -> build/lib.linux-i686-3.7/Bio/ExPASy
copying Bio/ExPASy/Enzyme.py -> build/lib.linux-i686-3.7/Bio/ExPASy
copying Bio/ExPASy/Prosite.py -> build/lib.linux-i686-3.7/Bio/ExPASy
copying Bio/ExPASy/__init__.py -> build/lib.linux-i686-3.7/Bio/ExPASy
creating build/lib.linux-i686-3.7/Bio/FSSP
copying Bio/FSSP/__init__.py -> build/lib.linux-i686-3.7/Bio/FSSP
copying Bio/FSSP/FSSPTools.py -> build/lib.linux-i686-3.7/Bio/FSSP
copying Bio/FSSP/fssp_rec.py -> build/lib.linux-i686-3.7/Bio/FSSP
creating build/lib.linux-i686-3.7/Bio/GenBank
copying Bio/GenBank/Record.py -> build/lib.linux-i686-3.7/Bio/GenBank
copying Bio/GenBank/Scanner.py -> build/lib.linux-i686-3.7/Bio/GenBank
copying Bio/GenBank/utils.py -> build/lib.linux-i686-3.7/Bio/GenBank
copying Bio/GenBank/__init__.py -> build/lib.linux-i686-3.7/Bio/GenBank
creating build/lib.linux-i686-3.7/Bio/Geo
copying Bio/Geo/__init__.py -> build/lib.linux-i686-3.7/Bio/Geo
copying Bio/Geo/Record.py -> build/lib.linux-i686-3.7/Bio/Geo
creating build/lib.linux-i686-3.7/Bio/Graphics
copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-i686-3.7/Bio/Graphics
copying Bio/Graphics/Comparative.py -> build/lib.linux-i686-3.7/Bio/Graphics
copying Bio/Graphics/Distribution.py -> build/lib.linux-i686-3.7/Bio/Graphics
copying Bio/Graphics/__init__.py -> build/lib.linux-i686-3.7/Bio/Graphics
copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-i686-3.7/Bio/Graphics
copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-i686-3.7/Bio/Graphics
copying Bio/Graphics/KGML_vis.py -> build/lib.linux-i686-3.7/Bio/Graphics
creating build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram
creating build/lib.linux-i686-3.7/Bio/HMM
copying Bio/HMM/MarkovModel.py -> build/lib.linux-i686-3.7/Bio/HMM
copying Bio/HMM/Utilities.py -> build/lib.linux-i686-3.7/Bio/HMM
copying Bio/HMM/__init__.py -> build/lib.linux-i686-3.7/Bio/HMM
copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-i686-3.7/Bio/HMM
copying Bio/HMM/Trainer.py -> build/lib.linux-i686-3.7/Bio/HMM
creating build/lib.linux-i686-3.7/Bio/KEGG
copying Bio/KEGG/REST.py -> build/lib.linux-i686-3.7/Bio/KEGG
copying Bio/KEGG/__init__.py -> build/lib.linux-i686-3.7/Bio/KEGG
creating build/lib.linux-i686-3.7/Bio/KEGG/Compound
copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-i686-3.7/Bio/KEGG/Compound
creating build/lib.linux-i686-3.7/Bio/KEGG/Enzyme
copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-i686-3.7/Bio/KEGG/Enzyme
creating build/lib.linux-i686-3.7/Bio/KEGG/Gene
copying Bio/KEGG/Gene/__init__.py -> build/lib.linux-i686-3.7/Bio/KEGG/Gene
creating build/lib.linux-i686-3.7/Bio/KEGG/Map
copying Bio/KEGG/Map/__init__.py -> build/lib.linux-i686-3.7/Bio/KEGG/Map
creating build/lib.linux-i686-3.7/Bio/PDB
creating build/lib.linux-i686-3.7/Bio/PDB/mmtf
copying Bio/PDB/mmtf/DefaultParser.py -> build/lib.linux-i686-3.7/Bio/PDB/mmtf
copying Bio/PDB/mmtf/__init__.py -> build/lib.linux-i686-3.7/Bio/PDB/mmtf
creating build/lib.linux-i686-3.7/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-i686-3.7/Bio/KEGG/KGML
copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-i686-3.7/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-i686-3.7/Bio/KEGG/KGML
creating build/lib.linux-i686-3.7/Bio/Medline
copying Bio/Medline/__init__.py -> build/lib.linux-i686-3.7/Bio/Medline
creating build/lib.linux-i686-3.7/Bio/motifs
copying Bio/motifs/__init__.py -> build/lib.linux-i686-3.7/Bio/motifs
copying Bio/motifs/mast.py -> build/lib.linux-i686-3.7/Bio/motifs
copying Bio/motifs/matrix.py -> build/lib.linux-i686-3.7/Bio/motifs
copying Bio/motifs/minimal.py -> build/lib.linux-i686-3.7/Bio/motifs
copying Bio/motifs/transfac.py -> build/lib.linux-i686-3.7/Bio/motifs
copying Bio/motifs/alignace.py -> build/lib.linux-i686-3.7/Bio/motifs
copying Bio/motifs/meme.py -> build/lib.linux-i686-3.7/Bio/motifs
copying Bio/motifs/thresholds.py -> build/lib.linux-i686-3.7/Bio/motifs
creating build/lib.linux-i686-3.7/Bio/motifs/applications
copying Bio/motifs/applications/__init__.py -> build/lib.linux-i686-3.7/Bio/motifs/applications
copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-i686-3.7/Bio/motifs/applications
creating build/lib.linux-i686-3.7/Bio/motifs/jaspar
copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-i686-3.7/Bio/motifs/jaspar
copying Bio/motifs/jaspar/db.py -> build/lib.linux-i686-3.7/Bio/motifs/jaspar
creating build/lib.linux-i686-3.7/Bio/Nexus
copying Bio/Nexus/Nodes.py -> build/lib.linux-i686-3.7/Bio/Nexus
copying Bio/Nexus/Trees.py -> build/lib.linux-i686-3.7/Bio/Nexus
copying Bio/Nexus/Nexus.py -> build/lib.linux-i686-3.7/Bio/Nexus
copying Bio/Nexus/StandardData.py -> build/lib.linux-i686-3.7/Bio/Nexus
copying Bio/Nexus/__init__.py -> build/lib.linux-i686-3.7/Bio/Nexus
creating build/lib.linux-i686-3.7/Bio/NMR
copying Bio/NMR/__init__.py -> build/lib.linux-i686-3.7/Bio/NMR
copying Bio/NMR/xpktools.py -> build/lib.linux-i686-3.7/Bio/NMR
copying Bio/NMR/NOEtools.py -> build/lib.linux-i686-3.7/Bio/NMR
creating build/lib.linux-i686-3.7/Bio/Pathway
copying Bio/Pathway/__init__.py -> build/lib.linux-i686-3.7/Bio/Pathway
creating build/lib.linux-i686-3.7/Bio/Pathway/Rep
copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-i686-3.7/Bio/Pathway/Rep
copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-i686-3.7/Bio/Pathway/Rep
copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-i686-3.7/Bio/Pathway/Rep
copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/Chain.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/Dice.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/FragmentMapper.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/Model.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/NeighborSearch.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/PDBIO.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/PDBParser.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/Polypeptide.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/ResidueDepth.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/Structure.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/StructureBuilder.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/Vector.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/mmcifio.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/vectors.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/Atom.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/DSSP.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/Entity.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/HSExposure.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/MMCIFParser.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/NACCESS.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/PDBExceptions.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/PDBList.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/PSEA.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/Residue.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/Selection.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/StructureAlignment.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/Superimposer.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/__init__.py -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-i686-3.7/Bio/PDB
creating build/lib.linux-i686-3.7/Bio/PopGen
copying Bio/PopGen/__init__.py -> build/lib.linux-i686-3.7/Bio/PopGen
creating build/lib.linux-i686-3.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/Controller.py -> build/lib.linux-i686-3.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-i686-3.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/Utils.py -> build/lib.linux-i686-3.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/EasyController.py -> build/lib.linux-i686-3.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-i686-3.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-i686-3.7/Bio/PopGen/GenePop
creating build/lib.linux-i686-3.7/Bio/Restriction
copying Bio/Restriction/RanaConfig.py -> build/lib.linux-i686-3.7/Bio/Restriction
copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-i686-3.7/Bio/Restriction
copying Bio/Restriction/PrintFormat.py -> build/lib.linux-i686-3.7/Bio/Restriction
copying Bio/Restriction/Restriction.py -> build/lib.linux-i686-3.7/Bio/Restriction
copying Bio/Restriction/__init__.py -> build/lib.linux-i686-3.7/Bio/Restriction
creating build/lib.linux-i686-3.7/Bio/SCOP
copying Bio/SCOP/Des.py -> build/lib.linux-i686-3.7/Bio/SCOP
copying Bio/SCOP/Hie.py -> build/lib.linux-i686-3.7/Bio/SCOP
copying Bio/SCOP/Residues.py -> build/lib.linux-i686-3.7/Bio/SCOP
copying Bio/SCOP/Cla.py -> build/lib.linux-i686-3.7/Bio/SCOP
copying Bio/SCOP/Dom.py -> build/lib.linux-i686-3.7/Bio/SCOP
copying Bio/SCOP/Raf.py -> build/lib.linux-i686-3.7/Bio/SCOP
copying Bio/SCOP/__init__.py -> build/lib.linux-i686-3.7/Bio/SCOP
creating build/lib.linux-i686-3.7/Bio/SearchIO
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copying Bio/SearchIO/__init__.py -> build/lib.linux-i686-3.7/Bio/SearchIO
copying Bio/SearchIO/_utils.py -> build/lib.linux-i686-3.7/Bio/SearchIO
copying Bio/SearchIO/FastaIO.py -> build/lib.linux-i686-3.7/Bio/SearchIO
copying Bio/SearchIO/_index.py -> build/lib.linux-i686-3.7/Bio/SearchIO
creating build/lib.linux-i686-3.7/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/ParserSupport.py -> build/lib.linux-i686-3.7/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/NCBIStandalone.py -> build/lib.linux-i686-3.7/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/__init__.py -> build/lib.linux-i686-3.7/Bio/SearchIO/_legacy
creating build/lib.linux-i686-3.7/Bio/SearchIO/_model
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copying Bio/SearchIO/_model/hsp.py -> build/lib.linux-i686-3.7/Bio/SearchIO/_model
copying Bio/SearchIO/_model/__init__.py -> build/lib.linux-i686-3.7/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hit.py -> build/lib.linux-i686-3.7/Bio/SearchIO/_model
copying Bio/SearchIO/_model/query.py -> build/lib.linux-i686-3.7/Bio/SearchIO/_model
creating build/lib.linux-i686-3.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-i686-3.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-i686-3.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-i686-3.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_text.py -> build/lib.linux-i686-3.7/Bio/SearchIO/BlastIO
creating build/lib.linux-i686-3.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-i686-3.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-i686-3.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-i686-3.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-i686-3.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-i686-3.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-i686-3.7/Bio/SearchIO/HmmerIO
creating build/lib.linux-i686-3.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-i686-3.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-i686-3.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.linux-i686-3.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-i686-3.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.linux-i686-3.7/Bio/SearchIO/ExonerateIO
creating build/lib.linux-i686-3.7/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/__init__.py -> build/lib.linux-i686-3.7/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/lib.linux-i686-3.7/Bio/SearchIO/InterproscanIO
creating build/lib.linux-i686-3.7/Bio/SeqIO
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copying Bio/SeqIO/IgIO.py -> build/lib.linux-i686-3.7/Bio/SeqIO
copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-i686-3.7/Bio/SeqIO
copying Bio/SeqIO/PdbIO.py -> build/lib.linux-i686-3.7/Bio/SeqIO
copying Bio/SeqIO/PirIO.py -> build/lib.linux-i686-3.7/Bio/SeqIO
copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-i686-3.7/Bio/SeqIO
copying Bio/SeqIO/SwissIO.py -> build/lib.linux-i686-3.7/Bio/SeqIO
copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-i686-3.7/Bio/SeqIO
copying Bio/SeqIO/_convert.py -> build/lib.linux-i686-3.7/Bio/SeqIO
copying Bio/SeqIO/AbiIO.py -> build/lib.linux-i686-3.7/Bio/SeqIO
copying Bio/SeqIO/FastaIO.py -> build/lib.linux-i686-3.7/Bio/SeqIO
copying Bio/SeqIO/Interfaces.py -> build/lib.linux-i686-3.7/Bio/SeqIO
copying Bio/SeqIO/PhdIO.py -> build/lib.linux-i686-3.7/Bio/SeqIO
copying Bio/SeqIO/QualityIO.py -> build/lib.linux-i686-3.7/Bio/SeqIO
copying Bio/SeqIO/SffIO.py -> build/lib.linux-i686-3.7/Bio/SeqIO
copying Bio/SeqIO/TabIO.py -> build/lib.linux-i686-3.7/Bio/SeqIO
copying Bio/SeqIO/__init__.py -> build/lib.linux-i686-3.7/Bio/SeqIO
copying Bio/SeqIO/_index.py -> build/lib.linux-i686-3.7/Bio/SeqIO
creating build/lib.linux-i686-3.7/Bio/SeqUtils
copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-i686-3.7/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsageIndices.py -> build/lib.linux-i686-3.7/Bio/SeqUtils
copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-i686-3.7/Bio/SeqUtils
copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-i686-3.7/Bio/SeqUtils
copying Bio/SeqUtils/lcc.py -> build/lib.linux-i686-3.7/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsage.py -> build/lib.linux-i686-3.7/Bio/SeqUtils
copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-i686-3.7/Bio/SeqUtils
copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-i686-3.7/Bio/SeqUtils
copying Bio/SeqUtils/__init__.py -> build/lib.linux-i686-3.7/Bio/SeqUtils
creating build/lib.linux-i686-3.7/Bio/Sequencing
copying Bio/Sequencing/Phd.py -> build/lib.linux-i686-3.7/Bio/Sequencing
copying Bio/Sequencing/Ace.py -> build/lib.linux-i686-3.7/Bio/Sequencing
copying Bio/Sequencing/__init__.py -> build/lib.linux-i686-3.7/Bio/Sequencing
creating build/lib.linux-i686-3.7/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/__init__.py -> build/lib.linux-i686-3.7/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_samtools.py -> build/lib.linux-i686-3.7/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_Novoalign.py -> build/lib.linux-i686-3.7/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_bwa.py -> build/lib.linux-i686-3.7/Bio/Sequencing/Applications
creating build/lib.linux-i686-3.7/Bio/Statistics
copying Bio/Statistics/__init__.py -> build/lib.linux-i686-3.7/Bio/Statistics
copying Bio/Statistics/lowess.py -> build/lib.linux-i686-3.7/Bio/Statistics
creating build/lib.linux-i686-3.7/Bio/SubsMat
copying Bio/SubsMat/FreqTable.py -> build/lib.linux-i686-3.7/Bio/SubsMat
copying Bio/SubsMat/__init__.py -> build/lib.linux-i686-3.7/Bio/SubsMat
copying Bio/SubsMat/MatrixInfo.py -> build/lib.linux-i686-3.7/Bio/SubsMat
creating build/lib.linux-i686-3.7/Bio/SVDSuperimposer
copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-i686-3.7/Bio/SVDSuperimposer
creating build/lib.linux-i686-3.7/Bio/PDB/QCPSuperimposer
copying Bio/PDB/QCPSuperimposer/__init__.py -> build/lib.linux-i686-3.7/Bio/PDB/QCPSuperimposer
creating build/lib.linux-i686-3.7/Bio/SwissProt
copying Bio/SwissProt/__init__.py -> build/lib.linux-i686-3.7/Bio/SwissProt
copying Bio/SwissProt/KeyWList.py -> build/lib.linux-i686-3.7/Bio/SwissProt
creating build/lib.linux-i686-3.7/Bio/TogoWS
copying Bio/TogoWS/__init__.py -> build/lib.linux-i686-3.7/Bio/TogoWS
creating build/lib.linux-i686-3.7/Bio/Phylo
copying Bio/Phylo/BaseTree.py -> build/lib.linux-i686-3.7/Bio/Phylo
copying Bio/Phylo/CDAOIO.py -> build/lib.linux-i686-3.7/Bio/Phylo
copying Bio/Phylo/NeXML.py -> build/lib.linux-i686-3.7/Bio/Phylo
copying Bio/Phylo/Newick.py -> build/lib.linux-i686-3.7/Bio/Phylo
copying Bio/Phylo/NexusIO.py -> build/lib.linux-i686-3.7/Bio/Phylo
copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-i686-3.7/Bio/Phylo
copying Bio/Phylo/__init__.py -> build/lib.linux-i686-3.7/Bio/Phylo
copying Bio/Phylo/_io.py -> build/lib.linux-i686-3.7/Bio/Phylo
copying Bio/Phylo/CDAO.py -> build/lib.linux-i686-3.7/Bio/Phylo
copying Bio/Phylo/Consensus.py -> build/lib.linux-i686-3.7/Bio/Phylo
copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-i686-3.7/Bio/Phylo
copying Bio/Phylo/NewickIO.py -> build/lib.linux-i686-3.7/Bio/Phylo
copying Bio/Phylo/PhyloXML.py -> build/lib.linux-i686-3.7/Bio/Phylo
copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-i686-3.7/Bio/Phylo
copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-i686-3.7/Bio/Phylo
copying Bio/Phylo/_utils.py -> build/lib.linux-i686-3.7/Bio/Phylo
creating build/lib.linux-i686-3.7/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Phyml.py -> build/lib.linux-i686-3.7/Bio/Phylo/Applications
copying Bio/Phylo/Applications/__init__.py -> build/lib.linux-i686-3.7/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Fasttree.py -> build/lib.linux-i686-3.7/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Raxml.py -> build/lib.linux-i686-3.7/Bio/Phylo/Applications
creating build/lib.linux-i686-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-i686-3.7/warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.py{}' found anywhere in distribution
warning: no previously-included files matching '*.py-e' found anywhere in distribution
Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.linux-i686-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-i686-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/codeml.py -> build/lib.linux-i686-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-i686-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.linux-i686-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-i686-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-i686-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-i686-3.7/Bio/Phylo/PAML
creating build/lib.linux-i686-3.7/Bio/UniGene
copying Bio/UniGene/__init__.py -> build/lib.linux-i686-3.7/Bio/UniGene
creating build/lib.linux-i686-3.7/Bio/UniProt
copying Bio/UniProt/__init__.py -> build/lib.linux-i686-3.7/Bio/UniProt
copying Bio/UniProt/GOA.py -> build/lib.linux-i686-3.7/Bio/UniProt
creating build/lib.linux-i686-3.7/Bio/Wise
copying Bio/Wise/dnal.py -> build/lib.linux-i686-3.7/Bio/Wise
copying Bio/Wise/__init__.py -> build/lib.linux-i686-3.7/Bio/Wise
copying Bio/Wise/psw.py -> build/lib.linux-i686-3.7/Bio/Wise
creating build/lib.linux-i686-3.7/Bio/_py3k
copying Bio/_py3k/__init__.py -> build/lib.linux-i686-3.7/Bio/_py3k
creating build/lib.linux-i686-3.7/BioSQL
copying BioSQL/__init__.py -> build/lib.linux-i686-3.7/BioSQL
copying BioSQL/Loader.py -> build/lib.linux-i686-3.7/BioSQL
copying BioSQL/DBUtils.py -> build/lib.linux-i686-3.7/BioSQL
copying BioSQL/BioSeqDatabase.py -> build/lib.linux-i686-3.7/BioSQL
copying BioSQL/BioSeq.py -> build/lib.linux-i686-3.7/BioSQL
creating build/lib.linux-i686-3.7/Bio/Affy
copying Bio/Affy/CelFile.py -> build/lib.linux-i686-3.7/Bio/Affy
copying Bio/Affy/__init__.py -> build/lib.linux-i686-3.7/Bio/Affy
creating build/lib.linux-i686-3.7/Bio/Cluster
copying Bio/Cluster/__init__.py -> build/lib.linux-i686-3.7/Bio/Cluster
creating build/lib.linux-i686-3.7/Bio/KDTree
copying Bio/KDTree/__init__.py -> build/lib.linux-i686-3.7/Bio/KDTree
copying Bio/KDTree/KDTree.py -> build/lib.linux-i686-3.7/Bio/KDTree
creating build/lib.linux-i686-3.7/Bio/phenotype
copying Bio/phenotype/phen_micro.py -> build/lib.linux-i686-3.7/Bio/phenotype
copying Bio/phenotype/__init__.py -> build/lib.linux-i686-3.7/Bio/phenotype
copying Bio/phenotype/pm_fitting.py -> build/lib.linux-i686-3.7/Bio/phenotype
running egg_info
writing biopython.egg-info/PKG-INFO
writing dependency_links to biopython.egg-info/dependency_links.txt
writing requirements to biopython.egg-info/requires.txt
writing top-level names to biopython.egg-info/top_level.txt
reading manifest file 'biopython.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'biopython.egg-info/SOURCES.txt'
copying Bio/cpairwise2module.c -> build/lib.linux-i686-3.7/Bio
copying Bio/trie.c -> build/lib.linux-i686-3.7/Bio
copying Bio/trie.h -> build/lib.linux-i686-3.7/Bio
copying Bio/triemodule.c -> build/lib.linux-i686-3.7/Bio
copying Bio/Align/_aligners.c -> build/lib.linux-i686-3.7/Bio/Align
creating build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Features.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Access.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_General.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Project.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_all.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NSE.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NSE.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/OMSSA.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PDB_General.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PIR_General.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PRF_General.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/SP_General.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/SP_General.mod.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivearticle.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-classes.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-models.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-modules.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/articlemeta.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/backmatter.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/chars.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/common.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/default-classes.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/default-mixes.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/display.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eInfo_020511.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eLink_090910.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eLink_101123.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/ePost_020511.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eSearch_020511.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eSpell.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/eSummary_041029.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/egquery.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/einfo.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/elink_020122.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/esearch.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/esummary-v1.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/format.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/htmltable.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsa.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsb.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsc.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsn.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamso.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsr.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isobox.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isocyr1.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isocyr2.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isodia.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk1.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk2.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk3.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk4.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isolat1.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isolat2.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomfrk.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomopf.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomscr.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isonum.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isopub.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isotech.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/journalmeta.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/link.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/list.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/math.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml2.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml3-qname1.mod -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml3.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathmlsetup.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mmlalias.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mmlextra.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/modules.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/notat.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/para.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/phrase.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pmc-1.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_020114.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_080101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_090101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_100101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_100301.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_110101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_120101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_130101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_130501.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_140101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_150101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_180101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_180601.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_190101.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/references.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/section.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/taxon.dtd -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.linux-i686-3.7/Bio/Entrez/DTDs
creating build/lib.linux-i686-3.7/Bio/Entrez/XSDs
copying Bio/Entrez/XSDs/IPGReportSet.xsd -> build/lib.linux-i686-3.Bio/Align/_aligners.c: In function ‘PathGenerator_length’:
Bio/Align/_aligners.c:701:22: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized]
701 | self->length = length;
| ~~~~~~~~~~~~~^~~~~~~~
In file included from /usr/include/python3.7m/Python.h:108,
from Bio/cpairwise2module.c:14:
Bio/cpairwise2module.c: In function ‘cpairwise2__make_score_matrix_fast’:
/usr/include/python3.7m/listobject.h:73:58: warning: ‘py_trace_row’ may be used uninitialized in this function [-Wmaybe-uninitialized]
73 | #define PyList_SET_ITEM(op, i, v) (((PyListObject *)(op))->ob_item[i] = (v))
| ^~
Bio/cpairwise2module.c:343:34: note: ‘py_trace_row’ was declared here
343 | PyObject *py_score_row, *py_trace_row;
| ^~~~~~~~~~~~
7/Bio/Entrez/XSDs
copying Bio/motifs/_pwm.c -> build/lib.linux-i686-3.7/Bio/motifs
copying Bio/Nexus/cnexus.c -> build/lib.linux-i686-3.7/Bio/Nexus
copying Bio/PDB/kdtrees.c -> build/lib.linux-i686-3.7/Bio/PDB
copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> build/lib.linux-i686-3.7/Bio/PDB/QCPSuperimposer
copying Bio/Cluster/cluster.c -> build/lib.linux-i686-3.7/Bio/Cluster
copying Bio/Cluster/cluster.h -> build/lib.linux-i686-3.7/Bio/Cluster
copying Bio/Cluster/clustermodule.c -> build/lib.linux-i686-3.7/Bio/Cluster
copying Bio/KDTree/KDTree.c -> build/lib.linux-i686-3.7/Bio/KDTree
copying Bio/KDTree/KDTree.h -> build/lib.linux-i686-3.7/Bio/KDTree
copying Bio/KDTree/KDTreemodule.c -> build/lib.linux-i686-3.7/Bio/KDTree
copying Bio/KDTree/Neighbor.h -> build/lib.linux-i686-3.7/Bio/KDTree
running build_ext
building 'Bio.Align._aligners' extension
creating build/temp.linux-i686-3.7
creating build/temp.linux-i686-3.7/Bio
creating build/temp.linux-i686-3.7/Bio/Align
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.7m -c Bio/Align/_aligners.c -o build/temp.linux-i686-3.7/Bio/Align/_aligners.o
gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.7/Bio/Align/_aligners.o -L/usr/lib -lpython3.7m -o build/lib.linux-i686-3.7/Bio/Align/_aligners.cpython-37m-i386-linux-gnu.so
building 'Bio.cpairwise2' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.7m -c Bio/cpairwise2module.c -o build/temp.linux-i686-3.7/Bio/cpairwise2module.o
gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.7/Bio/cpairwise2module.o -L/usr/lib -lpython3.7m -o build/lib.linux-i686-3.7/Bio/cpairwise2.cpython-37m-i386-linux-gnu.so
building 'Bio.Nexus.cnexus' extension
creating build/temp.linux-i686-3.7/Bio/Nexus
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.7m -c Bio/Nexus/cnexus.c -o build/temp.linux-i686-3.7/Bio/Nexus/cnexus.o
gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.7/Bio/Nexus/cnexus.o -L/usr/lib -lpython3.7m -o build/lib.linux-i686-3.7/Bio/Nexus/cnexus.cpython-37m-i386-linux-gnu.so
building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension
creating build/temp.linux-i686-3.7/Bio/PDB
creating build/temp.linux-i686-3.7/Bio/PDB/QCPSuperimposer
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.7m -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-i686-3.7/Bio/PDB/QCPSuperimposer/qcprotmodule.o
gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.7/Bio/PDB/QCPSuperimposer/qcprotmodule.o -L/usr/lib -lpython3.7m -o build/lib.linux-i686-3.7/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-37m-i386-linux-gnu.so
building 'Bio.motifs._pwm' extension
creating build/temp.linux-i686-3.7/Bio/motifs
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.7m -c Bio/motifs/_pwm.c -o build/temp.linux-i686-3.7/Bio/motifs/_pwm.o
gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.7/Bio/motifs/_pwm.o -L/usr/lib -lpython3.7m -o build/lib.linux-i686-3.7/Bio/motifs/_pwm.cpython-37m-i386-linux-gnu.so
building 'Bio.Cluster._cluster' extension
creating build/temp.linux-i686-3.7/Bio/Cluster
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.7m -c Bio/Cluster/cluster.c -o build/temp.linux-i686-3.7/Bio/Cluster/cluster.o
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.7m -c Bio/Cluster/clustermodule.c -o build/temp.linux-i686-3.7/Bio/Cluster/clustermodule.o
gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.7/Bio/Cluster/cluster.o build/temp.linux-i686-3.7/Bio/Cluster/clustermodule.o -L/usr/lib -lpython3.7m -o build/lib.linux-i686-3.7/Bio/Cluster/_cluster.cpython-37m-i386-linux-gnu.so
building 'Bio.PDB.kdtrees' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.7m -c Bio/PDB/kdtrees.c -o build/temp.linux-i686-3.7/Bio/PDB/kdtrees.o
gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.7/Bio/PDB/kdtrees.o -L/usr/lib -lpython3.7m -o build/lib.linux-i686-3.7/Bio/PDB/kdtrees.cpython-37m-i386-linux-gnu.so
building 'Bio.KDTree._CKDTree' extension
creating build/temp.linux-i686-3.7/Bio/KDTree
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.7m -c Bio/KDTree/KDTree.c -o build/temp.linux-i686-3.7/Bio/KDTree/KDTree.o
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.7m -c Bio/KDTree/KDTreemodule.c -o build/temp.linux-i686-3.7/Bio/KDTree/KDTreemodule.o
gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.7/Bio/KDTree/KDTree.o build/temp.linux-i686-3.7/Bio/KDTree/KDTreemodule.o -L/usr/lib -lpython3.7m -o build/lib.linux-i686-3.7/Bio/KDTree/_CKDTree.cpython-37m-i386-linux-gnu.so
building 'Bio.trie' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -greBio/triemodule.c:585:5: warning: initialization of ‘Py_hash_t (*)(PyObject *)’ {aka ‘int (*)(struct _object *)’} from incompatible pointer type ‘long int (*)(PyObject *)’ {aka ‘long int (*)(struct _object *)’} [-Wincompatible-pointer-types]
585 | trie_nohash, /*tp_hash */
| ^~~~~~~~~~~
Bio/triemodule.c:585:5: note: (near initialization for ‘Trie_Type.tp_hash’)
Bio/trie.c: In function ‘_iterate_helper’:
Bio/trie.c:510:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
510 | if(keylen + strlen(suffix) >= max_key) {
| ^~
In file included from /usr/include/string.h:494,
from Bio/trie.c:17:
In function ‘strncat’,
inlined from ‘_with_prefix_helper.constprop’ at Bio/trie.c:595:6:
/usr/include/bits/string_fortified.h:136:10: warning: ‘__builtin___strncat_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Bio/trie.c: In function ‘_with_prefix_helper.constprop’:
Bio/trie.c:561:14: note: length computed here
561 | suffixlen = strlen(suffix);
| ^~~~~~~~~~~~~~
+ popd
+ RPM_EC=0
++ jobs -p
+ exit 0
cord-gcc-switches -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -IBio -I/usr/include/python3.7m -c Bio/triemodule.c -o build/temp.linux-i686-3.7/Bio/triemodule.o
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -IBio -I/usr/include/python3.7m -c Bio/trie.c -o build/temp.linux-i686-3.7/Bio/trie.o
gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.7/Bio/triemodule.o build/temp.linux-i686-3.7/Bio/trie.o -L/usr/lib -lpython3.7m -o build/lib.linux-i686-3.7/Bio/trie.cpython-37m-i386-linux-gnu.so
~/build/BUILD/python-biopython-1.73
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.IJ3tkv
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386
++ dirname /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386
+ cd python-biopython-1.73
+ pushd python3
+ /usr/bin/python3 setup.py install -O1 --skip-build --root=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386 --install-data=/usr/share/python-biopython
~/build/BUILD/python-biopython-1.73/python3 ~/build/BUILD/python-biopython-1.73
running install
running install_lib
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/BioSQL
copying build/lib.linux-i686-3.7/BioSQL/BioSeq.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/BioSQL
copying build/lib.linux-i686-3.7/BioSQL/BioSeqDatabase.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/BioSQL
copying build/lib.linux-i686-3.7/BioSQL/DBUtils.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/BioSQL
copying build/lib.linux-i686-3.7/BioSQL/Loader.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/BioSQL
copying build/lib.linux-i686-3.7/BioSQL/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/BioSQL
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/trie.cpython-37m-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/cpairwise2.cpython-37m-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/triemodule.c -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/trie.h -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/trie.c -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/cpairwise2module.c -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/phenotype
copying build/lib.linux-i686-3.7/Bio/phenotype/pm_fitting.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/phenotype
copying build/lib.linux-i686-3.7/Bio/phenotype/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/phenotype
copying build/lib.linux-i686-3.7/Bio/phenotype/phen_micro.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/phenotype
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-i686-3.7/Bio/KDTree/_CKDTree.cpython-37m-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-i686-3.7/Bio/KDTree/Neighbor.h -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-i686-3.7/Bio/KDTree/KDTreemodule.c -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-i686-3.7/Bio/KDTree/KDTree.h -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-i686-3.7/Bio/KDTree/KDTree.c -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-i686-3.7/Bio/KDTree/KDTree.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-i686-3.7/Bio/KDTree/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KDTree
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Cluster
copying build/lib.linux-i686-3.7/Bio/Cluster/_cluster.cpython-37m-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Cluster
copying build/lib.linux-i686-3.7/Bio/Cluster/clustermodule.c -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Cluster
copying build/lib.linux-i686-3.7/Bio/Cluster/cluster.h -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Cluster
copying build/lib.linux-i686-3.7/Bio/Cluster/cluster.c -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Cluster
copying build/lib.linux-i686-3.7/Bio/Cluster/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Cluster
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Affy
copying build/lib.linux-i686-3.7/Bio/Affy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Affy
copying build/lib.linux-i686-3.7/Bio/Affy/CelFile.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Affy
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/_py3k
copying build/lib.linux-i686-3.7/Bio/_py3k/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/_py3k
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Wise
copying build/lib.linux-i686-3.7/Bio/Wise/psw.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Wise
copying build/lib.linux-i686-3.7/Bio/Wise/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Wise
copying build/lib.linux-i686-3.7/Bio/Wise/dnal.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Wise
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/UniProt
copying build/lib.linux-i686-3.7/Bio/UniProt/GOA.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/UniProt
copying build/lib.linux-i686-3.7/Bio/UniProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/UniProt
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/UniGene
copying build/lib.linux-i686-3.7/Bio/UniGene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/UniGene
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-3.7/Bio/Phylo/PAML/yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-3.7/Bio/Phylo/PAML/chi2.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-3.7/Bio/Phylo/PAML/_parse_yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-3.7/Bio/Phylo/PAML/_parse_baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-3.7/Bio/Phylo/PAML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-3.7/Bio/Phylo/PAML/codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-3.7/Bio/Phylo/PAML/baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-3.7/Bio/Phylo/PAML/_parse_codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-3.7/Bio/Phylo/PAML/_paml.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-i686-3.7/Bio/Phylo/Applications/_Raxml.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-i686-3.7/Bio/Phylo/Applications/_Fasttree.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-i686-3.7/Bio/Phylo/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-i686-3.7/Bio/Phylo/Applications/_Phyml.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-i686-3.7/Bio/Phylo/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-3.7/Bio/Phylo/_cdao_owl.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-3.7/Bio/Phylo/TreeConstruction.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-3.7/Bio/Phylo/PhyloXML.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-3.7/Bio/Phylo/NewickIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-3.7/Bio/Phylo/NeXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-3.7/Bio/Phylo/Consensus.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-3.7/Bio/Phylo/CDAO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-3.7/Bio/Phylo/_io.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-3.7/Bio/Phylo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-3.7/Bio/Phylo/PhyloXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-3.7/Bio/Phylo/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-3.7/Bio/Phylo/Newick.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-3.7/Bio/Phylo/NeXML.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-3.7/Bio/Phylo/CDAOIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-3.7/Bio/Phylo/BaseTree.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/TogoWS
copying build/lib.linux-i686-3.7/Bio/TogoWS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/TogoWS
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SwissProt
copying build/lib.linux-i686-3.7/Bio/SwissProt/KeyWList.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SwissProt
copying build/lib.linux-i686-3.7/Bio/SwissProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SwissProt
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SVDSuperimposer
copying build/lib.linux-i686-3.7/Bio/SVDSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SVDSuperimposer
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SubsMat
copying build/lib.linux-i686-3.7/Bio/SubsMat/MatrixInfo.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SubsMat
copying build/lib.linux-i686-3.7/Bio/SubsMat/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SubsMat
copying build/lib.linux-i686-3.7/Bio/SubsMat/FreqTable.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SubsMat
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Statistics
copying build/lib.linux-i686-3.7/Bio/Statistics/lowess.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Statistics
copying build/lib.linux-i686-3.7/Bio/Statistics/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Statistics
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Sequencing
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-i686-3.7/Bio/Sequencing/Applications/_bwa.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-i686-3.7/Bio/Sequencing/Applications/_Novoalign.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-i686-3.7/Bio/Sequencing/Applications/_samtools.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-i686-3.7/Bio/Sequencing/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-i686-3.7/Bio/Sequencing/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Sequencing
copying build/lib.linux-i686-3.7/Bio/Sequencing/Ace.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Sequencing
copying build/lib.linux-i686-3.7/Bio/Sequencing/Phd.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Sequencing
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-3.7/Bio/SeqUtils/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-3.7/Bio/SeqUtils/ProtParam.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-3.7/Bio/SeqUtils/IsoelectricPoint.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-3.7/Bio/SeqUtils/CodonUsage.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-3.7/Bio/SeqUtils/lcc.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-3.7/Bio/SeqUtils/ProtParamData.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-3.7/Bio/SeqUtils/MeltingTemp.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-3.7/Bio/SeqUtils/CodonUsageIndices.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-3.7/Bio/SeqUtils/CheckSum.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqUtils
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-3.7/Bio/SeqIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-3.7/Bio/SeqIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-3.7/Bio/SeqIO/TabIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-3.7/Bio/SeqIO/SffIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-3.7/Bio/SeqIO/QualityIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-3.7/Bio/SeqIO/PhdIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-3.7/Bio/SeqIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-3.7/Bio/SeqIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-3.7/Bio/SeqIO/AbiIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-3.7/Bio/SeqIO/_convert.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-3.7/Bio/SeqIO/UniprotIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-3.7/Bio/SeqIO/SwissIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-3.7/Bio/SeqIO/SeqXmlIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-3.7/Bio/SeqIO/PirIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-3.7/Bio/SeqIO/PdbIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-3.7/Bio/SeqIO/InsdcIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-3.7/Bio/SeqIO/IgIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-3.7/Bio/SeqIO/AceIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/InterproscanIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/InterproscanIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/InterproscanIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/InterproscanIO
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/ExonerateIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/ExonerateIO/exonerate_text.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/ExonerateIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/HmmerIO/hmmer3_text.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/HmmerIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/HmmerIO/hmmer2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/HmmerIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/BlastIO/blast_text.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/BlastIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/BlastIO/blast_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/BlastIO/blast_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/BlastIO
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-i686-3.7/Bio/SearchIO/_model/query.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-i686-3.7/Bio/SearchIO/_model/hit.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-i686-3.7/Bio/SearchIO/_model/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-i686-3.7/Bio/SearchIO/_model/hsp.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-i686-3.7/Bio/SearchIO/_model/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/_model
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-i686-3.7/Bio/SearchIO/_legacy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-i686-3.7/Bio/SearchIO/_legacy/NCBIStandalone.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-i686-3.7/Bio/SearchIO/_legacy/ParserSupport.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-i686-3.7/Bio/SearchIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO
copying build/lib.linux-i686-3.7/Bio/SearchIO/BlatIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-i686-3.7/Bio/SCOP/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-i686-3.7/Bio/SCOP/Raf.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-i686-3.7/Bio/SCOP/Dom.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-i686-3.7/Bio/SCOP/Cla.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-i686-3.7/Bio/SCOP/Residues.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-i686-3.7/Bio/SCOP/Hie.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-i686-3.7/Bio/SCOP/Des.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SCOP
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Restriction
copying build/lib.linux-i686-3.7/Bio/Restriction/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Restriction
copying build/lib.linux-i686-3.7/Bio/Restriction/Restriction.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Restriction
copying build/lib.linux-i686-3.7/Bio/Restriction/PrintFormat.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Restriction
copying build/lib.linux-i686-3.7/Bio/Restriction/Restriction_Dictionary.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Restriction
copying build/lib.linux-i686-3.7/Bio/Restriction/RanaConfig.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Restriction
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PopGen
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-i686-3.7/Bio/PopGen/GenePop/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-i686-3.7/Bio/PopGen/GenePop/LargeFileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-i686-3.7/Bio/PopGen/GenePop/EasyController.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-i686-3.7/Bio/PopGen/GenePop/Utils.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-i686-3.7/Bio/PopGen/GenePop/FileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-i686-3.7/Bio/PopGen/GenePop/Controller.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-i686-3.7/Bio/PopGen/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PopGen
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Pathway
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Pathway/Rep
copying build/lib.linux-i686-3.7/Bio/Pathway/Rep/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Pathway/Rep
copying build/lib.linux-i686-3.7/Bio/Pathway/Rep/Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Pathway/Rep
copying build/lib.linux-i686-3.7/Bio/Pathway/Rep/MultiGraph.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Pathway/Rep
copying build/lib.linux-i686-3.7/Bio/Pathway/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Pathway
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/NMR
copying build/lib.linux-i686-3.7/Bio/NMR/NOEtools.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/NMR
copying build/lib.linux-i686-3.7/Bio/NMR/xpktools.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/NMR
copying build/lib.linux-i686-3.7/Bio/NMR/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/NMR
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-i686-3.7/Bio/Nexus/cnexus.cpython-37m-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-i686-3.7/Bio/Nexus/cnexus.c -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-i686-3.7/Bio/Nexus/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-i686-3.7/Bio/Nexus/StandardData.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-i686-3.7/Bio/Nexus/Nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-i686-3.7/Bio/Nexus/Trees.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-i686-3.7/Bio/Nexus/Nodes.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Nexus
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-i686-3.7/Bio/motifs/_pwm.cpython-37m-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-i686-3.7/Bio/motifs/_pwm.c -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/motifs
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/motifs/jaspar
copying build/lib.linux-i686-3.7/Bio/motifs/jaspar/db.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/motifs/jaspar
copying build/lib.linux-i686-3.7/Bio/motifs/jaspar/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/motifs/jaspar
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/motifs/applications
copying build/lib.linux-i686-3.7/Bio/motifs/applications/_xxmotif.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/motifs/applications
copying build/lib.linux-i686-3.7/Bio/motifs/applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/motifs/applications
copying build/lib.linux-i686-3.7/Bio/motifs/thresholds.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-i686-3.7/Bio/motifs/meme.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-i686-3.7/Bio/motifs/alignace.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-i686-3.7/Bio/motifs/transfac.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-i686-3.7/Bio/motifs/minimal.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-i686-3.7/Bio/motifs/matrix.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-i686-3.7/Bio/motifs/mast.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-i686-3.7/Bio/motifs/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/motifs
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Medline
copying build/lib.linux-i686-3.7/Bio/Medline/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Medline
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/kdtrees.cpython-37m-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/kdtrees.c -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-i686-3.7/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-37m-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-i686-3.7/Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-i686-3.7/Bio/PDB/QCPSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-i686-3.7/Bio/PDB/parse_pdb_header.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/Superimposer.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/StructureAlignment.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/Selection.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/Residue.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/PSEA.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/PDBList.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/PDBExceptions.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/NACCESS.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/MMCIFParser.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/HSExposure.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/Entity.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/DSSP.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/Atom.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/vectors.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/mmcifio.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/Vector.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/StructureBuilder.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/Structure.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/ResidueDepth.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/Polypeptide.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/PDBParser.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/PDBIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/NeighborSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/Model.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/MMCIF2Dict.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/FragmentMapper.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/Dice.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/Chain.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-i686-3.7/Bio/PDB/AbstractPropertyMap.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB/mmtf
copying build/lib.linux-i686-3.7/Bio/PDB/mmtf/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB/mmtf
copying build/lib.linux-i686-3.7/Bio/PDB/mmtf/DefaultParser.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB/mmtf
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KEGG
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KEGG/KGML
copying build/lib.linux-i686-3.7/Bio/KEGG/KGML/KGML_pathway.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KEGG/KGML
copying build/lib.linux-i686-3.7/Bio/KEGG/KGML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KEGG/KGML
copying build/lib.linux-i686-3.7/Bio/KEGG/KGML/KGML_parser.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KEGG/KGML
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KEGG/Map
copying build/lib.linux-i686-3.7/Bio/KEGG/Map/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KEGG/Map
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KEGG/Gene
copying build/lib.linux-i686-3.7/Bio/KEGG/Gene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KEGG/Gene
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KEGG/Enzyme
copying build/lib.linux-i686-3.7/Bio/KEGG/Enzyme/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KEGG/Enzyme
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KEGG/Compound
copying build/lib.linux-i686-3.7/Bio/KEGG/Compound/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KEGG/Compound
copying build/lib.linux-i686-3.7/Bio/KEGG/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KEGG
copying build/lib.linux-i686-3.7/Bio/KEGG/REST.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KEGG
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/HMM
copying build/lib.linux-i686-3.7/Bio/HMM/Trainer.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/HMM
copying build/lib.linux-i686-3.7/Bio/HMM/DynamicProgramming.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/HMM
copying build/lib.linux-i686-3.7/Bio/HMM/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/HMM
copying build/lib.linux-i686-3.7/Bio/HMM/Utilities.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/HMM
copying build/lib.linux-i686-3.7/Bio/HMM/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/HMM
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram/_Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram/_Feature.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram/_CrossLink.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram/_Colors.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram/_Track.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram/_GraphSet.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram/_Diagram.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-3.7/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-3.7/Bio/Graphics/KGML_vis.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics
copying build/lib.linux-i686-3.7/Bio/Graphics/DisplayRepresentation.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics
copying build/lib.linux-i686-3.7/Bio/Graphics/ColorSpiral.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics
copying build/lib.linux-i686-3.7/Bio/Graphics/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics
copying build/lib.linux-i686-3.7/Bio/Graphics/Distribution.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics
copying build/lib.linux-i686-3.7/Bio/Graphics/Comparative.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics
copying build/lib.linux-i686-3.7/Bio/Graphics/BasicChromosome.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Geo
copying build/lib.linux-i686-3.7/Bio/Geo/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Geo
copying build/lib.linux-i686-3.7/Bio/Geo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Geo
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/GenBank
copying build/lib.linux-i686-3.7/Bio/GenBank/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/GenBank
copying build/lib.linux-i686-3.7/Bio/GenBank/utils.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/GenBank
copying build/lib.linux-i686-3.7/Bio/GenBank/Scanner.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/GenBank
copying build/lib.linux-i686-3.7/Bio/GenBank/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/GenBank
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/FSSP
copying build/lib.linux-i686-3.7/Bio/FSSP/fssp_rec.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/FSSP
copying build/lib.linux-i686-3.7/Bio/FSSP/FSSPTools.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/FSSP
copying build/lib.linux-i686-3.7/Bio/FSSP/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/FSSP
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/ExPASy
copying build/lib.linux-i686-3.7/Bio/ExPASy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/ExPASy
copying build/lib.linux-i686-3.7/Bio/ExPASy/Prosite.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/ExPASy
copying build/lib.linux-i686-3.7/Bio/ExPASy/Enzyme.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/ExPASy
copying build/lib.linux-i686-3.7/Bio/ExPASy/cellosaurus.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/ExPASy
copying build/lib.linux-i686-3.7/Bio/ExPASy/ScanProsite.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/ExPASy
copying build/lib.linux-i686-3.7/Bio/ExPASy/Prodoc.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/ExPASy
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/XSDs
copying build/lib.linux-i686-3.7/Bio/Entrez/XSDs/IPGReportSet.xsd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/XSDs
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/xmlspecchars.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/taxon.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/section.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/references.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/pubmed_190101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/pubmed_180601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/pubmed_180101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/pubmed_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/pubmed_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/pubmed_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/pubmed_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/pubmed_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/pubmed_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/pubmed_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/pubmed_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/pubmed_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/pubmed_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/pubmed_020114.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/pmc-1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/phrase.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/para.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/notat.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmserials_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmserials_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/mmlextra.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/mmlalias.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/mathmlsetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/mathml3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/mathml3-qname1.mod -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/mathml2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/mathml2-qname-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/math.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/list.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/link.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/journalmeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isotech.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isopub.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isonum.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isomscr.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isomopf.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isomfrk.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isolat2.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isolat1.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isogrk4.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isogrk3.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isogrk2.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isogrk1.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isodia.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isocyr2.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isocyr1.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isobox.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isoamsr.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isoamso.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isoamsn.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isoamsc.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isoamsb.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/isoamsa.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/htmltable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/format.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/esummary-v1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/esearch.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/elink_020122.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/einfo.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/egquery.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/eSummary_041029.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/eSpell.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/eSearch_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/ePost_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/eLink_101123.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/eLink_090910.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/eInfo_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/display.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/default-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/default-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/common.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/chars.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/bookdoc_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/bookdoc_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/bookdoc_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/bookdoc_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/bookdoc_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/bookdoc_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/backmatter.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/articlemeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/archivecustom-modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/archivecustom-models.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/archivecustom-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/archivecustom-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/archivearticle.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/SP_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/SP_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/PRF_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/PRF_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/PIR_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/PIR_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/PDB_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/PDB_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/OMSSA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/OMSSA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NSE.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NSE.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_all.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Variation.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Systems.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Submit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Remap.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_RNA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Pub.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Protein.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Project.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Organism.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Mime.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Mim.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Medline.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Gene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/NCBI_Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/MMDB_Features.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/MMDB.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/MMDB.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/HomoloGene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/GenBank_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/EMBL_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/Docsum_3_4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/Docsum_3_3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/Docsum_3_2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/Docsum_3_1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/DTDs/Docsum_3_0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-3.7/Bio/Entrez/Parser.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez
copying build/lib.linux-i686-3.7/Bio/Entrez/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Emboss
copying build/lib.linux-i686-3.7/Bio/Emboss/PrimerSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Emboss
copying build/lib.linux-i686-3.7/Bio/Emboss/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Emboss
copying build/lib.linux-i686-3.7/Bio/Emboss/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Emboss
copying build/lib.linux-i686-3.7/Bio/Emboss/Primer3.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Emboss
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Data
copying build/lib.linux-i686-3.7/Bio/Data/IUPACData.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Data
copying build/lib.linux-i686-3.7/Bio/Data/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Data
copying build/lib.linux-i686-3.7/Bio/Data/SCOPData.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Data
copying build/lib.linux-i686-3.7/Bio/Data/CodonTable.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Data
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Crystal
copying build/lib.linux-i686-3.7/Bio/Crystal/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Crystal
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Compass
copying build/lib.linux-i686-3.7/Bio/Compass/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Compass
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/codonalign
copying build/lib.linux-i686-3.7/Bio/codonalign/codonseq.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/codonalign
copying build/lib.linux-i686-3.7/Bio/codonalign/codonalignment.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/codonalign
copying build/lib.linux-i686-3.7/Bio/codonalign/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/codonalign
copying build/lib.linux-i686-3.7/Bio/codonalign/codonalphabet.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/codonalign
copying build/lib.linux-i686-3.7/Bio/codonalign/chisq.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/codonalign
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/CAPS
copying build/lib.linux-i686-3.7/Bio/CAPS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/CAPS
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Blast
copying build/lib.linux-i686-3.7/Bio/Blast/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Blast
copying build/lib.linux-i686-3.7/Bio/Blast/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Blast
copying build/lib.linux-i686-3.7/Bio/Blast/NCBIXML.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Blast
copying build/lib.linux-i686-3.7/Bio/Blast/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Blast
copying build/lib.linux-i686-3.7/Bio/Blast/ParseBlastTable.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Blast
copying build/lib.linux-i686-3.7/Bio/Blast/NCBIWWW.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Blast
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Application
copying build/lib.linux-i686-3.7/Bio/Application/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Application
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Alphabet
copying build/lib.linux-i686-3.7/Bio/Alphabet/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Alphabet
copying build/lib.linux-i686-3.7/Bio/Alphabet/IUPAC.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Alphabet
copying build/lib.linux-i686-3.7/Bio/Alphabet/Reduced.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Alphabet
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-i686-3.7/Bio/AlignIO/StockholmIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-i686-3.7/Bio/AlignIO/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-i686-3.7/Bio/AlignIO/MafIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-i686-3.7/Bio/AlignIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-i686-3.7/Bio/AlignIO/ClustalIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-i686-3.7/Bio/AlignIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-i686-3.7/Bio/AlignIO/PhylipIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-i686-3.7/Bio/AlignIO/MauveIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-i686-3.7/Bio/AlignIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-i686-3.7/Bio/AlignIO/EmbossIO.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/AlignIO
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Align
copying build/lib.linux-i686-3.7/Bio/Align/_aligners.cpython-37m-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Align
copying build/lib.linux-i686-3.7/Bio/Align/_aligners.c -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Align
creating /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-3.7/Bio/Align/Applications/_TCoffee.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-3.7/Bio/Align/Applications/_Prank.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-3.7/Bio/Align/Applications/_Mafft.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-3.7/Bio/Align/Applications/_Dialign.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-3.7/Bio/Align/Applications/_ClustalOmega.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-3.7/Bio/Align/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-3.7/Bio/Align/Applications/_Probcons.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-3.7/Bio/Align/Applications/_Muscle.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-3.7/Bio/Align/Applications/_MSAProbs.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-3.7/Bio/Align/Applications/_Clustalw.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-3.7/Bio/Align/AlignInfo.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Align
copying build/lib.linux-i686-3.7/Bio/Align/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Align
copying build/lib.linux-i686-3.7/Bio/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/Index.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/triefind.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/pairwise2.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/kNN.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/bgzf.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/SeqRecord.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/SeqFeature.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/Seq.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/NaiveBayes.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/MaxEntropy.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/LogisticRegression.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-i686-3.7/Bio/File.py -> /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/BioSQL/BioSeq.py to BioSeq.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/BioSQL/BioSeqDatabase.py to BioSeqDatabase.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/BioSQL/DBUtils.py to DBUtils.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/BioSQL/Loader.py to Loader.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/BioSQL/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/phenotype/pm_fitting.py to pm_fitting.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/phenotype/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/phenotype/phen_micro.py to phen_micro.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KDTree/KDTree.py to KDTree.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KDTree/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Cluster/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Affy/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Affy/CelFile.py to CelFile.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/_py3k/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Wise/psw.py to psw.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Wise/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Wise/dnal.py to dnal.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/UniProt/GOA.py to GOA.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/UniProt/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/UniGene/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PAML/yn00.py to yn00.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PAML/chi2.py to chi2.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PAML/_parse_yn00.py to _parse_yn00.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PAML/_parse_baseml.py to _parse_baseml.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PAML/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PAML/codeml.py to codeml.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PAML/baseml.py to baseml.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PAML/_parse_codeml.py to _parse_codeml.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PAML/_paml.py to _paml.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/Applications/_Raxml.py to _Raxml.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/Applications/_Fasttree.py to _Fasttree.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/Applications/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/Applications/_Phyml.py to _Phyml.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/_utils.py to _utils.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/_cdao_owl.py to _cdao_owl.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/TreeConstruction.py to TreeConstruction.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PhyloXML.py to PhyloXML.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/NewickIO.py to NewickIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/NeXMLIO.py to NeXMLIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/Consensus.py to Consensus.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/CDAO.py to CDAO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/_io.py to _io.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/PhyloXMLIO.py to PhyloXMLIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/NexusIO.py to NexusIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/Newick.py to Newick.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/NeXML.py to NeXML.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/CDAOIO.py to CDAOIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Phylo/BaseTree.py to BaseTree.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/TogoWS/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SwissProt/KeyWList.py to KeyWList.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SwissProt/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SVDSuperimposer/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SubsMat/MatrixInfo.py to MatrixInfo.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SubsMat/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SubsMat/FreqTable.py to FreqTable.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Statistics/lowess.py to lowess.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Statistics/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Sequencing/Applications/_bwa.py to _bwa.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Sequencing/Applications/_Novoalign.py to _Novoalign.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Sequencing/Applications/_samtools.py to _samtools.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Sequencing/Applications/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Sequencing/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Sequencing/Ace.py to Ace.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Sequencing/Phd.py to Phd.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqUtils/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqUtils/ProtParam.py to ProtParam.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqUtils/IsoelectricPoint.py to IsoelectricPoint.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqUtils/CodonUsage.py to CodonUsage.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqUtils/lcc.py to lcc.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqUtils/ProtParamData.py to ProtParamData.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqUtils/MeltingTemp.py to MeltingTemp.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqUtils/CodonUsageIndices.py to CodonUsageIndices.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqUtils/CheckSum.py to CheckSum.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO/_index.py to _index.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO/TabIO.py to TabIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO/SffIO.py to SffIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO/QualityIO.py to QualityIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO/PhdIO.py to PhdIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO/Interfaces.py to Interfaces.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO/FastaIO.py to FastaIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO/AbiIO.py to AbiIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO/_convert.py to _convert.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO/UniprotIO.py to UniprotIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO/SwissIO.py to SwissIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO/SeqXmlIO.py to SeqXmlIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO/PirIO.py to PirIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO/PdbIO.py to PdbIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO/InsdcIO.py to InsdcIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO/IgIO.py to IgIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SeqIO/AceIO.py to AceIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/InterproscanIO/interproscan_xml.py to interproscan_xml.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/InterproscanIO/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py to exonerate_vulgar.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO/exonerate_cigar.py to exonerate_cigar.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO/exonerate_text.py to exonerate_text.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO/_base.py to _base.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO/hmmer3_text.py to hmmer3_text.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO/hmmer3_domtab.py to hmmer3_domtab.cpython-37.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_Graph.py to _Graph.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_Feature.py to _Feature.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_CrossLink.py to _CrossLink.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_Colors.py to _Colors.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py to _AbstractDrawer.cpython-37.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_GraphSet.py to _GraphSet.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_FeatureSet.py to _FeatureSet.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_Diagram.py to _Diagram.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_CircularDrawer.py to _CircularDrawer.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/KGML_vis.py to KGML_vis.cpython-37.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/ColorSpiral.py to ColorSpiral.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/Distribution.py to Distribution.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Graphics/Comparative.py to Comparative.cpython-37.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/GenBank/__init__.py to __init__.cpython-37.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/FSSP/FSSPTools.py to FSSPTools.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/FSSP/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/ExPASy/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/ExPASy/Prosite.py to Prosite.cpython-37.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/ExPASy/cellosaurus.py to cellosaurus.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/ExPASy/ScanProsite.py to ScanProsite.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/ExPASy/Prodoc.py to Prodoc.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/Parser.py to Parser.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Entrez/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Emboss/PrimerSearch.py to PrimerSearch.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Emboss/Applications.py to Applications.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Emboss/__init__.py to __init__.cpython-37.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Data/SCOPData.py to SCOPData.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Data/CodonTable.py to CodonTable.cpython-37.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Blast/Record.py to Record.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Blast/NCBIXML.py to NCBIXML.cpython-37.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Alphabet/Reduced.py to Reduced.cpython-37.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/AlignIO/MauveIO.py to MauveIO.cpython-37.pyc
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+ find Scripts -name '*.py'
+ xargs sed -i '1s|^#!/usr/bin/env python|#!/usr/bin/python3|'
+ popd
+ /usr/lib/rpm/find-debuginfo.sh -j2 --strict-build-id -m -i --build-id-seed 1.73-5.fc31 --unique-debug-suffix -1.73-5.fc31.i386 --unique-debug-src-base python-biopython-1.73-5.fc31.i386 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/python-biopython-1.73
1175 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 0
g install_egg_info
running egg_info
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Copying biopython.egg-info to /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/biopython-1.73-py3.7.egg-info
running install_scripts
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extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Cluster/_cluster.cpython-37m-i386-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Align/_aligners.cpython-37m-i386-linux-gnu.so
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extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/KDTree/_CKDTree.cpython-37m-i386-linux-gnu.so
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Nexus/cnexus.cpython-37m-i386-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/Nexus/cnexus.cpython-37m-i386-linux-gnu.so
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-37m-i386-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-37m-i386-linux-gnu.so
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB/kdtrees.cpython-37m-i386-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/PDB/kdtrees.cpython-37m-i386-linux-gnu.so
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/cpairwise2.cpython-37m-i386-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/cpairwise2.cpython-37m-i386-linux-gnu.so
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/motifs/_pwm.cpython-37m-i386-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/motifs/_pwm.cpython-37m-i386-linux-gnu.so
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/trie.cpython-37m-i386-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages/Bio/trie.cpython-37m-i386-linux-gnu.so
original debug info size: 904kB, size after compression: 828kB
/usr/lib/rpm/sepdebugcrcfix: Updated 9 CRC32s, 0 CRC32s did match.
Bytecompiling .py files below /build+ /usr/lib/rpm/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
dir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/debug/usr/lib/python3.7 using /usr/bin/python3.7
Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7 using /usr/bin/python3.7
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.jrFWYu
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.73
+ pushd python3/Tests
+ find . -name run_tests.py
+ xargs sed -i '1s|^#!/usr/bin/env python|#!/usr/bin/python3|'
++ grep -v Nexus
++ ls test_Ace.py test_Affy.py test_AlignIO.py test_AlignIO_ClustalIO.py test_AlignIO_EmbossIO.py test_AlignIO_FastaIO.py test_AlignIO_MauveIO.py test_AlignIO_PhylipIO.py test_AlignIO_convert.py test_AlignInfo.py test_Application.py test_BWA_tool.py test_BioSQL_MySQLdb.py test_BioSQL_MySQLdb_online.py test_BioSQL_mysql_connector.py test_BioSQL_mysql_connector_online.py test_BioSQL_psycopg2.py test_BioSQL_psycopg2_online.py test_BioSQL_sqlite3.py test_BioSQL_sqlite3_online.py test_CAPS.py test_CelFile.py test_Chi2.py test_ClustalOmega_tool.py test_Clustalw_tool.py test_Cluster.py test_CodonTable.py test_CodonUsage.py test_ColorSpiral.py test_Compass.py test_Consensus.py test_Crystal.py test_DSSP_tool.py test_Dialign_tool.py test_EMBL_unittest.py test_Emboss.py test_EmbossPhylipNew.py test_EmbossPrimer.py test_Entrez.py test_Entrez_online.py test_Entrez_parser.py test_Enzyme.py test_ExPASy.py test_FSSP.py test_Fasttree_tool.py test_File.py test_GenBank.py test_GenBank_unittest.py test_GenomeDiagram.py test_GraphicsBitmaps.py test_GraphicsChromosome.py test_GraphicsDistribution.py test_GraphicsGeneral.py test_HMMCasino.py test_HMMGeneral.py test_KDTree.py test_KEGG.py test_KEGG_online.py test_KGML_graphics.py test_KGML_graphics_online.py test_KGML_nographics.py test_KeyWList.py test_Location.py test_LogisticRegression.py test_MSAProbs_tool.py test_MafIO_index.py test_Mafft_tool.py test_MarkovModel.py test_Medline.py test_Muscle_tool.py test_NACCESS_tool.py test_NCBITextParser.py test_NCBIXML.py test_NCBI_BLAST_tools.py test_NCBI_qblast.py test_NaiveBayes.py test_Nexus.py test_PAML_baseml.py test_PAML_codeml.py test_PAML_tools.py test_PAML_yn00.py test_PDB.py test_PDBList.py test_PDB_FragmentMapper.py test_PDB_KDTree.py test_PDB_MMCIF2Dict.py test_PDB_MMCIFParser.py test_PDB_Polypetide.py test_PDB_ResidueDepth.py test_PDB_StructureAlignment.py test_PDB_Superimposer.py test_PDB_vectors.py test_Pathway.py test_Phd.py test_Phylo.py test_PhyloXML.py test_Phylo_CDAO.py test_Phylo_NeXML.py test_Phylo_matplotlib.py test_Phylo_networkx.py test_PopGen_GenePop.py test_PopGen_GenePop_EasyController.py test_PopGen_GenePop_nodepend.py test_Prank_tool.py test_Probcons_tool.py test_ProtParam.py test_QCPSuperimposer.py test_RCSBFormats.py test_Restriction.py test_SCOP_Astral.py test_SCOP_Cla.py test_SCOP_Des.py test_SCOP_Dom.py test_SCOP_Hie.py test_SCOP_Raf.py test_SCOP_Residues.py test_SCOP_Scop.py test_SCOP_online.py test_SVDSuperimposer.py test_SearchIO_blast_tab.py test_SearchIO_blast_tab_index.py test_SearchIO_blast_text.py test_SearchIO_blast_xml.py test_SearchIO_blast_xml_index.py test_SearchIO_blat_psl.py test_SearchIO_blat_psl_index.py test_SearchIO_exonerate.py test_SearchIO_exonerate_text_index.py test_SearchIO_exonerate_vulgar_index.py test_SearchIO_fasta_m10.py test_SearchIO_fasta_m10_index.py test_SearchIO_hmmer2_text.py test_SearchIO_hmmer2_text_index.py test_SearchIO_hmmer3_domtab.py test_SearchIO_hmmer3_domtab_index.py test_SearchIO_hmmer3_tab.py test_SearchIO_hmmer3_tab_index.py test_SearchIO_hmmer3_text.py test_SearchIO_hmmer3_text_index.py test_SearchIO_interproscan_xml.py test_SearchIO_legacy.py test_SearchIO_model.py test_SearchIO_write.py test_SeqFeature.py test_SeqIO.py test_SeqIO_AbiIO.py test_SeqIO_FastaIO.py test_SeqIO_Insdc.py test_SeqIO_PdbIO.py test_SeqIO_QualityIO.py test_SeqIO_SeqXML.py test_SeqIO_convert.py test_SeqIO_features.py test_SeqIO_index.py test_SeqIO_online.py test_SeqIO_write.py test_SeqRecord.py test_SeqUtils.py test_Seq_objs.py test_SffIO.py test_SubsMat.py test_SwissProt.py test_TCoffee_tool.py test_TogoWS.py test_TreeConstruction.py test_Tutorial.py test_UniGene.py test_Uniprot.py test_Wise.py test_XXmotif_tool.py test_align.py test_bgzf.py test_cellosaurus.py test_codonalign.py test_geo.py test_kNN.py test_lowess.py test_mmtf.py test_mmtf_online.py test_motifs.py test_motifs_online.py test_pairwise2.py test_pairwise_aligner.py test_phenotype.py test_phenotype_fit.py test_phyml_tool.py test_prodoc.py test_prosite1.py test_prosite2.py test_psw.py test_raxml_tool.py test_samtools_tool.py test_s++ grep -v Phylo
eq.py test_translate.py test_trie.py
++ grep -v Tutorial
++ grep -v bgzf
++ grep -v SearchIO_blast
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Ace.py
test_Ace ... ok
test_check_ACEParser (test_Ace.AceTestOne)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestOne)
Test to check that contig parser parses each contig into a contig. ... ok
test_check_ACEParser (test_Ace.AceTestThree)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestThree)
Test to check that record parser parses each contig into a record. ... ok
test_check_ACEParser (test_Ace.AceTestTwo)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestTwo)
Test to check that record parser parses each contig into a record. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.061 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Affy.py
test_Affy ... ok
testAffy3 (test_Affy.AffyTest) ... ok
testAffy3Backwards (test_Affy.AffyTest) ... ok
testAffy4 (test_Affy.AffyTest) ... ok
testAffyBadHeader (test_Affy.AffyTest) ... ok
testAffyStrict (test_Affy.AffyTest) ... ok
testAffyWrongModeRead (test_Affy.AffyTest) ... ok
testAffyWrongModeReadV4 (test_Affy.AffyTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.014 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO.py
test_AlignIO ... ok
runTest (__main__.ComparisonTestCase)
test_AlignIO ... ok
----------------------------------------------------------------------
Ran 1 test in 2.442 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_ClustalIO.py
test_AlignIO_ClustalIO ... ok
test_cat_one_two (test_AlignIO_ClustalIO.TestClustalIO) ... ok
test_empy (test_AlignIO_ClustalIO.TestClustalIO)
Checking empty file. ... ok
test_kalign_header (test_AlignIO_ClustalIO.TestClustalIO)
Make sure we can parse the Kalign header. ... ok
test_one (test_AlignIO_ClustalIO.TestClustalIO) ... ok
test_three (test_AlignIO_ClustalIO.TestClustalIO) ... ok
test_two (test_AlignIO_ClustalIO.TestClustalIO) ... ok
test_write_read (test_AlignIO_ClustalIO.TestClustalIO)
Checking write/read. ... ok
test_write_read_single (test_AlignIO_ClustalIO.TestClustalIO)
Testing write/read when there is only one sequence. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.082 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_EmbossIO.py
test_AlignIO_EmbossIO ... ok
test_pair_example (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
test_pair_example2 (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
test_pair_example3 (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
test_pair_plus_simple (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
test_simple_example (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.080 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_FastaIO.py
test_AlignIO_FastaIO ... ok
test_output001 (test_AlignIO_FastaIO.FastaIOTests)
Check output001.m10 file. ... ok
test_output002 (test_AlignIO_FastaIO.FastaIOTests)
Check output002.m10 file. ... ok
test_output003 (test_AlignIO_FastaIO.FastaIOTests)
Check output003.m10 file. ... ok
test_output004 (test_AlignIO_FastaIO.FastaIOTests)
Check output004.m10 file. ... ok
test_output005 (test_AlignIO_FastaIO.FastaIOTests)
Check output005.m10 file. ... ok
test_output006 (test_AlignIO_FastaIO.FastaIOTests)
Check output006.m10 file. ... ok
test_output007 (test_AlignIO_FastaIO.FastaIOTests)
Check output007.m10 file. ... ok
test_output008 (test_AlignIO_FastaIO.FastaIOTests)
Check output008.m10 file. ... ok
test_output009 (test_AlignIO_FastaIO.FastaIOTests)
Check output009.m10 file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.105 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_MauveIO.py
test_AlignIO_MauveIO ... ok
test_one (test_AlignIO_MauveIO.TestMauveIO) ... ok
test_sequence_positions (test_AlignIO_MauveIO.TestMauveIO) ... ok
test_write_read (test_AlignIO_MauveIO.TestMauveIO) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.117 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_PhylipIO.py
test_AlignIO_PhylipIO ... ok
test_concatenation (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
test_five (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
test_five_a (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
test_four (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
test_one (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
test_two_and_three (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
test_write_read (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.081 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_convert.py
test_AlignIO_convert ... ok
test_Clustalw_hedgehog_aln_clustal_to_clustal (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to clustal ... ok
test_Clustalw_hedgehog_aln_clustal_to_fasta (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to fasta ... ok
test_Clustalw_hedgehog_aln_clustal_to_maf (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to maf ... ok
test_Clustalw_hedgehog_aln_clustal_to_mauve (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to mauve ... ok
test_Clustalw_hedgehog_aln_clustal_to_nexus (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to nexus ... ok
test_Clustalw_hedgehog_aln_clustal_to_phylip (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to phylip ... ok
test_Clustalw_hedgehog_aln_clustal_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to phylip-relaxed ... ok
test_Clustalw_hedgehog_aln_clustal_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to phylip-sequential ... ok
test_Clustalw_hedgehog_aln_clustal_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to stockholm ... ok
test_Fasta_output001_m10_fasta-m10_to_clustal (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to clustal ... ok
test_Fasta_output001_m10_fasta-m10_to_fasta (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to fasta ... ok
test_Fasta_output001_m10_fasta-m10_to_maf (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to maf ... ok
test_Fasta_output001_m10_fasta-m10_to_mauve (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to mauve ... ok
test_Fasta_output001_m10_fasta-m10_to_nexus (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to nexus ... ok
test_Fasta_output001_m10_fasta-m10_to_phylip (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to phylip ... ok
test_Fasta_output001_m10_fasta-m10_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to phylip-relaxed ... ok
test_Fasta_output001_m10_fasta-m10_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to phylip-sequential ... ok
test_Fasta_output001_m10_fasta-m10_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to stockholm ... ok
test_GFF_multi_fna_fasta_to_clustal (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to clustal ... ok
test_GFF_multi_fna_fasta_to_fasta (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to fasta ... ok
test_GFF_multi_fna_fasta_to_maf (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to maf ... ok
test_GFF_multi_fna_fasta_to_mauve (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to mauve ... ok
test_GFF_multi_fna_fasta_to_nexus (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to nexus ... ok
test_GFF_multi_fna_fasta_to_phylip (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to phylip ... ok
test_GFF_multi_fna_fasta_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to phylip-relaxed ... ok
test_GFF_multi_fna_fasta_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to phylip-sequential ... ok
test_GFF_multi_fna_fasta_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to stockholm ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_clustal (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to clustal ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_fasta (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to fasta ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_maf (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to maf ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_mauve (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to mauve ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_nexus (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to nexus ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_phylip (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to phylip ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to phylip-relaxed ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to phylip-sequential ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to stockholm ... ok
test_NBRF_clustalw_pir_pir_to_clustal (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to clustal ... ok
test_NBRF_clustalw_pir_pir_to_fasta (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to fasta ... ok
test_NBRF_clustalw_pir_pir_to_maf (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to maf ... ok
test_NBRF_clustalw_pir_pir_to_mauve (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to mauve ... ok
test_NBRF_clustalw_pir_pir_to_nexus (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to nexus ... ok
test_NBRF_clustalw_pir_pir_to_phylip (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to phylip ... ok
test_NBRF_clustalw_pir_pir_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to phylip-relaxed ... ok
test_NBRF_clustalw_pir_pir_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to phylip-sequential ... ok
test_NBRF_clustalw_pir_pir_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to stockholm ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_clustal (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to clustal ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_fasta (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to fasta ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_maf (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to maf ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_mauve (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to mauve ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_nexus (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to nexus ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_phylip (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to phylip ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to phylip-relaxed ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to phylip-sequential ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to stockholm ... ok
test_Quality_example_fastq_fastq-sanger_to_clustal (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to clustal ... ok
test_Quality_example_fastq_fastq-sanger_to_fasta (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to fasta ... ok
test_Quality_example_fastq_fastq-sanger_to_maf (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to maf ... ok
test_Quality_example_fastq_fastq-sanger_to_mauve (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to mauve ... ok
test_Quality_example_fastq_fastq-sanger_to_nexus (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to nexus ... ok
test_Quality_example_fastq_fastq-sanger_to_phylip (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to phylip ... ok
test_Quality_example_fastq_fastq-sanger_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to phylip-relaxed ... ok
test_Quality_example_fastq_fastq-sanger_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to phylip-sequential ... ok
test_Quality_example_fastq_fastq-sanger_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to stockholm ... ok
test_Quality_example_fastq_fastq_to_clustal (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to clustal ... ok
test_Quality_example_fastq_fastq_to_fasta (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to fasta ... ok
test_Quality_example_fastq_fastq_to_maf (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to maf ... ok
test_Quality_example_fastq_fastq_to_mauve (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to mauve ... ok
test_Quality_example_fastq_fastq_to_nexus (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to nexus ... ok
test_Quality_example_fastq_fastq_to_phylip (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to phylip ... ok
test_Quality_example_fastq_fastq_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to phylip-relaxed ... ok
test_Quality_example_fastq_fastq_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to phylip-sequential ... ok
test_Quality_example_fastq_fastq_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to stockholm ... ok
test_Stockholm_simple_sth_stockholm_to_clustal (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to clustal ... ok
test_Stockholm_simple_sth_stockholm_to_fasta (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to fasta ... ok
test_Stockholm_simple_sth_stockholm_to_maf (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to maf ... ok
test_Stockholm_simple_sth_stockholm_to_mauve (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to mauve ... ok
test_Stockholm_simple_sth_stockholm_to_nexus (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to nexus ... ok
test_Stockholm_simple_sth_stockholm_to_phylip (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to phylip ... ok
test_Stockholm_simple_sth_stockholm_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to phylip-relaxed ... ok
test_Stockholm_simple_sth_stockholm_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to phylip-sequential ... ok
test_Stockholm_simple_sth_stockholm_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to stockholm ... ok
----------------------------------------------------------------------
Ran 1 test in 0.447 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignInfo.py
test_AlignInfo ... ok
test_nucleotides (test_AlignInfo.AlignInfoTests) ... ok
test_proteins (test_AlignInfo.AlignInfoTests) ... ok
test_pseudo_count (test_AlignInfo.AlignInfoTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.132 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Application.py
test_Application ... ok
test_echo (test_Application.TestApp) ... ok
test_echo_capture_both (test_Application.TestApp) ... ok
test_echo_capture_neither (test_Application.TestApp) ... ok
test_echo_capture_stderr (test_Application.TestApp) ... ok
test_echo_capture_stdout (test_Application.TestApp) ... ok
test_echo_file_both (test_Application.TestApp) ... ok
test_echo_file_same (test_Application.TestApp) ... ok
test_echo_file_stderr (test_Application.TestApp) ... ok
test_echo_file_stdout (test_Application.TestApp) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.046 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BWA_tool.py
test_BWA_tool ... skipping. Install bwa and correctly set the file path to the program if you want to use it from Biopython
----------------------------------------------------------------------
Ran 1 test in 0.040 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_MySQLdb.py
test_BioSQL_MySQLdb ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
----------------------------------------------------------------------
Ran 1 test in 0.151 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_MySQLdb_online.py
test_BioSQL_MySQLdb_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.123 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_mysql_connector.py
test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
----------------------------------------------------------------------
Ran 1 test in 0.118 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_mysql_connector_online.py
test_BioSQL_mysql_connector_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.115 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_psycopg2.py
test_BioSQL_psycopg2 ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
----------------------------------------------------------------------
Ran 1 test in 0.112 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_psycopg2_online.py
test_BioSQL_psycopg2_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.126 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_sqlite3.py
test_BioSQL_sqlite3 ... ok
test_SeqIO_loading (common_BioSQL.AutoSeqIOTests) ... ok
test_backwards_compatibility (test_BioSQL_sqlite3.BackwardsCompatibilityTest)
Check can re-use an old BioSQL SQLite3 database. ... ok
test_NC_000932 (common_BioSQL.ClosedLoopTest)
From GenBank file to BioSQL and back to a GenBank file, NC_000932. ... ok
test_NC_005816 (common_BioSQL.ClosedLoopTest)
From GenBank file to BioSQL and back to a GenBank file, NC_005816. ... ok
test_NT_019265 (common_BioSQL.ClosedLoopTest)
From GenBank file to BioSQL and back to a GenBank file, NT_019265. ... ok
test_arab1 (common_BioSQL.ClosedLoopTest)
From GenBank file to BioSQL and back to a GenBank file, arab1. ... ok
test_cor6_6 (common_BioSQL.ClosedLoopTest)
From GenBank file to BioSQL and back to a GenBank file, cor6_6. ... ok
test_no_ref (common_BioSQL.ClosedLoopTest)
From GenBank file to BioSQL and back to a GenBank file, noref. ... ok
test_one_of (common_BioSQL.ClosedLoopTest)
From GenBank file to BioSQL and back to a GenBank file, one_of. ... ok
test_protein_refseq2 (common_BioSQL.ClosedLoopTest)
From GenBank file to BioSQL and back to a GenBank file, protein_refseq2. ... ok
test_del_db_items (common_BioSQL.DeleteTest)
Check all associated data is deleted from an item. ... ok
test_server (common_BioSQL.DeleteTest)
Check BioSeqDatabase methods. ... ok
test_duplicate_id_load (common_BioSQL.DupLoadTest)
Make sure can't import records with same ID (in one go). ... ok
test_duplicate_load (common_BioSQL.DupLoadTest)
Make sure can't import a single record twice (in one go). ... ok
test_duplicate_load2 (common_BioSQL.DupLoadTest)
Make sure can't import a single record twice (in steps). ... ok
test_record_loading (common_BioSQL.InDepthLoadTest)
Make sure all records are correctly loaded. ... ok
test_reload (common_BioSQL.InDepthLoadTest)
Make sure can't reimport existing records. ... ok
test_seq_feature (common_BioSQL.InDepthLoadTest)
In depth check that SeqFeatures are transmitted through the db. ... ok
test_transfer (common_BioSQL.InDepthLoadTest)
Make sure can load record into another namespace. ... ok
test_load_database (common_BioSQL.LoaderTest)
Load SeqRecord objects into a BioSQL database. ... ok
test_cross_retrieval_of_items (common_BioSQL.MultiReadTest)
Test that valid ids can't be retrieved between namespaces. ... ok
test_get_db_items (common_BioSQL.MultiReadTest)
Check list, keys, length etc. ... ok
test_server (common_BioSQL.MultiReadTest)
Check BioSeqDatabase methods. ... ok
test_get_db_items (common_BioSQL.ReadTest)
Check list, keys, length etc. ... ok
test_lookup_items (common_BioSQL.ReadTest)
Test retrieval of items using various ids. ... ok
test_server (common_BioSQL.ReadTest)
Check BioSeqDatabase methods. ... ok
test_addition (common_BioSQL.SeqInterfaceTest)
Check can add DBSeq objects together. ... ok
test_convert (common_BioSQL.SeqInterfaceTest)
Check can turn a DBSeq object into a Seq or MutableSeq. ... ok
test_multiplication (common_BioSQL.SeqInterfaceTest)
Check can multiply DBSeq objects by integers. ... ok
test_record_slicing (common_BioSQL.SeqInterfaceTest)
Check that slices of DBSeqRecord are retrieved properly. ... ok
test_seq (common_BioSQL.SeqInterfaceTest)
Make sure Seqs from BioSQL implement the right interface. ... ok
test_seq_features (common_BioSQL.SeqInterfaceTest)
Check SeqFeatures of a sequence. ... ok
test_seq_record (common_BioSQL.SeqInterfaceTest)
Make sure SeqRecords from BioSQL implement the right interface. ... ok
test_seq_slicing (common_BioSQL.SeqInterfaceTest)
Check that slices of sequences are retrieved properly. ... ok
test_ambiguous_location (common_BioSQL.SwissProtUnknownPositionTest)
Loaded uniprot-xml with ambiguous location in BioSQL. ... ok
test_NC_000932 (common_BioSQL.TransferTest)
From GenBank file to BioSQL, then again to a new namespace, NC_000932. ... ok
test_NC_005816 (common_BioSQL.TransferTest)
From GenBank file to BioSQL, then again to a new namespace, NC_005816. ... ok
test_NT_019265 (common_BioSQL.TransferTest)
From GenBank file to BioSQL, then again to a new namespace, NT_019265. ... ok
test_arab1 (common_BioSQL.TransferTest)
From GenBank file to BioSQL, then again to a new namespace, arab1. ... ok
test_cor6_6 (common_BioSQL.TransferTest)
From GenBank file to BioSQL, then again to a new namespace, cor6_6. ... ok
test_no_ref (common_BioSQL.TransferTest)
From GenBank file to BioSQL, then again to a new namespace, noref. ... ok
test_one_of (common_BioSQL.TransferTest)
From GenBank file to BioSQL, then again to a new namespace, one_of. ... ok
test_protein_refseq2 (common_BioSQL.TransferTest)
From GenBank file to BioSQL, then again to a new namespace, protein_refseq2. ... ok
----------------------------------------------------------------------
Ran 1 test in 11.650 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_sqlite3_online.py
test_BioSQL_sqlite3_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.118 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_CAPS.py
test_CAPS ... ok
test (test_CAPS.TestCAPS) ... ok
testNoCAPS (test_CAPS.TestCAPS) ... ok
test_trivial (test_CAPS.TestCAPS) ... ok
test_uneven (test_CAPS.TestCAPS) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.409 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_CelFile.py
test_CelFile ... ok
test_read (test_CelFile.testCelFile) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.008 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Chi2.py
test_Chi2 ... ok
test_cdf_chi2 (test_Chi2.ModTest) ... ok
test_incomplete_gamma (test_Chi2.ModTest) ... ok
test_ln_gamma (test_Chi2.ModTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.254 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ClustalOmega_tool.py
test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.132 seconds
~/build/BUILD/python-biopython-1.73/python3/Tests ~/build/BUILD/python-biopython-1.73
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Clustalw_tool.py
test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.125 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Cluster.py
test_Cluster ... ok
test_clusterdistance (test_Cluster.TestCluster) ... ok
test_distancematrix_kmedoids (test_Cluster.TestCluster) ... ok
test_kcluster (test_Cluster.TestCluster) ... ok
test_mask_parse (test_Cluster.TestCluster) ... ok
test_matrix_parse (test_Cluster.TestCluster) ... ok
test_pca (test_Cluster.TestCluster) ... ok
test_somcluster (test_Cluster.TestCluster) ... ok
test_tree (test_Cluster.TestCluster) ... ok
test_treecluster (test_Cluster.TestCluster) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.037 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_CodonTable.py
test_CodonTable ... ok
test_coding (test_CodonTable.AmbiguousCodonsTests)
Check a few ambiguous codons for correct coding. ... ok
test_list_ambiguous_codons (test_CodonTable.AmbiguousCodonsTests)
Check if stop codons are properly extended. ... ok
test_start_codons (test_CodonTable.AmbiguousCodonsTests)
Test various ambiguous codons as start codon. ... ok
test_stop_codons (test_CodonTable.AmbiguousCodonsTests)
Test various ambiguous codons as stop codon. ... ok
test_ambiguous_tables (test_CodonTable.BasicSanityTests)
Check if all IDs and all names are present in ambiguous tables. ... ok
test_complete_tables (test_CodonTable.BasicSanityTests)
Check if all unambiguous codon tables have all entries. ... ok
test_number_of_tables (test_CodonTable.BasicSanityTests)
Check if we have the same number of tables for each type. ... ok
test_ambiguous_forward_table (test_CodonTable.ErrorConditions)
Raise errors in AmbiguousForwardTable. ... ok
test_list_possible_proteins (test_CodonTable.ErrorConditions)
Raise errors in list_possible proteins. ... ok
test_print_table (test_CodonTable.PrintTable)
Test output of __str__ function. ... ok
test_table01 (test_CodonTable.SingleTableTests)
Check table 1: Standard. ... ok
test_table02 (test_CodonTable.SingleTableTests)
Check table 2: Vertebrate Mitochondrial. ... ok
test_table03 (test_CodonTable.SingleTableTests)
Check table 3: Yeast Mitochondrial. ... ok
test_table04 (test_CodonTable.SingleTableTests)
Check table 4: Mold Mitochondrial and others. ... ok
test_table05 (test_CodonTable.SingleTableTests)
Check table 5: Invertebrate Mitochondrial. ... ok
test_table06 (test_CodonTable.SingleTableTests)
Check table 6: Ciliate and Other Nuclear. ... ok
test_table09 (test_CodonTable.SingleTableTests)
Check table 9: Echinoderm and Flatworm Mitochondrial. ... ok
test_table10 (test_CodonTable.SingleTableTests)
Check table 10: Euplotid Nuclear. ... ok
test_table11 (test_CodonTable.SingleTableTests)
Check table 11: Bacterial, Archaeal and Plant Plastid. ... ok
test_table12 (test_CodonTable.SingleTableTests)
Check table 12: Alternative Yeast Nuclear. ... ok
test_table13 (test_CodonTable.SingleTableTests)
Check table 13: Ascidian Mitochondrial. ... ok
test_table14 (test_CodonTable.SingleTableTests)
Check table 14: Alternative Flatworm Mitochondrial. ... ok
test_table16 (test_CodonTable.SingleTableTests)
Check table 16: Chlorophycean Mitochondrial. ... ok
test_table21 (test_CodonTable.SingleTableTests)
Check table 21: Trematode Mitochondrial. ... ok
test_table22 (test_CodonTable.SingleTableTests)
Check table 22: Scenedesmus obliquus Mitochondrial. ... ok
test_table23 (test_CodonTable.SingleTableTests)
Check table 9: Thraustochytrium Mitochondrial. ... ok
test_table24 (test_CodonTable.SingleTableTests)
Check table 24: Pterobranchia Mitochondrial. ... ok
test_table25 (test_CodonTable.SingleTableTests)
Check table 25: Candidate Division SR1 and Gracilibacteria. ... ok
test_table26 (test_CodonTable.SingleTableTests)
Check table 26: Pachysolen tannophilus Nuclear. ... ok
test_table27 (test_CodonTable.SingleTableTests)
Check table 27: Karyorelict Nuclear. ... ok
test_table28 (test_CodonTable.SingleTableTests)
Check table 28: Condylostoma Nuclear. ... ok
test_table29 (test_CodonTable.SingleTableTests)
Check table 29: Mesodinium Nuclear. ... ok
test_table30 (test_CodonTable.SingleTableTests)
Check table 30: Peritrich Nuclear. ... ok
test_table31 (test_CodonTable.SingleTableTests)
Check table 31: Blastocrithidia Nuclear. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.075 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_CodonUsage.py
test_CodonUsage ... ok
runTest (__main__.ComparisonTestCase)
test_CodonUsage ... ok
----------------------------------------------------------------------
Ran 1 test in 0.131 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ColorSpiral.py
test_ColorSpiral ... ok
test_dict (test_ColorSpiral.DictTest)
get_color_dict() for classes A-D, no jitter. ... ok
test_colorlist (test_ColorSpiral.SpiralTest)
Get set of eight colours, no jitter, using ColorSpiral. ... ok
test_colorspiral (test_ColorSpiral.SpiralTest)
Get set of 16 colours, no jitter, using ColorSpiral. ... ok
test_colorspiral (test_ColorSpiral.SquareTest)
Set of 625 colours, with jitter, using get_colors(). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.071 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Compass.py
test_Compass ... ok
testAlignmentParsingOne (test_Compass.CompassTest) ... ok
testAlignmentParsingTwo (test_Compass.CompassTest) ... ok
testCompassIteratorEasy (test_Compass.CompassTest) ... ok
testCompassIteratorHard (test_Compass.CompassTest) ... ok
testCompassParser (test_Compass.CompassTest) ... ok
testCompassScanAndConsume (test_Compass.CompassTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.012 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Consensus.py
test_Consensus ... ok
test_bitstring (test_Consensus.BitStringTest) ... ok
test_bootstrap (test_Consensus.BootstrapTest) ... ok
test_bootstrap_consensus (test_Consensus.BootstrapTest) ... ok
test_bootstrap_trees (test_Consensus.BootstrapTest) ... ok
test_adam_consensus (test_Consensus.ConsensusTest) ... ok
test_count_clades (test_Consensus.ConsensusTest) ... ok
test_get_support (test_Consensus.ConsensusTest) ... ok
test_majority_consensus (test_Consensus.ConsensusTest) ... ok
test_strict_consensus (test_Consensus.ConsensusTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 2.221 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Crystal.py
test_Crystal ... ok
testAdd (test_Crystal.ChainTestCase) ... ok
testAppend (test_Crystal.ChainTestCase) ... ok
testContains (test_Crystal.ChainTestCase) ... ok
testCount (test_Crystal.ChainTestCase) ... ok
testDelItem (test_Crystal.ChainTestCase) ... ok
testDelSlice (test_Crystal.ChainTestCase) ... ok
testEquals (test_Crystal.ChainTestCase) ... ok
testGetItem (test_Crystal.ChainTestCase) ... ok
testGetSlice (test_Crystal.ChainTestCase) ... ok
testIndex (test_Crystal.ChainTestCase) ... ok
testInsert (test_Crystal.ChainTestCase) ... ok
testLen (test_Crystal.ChainTestCase) ... ok
testRemove (test_Crystal.ChainTestCase) ... ok
testSetItem (test_Crystal.ChainTestCase) ... ok
testSetSlice (test_Crystal.ChainTestCase) ... ok
testClear (test_Crystal.CrystalTestCase) ... ok
testDelItem (test_Crystal.CrystalTestCase) ... ok
testGetItem (test_Crystal.CrystalTestCase) ... ok
testHasKey (test_Crystal.CrystalTestCase) ... ok
testItems (test_Crystal.CrystalTestCase) ... ok
testKeys (test_Crystal.CrystalTestCase) ... ok
testLen (test_Crystal.CrystalTestCase) ... ok
testSetItem (test_Crystal.CrystalTestCase) ... ok
testValues (test_Crystal.CrystalTestCase) ... ok
testEquals (test_Crystal.HeteroTestCase) ... ok
testInit (test_Crystal.HeteroTestCase) ... ok
testLen (test_Crystal.HeteroTestCase) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.022 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_DSSP_tool.py
test_DSSP_tool ... skipping. Install dssp if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.130 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Dialign_tool.py
test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.078 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_EMBL_unittest.py
test_EMBL_unittest ... ok
test_embl_0_line (test_EMBL_unittest.EMBLTests)
Test SQ line with 0 length sequence ... ok
test_embl_content_after_co (test_EMBL_unittest.EMBLTests)
Test a ValueError is thrown by content after a CO line ... ok
test_embl_no_coords (test_EMBL_unittest.EMBLTests)
Test sequence lines without coordinates. ... ok
test_embl_wrong_dr_line (test_EMBL_unittest.EMBLTests)
Test files with wrong DR lines ... ok
----------------------------------------------------------------------
Ran 1 test in 0.120 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Emboss.py
test_Emboss ... skipping. Install EMBOSS if you want to use Bio.Emboss.
----------------------------------------------------------------------
Ran 1 test in 0.135 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_EmbossPhylipNew.py
test_EmbossPhylipNew ... skipping. Install the Emboss package 'PhylipNew' if you want to use the Bio.Emboss.Applications wrappers for phylogenetic tools.
----------------------------------------------------------------------
Ran 1 test in 0.100 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_EmbossPrimer.py
test_EmbossPrimer ... ok
test_in_depth_single_parse (test_EmbossPrimer.Primer3ParseTest)
Make sure we get info right from a single primer find. ... ok
test_indepth_regular_parse (test_EmbossPrimer.Primer3ParseTest)
Make sure we get the data from normal primer3 files okay. ... ok
test_internal_oligo_single_parse (test_EmbossPrimer.Primer3ParseTest)
Make sure we can parse an internal oligo file correctly. ... ok
test_mutli_record_full (test_EmbossPrimer.Primer3ParseTest)
Test parsing multiple primer sets (NirK full) ... ok
test_mutli_record_fwd (test_EmbossPrimer.Primer3ParseTest)
Test parsing multiple primer sets (NirK forward). ... ok
test_simple_parse (test_EmbossPrimer.Primer3ParseTest)
Make sure that we can use all single target primer3 files. ... ok
test_primer_representation (test_EmbossPrimer.PrimerSearchInputTest)
Make sure we can output primer information correctly. ... ok
test_in_depth_normal_parse (test_EmbossPrimer.PrimersearchParseTest)
Make sure the output from a simple primersearch file is correct. ... ok
test_simple_parse (test_EmbossPrimer.PrimersearchParseTest)
Make sure that we can parse all primersearch files. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.019 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Entrez.py
test_Entrez ... ok
test_custom_directory (test_Entrez.CustomDirectoryTest) ... ok
test_construct_cgi_ecitmatch (test_Entrez.TestURLConstruction) ... ok
test_construct_cgi_efetch (test_Entrez.TestURLConstruction) ... ok
test_construct_cgi_einfo (test_Entrez.TestURLConstruction)
Test constructed url for request to Entrez. ... ok
test_construct_cgi_elink1 (test_Entrez.TestURLConstruction) ... ok
test_construct_cgi_elink2 (test_Entrez.TestURLConstruction)
Commas: Link from protein to gene. ... ok
test_construct_cgi_elink3 (test_Entrez.TestURLConstruction)
Multiple ID entries: Find one-to-one links from protein to gene. ... ok
test_construct_cgi_epost1 (test_Entrez.TestURLConstruction) ... ok
test_construct_cgi_epost2 (test_Entrez.TestURLConstruction) ... ok
test_email_warning (test_Entrez.TestURLConstruction)
Test issuing warning when user does not specify email address. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.024 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Entrez_online.py
test_Entrez_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.102 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Entrez_parser.py
test_Entrez_parser ... ok
test_efetch_schemas (test_Entrez_parser.EFetchTest)
Test parsing XML using Schemas. ... ok
test_fasta (test_Entrez_parser.EFetchTest)
Test error handling when presented with Fasta non-XML data. ... ok
test_genbank (test_Entrez_parser.EFetchTest)
Test error handling when presented with GenBank non-XML data. ... ok
test_nucleotide1 (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, Nucleotide database (first test). ... ok
test_nucleotide2 (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, Nucleotide database (second test). ... ok
test_omim (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, OMIM database. ... ok
test_protein (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, Protein database. ... ok
test_pubmed1 (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, PubMed database (first test). ... ok
test_pubmed2 (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, PubMed database (second test). ... ok
test_pubmed_html (test_Entrez_parser.EFetchTest)
Test error handling when presented with HTML (so XML-like) data. ... ok
test_pubmed_html_escaping (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, PubMed database with HTML tags and HTML escape characters. ... ok
test_pubmed_html_mathml_tags (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, PubMed database, with both HTML and MathML tags ... ok
test_pubmed_html_tags (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, PubMed database with HTML tags. ... ok
test_taxonomy (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, Taxonomy database. ... ok
test_truncated_xml (test_Entrez_parser.EFetchTest)
Test error handling for a truncated XML declaration. ... ok
test_xml_without_declaration (test_Entrez_parser.EFetchTest)
Test error handling for a missing XML declaration. ... ok
test_egquery1 (test_Entrez_parser.EGQueryTest)
Test parsing XML output returned by EGQuery (first test). ... ok
test_egquery2 (test_Entrez_parser.EGQueryTest)
Test parsing XML output returned by EGQuery (second test). ... ok
test_corrupted (test_Entrez_parser.EInfoTest)
Test if corrupted XML is handled correctly. ... ok
test_list (test_Entrez_parser.EInfoTest)
Test parsing database list returned by EInfo. ... ok
test_pubmed1 (test_Entrez_parser.EInfoTest)
Test parsing database info returned by EInfo. ... ok
test_pubmed2 (test_Entrez_parser.EInfoTest)
Test validating the XML against the DTD. ... ok
test_pubmed3 (test_Entrez_parser.EInfoTest)
Test non-validating parser on XML with an inconsistent DTD. ... ok
test_medline (test_Entrez_parser.ELinkTest)
Test parsing medline indexed articles returned by ELink. ... ok
test_nucleotide (test_Entrez_parser.ELinkTest)
Test parsing Nucleotide to Protein links returned by ELink. ... ok
test_pubmed1 (test_Entrez_parser.ELinkTest)
Test parsing pubmed links returned by ELink (first test). ... ok
test_pubmed2 (test_Entrez_parser.ELinkTest)
Test parsing pubmed links returned by ELink (second test). ... ok
test_pubmed3 (test_Entrez_parser.ELinkTest)
Test parsing pubmed link returned by ELink (third test). ... ok
test_pubmed4 (test_Entrez_parser.ELinkTest)
Test parsing pubmed links returned by ELink (fourth test). ... ok
test_pubmed5 (test_Entrez_parser.ELinkTest)
Test parsing pubmed links returned by ELink (fifth test). ... ok
test_pubmed6 (test_Entrez_parser.ELinkTest)
Test parsing pubmed links returned by ELink (sixth test). ... ok
test_epost (test_Entrez_parser.EPostTest)
Test parsing XML returned by EPost. ... ok
test_invalid (test_Entrez_parser.EPostTest)
Test parsing XML returned by EPost with invalid id (overflow tag). ... ok
test_wrong (test_Entrez_parser.EPostTest)
Test parsing XML returned by EPost with incorrect arguments. ... ok
test_journals (test_Entrez_parser.ESearchTest)
Test parsing XML returned by ESearch from the Journals database. ... ok
test_notfound (test_Entrez_parser.ESearchTest)
Test parsing XML returned by ESearch when no items were found. ... ok
test_nucleotide (test_Entrez_parser.ESearchTest)
Test parsing XML returned by ESearch from the Nucleotide database. ... ok
test_pmc (test_Entrez_parser.ESearchTest)
Test parsing XML returned by ESearch from PubMed Central. ... ok
test_protein (test_Entrez_parser.ESearchTest)
Test parsing XML returned by ESearch from the Protein database. ... ok
test_pubmed1 (test_Entrez_parser.ESearchTest)
Test parsing XML returned by ESearch from PubMed (first test). ... ok
test_pubmed2 (test_Entrez_parser.ESearchTest)
Test parsing XML returned by ESearch from PubMed (second test). ... ok
test_pubmed3 (test_Entrez_parser.ESearchTest)
Test parsing XML returned by ESearch from PubMed (third test). ... ok
test_espell (test_Entrez_parser.ESpellTest)
Test parsing XML output returned by ESpell. ... ok
test_journals (test_Entrez_parser.ESummaryTest)
Test parsing XML returned by ESummary from the Journals database. ... ok
test_nucleotide (test_Entrez_parser.ESummaryTest)
Test parsing XML returned by ESummary from the Nucleotide database. ... ok
test_protein (test_Entrez_parser.ESummaryTest)
Test parsing XML returned by ESummary from the Protein database. ... ok
test_pubmed (test_Entrez_parser.ESummaryTest)
Test parsing XML returned by ESummary from PubMed. ... ok
test_structure (test_Entrez_parser.ESummaryTest)
Test parsing XML returned by ESummary from the Structure database. ... ok
test_taxonomy (test_Entrez_parser.ESummaryTest)
Test parsing XML returned by ESummary from the Taxonomy database. ... ok
test_unists (test_Entrez_parser.ESummaryTest)
Test parsing XML returned by ESummary from the UniSTS database. ... ok
test_wrong (test_Entrez_parser.ESummaryTest)
Test parsing XML returned by ESummary with incorrect arguments. ... ok
test_BytesIO (test_Entrez_parser.GeneralTests)
Test parsing a BytesIO handle (bytes not unicode). ... ok
test_StringIO (test_Entrez_parser.GeneralTests)
Test parsing a StringIO handle (unicode not bytes). ... ok
test_bytes_handle (test_Entrez_parser.GeneralTests)
Test parsing a handle opened in binary mode. ... ok
test_closed_handle (test_Entrez_parser.GeneralTests)
Test parsing closed handle fails gracefully. ... ok
test_text_handle (test_Entrez_parser.GeneralTests)
Test parsing a handle opened in text mode. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.365 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Enzyme.py
test_Enzyme ... ok
test_lactate (test_Enzyme.TestEnzyme)
Parsing ENZYME record for lactate racemase (5.1.2.1) ... ok
test_lipoprotein (test_Enzyme.TestEnzyme)
Parsing ENZYME record for lipoprotein lipase (3.1.1.34) ... ok
test_parse_many (test_Enzyme.TestEnzyme)
Check parse function with multiple records. ... ok
test_parse_one (test_Enzyme.TestEnzyme)
Check parse function with one record. ... ok
test_parse_zero (test_Enzyme.TestEnzyme) ... ok
test_proline (test_Enzyme.TestEnzyme)
Parsing ENZYME record for proline racemase (5.1.1.4) ... ok
test_valine (test_Enzyme.TestEnzyme)
Parsing ENZYME record for valine decarboxylase (4.1.1.14) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.010 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ExPASy.py
test_ExPASy ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.005 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_FSSP.py
test_FSSP ... ok
runTest (__main__.ComparisonTestCase)
test_FSSP ... ok
----------------------------------------------------------------------
Ran 1 test in 1.647 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Fasttree_tool.py
test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.245 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_File.py
test_File ... ok
test_custom_path_like_object (test_File.AsHandleTestCase)
Test as_handle with a custom path-like object ... ok
test_handle (test_File.AsHandleTestCase)
Test as_handle with a file-like object argument ... ok
test_path_object (test_File.AsHandleTestCase)
Test as_handle with a pathlib.Path object ... ok
test_string_path (test_File.AsHandleTestCase)
Test as_handle with a string path argument ... ok
test_stringio (test_File.AsHandleTestCase) ... ok
test_bgzf (test_File.RandomAccess) ... ok
test_gzip (test_File.RandomAccess) ... ok
test_plain (test_File.RandomAccess) ... ok
test_one (test_File.UndoHandleTests) ... ok
test_read (test_File.UndoHandleTests)
Test read method ... ok
test_undohandle_read_block (test_File.UndoHandleTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.020 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GenBank.py
test_GenBank ... ok
runTest (__main__.ComparisonTestCase)
test_GenBank ... ok
----------------------------------------------------------------------
Ran 1 test in 0.307 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GenBank_unittest.py
version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests rtest_GenBank_unittest ... ok
test_000_genbank_bad_loc_wrap_warning (test_GenBank_unittest.GenBankTests)
Feature line wrapping warning. ... ok
test_001_genbank_bad_origin_wrapping_location (test_GenBank_unittest.GenBankTests)
Bad origin wrapping. ... ok
test_001_negative_location_warning (test_GenBank_unittest.GenBankTests)
Un-parsable feature location warning. ... ok
test_dbline_embl_gb (test_GenBank_unittest.GenBankTests)
Parse GenBank/EMBL paired records with PR project entry: EMBL ... ok
test_dbline_gb_embl (test_GenBank_unittest.GenBankTests)
Parse GenBank/EMBL paired records with PR project entry: GenBank ... ok
test_dblink (test_GenBank_unittest.GenBankTests)
Parse GenBank record with old DBLINK project entry. ... ok
test_dblink_two (test_GenBank_unittest.GenBankTests)
Parse GenBank record with old and new DBLINK project entries. ... ok
test_dot_lineage (test_GenBank_unittest.GenBankTests)
Missing taxonomy lineage. ... ok
test_genbank_bad_loc_wrap_parsing (test_GenBank_unittest.GenBankTests)
Bad location wrapping. ... ok
test_genbank_date_correct (test_GenBank_unittest.GenBankTests)
Check if user provided date is inserted correctly ... ok
test_genbank_date_datetime (test_GenBank_unittest.GenBankTests)
Check if datetime objects are handled correctly ... ok
test_genbank_date_default (test_GenBank_unittest.GenBankTests)
Check if default date is handled correctly ... ok
test_genbank_date_invalid (test_GenBank_unittest.GenBankTests)
Check if invalid dates are treated as default ... ok
test_genbank_date_list (test_GenBank_unittest.GenBankTests)
Check if date lists are handled correctly ... ok
test_genbank_read (test_GenBank_unittest.GenBankTests)
GenBank.read(...) simple test. ... ok
test_genbank_read_invalid (test_GenBank_unittest.GenBankTests)
GenBank.read(...) error on invalid file (e.g. FASTA file). ... ok
test_genbank_read_multirecord (test_GenBank_unittest.GenBankTests)
GenBank.read(...) error on multiple record input. ... ok
test_genbank_read_no_origin_no_end (test_GenBank_unittest.GenBankTests)
GenBank.read(...) error on malformed file. ... ok
test_implicit_orign_wrap_extract_and_translate (test_GenBank_unittest.GenBankTests)
Test that features wrapped around origin give expected data. ... ok
test_implicit_orign_wrap_fix (test_GenBank_unittest.GenBankTests)
Attempt to fix implied origin wrapping. ... ok
test_invalid_product_line_raises_value_error (test_GenBank_unittest.GenBankTests)
Parsing invalid product line. ... ok
test_locus_line_topogoly (test_GenBank_unittest.GenBankTests)
Test if chromosome topology is conserved ... ok
test_long_names (test_GenBank_unittest.GenBankTests)
Various GenBank names which push the column based LOCUS line. ... ok
test_negative_location (test_GenBank_unittest.GenBankTests)
Negative feature locations. ... ok
test_qualifier_escaping_read (test_GenBank_unittest.GenBankTests)
Check qualifier escaping is preserved when parsing. ... ok
test_qualifier_escaping_write (test_GenBank_unittest.GenBankTests)
Check qualifier escaping is preserved when writing. ... ok
test_qualifier_order (test_GenBank_unittest.GenBankTests)
Check the qualifier order is preserved. ... ok
test_structured_comment_parsing (test_GenBank_unittest.GenBankTests)
Structued comment parsing. ... ok
test_first_line_imgt (test_GenBank_unittest.LineOneTests)
Check IMGT ID line parsing. ... ok
test_topology_embl (test_GenBank_unittest.LineOneTests)
Check EMBL ID line parsing. ... ok
test_topology_genbank (test_GenBank_unittest.LineOneTests)
Check GenBank LOCUS line parsing. ... ok
test_000_write_invalid_but_parsed_locus_line (test_GenBank_unittest.OutputTests)
Make sure we survive writing slightly invalid LOCUS lines we could parse. ... ok
test_mad_dots (test_GenBank_unittest.OutputTests)
Writing and reading back accesssion.version variants. ... ok
test_seqrecord_default_description (test_GenBank_unittest.OutputTests)
Read in file using SeqRecord default description. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.258 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GenomeDiagram.py
x_order_2: colinear!
x_order_2: colinear!
x_order_2: colinear!
test_GenomeDiagram ... ok
test_color_conversions (test_GenomeDiagram.ColorsTest)
Test color translations. ... ok
test_add_track (test_GenomeDiagram.DiagramTest) ... ok
test_add_track_error (test_GenomeDiagram.DiagramTest)
Test adding unspecified track. ... ok
test_add_track_to_occupied_level (test_GenomeDiagram.DiagramTest) ... ok
test_del_tracks (test_GenomeDiagram.DiagramTest) ... ok
test_diagram_via_methods_pdf (test_GenomeDiagram.DiagramTest)
Construct and draw PDF using method approach. ... ok
test_diagram_via_object_pdf (test_GenomeDiagram.DiagramTest)
Construct and draw PDF using object approach. ... ok
test_get_tracks (test_GenomeDiagram.DiagramTest) ... ok
test_move_track (test_GenomeDiagram.DiagramTest) ... ok
test_partial_diagram (test_GenomeDiagram.DiagramTest)
Construct and draw SVG and PDF for just part of a SeqRecord. ... ok
test_renumber (test_GenomeDiagram.DiagramTest)
Test renumbering tracks. ... ok
test_str (test_GenomeDiagram.DiagramTest)
Test diagram's info as string. ... ok
test_write_arguments (test_GenomeDiagram.DiagramTest)
Check how the write methods respond to output format arguments. ... ok
test_limits (test_GenomeDiagram.GraphTest)
Check line graphs. ... ok
test_slicing (test_GenomeDiagram.GraphTest)
Check GraphData slicing. ... ok
test_label_default (test_GenomeDiagram.LabelTest)
Feature labels - default. ... ok
test_all_sigils (test_GenomeDiagram.SigilsTest)
All sigils. ... ok
test_arrow_heads (test_GenomeDiagram.SigilsTest)
Feature arrow sigils, varying heads. ... ok
test_arrow_shafts (test_GenomeDiagram.SigilsTest)
Feature arrow sigils, varying shafts. ... ok
test_big_arrow_shafts (test_GenomeDiagram.SigilsTest)
Feature big-arrow sigils, varying shafts. ... ok
test_labels (test_GenomeDiagram.SigilsTest)
Feature labels. ... ok
test_long_arrow_heads (test_GenomeDiagram.SigilsTest)
Feature ARROW sigil heads within bounding box. ... ok
test_long_bigarrow_heads (test_GenomeDiagram.SigilsTest)
Feature BIGARROW sigil heads within bounding box. ... ok
test_long_jaggy (test_GenomeDiagram.SigilsTest)
Feature JAGGY sigil heads within bounding box. ... ok
test_long_octo_heads (test_GenomeDiagram.SigilsTest)
Feature OCTO sigil heads within bounding box. ... ok
test_short_arrow (test_GenomeDiagram.SigilsTest)
Feature arrow sigil heads within bounding box. ... ok
test_short_bigarrow (test_GenomeDiagram.SigilsTest)
Feature big-arrow sigil heads within bounding box. ... ok
test_short_jaggy (test_GenomeDiagram.SigilsTest)
Feature arrow sigil heads within bounding box. ... ok
test_short_octo (test_GenomeDiagram.SigilsTest)
Feature big-arrow sigil heads within bounding box. ... ok
----------------------------------------------------------------------
Ran 1 test in 4.351 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsBitmaps.py
test_GraphicsBitmaps ... ok
test_simple_scatter_plot (test_GraphicsBitmaps.ComparativeTest)
Test creation of a simple PNG scatter plot. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.487 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsChromosome.py
test_GraphicsChromosome ... ok
test_add_count (test_GraphicsChromosome.ChromosomeCountTest)
Add counts to specific chromosome segments. ... ok
test_add_label (test_GraphicsChromosome.ChromosomeCountTest)
Add labels to chromosome segments. ... ok
test_color_from_count (test_GraphicsChromosome.ChromosomeCountTest)
Retrieve a color from a count number with the default color scheme. ... ok
test_fill_chromosome (test_GraphicsChromosome.ChromosomeCountTest)
Test filling out the information on a chromosome. ... ok
test_get_segment_info (test_GraphicsChromosome.ChromosomeCountTest)
Test retrieval of segment information. ... ok
test_set_scale (test_GraphicsChromosome.ChromosomeCountTest)
Set the scale for a chromosome segment. ... ok
test_random_organism (test_GraphicsChromosome.OrganismGraphicTest)
Generate an organism with random chromosome info. ... ok
test_simple_organism (test_GraphicsChromosome.OrganismGraphicTest)
Test the basic functionality of drawing an organism. ... ok
test_simple_organism_pdf (test_GraphicsChromosome.OrganismGraphicTest)
Output a simple organism to a PDF file. ... ok
test_simple_organism_ps (test_GraphicsChromosome.OrganismGraphicTest)
Output a simple organism to a postscript file. ... ok
test_simple_organism_svg (test_GraphicsChromosome.OrganismGraphicTest)
Output a simple organism to an SVG file. ... ok
test_widget (test_GraphicsChromosome.OrganismGraphicTest)
Try widget derived functionality. ... ok
test_simple_tRNA_seqfeatures (test_GraphicsChromosome.OrganismSubAnnotationsTest)
Test sub-annotations (as SeqFeatures) on a genome segment, tRNA for Arabidopsis ... ok
test_simple_tRNA_tuples (test_GraphicsChromosome.OrganismSubAnnotationsTest)
Test sub-annotations (as tuples) on a genome segment, tRNA for Arabidopsis ... ok
----------------------------------------------------------------------
Ran 1 test in 1.281 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsDistribution.py
test_GraphicsDistribution ... ok
test_multi_page (test_GraphicsDistribution.BarChartTest)
Create a page with multiple distributions on it. ... ok
test_simple_page (test_GraphicsDistribution.BarChartTest)
Test displaying a page with single distribution. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.291 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsGeneral.py
test_GraphicsGeneral ... ok
test_simple_scatter_plot_1 (test_GraphicsGeneral.ComparativeTest)
Test creation of a simple ScatterPlot with one list. ... ok
test_simple_scatter_plot_7 (test_GraphicsGeneral.ComparativeTest)
Test creation of a simple ScatterPlot with more lists. ... ok
----------------------------------------------------------------------
Ran 1 test in 1.997 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_HMMCasino.py
test_HMMCasino ... ok
runTest (__main__.ComparisonTestCase)
test_HMMCasino ... ok
----------------------------------------------------------------------
Ran 1 test in 0.864 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_HMMGeneral.py
test_HMMGeneral ... ok
test_log_likelihood (test_HMMGeneral.AbstractTrainerTest)
Calculate log likelihood. ... ok
test_ml_estimator (test_HMMGeneral.AbstractTrainerTest)
Test the maximum likelihood estimator for simple cases. ... ok
test_allow_transition (test_HMMGeneral.HiddenMarkovModelTest)
Testing allow_transition ... ok
test_non_ergodic (test_HMMGeneral.HiddenMarkovModelTest)
Non-ergodic model (meaning that some transitions are not allowed). ... ok
test_simple_hmm (test_HMMGeneral.HiddenMarkovModelTest)
Test a simple model with 2 states and 2 symbols. ... ok
test_transitions_from (test_HMMGeneral.HiddenMarkovModelTest)
Testing the calculation of transitions_from ... ok
test_transitions_to (test_HMMGeneral.HiddenMarkovModelTest)
Testing the calculation of transitions_to ... ok
test_allow_all_transitions (test_HMMGeneral.MarkovModelBuilderTest)
Testing allow_all_transitions. ... ok
test_set_equal_probabilities (test_HMMGeneral.MarkovModelBuilderTest) ... ok
test_set_initial_probabilities (test_HMMGeneral.MarkovModelBuilderTest) ... ok
test_set_random_probabilities (test_HMMGeneral.MarkovModelBuilderTest) ... ok
test_test_initialize (test_HMMGeneral.MarkovModelBuilderTest)
Making sure MarkovModelBuilder is initialized correctly. ... ok
test_calculate_s_value (test_HMMGeneral.ScaledDPAlgorithmsTest)
Testing the calculation of s values. ... ok
test_empty_state_training_sequence (test_HMMGeneral.TrainingSequenceTest) ... ok
test_invalid_training_sequence (test_HMMGeneral.TrainingSequenceTest) ... ok
test_valid_training_sequence (test_HMMGeneral.TrainingSequenceTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.071 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KDTree.py
test_KDTree ... ok
test_KDTree (test_KDTree.KDTreeTest) ... ok
test_KDTree_exceptions (test_KDTree.KDTreeTest) ... ok
test_KDTree_neighbour (test_KDTree.KDTreeTest) ... ok
test_all_search (test_KDTree.KDTreeTest) ... ok
test_search (test_KDTree.KDTreeTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 2.566 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KEGG.py
test_KEGG ... ok
test_irregular (test_KEGG.CompoundTests) ... ok
test_sample (test_KEGG.CompoundTests) ... ok
test_4letter (test_KEGG.EnzymeTests) ... ok
test_exceptions (test_KEGG.EnzymeTests) ... ok
test_irregular (test_KEGG.EnzymeTests) ... ok
test_new (test_KEGG.EnzymeTests) ... ok
test_sample (test_KEGG.EnzymeTests) ... ok
test_map00950 (test_KEGG.MapTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.199 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KEGG_online.py
test_KEGG_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.115 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KGML_graphics.py
test_KGML_graphics ... ok
test_render_KGML_basic (test_KGML_graphics.KGMLPathwayTest)
Basic rendering of KGML: write to PDF without modification. ... ok
test_render_KGML_modify (test_KGML_graphics.KGMLPathwayTest)
Rendering of KGML to PDF, with modification. ... ok
test_render_KGML_transparency (test_KGML_graphics.KGMLPathwayTest)
Rendering of KGML to PDF, with color alpha channel. ... ok
----------------------------------------------------------------------
Ran 1 test in 10.452 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KGML_graphics_online.py
test_KGML_graphics_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.005 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KGML_nographics.py
test_KGML_nographics ... ok
test_read_and_write_KGML_files (test_KGML_nographics.KGMLPathwayTest)
Read KGML from, and write KGML to, local files. ... ok
----------------------------------------------------------------------
Ran 1 test in 1.690 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KeyWList.py
test_KeyWList ... ok
test_parse (test_KeyWList.KeyWListTest)
Parsing keywlist.txt ... ok
test_parse2 (test_KeyWList.KeyWListTest)
Parsing keywlist2.txt (without header and footer) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.008 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Location.py
test_Location ... ok
runTest (__main__.ComparisonTestCase)
test_Location ... ok
----------------------------------------------------------------------
Ran 1 test in 0.064 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_LogisticRegression.py
test_LogisticRegression ... ok
test_calculate_model (test_LogisticRegression.TestLogisticRegression) ... ok
test_calculate_model_with_update_callback (test_LogisticRegression.TestLogisticRegression) ... ok
test_calculate_probability (test_LogisticRegression.TestLogisticRegression) ... ok
test_classify (test_LogisticRegression.TestLogisticRegression) ... ok
test_dimensionality_of_input_xs (test_LogisticRegression.TestLogisticRegression) ... ok
test_leave_one_out (test_LogisticRegression.TestLogisticRegression) ... ok
test_model_accuracy (test_LogisticRegression.TestLogisticRegression) ... ok
test_xs_and_ys_input_parameter_lengths (test_LogisticRegression.TestLogisticRegression) ... ok
test_ys_input_class_assignments (test_LogisticRegression.TestLogisticRegression) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.113 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_MSAProbs_tool.py
test_MSAProbs_tool ... skipping. Install msaprobs if you want to use MSAProbs from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.117 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_MafIO_index.py
test_MafIO_index ... ok
test_bundle_without_target (test_MafIO_index.NewIndexTest) ... ok
test_good_big (test_MafIO_index.NewIndexTest) ... ok
test_good_small (test_MafIO_index.NewIndexTest) ... ok
test_length_coords_mismatch (test_MafIO_index.NewIndexTest) ... ok
test_old (test_MafIO_index.PreBuiltIndexTest) ... ok
test_old_corrupt_index (test_MafIO_index.PreBuiltIndexTest) ... ok
test_old_file_not_found (test_MafIO_index.PreBuiltIndexTest) ... ok
test_old_invalid_sqlite (test_MafIO_index.PreBuiltIndexTest) ... ok
test_old_unfinished_index (test_MafIO_index.PreBuiltIndexTest) ... ok
test_old_wrong_filename (test_MafIO_index.PreBuiltIndexTest) ... ok
test_old_wrong_target_seqname (test_MafIO_index.PreBuiltIndexTest) ... ok
test_old_wrong_version (test_MafIO_index.PreBuiltIndexTest) ... ok
test_region2bin (test_MafIO_index.StaticMethodTest) ... ok
test_ucscbin (test_MafIO_index.StaticMethodTest) ... ok
test_records_begin (test_MafIO_index.TestGetRecord) ... ok
test_records_end (test_MafIO_index.TestGetRecord) ... ok
test_incorrect_bundle_coords (test_MafIO_index.TestSearchBadMAF) ... ok
test_correct_block_boundary (test_MafIO_index.TestSearchGoodMAF)
Following issues 504 and 1086. ... ok
test_correct_block_length (test_MafIO_index.TestSearchGoodMAF)
Following issues 504 and 1086. ... ok
test_correct_retrieval_1 (test_MafIO_index.TestSearchGoodMAF)
Correct retrieval of Cnksr3 in mouse. ... ok
test_correct_retrieval_2 (test_MafIO_index.TestSearchGoodMAF) ... ok
test_correct_retrieval_3 (test_MafIO_index.TestSearchGoodMAF)
Following issue 1083. ... ok
test_correct_spliced_sequences_1 (test_MafIO_index.TestSearchGoodMAF)
Checking that spliced sequences are correct. ... ok
test_correct_spliced_sequences_2 (test_MafIO_index.TestSearchGoodMAF)
Checking that spliced sequences are correct. ... ok
test_invalid_exon_count (test_MafIO_index.TestSearchGoodMAF) ... ok
test_invalid_exon_schema (test_MafIO_index.TestSearchGoodMAF) ... ok
test_invalid_type_1 (test_MafIO_index.TestSearchGoodMAF) ... ok
test_invalid_type_2 (test_MafIO_index.TestSearchGoodMAF) ... ok
test_bundle_without_target (test_MafIO_index.TestSpliceBadMAF) ... ok
test_inconsistent_strand (test_MafIO_index.TestSpliceBadMAF) ... ok
test_correct_retrieval_1 (test_MafIO_index.TestSpliceGoodMAF)
Correct retrieval of Cnksr3 in mouse. ... ok
test_invalid_strand (test_MafIO_index.TestSpliceGoodMAF) ... ok
test_no_alignment (test_MafIO_index.TestSpliceGoodMAF) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.203 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Mafft_tool.py
test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.083 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_MarkovModel.py
test_MarkovModel ... ok
test_argmaxes (test_MarkovModel.TestMarkovModel) ... ok
test_backward (test_MarkovModel.TestMarkovModel) ... ok
test_baum_welch (test_MarkovModel.TestMarkovModel) ... ok
test_forward (test_MarkovModel.TestMarkovModel) ... ok
test_logsum_and_exp_logsum (test_MarkovModel.TestMarkovModel) ... ok
test_logvecadd (test_MarkovModel.TestMarkovModel) ... ok
test_mle (test_MarkovModel.TestMarkovModel) ... ok
test_normalize_and_copy_and_check (test_MarkovModel.TestMarkovModel) ... ok
test_random_norm (test_MarkovModel.TestMarkovModel) ... ok
test_readline_and_check_start (test_MarkovModel.TestMarkovModel) ... ok
test_save_and_load (test_MarkovModel.TestMarkovModel) ... ok
test_topcoder1 (test_MarkovModel.TestMarkovModel) ... ok
test_topcoder2 (test_MarkovModel.TestMarkovModel) ... ok
test_topcoder3 (test_MarkovModel.TestMarkovModel) ... ok
test_topcoder4 (test_MarkovModel.TestMarkovModel) ... ok
test_topcoder5 (test_MarkovModel.TestMarkovModel) ... ok
test_train_bw (test_MarkovModel.TestMarkovModel) ... ok
test_train_visible (test_MarkovModel.TestMarkovModel) ... ok
test_uniform_norm (test_MarkovModel.TestMarkovModel) ... ok
test_viterbi (test_MarkovModel.TestMarkovModel) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.490 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Medline.py
test_Medline ... ok
test_multiline_mesh (test_Medline.TestMedline) ... ok
test_parse (test_Medline.TestMedline) ... ok
test_read (test_Medline.TestMedline) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.010 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Muscle_tool.py
test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.118 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NACCESS_tool.py
equiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: potest_NACCESS_tool ... skipping. Install naccess if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.085 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBITextParser.py
test_NCBITextParser ... ok
test_conversion (test_NCBITextParser.TestBlastRecord)
Test converting a Blast record multiple alignment ... ok
test_text_2010L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.10 output (text_2010L_blastn_001) ... ok
test_text_2010L_blastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.10 output without alignments (text_2010L_blastn_002) ... ok
test_text_2010L_blastn_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.10 output without descriptions (text_2010L_blastn_003) ... ok
test_text_2010L_blastn_004 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.10 output (text_2010L_blastn_004) ... ok
test_text_2010L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output (text_2010L_blastp_001) ... ok
test_text_2010L_blastp_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output without hits (text_2010L_blastp_002) ... ok
test_text_2010L_blastp_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output (text_2010L_blastp_003) ... ok
test_text_2010L_blastp_004 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output without descriptions (text_2010L_blastp_004) ... ok
test_text_2010L_blastp_005 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output without alignments (text_2010L_blastp_005) ... ok
test_text_2010L_blastp_006 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output (text_2010L_blastp_006) ... ok
test_text_2010L_blastp_007 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output (text_2010L_blastp_007) ... ok
test_text_2010L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.0.10 output (text_2010L_blastx_001) ... ok
test_text_2010L_blastx_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.0.10 output without hits (text_2010L_blastx_002) ... ok
test_text_2010L_phiblast_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing PHI-BLAST, BLASTP 2.0.10 output, one round (text_2010L_phiblast_001) ... ok
test_text_2010L_phiblast_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing PHI-BLAST, BLASTP 2.0.10 output, three rounds (text_2010L_phiblast_002) ... ok
test_text_2010L_phiblast_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing PHI-BLAST, BLASTP 2.0.10 output, two rounds (text_2010L_phiblast_003) ... ok
test_text_2010L_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.0.10 output (text_2010L_tblastn_001) ... ok
test_text_2010L_tblastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.0.10 output without hits (text_2010L_tblastn_002) ... ok
test_text_2010L_tblastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTX 2.0.10 output (text_2010L_tblastx_001) ... ok
test_text_2011L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.11 output (text_2011L_blastn_001) ... ok
test_text_2011L_blastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.11 output without alignments (text_2011L_blastn_002) ... ok
test_text_2011L_blastn_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.11 output without descriptions (text_2011L_blastn_003) ... ok
test_text_2011L_blastn_004 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.11 output (text_2011L_blastn_004) ... ok
test_text_2011L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output (text_2011L_blastp_001) ... ok
test_text_2011L_blastp_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output without hits (text_2011L_blastp_002) ... ok
test_text_2011L_blastp_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output (text_2011L_blastp_003) ... ok
test_text_2011L_blastp_004 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output without descriptions (text_2011L_blastp_004) ... ok
test_text_2011L_blastp_005 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output without alignments (text_2011L_blastp_005) ... ok
test_text_2011L_blastp_006 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output (text_2011L_blastp_006) ... ok
test_text_2011L_blastp_007 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output (text_2011L_blastp_007) ... ok
test_text_2011L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.0.11 output (text_2011L_blastx_001) ... ok
test_text_2011L_blastx_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.0.11 output without hits (text_2011L_blastx_002) ... ok
test_text_2011L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_001) ... ok
test_text_2011L_psiblast_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_002) ... ok
test_text_2011L_psiblast_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output (text_2011L_psiblast_003) ... ok
test_text_2011L_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.0.11 output (text_2011L_tblastn_001) ... ok
test_text_2011L_tblastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.0.11 output without hits (text_2011L_tblastn_002) ... ok
test_text_2011L_tblastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTX 2.0.11 output (text_2011L_tblastx_001) ... ok
test_text_2012L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.12 output (text_2012L_psiblast_001) ... ok
test_text_2014L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.14 output (text_2014L_blastn_001) ... ok
test_text_2014L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.14 output (text_2014L_psiblast_001) ... ok
test_text_2201L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.1 output (text_2201L_blastx_001) ... ok
test_text_2202L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.2.2 output with error messages (text_2202L_blastn_001) ... ok
test_text_2202L_blastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.2.2 output with missing error messages (text_2202L_blastn_002) ... ok
test_text_2202L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.2 output with multiple records (text_2202L_blastp_001) ... ok
test_text_2208L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.8 output (text_2208L_psiblast_001) ... ok
test_text_2215L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.15 output with no hits (text_2215L_blastx_001) ... ok
test_text_2216L_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.2.16 output (text_2216L_tblastn_001) ... ok
test_text_2220L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.20 output (text_2220L_blastx_001) ... ok
test_text_2220L_blastx_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.20 output with multiple queries (text_2220L_blastx_002) ... ok
test_text_2221L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.21 output with multiple queries (text_2221L_blastp_001) ... ok
test_text_2222L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.22 output with multiple queries (text_2222L_blastx_001) ... ok
test_text_2222_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.22+ output with multiple queries (text_2222_blastx_001) ... ok
test_text_2226_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.2.26+ output with no results. ... ok
test_text_2226_blastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.2.26+ output with single hsp results. ... ok
test_text_2226_blastn_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.2.26+ output with multiple hsp results present. ... ok
test_text_2226_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.26+ with no results. ... ok
test_text_2226_blastp_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.26+ with single hsp results. ... ok
test_text_2226_blastp_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok
test_text_2226_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.26+ with no results. ... ok
test_text_2226_blastx_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.26+ with single hsp results. ... ok
test_text_2226_blastx_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok
test_text_2226_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.2.26+ output with no results. ... ok
test_text_2226_tblastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.2.26+ output with single hsp results. ... ok
test_text_2226_tblastn_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.2.26+ output with multiple hsp results present. ... ok
test_text_2226_tblastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTX 2.2.26+ output with no results. ... ok
test_text_2226_tblastx_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTX 2.2.26+ output with single hsp results. ... ok
test_text_2226_tblastx_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTX 2.2.26+ output with multiple hsp results present. ... ok
test_text_2230_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.30+ output with line of dashes. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.780 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBIXML.py
test_NCBIXML ... ok
test_xml_2212L_blastn_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTN 2.2.12, gi|1348916|gb|G26684.1|G26684 (xml_2212L_blastn_001) ... ok
test_xml_2212L_blastp_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTP 2.2.12, gi|49176427|ref|NP_418280.3| (xml_2212L_blastp_001) ... ok
test_xml_2212L_blastx_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTX 2.2.12, gi|1347369|gb|G25137.1|G25137 (xml_2212L_blastx_001) ... ok
test_xml_2212L_tblastn_001 (test_NCBIXML.TestNCBIXML)
Parsing TBLASTN 2.2.12, gi|729325|sp|P39483|DHG2_BACME (xml_2212L_tblastn_001) ... ok
test_xml_2212L_tblastx_001 (test_NCBIXML.TestNCBIXML)
Parsing TBLASTX 2.2.12, gi|1348853|gb|G26621.1|G26621, BLOSUM80 (xml_2212L_tblastx_001) ... ok
test_xml_2218L_blastp_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTP 2.2.18, Fake query (xml_2218L_blastp_001) ... ok
test_xml_2218L_rpsblast_001 (test_NCBIXML.TestNCBIXML)
Parsing PSI-BLASTP 2.2.18, single query which converges in 3 iterations (xml_2218L_rpsblast_001) ... ok
test_xml_2218_blastp_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTP 2.2.18+, gi|160837788|ref|NP_075631.2| (xml_2218_blastp_001) ... ok
test_xml_2218_blastp_002 (test_NCBIXML.TestNCBIXML)
Parsing BLASTP 2.2.18+, SwissProt Q08386 and P07175, no hits (xml_2218_blastp_002) ... ok
test_xml_2222_blastp_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTP 2.2.22+, multiple queries against NR (xml_2222_blastp_001) ... ok
test_xml_2222_blastx_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTX 2.2.22+, multiple queries against NR (xml_2222_blastx_001) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.384 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBI_BLAST_tools.py
test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.022 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBI_qblast.py
test_NCBI_qblast ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.075 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NaiveBayes.py
test_NaiveBayes ... ok
test_car_data (test_NaiveBayes.CarTest)
Simple example using car data. ... ok
test_calculate_function_with_scale (test_NaiveBayes.NaiveBayesTest) ... ok
test_calculate_function_wrong_dimensionality (test_NaiveBayes.NaiveBayesTest) ... ok
test_classify_function (test_NaiveBayes.NaiveBayesTest) ... ok
test_train_function_input_lengths (test_NaiveBayes.NaiveBayesTest) ... ok
test_train_function_no_training_set (test_NaiveBayes.NaiveBayesTest) ... ok
test_train_function_uneven_dimension_of_training_set (test_NaiveBayes.NaiveBayesTest) ... ok
test_train_function_with_priors (test_NaiveBayes.NaiveBayesTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.013 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_baseml.py
test_PAML_baseml ... ok
testAlignmentExists (test_PAML_baseml.ModTest) ... ok
testAlignmentFileIsValid (test_PAML_baseml.ModTest) ... ok
testAlignmentSpecified (test_PAML_baseml.ModTest) ... ok
testCtlFileExistsOnRead (test_PAML_baseml.ModTest) ... ok
testCtlFileExistsOnRun (test_PAML_baseml.ModTest) ... ok
testCtlFileValidOnRead (test_PAML_baseml.ModTest) ... ok
testCtlFileValidOnRun (test_PAML_baseml.ModTest) ... ok
testOptionExists (test_PAML_baseml.ModTest) ... ok
testOutputFileSpecified (test_PAML_baseml.ModTest) ... ok
testPamlErrorsCaught (test_PAML_baseml.ModTest) ... ok
testParseAllVersions (test_PAML_baseml.ModTest) ... ok
testParseAlpha1Rho1 (test_PAML_baseml.ModTest) ... ok
testParseModel (test_PAML_baseml.ModTest) ... ok
testParseNhomo (test_PAML_baseml.ModTest) ... ok
testParseSEs (test_PAML_baseml.ModTest) ... ok
testResultsExist (test_PAML_baseml.ModTest) ... ok
testResultsParsable (test_PAML_baseml.ModTest) ... ok
testResultsValid (test_PAML_baseml.ModTest) ... ok
testTreeExists (test_PAML_baseml.ModTest) ... ok
testTreeFileValid (test_PAML_baseml.ModTest) ... ok
testTreeSpecified (test_PAML_baseml.ModTest) ... ok
testWorkingDirValid (test_PAML_baseml.ModTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.361 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_codeml.py
test_PAML_codeml ... ok
testAlignmentExists (test_PAML_codeml.ModTest) ... ok
testAlignmentFileIsValid (test_PAML_codeml.ModTest) ... ok
testAlignmentSpecified (test_PAML_codeml.ModTest) ... ok
testCtlFileExistsOnRead (test_PAML_codeml.ModTest) ... ok
testCtlFileExistsOnRun (test_PAML_codeml.ModTest) ... ok
testCtlFileValidOnRead (test_PAML_codeml.ModTest) ... ok
testCtlFileValidOnRun (test_PAML_codeml.ModTest) ... ok
testOptionExists (test_PAML_codeml.ModTest) ... ok
testOutputFileSpecified (test_PAML_codeml.ModTest) ... ok
testPamlErrorsCaught (test_PAML_codeml.ModTest) ... ok
testParseAA (test_PAML_codeml.ModTest) ... ok
testParseAAPairwise (test_PAML_codeml.ModTest) ... ok
testParseAllNSsites (test_PAML_codeml.ModTest) ... ok
testParseBranchSiteA (test_PAML_codeml.ModTest) ... ok
testParseCladeModelC (test_PAML_codeml.ModTest) ... ok
testParseFreeRatio (test_PAML_codeml.ModTest) ... ok
testParseM2arel (test_PAML_codeml.ModTest) ... ok
testParseNSsite3 (test_PAML_codeml.ModTest) ... ok
testParseNgene2Mgene02 (test_PAML_codeml.ModTest) ... ok
testParseNgene2Mgene1 (test_PAML_codeml.ModTest) ... ok
testParseNgene2Mgene34 (test_PAML_codeml.ModTest) ... ok
testParsePairwise (test_PAML_codeml.ModTest) ... ok
testParseSEs (test_PAML_codeml.ModTest) ... ok
testParseSitesParamsForPairwise (test_PAML_codeml.ModTest)
Verify that pairwise site estimates are indeed parsed. Fixes #483 ... ok
testResultsExist (test_PAML_codeml.ModTest) ... ok
testResultsParsable (test_PAML_codeml.ModTest) ... ok
testResultsValid (test_PAML_codeml.ModTest) ... ok
testTreeExists (test_PAML_codeml.ModTest) ... ok
testTreeFileValid (test_PAML_codeml.ModTest) ... ok
testTreeParseVersatility (test_PAML_codeml.ModTest)
Test finding trees in the results. ... ok
testTreeSpecified (test_PAML_codeml.ModTest) ... ok
testWorkingDirValid (test_PAML_codeml.ModTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.539 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_tools.py
test_PAML_tools ... skipping. Install PAML if you want to use the Bio.Phylo.PAML wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.218 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_yn00.py
test_PAML_yn00 ... ok
testAlignmentExists (test_PAML_yn00.ModTest) ... ok
testAlignmentFileIsValid (test_PAML_yn00.ModTest) ... ok
testAlignmentSpecified (test_PAML_yn00.ModTest) ... ok
testCtlFileExistsOnRead (test_PAML_yn00.ModTest) ... ok
testCtlFileExistsOnRun (test_PAML_yn00.ModTest) ... ok
testCtlFileValidOnRead (test_PAML_yn00.ModTest) ... ok
testCtlFileValidOnRun (test_PAML_yn00.ModTest) ... ok
testOptionExists (test_PAML_yn00.ModTest) ... ok
testOutputFileSpecified (test_PAML_yn00.ModTest) ... ok
testParseAllVersions (test_PAML_yn00.ModTest) ... ok
testParseLongNames (test_PAML_yn00.ModTest) ... ok
testResultsExist (test_PAML_yn00.ModTest) ... ok
testResultsParsable (test_PAML_yn00.ModTest) ... ok
testResultsValid (test_PAML_yn00.ModTest) ... ok
testWorkingDirValid (test_PAML_yn00.ModTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.222 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB.py
test_PDB ... ok
test_1_warnings (test_PDB.A_ExceptionTest)
Check warnings: Parse a flawed PDB file in permissive mode. ... ok
test_2_strict (test_PDB.A_ExceptionTest)
Check error: Parse a flawed PDB file in strict mode. ... ok
test_3_bad_xyz (test_PDB.A_ExceptionTest)
Check error: Parse an entry with bad x,y,z value. ... ok
test_4_occupancy (test_PDB.A_ExceptionTest)
Parse file with missing occupancy ... ok
test_AtomElement (test_PDB.Atom_Element)
Atom Element. ... ok
test_hydrogens (test_PDB.Atom_Element) ... ok
test_ions (test_PDB.Atom_Element)
Element for magnesium is assigned correctly. ... ok
test_change_chain_id (test_PDB.ChangingIdTests)
Change the id of a model. ... ok
test_change_id_to_self (test_PDB.ChangingIdTests)
Changing the id to itself does nothing (does not raise). ... ok
test_change_model_id (test_PDB.ChangingIdTests)
Change the id of a model. ... ok
test_change_model_id_raises (test_PDB.ChangingIdTests)
Cannot change id to a value already in use by another child. ... ok
test_change_residue_id (test_PDB.ChangingIdTests)
Change the id of a residue. ... ok
test_full_id_is_updated_chain (test_PDB.ChangingIdTests)
Invalidate cached full_ids if an id is changed. ... ok
test_full_id_is_updated_residue (test_PDB.ChangingIdTests)
Invalidate cached full_ids if an id is changed. ... ok
test_atom_copy (test_PDB.CopyTests) ... ok
test_entity_copy (test_PDB.CopyTests)
Make a copy of a residue. ... ok
test_DSSP_RSA (test_PDB.DsspTests)
Tests the usage of different ASA tables. ... ok
test_DSSP_file (test_PDB.DsspTests)
Test parsing of pregenerated DSSP. ... ok
test_DSSP_hbonds (test_PDB.DsspTests)
Test parsing of DSSP hydrogen bond information. ... ok
test_DSSP_in_model_obj (test_PDB.DsspTests)
All elements correctly added to xtra attribute of input model object. ... ok
test_DSSP_noheader_file (test_PDB.DsspTests)
Test parsing of pregenerated DSSP missing header information. ... ok
test_ExposureCN (test_PDB.Exposure)
HSExposureCN. ... ok
test_HSExposureCA (test_PDB.Exposure)
HSExposureCA. ... ok
test_HSExposureCB (test_PDB.Exposure)
HSExposureCB. ... ok
test_capsid (test_PDB.HeaderTests)
Parse the header of a known PDB file (1A8O). ... ok
test_fibril (test_PDB.HeaderTests)
Parse the header of another PDB file (2BEG). ... ok
test_get_atoms (test_PDB.IterationTests)
Yields all atoms from the structure, excluding duplicates and ALTLOCs which are not parsed. ... ok
test_get_chains (test_PDB.IterationTests)
Yields chains from different models separately. ... ok
test_get_residues (test_PDB.IterationTests)
Yields all residues from all models. ... ok
test_NACCESS_asa_file (test_PDB.NACCESSTests)
Test parsing of pregenerated asa NACCESS file ... ok
test_NACCESS_rsa_file (test_PDB.NACCESSTests)
Test parsing of pregenerated rsa NACCESS file ... ok
test_PDBParser (test_PDB.PDBParserTests)
Walk down the structure hierarchy and test parser reliability. ... ok
test_c_n (test_PDB.ParseReal)
Extract polypeptides from 1A80. ... ok
test_empty (test_PDB.ParseReal)
Parse an empty file. ... ok
test_model_numbering (test_PDB.ParseReal)
Preserve model serial numbers during I/O. ... ok
test_residue_sort (test_PDB.ParseReal)
Sorting atoms in residues. ... ok
test_strict (test_PDB.ParseReal)
Parse 1A8O.pdb file in strict mode. ... ok
test_c_n (test_PDB.ParseTest)
Extract polypeptides using C-N. ... ok
test_ca_ca (test_PDB.ParseTest)
Extract polypeptides using CA-CA. ... ok
test_comparison_entities (test_PDB.ParseTest)
Test comparing and sorting the several SMCRA objects ... ok
test_details (test_PDB.ParseTest)
Verify details of the parsed example PDB file. ... ok
test_pdbio_write_truncated (test_PDB.ParseTest)
Test parsing of truncated lines. ... ok
test_structure (test_PDB.ParseTest)
Verify the structure of the parsed example PDB file. ... ok
test_pdb_to_xyzr (test_PDB.ResidueDepthTests)
Test generation of xyzr (atomic radii) file ... ok
test_Vector (test_PDB.TransformTests)
Test Vector object. ... ok
test_Vector_angles (test_PDB.TransformTests) ... ok
test_m2rotaxis (test_PDB.TransformTests) ... ok
test_refmat (test_PDB.TransformTests) ... ok
test_rotmat (test_PDB.TransformTests) ... ok
test_transform (test_PDB.TransformTests)
Transform entities (rotation and translation). ... ok
test_mmcifio_multimodel (test_PDB.WriteTest)
Write a multi-model, multi-chain mmCIF file. ... ok
test_mmcifio_select (test_PDB.WriteTest)
Write a selection of the structure using a Select subclass. ... ok
test_mmcifio_write_dict (test_PDB.WriteTest)
Write an mmCIF dictionary out, read it in and compare them. ... ok
test_mmcifio_write_residue (test_PDB.WriteTest)
Write a single residue using MMCIFIO. ... ok
test_mmcifio_write_structure (test_PDB.WriteTest)
Write a full structure using MMCIFIO. ... ok
test_pdbio_missing_occupancy (test_PDB.WriteTest)
Write PDB file with missing occupancy. ... ok
test_pdbio_select (test_PDB.WriteTest)
Write a selection of the structure using a Select subclass. ... ok
test_pdbio_write_custom_residue (test_PDB.WriteTest)
Write a chainless residue using PDBIO. ... ok
test_pdbio_write_residue (test_PDB.WriteTest)
Write a single residue using PDBIO ... ok
test_pdbio_write_structure (test_PDB.WriteTest)
Write a full structure using PDBIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 3.612 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDBList.py
test_PDBList ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.005 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_FragmentMapper.py
test_PDB_FragmentMapper ... ok
test_fragment_mapper (test_PDB_FragmentMapper.FragmentMapperTests)
Self test for FragmentMapper module. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.208 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_KDTree.py
test_PDB_KDTree ... ok
test_KDTree_exceptions (test_PDB_KDTree.KDTreeTest) ... ok
test_KDTree_neighbor_search_manual (test_PDB_KDTree.KDTreeTest)
Test all fixed radius neighbor search. ... ok
test_KDTree_neighbor_search_simple (test_PDB_KDTree.KDTreeTest)
Test all fixed radius neighbor search. ... ok
test_KDTree_point_search (test_PDB_KDTree.KDTreeTest)
Test searching all points within a certain radius of center. ... ok
test_neighbor_search (test_PDB_KDTree.NeighborTest)
NeighborSearch: Find nearby randomly generated coordinates. ... ok
----------------------------------------------------------------------
Ran 1 test in 4.369 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIF2Dict.py
test_PDB_MMCIF2Dict ... ok
test_MMCIF2dict (test_PDB_MMCIF2Dict.MMCIF2dictTests) ... ok
test_inline_comments (test_PDB_MMCIF2Dict.MMCIF2dictTests)
Comments may begin outside of column 1 if preceded by whitespace. ... ok
test_loop_keyword_case_insensitive (test_PDB_MMCIF2Dict.MMCIF2dictTests)
Comments may begin outside of column 1. ... ok
test_quotefix (test_PDB_MMCIF2Dict.MMCIF2dictTests) ... ok
test_splitline (test_PDB_MMCIF2Dict.MMCIF2dictTests) ... ok
test_underscores (test_PDB_MMCIF2Dict.MMCIF2dictTests) ... ok
test_verbatim_block (test_PDB_MMCIF2Dict.MMCIF2dictTests)
Verbatim bocks parsed correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.148 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIFParser.py
test_PDB_MMCIFParser ... ok
test_conversion (test_PDB_MMCIFParser.CIFtoPDB)
Parse 1A8O.cif, write 1A8O.pdb, parse again and compare ... ok
testModels (test_PDB_MMCIFParser.ParseReal)
Test file with multiple models ... ok
test_filehandle (test_PDB_MMCIFParser.ParseReal)
Test if the parser can handle file handle as well as filename ... ok
test_insertions (test_PDB_MMCIFParser.ParseReal)
Test file with residue insertion codes ... ok
test_parsers (test_PDB_MMCIFParser.ParseReal)
Extract polypeptides from 1A80. ... ok
test_point_mutations_fast (test_PDB_MMCIFParser.ParseReal)
Test if FastMMCIFParser can parse point mutations correctly. ... ok
test_point_mutations_main (test_PDB_MMCIFParser.ParseReal)
Test if MMCIFParser parse point mutations correctly. ... ok
test_with_anisotrop (test_PDB_MMCIFParser.ParseReal) ... ok
----------------------------------------------------------------------
Ran 1 test in 2.412 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Polypetide.py
test_PDB_Polypetide ... ok
test_polypeptide (test_PDB_Polypetide.PolypeptideTests)
Tests on polypetide class and methods. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.165 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_ResidueDepth.py
test_PDB_ResidueDepth ... skipping. Install MSMS if you want to use it in Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.086 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_StructureAlignment.py
test_PDB_StructureAlignment ... /builddir/build/BUILD/python-biopython-1.73/python3/build/lib.linux-i686-3.7/Bio/PDB/StructureBuilder.py:91: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 13298.
PDBConstructionWarning)
/builddir/build/BUILD/python-biopython-1.73/python3/build/lib.linux-i686-3.7/Bio/PDB/StructureBuilder.py:91: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 13344.
PDBConstructionWarning)
ok
test_StructAlign (test_PDB_StructureAlignment.StructureAlignTests)
Tests on module to align two proteins according to a FASTA alignment file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.522 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Superimposer.py
test_PDB_Superimposer ... ok
test_Superimposer (test_PDB_Superimposer.SuperimposerTests)
Test on module that superimpose two protein structures. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.148 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_vectors.py
test_PDB_vectors ... ok
test_legacy_imports (test_PDB_vectors.LegacyImportTests)
Confirm legacy (deprecated) vector imports still work. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.084 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Pathway.py
test_Pathway ... ok
testAdditionalFunctions (test_Pathway.GraphTestCase) ... ok
test_Edges (test_Pathway.GraphTestCase) ... ok
test_Equals (test_Pathway.GraphTestCase) ... ok
test_Nodes (test_Pathway.GraphTestCase) ... ok
test_RemoveNode (test_Pathway.GraphTestCase) ... ok
testAdditionalFunctions (test_Pathway.MultiGraphTestCase) ... ok
test_Edges (test_Pathway.MultiGraphTestCase) ... ok
test_Equals (test_Pathway.MultiGraphTestCase) ... ok
test_Nodes (test_Pathway.MultiGraphTestCase) ... ok
test_RemoveNode (test_Pathway.MultiGraphTestCase) ... ok
test_eq (test_Pathway.ReactionTestCase) ... ok
test_rev (test_Pathway.ReactionTestCase) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.011 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Phd.py
test_Phd ... ok
test_check_SeqIO (test_Phd.PhdTest454)
Test phd_454 using parser via SeqIO. ... ok
test_check_SeqIO (test_Phd.PhdTestOne)
Test phd1 using parser via SeqIO. ... ok
test_check_record_parser (test_Phd.PhdTestOne)
Test phd1 file in detail. ... ok
test_check_SeqIO (test_Phd.PhdTestSolexa)
Test phd2 using parser via SeqIO. ... ok
test_check_SeqIO (test_Phd.PhdTestTwo)
Test phd2 using parser via SeqIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.122 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop.py
test_PopGen_GenePop ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
----------------------------------------------------------------------
Ran 1 test in 0.023 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop_EasyController.py
six linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hatest_PopGen_GenePop_EasyController ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
----------------------------------------------------------------------
Ran 1 test in 0.016 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop_nodepend.py
test_PopGen_GenePop_nodepend ... ok
test_file_record_parser (test_PopGen_GenePop_nodepend.FileParserTest)
Basic operation of the File Record Parser. ... ok
test_remove_features (test_PopGen_GenePop_nodepend.FileParserTest)
Testing the ability to remove population/loci via class methods. ... ok
test_wrong_file_parser (test_PopGen_GenePop_nodepend.FileParserTest)
Testing the ability to deal with wrongly formatted files. ... ok
test_record_parser (test_PopGen_GenePop_nodepend.ParserTest)
Basic operation of the Record Parser. ... ok
test_wrong_file_parser (test_PopGen_GenePop_nodepend.ParserTest)
Testing the ability to deal with wrongly formatted files. ... ok
test_record_basic (test_PopGen_GenePop_nodepend.RecordTest)
Basic test on Record. ... ok
test_utils (test_PopGen_GenePop_nodepend.UtilsTest)
Basic operation of GenePop Utils. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.036 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Prank_tool.py
test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.118 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Probcons_tool.py
test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.114 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ProtParam.py
test_ProtParam ... ok
test_aromaticity (test_ProtParam.ProtParamTest)
Test calculating protein aromaticity ... ok
test_count_amino_acids (test_ProtParam.ProtParamTest)
Test getting amino acid counts ... ok
test_flexibility (test_ProtParam.ProtParamTest)
Test calculating protein flexibility ... ok
test_get_amino_acids_percent (test_ProtParam.ProtParamTest)
Test getting amino acid percentage ... ok
test_get_molecular_weight (test_ProtParam.ProtParamTest)
Test calculating protein molecular weight ... ok
test_get_molecular_weight_identical (test_ProtParam.ProtParamTest)
Test calculating the protein molecular weight agrees with calculation from Bio.SeqUtils ... ok
test_get_monoisotopic_molecular_weight (test_ProtParam.ProtParamTest)
Test calculating the monoisotopic molecular weight ... ok
test_get_monoisotopic_molecular_weight_identical (test_ProtParam.ProtParamTest)
Test calculating the protein molecular weight agrees with calculation from Bio.SeqUtils ... ok
test_gravy (test_ProtParam.ProtParamTest)
Test calculating gravy ... ok
test_instability_index (test_ProtParam.ProtParamTest)
Test calculating protein instability index ... ok
test_isoelectric_point (test_ProtParam.ProtParamTest)
Test calculating the isoelectric point ... ok
test_molar_extinction_coefficient (test_ProtParam.ProtParamTest)
Test molar extinction coefficient ... ok
test_protein_scale (test_ProtParam.ProtParamTest)
Test calculating the Kite Doolittle scale ... ok
test_secondary_structure_fraction (test_ProtParam.ProtParamTest)
Test calculating secondary structure fractions ... ok
----------------------------------------------------------------------
Ran 1 test in 0.075 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_QCPSuperimposer.py
test_QCPSuperimposer ... ok
test_get_init_rms (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
test_get_rms (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
test_get_rotran (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
test_get_transformed (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
test_oldTest (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
test_run (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
test_set (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.084 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_RCSBFormats.py
test_RCSBFormats ... ok
test_compare_chains (test_RCSBFormats.CompareStructures)
Compare parsed chains ... ok
test_compare_models (test_RCSBFormats.CompareStructures)
Compared parsed models ... ok
----------------------------------------------------------------------
Ran 1 test in 1.115 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Restriction.py
test_Restriction ... ok
test_basic_isochizomers (test_Restriction.EnzymeComparison)
Test to be sure isochizomer and neoschizomers are as expected. ... ok
test_comparisons (test_Restriction.EnzymeComparison)
Test comparison operators between different enzymes. ... ok
test_change (test_Restriction.RestrictionBatchPrintTest)
Test that change() changes something. ... ok
test_make_format_map1 (test_Restriction.RestrictionBatchPrintTest)
Test that print_as('map'); print_that() correctly wraps round. ... ok
test_make_format_map2 (test_Restriction.RestrictionBatchPrintTest)
Test that print_as('map'); print_that() correctly wraps round. ... ok
test_make_format_map3 (test_Restriction.RestrictionBatchPrintTest)
Test that print_as('map'); print_that() correctly wraps round. ... ok
test_analysis_restrictions (test_Restriction.RestrictionBatches)
Test Fancier restriction analysis. ... ok
test_batch_analysis (test_Restriction.RestrictionBatches)
Sequence analysis with a restriction batch. ... ok
test_creating_batch (test_Restriction.RestrictionBatches)
Creating and modifying a restriction batch. ... ok
test_premade_batches (test_Restriction.RestrictionBatches)
Test content of premade batches CommOnly, NoComm, AllEnzymes. ... ok
test_search_premade_batches (test_Restriction.RestrictionBatches)
Test search with pre-made batches CommOnly, NoComm, AllEnzymes. ... ok
test_formatted_seq (test_Restriction.SequenceTesting)
Test several methods of FormattedSeq. ... ok
test_non_iupac_letters (test_Restriction.SequenceTesting)
Test if non-IUPAC letters raise a TypeError. ... ok
test_sequence_object (test_Restriction.SequenceTesting)
Test if sequence must be a Seq or MutableSeq object. ... ok
test_circular_sequences (test_Restriction.SimpleEnzyme)
Deal with cutting circular sequences. ... ok
test_cutting_border_positions (test_Restriction.SimpleEnzyme)
Check if cutting after first and penultimate position works. ... ok
test_ear_cutting (test_Restriction.SimpleEnzyme)
Test basic cutting with EarI (ambiguous overhang). ... ok
test_eco_cutting (test_Restriction.SimpleEnzyme)
Test basic cutting with EcoRI (5'overhang). ... ok
test_init (test_Restriction.SimpleEnzyme)
Check for error during __init__. ... ok
test_kpn_cutting (test_Restriction.SimpleEnzyme)
Test basic cutting with KpnI (3'overhang). ... ok
test_overlapping_cut_sites (test_Restriction.SimpleEnzyme)
Check if overlapping recognition sites are properly handled. ... ok
test_recognition_site_on_both_strands (test_Restriction.SimpleEnzyme)
Check if recognition sites on both strands are properly handled. ... ok
test_shortcuts (test_Restriction.SimpleEnzyme)
Check if '/' and '//' work as '.search' and '.catalyse'. ... ok
test_sma_cutting (test_Restriction.SimpleEnzyme)
Test basic cutting with SmaI (blunt cutter). ... ok
test_sna_cutting (test_Restriction.SimpleEnzyme)
Test basic cutting with SnaI (unknown). ... ok
test_print_that (test_Restriction.TestPrintOutputs)
Test print_that function. ... ok
test_str_method (test_Restriction.TestPrintOutputs)
Test __str__ and __repr__ outputs. ... ok
test_supplier (test_Restriction.TestPrintOutputs)
Test output of supplier list for different enzyme types. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.350 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Astral.py
test_SCOP_Astral ... ok
testConstructWithCustomFile (test_SCOP_Astral.AstralTests) ... ok
testGetDomainsClustered (test_SCOP_Astral.AstralTests) ... ok
testGetDomainsFromFile (test_SCOP_Astral.AstralTests) ... ok
testGetSeq (test_SCOP_Astral.AstralTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.123 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Cla.py
test_SCOP_Cla ... ok
testError (test_SCOP_Cla.ClaTests)
Test if a corrupt record raises the appropriate exception ... ok
testIndex (test_SCOP_Cla.ClaTests)
Test CLA file indexing ... ok
testParse (test_SCOP_Cla.ClaTests)
Test if all records in a CLA file are being read ... ok
testRecord (test_SCOP_Cla.ClaTests)
Test one record in detail ... ok
testStr (test_SCOP_Cla.ClaTests)
Test if we can convert each record to a string correctly ... ok
----------------------------------------------------------------------
Ran 1 test in 0.103 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Des.py
test_SCOP_Des ... ok
testError (test_SCOP_Des.DesTests)
Test if a corrupt record raises the appropriate exception ... ok
testParse (test_SCOP_Des.DesTests)
Test if all records in a DES file are being read ... ok
testRecord (test_SCOP_Des.DesTests)
Test one record in detail ... ok
testStr (test_SCOP_Des.DesTests)
Test if we can convert each record to a string correctly ... ok
----------------------------------------------------------------------
Ran 1 test in 0.102 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Dom.py
test_SCOP_Dom ... ok
testError (test_SCOP_Dom.DomTests)
Test if a corrupt record raises the appropriate exception ... ok
testParse (test_SCOP_Dom.DomTests)
Test if all records in a DOM file are being read ... ok
testRecord (test_SCOP_Dom.DomTests)
Test one record in detail ... ok
testStr (test_SCOP_Dom.DomTests)
Test if we can convert each record to a string correctly ... ok
----------------------------------------------------------------------
Ran 1 test in 0.101 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Hie.py
test_SCOP_Hie ... ok
testError (test_SCOP_Hie.HieTests)
Test if a corrupt record raises the appropriate exception ... ok
testParse (test_SCOP_Hie.HieTests)
Test if all records in a HIE file are being read ... ok
testStr (test_SCOP_Hie.HieTests)
Test if we can convert each record to a string correctly ... ok
----------------------------------------------------------------------
Ran 1 test in 0.100 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Raf.py
test_SCOP_Raf ... ok
testParse (test_SCOP_Raf.RafTests)
Can we parse a RAF record? ... ok
testSeqMapAdd (test_SCOP_Raf.RafTests) ... ok
testSeqMapIndex (test_SCOP_Raf.RafTests) ... ok
testSeqMapSlice (test_SCOP_Raf.RafTests) ... ok
test_SeqMap_getAtoms_err (test_SCOP_Raf.RafTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.110 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Residues.py
test_SCOP_Residues ... ok
testAstralParse (test_SCOP_Residues.ResiduesTests)
Test if we can parse residue subsets enclosed in brackets ... ok
testJustPdbId (test_SCOP_Residues.ResiduesTests) ... ok
testParse (test_SCOP_Residues.ResiduesTests) ... ok
testParseError (test_SCOP_Residues.ResiduesTests) ... ok
testPdbId (test_SCOP_Residues.ResiduesTests) ... ok
testStr (test_SCOP_Residues.ResiduesTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.105 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Scop.py
test_SCOP_Scop ... ok
testConstructFromDirectory (test_SCOP_Scop.ScopTests) ... ok
testGetAscendent (test_SCOP_Scop.ScopTests) ... ok
testParse (test_SCOP_Scop.ScopTests) ... ok
testParseDomain (test_SCOP_Scop.ScopTests) ... ok
testSccsOrder (test_SCOP_Scop.ScopTests) ... ok
test_get_descendents (test_SCOP_Scop.ScopTests)
Test getDescendents method ... ok
----------------------------------------------------------------------
Ran 1 test in 0.106 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_online.py
test_SCOP_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.004 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SVDSuperimposer.py
test_SVDSuperimposer ... ok
test_get_init_rms (test_SVDSuperimposer.SVDSuperimposerTest) ... ok
test_oldTest (test_SVDSuperimposer.SVDSuperimposerTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.010 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_blat_psl.py
test_SearchIO_blat_psl ... ok
test_psl_34_001 (test_SearchIO_blat_psl.BlatPslCases)
Test parsing blat output (psl_34_001.psl) ... ok
test_psl_34_002 (test_SearchIO_blat_psl.BlatPslCases)
Test parsing blat output (psl_34_001.psl) ... ok
test_psl_34_003 (test_SearchIO_blat_psl.BlatPslCases)
Test parsing blat output (psl_34_003.psl) ... ok
test_psl_34_004 (test_SearchIO_blat_psl.BlatPslCases)
Test parsing blat output (psl_34_004.psl) ... ok
test_psl_34_005 (test_SearchIO_blat_psl.BlatPslCases)
Test parsing blat output (psl_34_005.psl) ... ok
test_psl_35_001 (test_SearchIO_blat_psl.BlatPslCases)
Test parsing blat output (psl_35_001.psl) ... ok
test_psl_35_002 (test_SearchIO_blat_psl.BlatPslCases)
Test parsing blat output (psl_35_002.psl) ... ok
test_psl_34_001 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (psl_34_001.psl) ... ok
test_psl_34_002 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (psl_34_001.psl) ... ok
test_psl_34_003 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (psl_34_003.psl) ... ok
test_psl_34_004 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (psl_34_004.psl) ... ok
test_psl_34_005 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (psl_34_005.psl) ... ok
test_psl_35_001 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (psl_35_001.psl) ... ok
test_psl_35_002 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (psl_35_002.psl) ... ok
test_pslx_34_001 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (pslx_34_001.pslx) ... ok
test_pslx_34_002 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (pslx_34_002.pslx) ... ok
test_pslx_34_003 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (pslx_34_003.pslx) ... ok
test_pslx_34_004 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (pslx_34_004.pslx) ... ok
test_pslx_34_005 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (pslx_34_005.pslx) ... ok
test_pslx_35_002 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (pslx_35_002.pslx) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.177 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_blat_psl_index.py
test_SearchIO_blat_psl_index ... ok
test_psl_34_001 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-psl indexing, multiple queries ... ok
test_psl_34_002 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-psl indexing, single query, no hits ... ok
test_psl_34_003 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-psl indexing, single query, single hit ... ok
test_psl_34_004 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-psl indexing, single query, multiple hits with multiple hsps ... ok
test_psl_34_005 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-psl indexing, multiple queries, no header ... ok
test_psl_34_006 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-pslx indexing, multiple queries ... ok
test_psl_34_007 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-pslx indexing, single query, no hits ... ok
test_psl_34_008 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-pslx indexing, single query, single hit ... ok
test_psl_34_009 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-pslx indexing, single query, multiple hits with multiple hsps ... ok
test_psl_34_010 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-pslx indexing, multiple queries, no header ... ok
----------------------------------------------------------------------
Ran 1 test in 0.215 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate.py
test_SearchIO_exonerate ... ok
test_exn_22_o_vulgar_cigar (test_SearchIO_exonerate.ExonerateCigarCases)
Test parsing exonerate output (exn_22_o_vulgar_cigar.exn) ... ok
test_vulgar_text_similar_c2c (test_SearchIO_exonerate.ExonerateSpcCases)
Compares vulgar-text coordinate parsing for the coding2coding model. ... ok
test_vulgar_text_similar_g2g (test_SearchIO_exonerate.ExonerateSpcCases)
Compares vulgar-text coordinate parsing for the genome2genome model. ... ok
test_vulgar_text_similar_p2d (test_SearchIO_exonerate.ExonerateSpcCases)
Compares vulgar-text coordinate parsing for the protein2dna model. ... ok
test_exn_22_m_affine_local (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_affine_local.exn) ... ok
test_exn_22_m_cdna2genome (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_cdna2genome.exn) ... ok
test_exn_22_m_coding2coding (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_coding2coding.exn) ... ok
test_exn_22_m_coding2coding_fshifts (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_coding2coding_fshifts.exn) ... ok
test_exn_22_m_coding2genome (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_coding2genome.exn) ... ok
test_exn_22_m_dna2protein (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_dna2protein.exn) ... ok
test_exn_22_m_est2genome (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_est2genome.exn) ... ok
test_exn_22_m_genome2genome (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_genome2genome.exn) ... ok
test_exn_22_m_ner (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_ner.exn) ... ok
test_exn_22_m_protein2dna_fshifts (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_protein2dna_fshifts.exn) ... ok
test_exn_22_m_protein2genome (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_protein2genome.exn) ... ok
test_exn_22_m_ungapped (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_ungapped.exn) ... ok
test_exn_22_m_ungapped_trans (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_ungapped_trans.exn) ... ok
test_exn_22_q_multiple (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_q_multiple.exn) ... ok
test_exn_22_q_none (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_q_none.exn) ... ok
test_exn_22_o_vulgar (test_SearchIO_exonerate.ExonerateVulgarCases)
Test parsing exonerate output (exn_22_o_vulgar.exn) ... ok
test_exn_22_o_vulgar_fshifts (test_SearchIO_exonerate.ExonerateVulgarCases)
Test parsing exonerate output (exn_22_o_vulgar_fshifts.exn) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.227 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate_text_index.py
test_SearchIO_exonerate_text_index ... ok
test_exn_22_m_est2genome (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases)
Test exonerate-text indexing, single ... ok
test_exn_22_q_multiple (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases)
Test exonerate-text indexing, single ... ok
----------------------------------------------------------------------
Ran 1 test in 0.125 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate_vulgar_index.py
test_SearchIO_exonerate_vulgar_index ... ok
test_exn_22_m_est2genome (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases)
Test exonerate-vulgar indexing, single ... ok
test_exn_22_q_multiple (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases)
Test exonerate-vulgar indexing, single ... ok
----------------------------------------------------------------------
Ran 1 test in 0.105 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_fasta_m10.py
test_SearchIO_fasta_m10 ... ok
test_output002 (test_SearchIO_fasta_m10.Fasta34Cases)
Test parsing fasta34 output (output002.m10) ... ok
test_output003 (test_SearchIO_fasta_m10.Fasta34Cases)
Test parsing fasta34 output (output003.m10) ... ok
test_output001 (test_SearchIO_fasta_m10.Fasta35Cases)
Test parsing fasta35 output (output001.m10) ... ok
test_output004 (test_SearchIO_fasta_m10.Fasta35Cases)
Test parsing fasta35 output (output004.m10) ... ok
test_output005 (test_SearchIO_fasta_m10.Fasta35Cases)
Test parsing ssearch35 output (output005.m10) ... ok
test_output006 (test_SearchIO_fasta_m10.Fasta35Cases)
Test parsing fasta35 output (output006.m10) ... ok
test_output007 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output007.m10) ... ok
test_output008 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing tfastx36 output (output008.m10) ... ok
test_output009 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output009.m10) ... ok
test_output010 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output010.m10) ... ok
test_output011 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output011.m10) ... ok
test_output012 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output012.m10) ... ok
test_output013 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output013.m10) ... ok
test_output014 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output014.m10) ... ok
test_output015 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output015.m10) ... ok
test_output016 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output016.m10) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.182 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_fasta_m10_index.py
t 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:test_SearchIO_fasta_m10_index ... ok
test_output_001 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, fasta35, multiple queries ... ok
test_output_002 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, fasta34, multiple queries ... ok
test_output_005 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, ssearch35, multiple queries ... ok
test_output_008 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, tfastx36, multiple queries ... ok
test_output_009 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, fasta36, multiple queries ... ok
test_output_010 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, fasta36, single query, no hits ... ok
test_output_011 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, fasta36, single query, hits with single hsp ... ok
test_output_012 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, fasta36, single query with multiple hsps ... ok
----------------------------------------------------------------------
Ran 1 test in 0.261 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer2_text.py
test_SearchIO_hmmer2_text ... ok
test_hmmpfam_21 (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.1 file (text_21_hmmpfam_001.out) ... ok
test_hmmpfam_22 (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.2 file (text_22_hmmpfam_001.out) ... ok
test_hmmpfam_23 (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.3 file (text_23_hmmpfam_001.out) ... ok
test_hmmpfam_23_break_in_end_of_seq (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.3 file with a line break in the end of seq marker. ... ok
test_hmmpfam_23_missing_consensus (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.3 file (text_23_hmmpfam_003.out) ... ok
test_hmmpfam_23_no_match (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.3 file (text_23_hmmpfam_002.out) ... ok
test_hmmpfam_24 (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.4 file (text_24_hmmpfam_001.out) ... ok
test_hmmsearch_20 (test_SearchIO_hmmer2_text.HmmsearchTests)
Test parsing hmmsearch 2.0 file (text_20_hmmsearch_001.out) ... ok
test_hmmsearch_22 (test_SearchIO_hmmer2_text.HmmsearchTests)
Test parsing hmmsearch 2.2 file (text_22_hmmsearch_001.out) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.375 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer2_text_index.py
test_SearchIO_hmmer2_text_index ... ok
test_hmmertext_text_21_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
Test hmmer2-text indexing, HMMER 2.1 ... ok
test_hmmertext_text_22_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
Test hmmer2-text indexing, HMMER 2.2 ... ok
test_hmmertext_text_22_hmmsearch_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
Test hmmer2-text indexing, HMMER 2.2 ... ok
test_hmmertext_text_23_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
Test hmmer2-text indexing, HMMER 2.3 ... ok
test_hmmertext_text_24_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
Test hmmer2-text indexing, HMMER 2.4 ... ok
test_hmmer2text_22_multiple_first_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
Test hmmer2-text raw string retrieval, multiple queries, hmmpfam ... ok
test_hmmer2text_22_multiple_last_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
Test hmmer2-text raw string retrieval, multiple queries, hmmpfam ... ok
test_hmmer2text_22_multiple_middle_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
Test hmmer2-text raw string retrieval, multiple queries, hmmpfam ... ok
test_hmmer2text_22_single_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
Test hmmer2-text raw string retrieval, single query, hmmpfam ... ok
test_hmmer2text_22_single_hmmsearch (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
Test hmmer2-text raw string retrieval, single query, hmmsearch ... ok
----------------------------------------------------------------------
Ran 1 test in 0.223 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_domtab.py
test_SearchIO_hmmer3_domtab ... ok
test_domtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases)
Test parsing hmmsearch-domtab, hmmsearch 3.0, multiple queries (domtab_30_hmmsearch_001) ... ok
test_domtab_31b1_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases)
Test parsing hmmsearch-domtab, hmmsearch 3.1b1, single query (domtab_31b1_hmmsearch_001) ... ok
test_domtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases)
Test parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_001) ... ok
test_domtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab.HmmscanCases)
Test parsing hmmscan-domtab, hmmscan 3.0, single query, no hits (domtab_30_hmmscan_002) ... ok
test_domtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab.HmmscanCases)
Test parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_003) ... ok
test_domtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab.HmmscanCases)
Test parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_004) ... ok
test_domtab_31b1_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases)
Test parsing hmmscan-domtab, hmmscan 3.1b1, multiple queries (domtab_31b1_hmmscan_001) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.099 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_domtab_index.py
test_SearchIO_hmmer3_domtab_index ... ok
test_hmmerdomtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
Test hmmscan-domtab indexing, HMMER 3.0, multiple queries ... ok
test_hmmerdomtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
Test hmmscan-domtab indexing, HMMER 3.0, single query, no hits ... ok
test_hmmerdomtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
Test hmmscan-domtab indexing, HMMER 3.0, single query, multiple hits ... ok
test_hmmerdomtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
Test hmmscan-domtab indexing, HMMER 3.0, single query, no alignments ... ok
test_hmmerdomtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
Test hmmsearch-domtab indexing, HMMER 3.0, single query, no alignments ... ok
test_hmmerdomtab_30_multiple_first (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, first (domtab_30_hmmscan_001.out) ... ok
test_hmmerdomtab_30_multiple_last (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, last (domtab_30_hmmscan_001.out) ... ok
test_hmmerdomtab_30_multiple_middle (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, middle (domtab_30_hmmscan_001.out) ... ok
test_hmmerdomtab_30_single (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, single query (domtab_30_hmmscan_004.out) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.117 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_tab.py
test_SearchIO_hmmer3_tab ... ok
test_30_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases)
Test parsing hmmer3-tab, hmmscan 3.0, multiple queries (tab_30_hmmscan_001) ... ok
test_30_hmmscan_002 (test_SearchIO_hmmer3_tab.HmmscanCases)
Test parsing hmmer3-tab, hmmscan 3.0, single query, no hits (tab_30_hmmscan_002) ... ok
test_30_hmmscan_003 (test_SearchIO_hmmer3_tab.HmmscanCases)
Test parsing hmmer3-tab, hmmscan 3.0, single query, single hit, single hsp (tab_30_hmmscan_003) ... ok
test_30_hmmscan_004 (test_SearchIO_hmmer3_tab.HmmscanCases)
Test parsing hmmer3-tab, hmmscan 3.0, single query, multiple hits (tab_30_hmmscan_004) ... ok
test_31b1_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases)
Test parsing hmmer3-tab, hmmscan 3.1b1, multiple queries (tab_31b1_hmmscan_001) ... ok
test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_tab.HmmsearchCases)
Test parsing hmmer3-tab, hmmsearch 3.1b1, multiple queries (tab_31b1_hmmscan_001) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.087 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_tab_index.py
test_SearchIO_hmmer3_tab_index ... ok
test_hmmer3tab_30_hmmscan_001 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases)
Test hmmer3-tab indexing, HMMER 3.0, multiple queries ... ok
test_hmmer3tab_30_hmmscan_002 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases)
Test hmmer3-tab indexing, HMMER 3.0, single query, no hits ... ok
test_hmmer3tab_30_hmmscan_003 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases)
Test hmmer3-tab indexing, HMMER 3.0, single query, multiple hits ... ok
test_hmmer3tab_30_hmmscan_004 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases)
Test hmmer3-tab indexing, HMMER 3.0, single query, no alignments ... ok
test_hmmer3tab_30_multiple_first (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases)
Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, first (tab_30_hmmscan_001.out) ... ok
test_hmmer3tab_30_multiple_last (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases)
Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, last (tab_30_hmmscan_001.out) ... ok
test_hmmer3tab_30_multiple_middle (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases)
Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, middle (tab_30_hmmscan_001.out) ... ok
test_hmmer3tab_30_single (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases)
Test hmmer3-tab raw string retrieval, HMMER 3.0, single query (tab_30_hmmscan_004.out) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.098 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_text.py
test_SearchIO_hmmer3_text ... ok
test_30_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmersearch 3.0 (text_30_hmmsearch_001) ... ok
test_30_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmersearch 3.0 (text_30_hmmsearch_002) ... ok
test_30_hmmsearch_003 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmersearch 3.0 (text_30_hmmsearch_003) ... ok
test_30_hmmsearch_004 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmersearch 3.0 (text_30_hmmsearch_004) ... ok
test_30_hmmsearch_005 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmersearch 3.0 (text_30_hmmsearch_005) ... ok
test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmsearch 3.1b1 (text_31b1_hmmsearch_001) ... ok
test_31b2_hmmscan_001 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmscan 3.1b2 (text_31b2_hmmscan_001) ... ok
test_31b2_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_001) ... ok
test_31b2_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_002) ... ok
test_30_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_001) ... ok
test_30_hmmscan_002 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_002) ... ok
test_30_hmmscan_003 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_003) ... ok
test_30_hmmscan_004 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_004) ... ok
test_30_hmmscan_005 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_005) ... ok
test_30_hmmscan_006 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_006) ... ok
test_30_hmmscan_007 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_007) ... ok
test_30_hmmscan_008 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_008) ... ok
test_30_hmmscan_009 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_009) ... ok
test_30_hmmscan_010 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_010) ... ok
test_31b1_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.1b1 (text_31b1_hmmscan_001) ... ok
test_31b2_phmmer_001 (test_SearchIO_hmmer3_text.PhmmerCases)
Test parsing phmmer 3.1b2 (text_31b2_phmmer_001) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.283 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_text_index.py
test_SearchIO_hmmer3_text_index ... ok
test_hmmertext_text_30_hmmscan_001 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
Test hmmer3-text indexing, HMMER 3.0, multiple queries ... ok
test_hmmertext_text_30_hmmscan_002 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
Test hmmer3-text indexing, HMMER 3.0, single query, no hits ... ok
test_hmmertext_text_30_hmmscan_006 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
Test hmmer3-text indexing, HMMER 3.0, single query, multiple hits ... ok
test_hmmertext_text_30_hmmscan_007 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
Test hmmer3-text indexing, HMMER 3.0, single query, no alignments ... ok
test_hmmertext_text_30_hmmscan_008 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
Test hmmer3-text indexing, HMMER 3.0, single query, no alignment width ... ok
test_hmmertext_text_30_hmmsearch_005 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
Test hmmer3-text indexing, HMMER 3.0, multiple queries ... ok
test_hmmer3text_30_multiple_first (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases)
Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, first (text_30_hmmscan_001.out) ... ok
test_hmmer3text_30_multiple_last (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases)
Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, last (text_30_hmmscan_001.out) ... ok
test_hmmer3text_30_multiple_middle (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases)
Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, middle (text_30_hmmscan_001.out) ... ok
test_hmmer3text_30_single (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases)
Test hmmer3-text raw string retrieval, HMMER 3.0, single query (text_30_hmmscan_003.out) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.168 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_interproscan_xml.py
test_SearchIO_interproscan_xml ... ok
test_xml_001 (test_SearchIO_interproscan_xml.InterproscanXmlCases) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.082 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_legacy.py
test_SearchIO_legacy ... ok
runTest (__main__.ComparisonTestCase)
test_SearchIO_legacy ... ok
----------------------------------------------------------------------
Ran 1 test in 0.076 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_model.py
test_SearchIO_model ... ok
test_alphabet_no_seq (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment alphabet property, query and hit sequences not present ... ok
test_alphabet_with_seq (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment alphabet property, query or hit sequences present ... ok
test_coords_setters_getters (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit coordinate-related setters and getters ... ok
test_coords_setters_readonly (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit coordinate-related read-only getters ... ok
test_default_attrs (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment attributes' default values ... ok
test_frame_set_error (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit frame setters, invalid values ... ok
test_frame_set_ok (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit frame setters ... ok
test_getitem (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__getitem__ ... ok
test_getitem_alignment_annot (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__getitem__, with alignment annotation ... ok
test_getitem_attrs (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__getitem__, with attributes ... ok
test_id_desc_set (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit id and description setters ... ok
test_init_with_seqrecord (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__init__, with SeqRecord ... ok
test_init_wrong_seqtypes (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__init__, wrong sequence argument types ... ok
test_len (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__len__ ... ok
test_pickle (test_SearchIO_model.HSPFragmentCases)
Test pickling and unpickling of HSPFragment ... ok
test_repr (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__repr__ ... ok
test_seq_unequal_hit_query_len (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment sequence setter with unequal hit and query lengths ... ok
test_seqmodel (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment sequence attribute types and default values ... ok
test_strand_set_error (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit strand setters, invalid values ... ok
test_strand_set_from_minus_frame (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit strand getters, from minus frame ... ok
test_strand_set_from_plus_frame (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit strand getters, from plus frame ... ok
test_strand_set_from_zero_frame (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit strand getters, from zero frame ... ok
test_strand_set_ok (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit strand setters ... ok
test_getitem (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment.__getitem__, no alignments ... ok
test_getitem_only_hit (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment.__getitem__, only hit ... ok
test_getitem_only_query (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment.__getitem__, only query ... ok
test_init (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment.__init__ attributes ... ok
test_iter (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSP.__iter__, no alignments ... ok
test_len (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment.__len__, no alignments ... ok
test_repr (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment.__repr__, no alignments ... ok
test_seqmodel (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment sequence attributes, no alignments ... ok
test_alphabet (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.alphabet getter ... ok
test_alphabet_set (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.alphabet setter ... ok
test_contains (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.__contains__ ... ok
test_delitem (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.__delitem__ ... ok
test_fragments (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.fragments property ... ok
test_getitem (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.__getitem__ ... ok
test_id_desc_set (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP query and hit id and description setters ... ok
test_is_fragmented (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.is_fragmented property ... ok
test_len (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.__len__ ... ok
test_pickle (test_SearchIO_model.HSPMultipleFragmentCases)
Test pickling and unpickling of HSP ... ok
test_range (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP range properties ... ok
test_ranges (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP ranges properties ... ok
test_seqs (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP sequence properties ... ok
test_setitem_multiple (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.__setitem__, multiple items ... ok
test_setitem_single (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.__setitem___, single item ... ok
test_setters_readonly (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP read-only properties ... ok
test_span (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP span properties ... ok
test_alignment (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP.alignment property ... ok
test_aln_span (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP.aln_span property ... ok
test_fragment (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP.fragment property ... ok
test_init_no_fragment (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP.__init__ without fragments ... ok
test_is_fragmented (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP.is_fragmented property ... ok
test_len (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP.__len__ ... ok
test_range (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP range properties ... ok
test_seq (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP sequence properties ... ok
test_setters_readonly (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP read-only properties ... ok
test_span (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP span properties ... ok
test_append (test_SearchIO_model.HitCases)
Test Hit.append ... ok
test_delitem (test_SearchIO_model.HitCases)
Test Hit.__delitem__ ... ok
test_desc_set (test_SearchIO_model.HitCases)
Test Hit.description setter ... ok
test_desc_set_no_seqrecord (test_SearchIO_model.HitCases)
Test Hit.description setter, without HSP SeqRecords ... ok
test_filter (test_SearchIO_model.HitCases)
Test Hit.filter ... ok
test_filter_no_filtered (test_SearchIO_model.HitCases)
Test Hit.hit_filter, all hits filtered out ... ok
test_filter_no_func (test_SearchIO_model.HitCases)
Test Hit.filter, without arguments ... ok
test_fragments (test_SearchIO_model.HitCases)
Test Hit.fragments ... ok
test_getitem_multiple (test_SearchIO_model.HitCases)
Test Hit.__getitem__, multiple items ... ok
test_getitem_single (test_SearchIO_model.HitCases)
Test Hit.__getitem__, single item ... ok
test_hsp_map_no_func (test_SearchIO_model.HitCases)
Test Hit.map, without arguments ... ok
test_hsps (test_SearchIO_model.HitCases)
Test Hit.hsps ... ok
test_id_set (test_SearchIO_model.HitCases)
Test Hit.id setter ... ok
test_index (test_SearchIO_model.HitCases)
Test Hit.index ... ok
test_index_not_present (test_SearchIO_model.HitCases)
Test Hit.index, when index is not present ... ok
test_init_hsps_only (test_SearchIO_model.HitCases)
Test Hit.__init__, with hsps only ... ok
test_init_id_only (test_SearchIO_model.HitCases)
Test Hit.__init__, with ID only ... ok
test_init_none (test_SearchIO_model.HitCases)
Test Hit.__init__, no arguments ... ok
test_item_multiple (test_SearchIO_model.HitCases)
Test Hit.__setitem__, multiple items ... ok
test_iter (test_SearchIO_model.HitCases)
Test Hit.__iter__ ... ok
test_len (test_SearchIO_model.HitCases)
Test Hit.__len__ ... ok
test_map (test_SearchIO_model.HitCases)
Test Hit.hsp_map ... ok
test_nonzero (test_SearchIO_model.HitCases)
Test Hit.__nonzero__ ... ok
test_pickle (test_SearchIO_model.HitCases)
Test pickling and unpickling of Hit ... ok
test_pop (test_SearchIO_model.HitCases)
Test Hit.pop ... ok
test_repr (test_SearchIO_model.HitCases)
Test Hit.__repr__ ... ok
test_setitem_single (test_SearchIO_model.HitCases)
Test Hit.__setitem__, single item ... ok
test_sort (test_SearchIO_model.HitCases)
Test Hit.sort ... ok
test_sort_not_in_place (test_SearchIO_model.HitCases)
Test Hit.sort, not in place ... ok
test_validate_hsp_ok (test_SearchIO_model.HitCases)
Test Hit._validate_hsp ... ok
test_validate_hsp_wrong_hit_id (test_SearchIO_model.HitCases)
Test Hit._validate_hsp, wrong hit ID ... ok
test_validate_hsp_wrong_query_id (test_SearchIO_model.HitCases)
Test Hit._validate_hsp, wrong query ID ... ok
test_validate_hsp_wrong_type (test_SearchIO_model.HitCases)
Test Hit._validate_hsp, wrong type ... ok
test_absorb_hit_does_not_exist (test_SearchIO_model.QueryResultCases)
Test QueryResult.absorb, hit does not exist ... ok
test_absorb_hit_exists (test_SearchIO_model.QueryResultCases)
Test QueryResult.absorb, hit with the same ID exists ... ok
test_append_alt_id_exists (test_SearchIO_model.QueryResultCases)
Test QueryResult.append, when alt ID exists ... ok
test_append_alt_id_exists_alt (test_SearchIO_model.QueryResultCases)
Test QueryResult.append, when alt ID exists as primary ... ok
test_append_custom_hit_key_function_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.append, with custom hit key function ... ok
test_append_id_exists (test_SearchIO_model.QueryResultCases)
Test QueryResult.append, when ID exists ... ok
test_append_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.append ... ok
test_contains (test_SearchIO_model.QueryResultCases)
Test QueryResult.__contains__ ... ok
test_contains_alt (test_SearchIO_model.QueryResultCases)
Test QueryResult.__contains__, with alternative IDs ... ok
test_delitem_alt_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__delitem__, with alt ID ... ok
test_delitem_int_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__delitem__ ... ok
test_delitem_slice_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__delitem__, with slice ... ok
test_delitem_string_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__getitem__, with string ... ok
test_description_set (test_SearchIO_model.QueryResultCases)
Test QueryResult.description setter ... ok
test_description_set_no_seqrecord (test_SearchIO_model.QueryResultCases)
Test QueryResult.description setter, without HSP SeqRecords ... ok
test_fragments (test_SearchIO_model.QueryResultCases)
Test QueryResult.fragments ... ok
test_getitem_alt_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__getitem__, single item with alternative ID ... ok
test_getitem_default_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__getitem__ ... ok
test_getitem_int_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__getitem__, with integer ... ok
test_getitem_slice_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__getitem__, with slice ... ok
test_getitm_slice_alt_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__getitem__, with slice and alt IDs ... ok
test_hit_filter (test_SearchIO_model.QueryResultCases)
Test QueryResult.hit_filter ... ok
test_hit_filter_no_filtered (test_SearchIO_model.QueryResultCases)
Test QueryResult.hit_filter, all hits filtered out ... ok
test_hit_filter_no_func (test_SearchIO_model.QueryResultCases)
Test QueryResult.hit_filter, without arguments ... ok
test_hit_keys (test_SearchIO_model.QueryResultCases)
Test QueryResult.hit_keys ... ok
test_hit_map (test_SearchIO_model.QueryResultCases)
Test QueryResult.hit_map ... ok
test_hit_map_no_func (test_SearchIO_model.QueryResultCases)
Test QueryResult.hit_map, without arguments ... ok
test_hits (test_SearchIO_model.QueryResultCases)
Test QueryResult.hits ... ok
test_hsp_filter (test_SearchIO_model.QueryResultCases)
Test QueryResult.hsp_filter ... ok
test_hsp_filter_no_filtered (test_SearchIO_model.QueryResultCases)
Test QueryResult.hsp_filter, all hits filtered out ... ok
test_hsp_filter_no_func (test_SearchIO_model.QueryResultCases)
Test QueryResult.hsp_filter, no arguments ... ok
test_hsp_map (test_SearchIO_model.QueryResultCases)
Test QueryResult.hsp_map ... ok
test_hsp_map_no_func (test_SearchIO_model.QueryResultCases)
Test QueryResult.hsp_map, without arguments ... ok
test_hsps (test_SearchIO_model.QueryResultCases)
Test QueryResult.hsps ... ok
test_id_set (test_SearchIO_model.QueryResultCases)
Test QueryResult.id setter ... ok
test_index (test_SearchIO_model.QueryResultCases)
Test QueryResult.index ... ok
test_index_alt (test_SearchIO_model.QueryResultCases)
Test QueryResult.index, with alt ID ... ok
test_index_not_present (test_SearchIO_model.QueryResultCases)
Test QueryResult.index, when index is not present ... ok
test_init_hits_only (test_SearchIO_model.QueryResultCases)
Test QueryResult.__init__, with hits only ... ok
test_init_id_only (test_SearchIO_model.QueryResultCases)
Test QueryResult.__init__, with ID only ... ok
test_init_none (test_SearchIO_model.QueryResultCases)
Test QueryResult.__init__, no arguments ... ok
test_items (test_SearchIO_model.QueryResultCases)
Test QueryResult.items ... ok
test_iter (test_SearchIO_model.QueryResultCases)
Test QueryResult.__iter__ ... ok
test_len (test_SearchIO_model.QueryResultCases)
Test QueryResult.__len__ ... ok
test_nonzero (test_SearchIO_model.QueryResultCases)
Test QueryResult.__nonzero__ ... ok
test_order (test_SearchIO_model.QueryResultCases) ... ok
test_pickle (test_SearchIO_model.QueryResultCases)
Test pickling and unpickling of QueryResult ... ok
test_pop_int_index_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.pop, with integer index ... ok
test_pop_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.pop ... ok
test_pop_string_alt_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.pop, with alternative ID ... ok
test_pop_string_index_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.pop, with string index ... ok
test_repr (test_SearchIO_model.QueryResultCases)
Test QueryResult.__repr__ ... ok
test_setitem_from_empty (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, from empty container ... ok
test_setitem_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__ ... ok
test_setitem_ok_alt (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, checking alt hit IDs ... ok
test_setitem_ok_alt_existing (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, existing key ... ok
test_setitem_ok_alt_ok_promote (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, previously alt ID ... ok
test_setitem_wrong_key_type (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, wrong key type ... ok
test_setitem_wrong_query_id (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, wrong query ID ... ok
test_setitem_wrong_type (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, wrong type ... ok
test_sort_key_not_in_place_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.sort, with custom key, not in place ... ok
test_sort_key_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.sort, with custom key ... ok
test_sort_not_in_place_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.sort, not in place ... ok
test_sort_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.sort ... ok
test_sort_reverse_not_in_place_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.sort, reverse, not in place ... ok
test_sort_reverse_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.sort, reverse ... ok
----------------------------------------------------------------------
Ran 1 test in 0.157 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_write.py
test_SearchIO_write ... /builddir/build/BUILD/python-biopython-1.73/python3/build/lib.linux-i686-3.7/Bio/SearchIO/_legacy/NCBIStandalone.py:45: BiopythonWarning: Parsing BLAST plain text output file is not a well supported functionality anymore. Consider generating your BLAST output for parsing as XML or tabular format instead.
BiopythonWarning
ok
test_write_multiple_from_blasttab (test_SearchIO_write.BlastTabWriteCases)
Test blast-tab writing from blast-tab, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_001.txt) ... ok
test_write_multiple_from_blasttabc (test_SearchIO_write.BlastTabWriteCases)
Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_005.txt) ... ok
test_write_multiple_from_blasttabc_allfields (test_SearchIO_write.BlastTabWriteCases)
Test blast-tabc writing from blast-tabc, BLAST 2.2.28+, multiple queries (tab_2228_tblastx_001.txt) ... ok
test_write_single_from_blasttab (test_SearchIO_write.BlastTabWriteCases)
Test blast-tab writing from blast-tab, BLAST 2.2.26+, single query (tab_2226_tblastn_004.txt) ... ok
test_write_single_from_blasttabc (test_SearchIO_write.BlastTabWriteCases)
Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, single query (tab_2226_tblastn_008.txt) ... ok
test_write_multiple_from_blastxml (test_SearchIO_write.BlastXmlWriteCases)
Test blast-xml writing from blast-xml, BLAST 2.2.26+, multiple queries (xml_2226_blastp_001.xml) ... ok
test_write_single_from_blastxml (test_SearchIO_write.BlastXmlWriteCases)
Test blast-xml writing from blast-xml, BLAST 2.2.26+, single query (xml_2226_blastp_004.xml) ... ok
test_write_multiple_from_blatpsl (test_SearchIO_write.BlatPslWriteCases)
Test blat-psl writing from blat-psl, multiple queries (psl_34_001.psl) ... ok
test_write_multiple_from_blatpslx (test_SearchIO_write.BlatPslWriteCases)
Test blat-pslx writing from blat-pslx, multiple queries (pslx_34_001.pslx) ... ok
test_write_single_from_blatpsl (test_SearchIO_write.BlatPslWriteCases)
Test blat-psl writing from blat-psl, single query (psl_34_004.psl) ... ok
test_write_single_from_blatpsl_protein_query (test_SearchIO_write.BlatPslWriteCases)
Test blat-psl writing from blat-psl, single query (psl_35_002.psl) ... ok
test_write_single_from_blatpslx (test_SearchIO_write.BlatPslWriteCases)
Test blat-pslx writing from blat-pslx, single query (pslx_34_004.pslx) ... ok
test_write_single_from_blatpslx_protein_query (test_SearchIO_write.BlatPslWriteCases)
Test blat-pslx writing from blat-pslx, single query (pslx_35_002.pslx) ... ok
test_write_multiple_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases)
Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out) ... ok
test_write_single_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases)
Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out) ... ok
test_write_single_from_hmmsearchdomtab (test_SearchIO_write.HmmerDomtabWriteCases)
Test hmmsearch-domtab writing from hmmsearch-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out) ... ok
test_write_multiple_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases)
Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out) ... ok
test_write_single_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases)
Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, single query (tab_30_hmmscan_004.out) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.526 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqFeature.py
test_SeqFeature ... ok
test_eq_identical (test_SeqFeature.TestCompoundLocation)
Test two identical locations are equal ... ok
test_eq_not_identical (test_SeqFeature.TestCompoundLocation)
Test two different locations are not equal ... ok
test_eq_identical (test_SeqFeature.TestFeatureLocation)
Test two identical locations are equal ... ok
test_eq_not_identical (test_SeqFeature.TestFeatureLocation)
Test two different locations are not equal ... ok
test_start_before_end (test_SeqFeature.TestFeatureLocation) ... ok
test_eq_identical (test_SeqFeature.TestReference)
Test two identical references eq() to True ... ok
----------------------------------------------------------------------
Ran 1 test in 0.109 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO.py
test_SeqIO ... ok
runTest (__main__.ComparisonTestCase)
test_SeqIO ... ok
----------------------------------------------------------------------
Ran 1 test in 70.660 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_AbiIO.py
test_SeqIO_AbiIO ... ok
test_file_type (test_SeqIO_AbiIO.TestAbi)
Test if filetype is ABIF. ... ok
test_no_smpl1 (test_SeqIO_AbiIO.TestAbi)
Test parsing of ABIF file without the normally expected SMPL1 tag. ... ok
test_raw (test_SeqIO_AbiIO.TestAbi)
Test access to raw ABIF tags. ... ok
test_seqrecord (test_SeqIO_AbiIO.TestAbi)
Test if the extracted seqrecords data are equal to expected values. ... ok
test_trim (test_SeqIO_AbiIO.TestAbi)
Test if trim works. ... ok
test_file_type (test_SeqIO_AbiIO.TestAbiFake)
Test if error is raised if filetype is not ABIF. ... ok
test_file_mode (test_SeqIO_AbiIO.TestAbiWrongMode)
Test if exception is raised if file is not opened in 'rb' mode. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.406 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_FastaIO.py
test_SeqIO_FastaIO ... ok
test_edgecases_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers)
Test FastaTwoLineParser edge-cases. ... ok
test_edgecases_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers)
Test SimpleFastaParser edge-cases. ... ok
test_exceptions_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers)
Test FastaTwoLineParser exceptions. ... ok
test_regular_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers)
Test regular FastaTwoLineParser cases. ... ok
test_regular_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers)
"Test regular SimpleFastaParser cases. ... ok
test_mutli_dna_Quality/example (test_SeqIO_FastaIO.TitleFunctions)
Checking multi DNA file Quality/example.fasta ... ok
test_mutli_pro_Fasta/f002 (test_SeqIO_FastaIO.TitleFunctions)
Checking multi protein file Fasta/f002 ... ok
test_mutli_pro_Fasta/fa01 (test_SeqIO_FastaIO.TitleFunctions)
Checking multi protein file Fasta/fa01 ... ok
test_no_name (test_SeqIO_FastaIO.TitleFunctions)
Test FASTA record with no identifier. ... ok
test_nuc_Fasta/centaurea (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/centaurea.nu ... ok
test_nuc_Fasta/elderberry (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/elderberry.nu ... ok
test_nuc_Fasta/f001 (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/f001 ... ok
test_nuc_Fasta/lavender (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/lavender.nu ... ok
test_nuc_Fasta/lupine (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/lupine.nu ... ok
test_nuc_Fasta/phlox (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/phlox.nu ... ok
test_nuc_Fasta/sweetpea (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/sweetpea.nu ... ok
test_nuc_Fasta/wisteria (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/wisteria.nu ... ok
test_pro_Fasta/aster (test_SeqIO_FastaIO.TitleFunctions)
Checking protein file Fasta/aster.pro ... ok
test_pro_Fasta/loveliesbleeding (test_SeqIO_FastaIO.TitleFunctions)
Checking protein file Fasta/loveliesbleeding.pro ... ok
test_pro_Fasta/rose (test_SeqIO_FastaIO.TitleFunctions)
Checking protein file Fasta/rose.pro ... ok
test_pro_Fasta/rosemary (test_SeqIO_FastaIO.TitleFunctions)
Checking protein file Fasta/rosemary.pro ... ok
test_fails (test_SeqIO_FastaIO.Wrapping) ... ok
test_passes (test_SeqIO_FastaIO.Wrapping) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.115 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Insdc.py
test_SeqIO_Insdc ... /builddir/build/BUILD/python-biopython-1.73/python3/build/lib.linux-i686-3.7/Bio/GenBank/Scanner.py:287: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)?
BiopythonParserWarning)
ok
test_annotation1 (test_SeqIO_Insdc.TestEmbl)
Check parsing of annotation from EMBL files (1). ... ok
test_annotation2 (test_SeqIO_Insdc.TestEmbl)
Check parsing of annotation from EMBL files (2). ... ok
test_annotation3 (test_SeqIO_Insdc.TestEmbl)
Check parsing of annotation from EMBL files (3). ... ok
test_annotation4 (test_SeqIO_Insdc.TestEmbl)
Check parsing of annotation from EMBL files (4). ... ok
test_writing_empty_qualifiers (test_SeqIO_Insdc.TestEmbl) ... ok
test_annotation1 (test_SeqIO_Insdc.TestEmblRewrite)
Check writing-and-parsing EMBL file (1). ... ok
test_annotation2 (test_SeqIO_Insdc.TestEmblRewrite)
Check writing-and-parsing EMBL file (2). ... ok
test_annotation3 (test_SeqIO_Insdc.TestEmblRewrite)
Check writing-and-parsing EMBL file (3). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.139 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_PdbIO.py
test_SeqIO_PdbIO ... ok
test_atom_parse (test_SeqIO_PdbIO.TestCifAtom)
Parse a multi-chain structure by ATOM entries. ... ok
test_atom_read (test_SeqIO_PdbIO.TestCifAtom)
Read a single-chain structure by ATOM entries. ... ok
test_atom_read_noheader (test_SeqIO_PdbIO.TestCifAtom)
Read a single-chain CIF without a header by ATOM entries. ... ok
test_seqres_missing (test_SeqIO_PdbIO.TestCifSeqres)
Parse a PDB with no SEQRES entries. ... ok
test_seqres_parse (test_SeqIO_PdbIO.TestCifSeqres)
Parse a multi-chain PDB by SEQRES entries. ... ok
test_seqres_read (test_SeqIO_PdbIO.TestCifSeqres)
Read a single-chain structure by sequence entries. ... ok
test_atom_noheader (test_SeqIO_PdbIO.TestPdbAtom)
Parse a PDB with no HEADER line. ... ok
test_atom_parse (test_SeqIO_PdbIO.TestPdbAtom)
Parse a multi-chain structure by ATOM entries. ... ok
test_atom_read (test_SeqIO_PdbIO.TestPdbAtom)
Read a single-chain structure by ATOM entries. ... ok
test_atom_read_noheader (test_SeqIO_PdbIO.TestPdbAtom)
Read a single-chain PDB without a header by ATOM entries. ... ok
test_seqres_missing (test_SeqIO_PdbIO.TestPdbSeqres)
Parse a PDB with no SEQRES entries. ... ok
test_seqres_parse (test_SeqIO_PdbIO.TestPdbSeqres)
Parse a multi-chain PDB by SEQRES entries. ... ok
test_seqres_read (test_SeqIO_PdbIO.TestPdbSeqres)
Read a single-chain structure by sequence entries. ... ok
----------------------------------------------------------------------
Ran 1 test in 10.147 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_QualityIO.py
test_SeqIO_QualityIO ... ok
test_illumina_to_sanger (test_SeqIO_QualityIO.MappingTests)
Mapping check for FASTQ Illumina (0 to 62) to Sanger (0 to 62) ... ok
test_phred_quality_from_solexa (test_SeqIO_QualityIO.MappingTests)
Mapping check for function phred_quality_from_solexa ... ok
test_sanger_to_illumina (test_SeqIO_QualityIO.MappingTests)
Mapping check for FASTQ Sanger (0 to 93) to Illumina (0 to 62) ... ok
test_sanger_to_solexa (test_SeqIO_QualityIO.MappingTests)
Mapping check for FASTQ Sanger (0 to 93) to Solexa (-5 to 62) ... ok
test_solexa_quality_from_phred (test_SeqIO_QualityIO.MappingTests)
Mapping check for function solexa_quality_from_phred ... ok
test_solexa_to_sanger (test_SeqIO_QualityIO.MappingTests)
Mapping check for FASTQ Solexa (-5 to 62) to Sanger (0 to 62) ... ok
test_fasta_as_fastq (test_SeqIO_QualityIO.NonFastqTests) ... ok
test_sff_as_fastq (test_SeqIO_QualityIO.NonFastqTests) ... ok
test_diff_ids (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with diff ids ... ok
test_double_qual (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with double qual ... ok
test_double_seq (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with double seq ... ok
test_long_qual (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with long qual ... ok
test_no_qual (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with no qual ... ok
test_qual_del (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with del in quality ... ok
test_qual_escape (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with escape in quality ... ok
test_qual_null (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with null in quality ... ok
test_qual_space (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with space in quality ... ok
test_qual_tab (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with tab in quality ... ok
test_qual_unit_sep (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with unit sep in quality ... ok
test_qual_vtab (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with vtab in quality ... ok
test_short_qual (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with short qual ... ok
test_spaces (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with spaces ... ok
test_tabs (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with tabs ... ok
test_trunc_at_plus (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc at plus ... ok
test_trunc_at_qual (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc at qual ... ok
test_trunc_at_seq (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc at seq ... ok
test_trunc_in_plus (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc in plus ... ok
test_trunc_in_qual (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc in qual ... ok
test_trunc_in_seq (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc in seq ... ok
test_trunc_in_title (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc in title ... ok
test_fasta (test_SeqIO_QualityIO.TestQual)
Check FASTQ parsing matches FASTA parsing ... ok
test_fasta_out (test_SeqIO_QualityIO.TestQual)
Check FASTQ to FASTA output ... ok
test_paired (test_SeqIO_QualityIO.TestQual)
Check FASTQ parsing matches FASTA+QUAL parsing ... ok
test_qual (test_SeqIO_QualityIO.TestQual)
Check FASTQ parsing matches QUAL parsing ... ok
test_qual_negative (test_SeqIO_QualityIO.TestQual)
Check QUAL negative scores mapped to PHRED zero ... ok
test_qual_out (test_SeqIO_QualityIO.TestQual)
Check FASTQ to QUAL output ... ok
test_fastq_1000 (test_SeqIO_QualityIO.TestReadWrite)
Read and write back simple example with mixed case 1000bp read ... ok
test_fastq_2000 (test_SeqIO_QualityIO.TestReadWrite)
Read and write back simple example with upper case 2000bp read ... ok
test_fastq_dna (test_SeqIO_QualityIO.TestReadWrite)
Read and write back simple example with ambiguous DNA ... ok
test_fastq_rna (test_SeqIO_QualityIO.TestReadWrite)
Read and write back simple example with ambiguous RNA ... ok
test_illumina_full_range_illumina (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of illumina file illumina_full_range ... ok
test_longreads_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of sanger file longreads ... ok
test_misc_dna_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of sanger file misc_dna ... ok
test_misc_rna_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of sanger file misc_rna ... ok
test_sanger_full_range_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of sanger file sanger_full_range ... ok
test_solexa_full_range_solexa (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of solexa file solexa_full_range ... ok
test_wrapping_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of sanger file wrapping ... ok
test_alt_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_alt_index_at_end into FASTA+QUAL ... ok
test_alt_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_alt_index_at_start into FASTA+QUAL ... ok
test_alt_index_in_middle (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_alt_index_in_middle into FASTA+QUAL ... ok
test_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_index_in_middle into FASTA+QUAL ... ok
test_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_index_at_start into FASTA+QUAL ... ok
test_no_manifest (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_no_manifest.sff into FASTA+QUAL ... ok
test_original (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_random_10_reads.sff into FASTA+QUAL ... ok
test_negative_clip (test_SeqIO_QualityIO.TestSFF) ... ok
test_overlapping_clip (test_SeqIO_QualityIO.TestSFF) ... ok
test_E3MFGYR02 (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_random_10_reads.sff ... ok
test_E3MFGYR02_alt_index_at_end (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_alt_index_at_end.sff ... ok
test_E3MFGYR02_alt_index_at_start (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_alt_index_at_start.sff ... ok
test_E3MFGYR02_alt_index_in_middle (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_alt_index_in_middle.sff ... ok
test_E3MFGYR02_index_at_start (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_index_at_start.sff ... ok
test_E3MFGYR02_index_in_middle (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_index_in_middle.sff ... ok
test_E3MFGYR02_no_manifest (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_no_manifest.sff ... ok
test_E3MFGYR02_trimmed (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_random_10_reads.sff (trimmed) ... ok
test_example_fasta (test_SeqIO_QualityIO.TestWriteRead)
Write and read back example.fasta ... ok
test_example_fastq (test_SeqIO_QualityIO.TestWriteRead)
Write and read back example.fastq ... ok
test_example_qual (test_SeqIO_QualityIO.TestWriteRead)
Write and read back example.qual ... ok
test_generated (test_SeqIO_QualityIO.TestWriteRead)
Write and read back odd SeqRecord objects ... ok
test_greek_sff (test_SeqIO_QualityIO.TestWriteRead)
Write and read back greek.sff ... ok
test_illumina_faked (test_SeqIO_QualityIO.TestWriteRead)
Write and read back illumina_faked.fastq ... ok
test_paired_sff (test_SeqIO_QualityIO.TestWriteRead)
Write and read back paired.sff ... ok
test_sanger_93 (test_SeqIO_QualityIO.TestWriteRead)
Write and read back sanger_93.fastq ... ok
test_sanger_faked (test_SeqIO_QualityIO.TestWriteRead)
Write and read back sanger_faked.fastq ... ok
test_solexa_example (test_SeqIO_QualityIO.TestWriteRead)
Write and read back solexa_example.fastq ... ok
test_solexa_faked (test_SeqIO_QualityIO.TestWriteRead)
Write and read back solexa_faked.fastq ... ok
test_tricky (test_SeqIO_QualityIO.TestWriteRead)
Write and read back tricky.fastq ... ok
----------------------------------------------------------------------
Ran 1 test in 0.864 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_SeqXML.py
test_SeqIO_SeqXML ... ok
test_duplicated_dbxref (test_SeqIO_SeqXML.TestDetailedRead)
Read multiple cross references to a single source ... ok
test_duplicated_property (test_SeqIO_SeqXML.TestDetailedRead)
Read property with multiple values ... ok
test_empty_description (test_SeqIO_SeqXML.TestDetailedRead)
Check empty description. ... ok
test_full_characters_set_read (test_SeqIO_SeqXML.TestDetailedRead)
Read full characters set for each type ... ok
test_global_species (test_SeqIO_SeqXML.TestDetailedRead)
Check global species. ... ok
test_local_source_definition (test_SeqIO_SeqXML.TestDetailedRead)
Check local source. ... ok
test_local_species (test_SeqIO_SeqXML.TestDetailedRead)
Check local species. ... ok
test_read_minimal_required (test_SeqIO_SeqXML.TestDetailedRead)
Check minimal record. ... ok
test_special_characters_desc (test_SeqIO_SeqXML.TestDetailedRead)
Read special XML characters in description. ... ok
test_unicode_characters_desc (test_SeqIO_SeqXML.TestDetailedRead)
Test special unicode characters in the description. ... ok
test_read_write_dna (test_SeqIO_SeqXML.TestReadAndWrite)
Read and write DNA. ... ok
test_read_write_globalSpecies (test_SeqIO_SeqXML.TestReadAndWrite)
Read and write global species. ... ok
test_read_write_protein (test_SeqIO_SeqXML.TestReadAndWrite)
Read and write protein. ... ok
test_read_write_rna (test_SeqIO_SeqXML.TestReadAndWrite)
Read and write RNA. ... ok
test_write_species (test_SeqIO_SeqXML.TestReadAndWrite)
Test writing species from annotation tags. ... ok
test_for_errors (test_SeqIO_SeqXML.TestReadCorruptFiles)
Handling of corrupt files. ... ok
test_check_SeqIO (test_SeqIO_SeqXML.TestSimpleRead)
Files readable using parser via SeqIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.203 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_convert.py
test_SeqIO_convert ... ok
test_EMBL_TRBG361_embl_embl_to_fasta (test_SeqIO_convert.ConvertTests)
Convert EMBL/TRBG361.embl from embl to fasta ... ok
test_EMBL_U87107_embl_embl_to_fasta (test_SeqIO_convert.ConvertTests)
Convert EMBL/U87107.embl from embl to fasta ... ok
test_GenBank_NC_005816_gb_gb_to_fasta (test_SeqIO_convert.ConvertTests)
Convert GenBank/NC_005816.gb from gb to fasta ... ok
test_GenBank_cor6_6_gb_genbank_to_fasta (test_SeqIO_convert.ConvertTests)
Convert GenBank/cor6_6.gb from genbank to fasta ... ok
test_Quality_error_diff_ids_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to fasta ... ok
test_Quality_error_diff_ids_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to fastq ... ok
test_Quality_error_diff_ids_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to fastq-illumina ... ok
test_Quality_error_diff_ids_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to fastq-sanger ... ok
test_Quality_error_diff_ids_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to fastq-solexa ... ok
test_Quality_error_diff_ids_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to qual ... ok
test_Quality_error_diff_ids_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to tab ... ok
test_Quality_error_double_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to fasta ... ok
test_Quality_error_double_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to fastq ... ok
test_Quality_error_double_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to fastq-illumina ... ok
test_Quality_error_double_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to fastq-sanger ... ok
test_Quality_error_double_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to fastq-solexa ... ok
test_Quality_error_double_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to qual ... ok
test_Quality_error_double_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to tab ... ok
test_Quality_error_double_seq_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to fasta ... ok
test_Quality_error_double_seq_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to fastq ... ok
test_Quality_error_double_seq_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to fastq-illumina ... ok
test_Quality_error_double_seq_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to fastq-sanger ... ok
test_Quality_error_double_seq_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to fastq-solexa ... ok
test_Quality_error_double_seq_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to qual ... ok
test_Quality_error_double_seq_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to tab ... ok
test_Quality_error_long_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to fasta ... ok
test_Quality_error_long_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to fastq ... ok
test_Quality_error_long_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to fastq-illumina ... ok
test_Quality_error_long_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to fastq-sanger ... ok
test_Quality_error_long_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to fastq-solexa ... ok
test_Quality_error_long_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to qual ... ok
test_Quality_error_long_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to tab ... ok
test_Quality_error_no_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to fasta ... ok
test_Quality_error_no_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to fastq ... ok
test_Quality_error_no_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to fastq-illumina ... ok
test_Quality_error_no_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to fastq-sanger ... ok
test_Quality_error_no_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to fastq-solexa ... ok
test_Quality_error_no_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to qual ... ok
test_Quality_error_no_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to tab ... ok
test_Quality_error_qual_del_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_del.fastq from fastq to fastq ... ok
test_Quality_error_qual_del_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_del.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_del_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_del.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_del_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_del.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_del_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_del.fastq from fastq to qual ... ok
test_Quality_error_qual_escape_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_escape.fastq from fastq to fastq ... ok
test_Quality_error_qual_escape_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_escape.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_escape_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_escape.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_escape_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_escape.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_escape_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_escape.fastq from fastq to qual ... ok
test_Quality_error_qual_null_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_null.fastq from fastq to fastq ... ok
test_Quality_error_qual_null_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_null.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_null_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_null.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_null_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_null.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_null_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_null.fastq from fastq to qual ... ok
test_Quality_error_qual_space_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_space.fastq from fastq to fastq ... ok
test_Quality_error_qual_space_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_space.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_space_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_space.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_space_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_space.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_space_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_space.fastq from fastq to qual ... ok
test_Quality_error_qual_tab_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_tab.fastq from fastq to fastq ... ok
test_Quality_error_qual_tab_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_tab.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_tab_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_tab.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_tab_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_tab.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_tab_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_tab.fastq from fastq to qual ... ok
test_Quality_error_qual_unit_sep_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_unit_sep.fastq from fastq to fastq ... ok
test_Quality_error_qual_unit_sep_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_unit_sep.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_unit_sep_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_unit_sep.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_unit_sep_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_unit_sep.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_unit_sep_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_unit_sep.fastq from fastq to qual ... ok
test_Quality_error_qual_vtab_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_vtab.fastq from fastq to fastq ... ok
test_Quality_error_qual_vtab_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_vtab.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_vtab_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_vtab.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_vtab_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_vtab.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_vtab_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_vtab.fastq from fastq to qual ... ok
test_Quality_error_short_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to fasta ... ok
test_Quality_error_short_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to fastq ... ok
test_Quality_error_short_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to fastq-illumina ... ok
test_Quality_error_short_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to fastq-sanger ... ok
test_Quality_error_short_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to fastq-solexa ... ok
test_Quality_error_short_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to qual ... ok
test_Quality_error_short_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to tab ... ok
test_Quality_error_spaces_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to fasta ... ok
test_Quality_error_spaces_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to fastq ... ok
test_Quality_error_spaces_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to fastq-illumina ... ok
test_Quality_error_spaces_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to fastq-sanger ... ok
test_Quality_error_spaces_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to fastq-solexa ... ok
test_Quality_error_spaces_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to qual ... ok
test_Quality_error_spaces_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to tab ... ok
test_Quality_error_tabs_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to fasta ... ok
test_Quality_error_tabs_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to fastq ... ok
test_Quality_error_tabs_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to fastq-illumina ... ok
test_Quality_error_tabs_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to fastq-sanger ... ok
test_Quality_error_tabs_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to fastq-solexa ... ok
test_Quality_error_tabs_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to qual ... ok
test_Quality_error_tabs_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to tab ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to fasta ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to fastq ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to qual ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to tab ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to fasta ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to fastq ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to qual ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to tab ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to fasta ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to fastq ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to qual ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to tab ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to fasta ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to fastq ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to qual ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to tab ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to fasta ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to fastq ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to qual ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to tab ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to fasta ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to fastq ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to qual ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to tab ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to fasta ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to fastq ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to qual ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to tab ... ok
test_Quality_example_fastq_fastq-sanger_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to fasta ... ok
test_Quality_example_fastq_fastq-sanger_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to fastq ... ok
test_Quality_example_fastq_fastq-sanger_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to fastq-illumina ... ok
test_Quality_example_fastq_fastq-sanger_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to fastq-sanger ... ok
test_Quality_example_fastq_fastq-sanger_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to fastq-solexa ... ok
test_Quality_example_fastq_fastq-sanger_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to qual ... ok
test_Quality_example_fastq_fastq-sanger_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to tab ... ok
test_Quality_example_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to fasta ... ok
test_Quality_example_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to fastq ... ok
test_Quality_example_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to fastq-illumina ... ok
test_Quality_example_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to fastq-sanger ... ok
test_Quality_example_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to fastq-solexa ... ok
test_Quality_example_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to qual ... ok
test_Quality_example_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to tab ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to fasta ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to fastq ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to fastq-illumina ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to fastq-sanger ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to fastq-solexa ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to qual ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to tab ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to fasta ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to fastq ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to fastq-illumina ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to fastq-sanger ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to fastq-solexa ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to qual ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to tab ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to fasta ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to fastq ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to fastq-illumina ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to fastq-sanger ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to fastq-solexa ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to qual ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to tab ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to fasta ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to fastq ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to fastq-illumina ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to fastq-sanger ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to fastq-solexa ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to qual ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to tab ... ok
test_Quality_tricky_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to fasta ... ok
test_Quality_tricky_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to fastq ... ok
test_Quality_tricky_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to fastq-illumina ... ok
test_Quality_tricky_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to fastq-sanger ... ok
test_Quality_tricky_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to fastq-solexa ... ok
test_Quality_tricky_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to qual ... ok
test_Quality_tricky_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to tab ... ok
----------------------------------------------------------------------
Ran 1 test in 0.249 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_features.py
test_SeqIO_features ... ok
test_after (test_SeqIO_features.FeatureWriting)
Features: write/read simple after locations. ... ok
test_before (test_SeqIO_features.FeatureWriting)
Features: write/read simple before locations. ... ok
test_between (test_SeqIO_features.FeatureWriting)
GenBank/EMBL write/read simple between locations. ... ok
test_exact (test_SeqIO_features.FeatureWriting)
GenBank/EMBL write/read simple exact locations. ... ok
test_fuzzy_join (test_SeqIO_features.FeatureWriting)
Features: write/read fuzzy join locations. ... ok
test_join (test_SeqIO_features.FeatureWriting)
GenBank/EMBL write/read simple join locations. ... ok
test_oneof (test_SeqIO_features.FeatureWriting)
Features: write/read simple one-of locations. ... ok
test_unknown (test_SeqIO_features.FeatureWriting)
GenBank/EMBL write/read with unknown end points. ... ok
test_within (test_SeqIO_features.FeatureWriting)
Features: write/read simple within locations. ... ok
test_mixed_strand (test_SeqIO_features.GenBankLocations) ... ok
test_rev_comp_styles (test_SeqIO_features.GenBankLocations) ... ok
test_CDS (test_SeqIO_features.NC_000932)
Checking GenBank CDS translations vs FASTA faa file. ... ok
test_CDS (test_SeqIO_features.NC_005816)
Checking GenBank CDS translations vs FASTA faa file. ... ok
test_Features (test_SeqIO_features.NC_005816)
Checking GenBank features sequences vs FASTA ffn file. ... ok
test_GenBank_vs_EMBL (test_SeqIO_features.NC_005816) ... ok
test_Genome (test_SeqIO_features.NC_005816)
Checking GenBank sequence vs FASTA fna file. ... ok
test_Translations (test_SeqIO_features.NC_005816)
Checking translation of FASTA features (faa vs ffn). ... ok
test_qualifiers (test_SeqIO_features.SeqFeatureCreation)
Pass in qualifiers to SeqFeatures. ... ok
test_mixed_strand_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (join, mixed strand) ... ok
test_mixed_strand_dna_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (multi-join, mixed strand) ... ok
test_protein_between (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on protein (between location, zero length) ... ok
test_protein_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on protein (join) ... ok
test_protein_join_fuzzy (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on protein (fuzzy join) ... ok
test_protein_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on protein (multi-join) ... ok
test_protein_oneof (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on protein (one-of positions) ... ok
test_protein_simple (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on protein (simple) ... ok
test_simple_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (simple, default strand) ... ok
test_simple_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (join, strand +1) ... ok
test_simple_dna_join_after (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (join, strand -1, after position) ... ok
test_simple_dna_join_before (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (join, strand -1, before position) ... ok
test_simple_dna_join_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (join, strand -1) ... ok
test_simple_dna_strand0 (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (simple, strand 0) ... ok
test_simple_dna_strand1 (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (simple, strand +1) ... ok
test_simple_dna_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (simple, strand -1) ... ok
test_simple_dna_strand_none (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (simple, strand None) ... ok
test_simple_rna (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on RNA (simple, default strand) ... ok
test_single_letter_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (single letter, default strand) ... ok
test_zero_len_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (between location, zero length, default strand) ... ok
test_zero_len_dna_end (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (between location at end, zero length, default strand) ... ok
test_AAA03323 (test_SeqIO_features.TestWriteRead)
Write and read back AAA03323.embl ... ok
test_AE017046 (test_SeqIO_features.TestWriteRead)
Write and read back AE017046.embl ... ok
test_DD231055_edited (test_SeqIO_features.TestWriteRead)
Write and read back DD231055_edited.embl ... ok
test_Human_contigs (test_SeqIO_features.TestWriteRead)
Write and read back Human_contigs.embl ... ok
test_NC_000932 (test_SeqIO_features.TestWriteRead)
Write and read back NC_000932.gb ... ok
test_NC_005816 (test_SeqIO_features.TestWriteRead)
Write and read back NC_005816.gb ... ok
test_NT_019265 (test_SeqIO_features.TestWriteRead)
Write and read back NT_019265.gb ... ok
test_SC10H5 (test_SeqIO_features.TestWriteRead)
Write and read back SC10H5.embl ... ok
test_TRBG361 (test_SeqIO_features.TestWriteRead)
Write and read back TRBG361.embl ... ok
test_U87107 (test_SeqIO_features.TestWriteRead)
Write and read back U87107.embl ... ok
test_arab1 (test_SeqIO_features.TestWriteRead)
Write and read back arab1.gb ... ok
test_blank_seq (test_SeqIO_features.TestWriteRead)
Write and read back blank_seq.gb ... ok
test_cor6 (test_SeqIO_features.TestWriteRead)
Write and read back cor6_6.gb ... ok
test_dbsource_wrap (test_SeqIO_features.TestWriteRead)
Write and read back dbsource_wrap.gb ... ok
test_extra_keywords (test_SeqIO_features.TestWriteRead)
Write and read back extra_keywords.gb ... ok
test_gbvrl1_start (test_SeqIO_features.TestWriteRead)
Write and read back gbvrl1_start.seq ... ok
test_noref (test_SeqIO_features.TestWriteRead)
Write and read back noref.gb ... ok
test_one_of (test_SeqIO_features.TestWriteRead)
Write and read back of_one.gb ... ok
test_origin_line (test_SeqIO_features.TestWriteRead)
Write and read back origin_line.gb ... ok
test_pri1 (test_SeqIO_features.TestWriteRead)
Write and read back pri1.gb ... ok
test_protein_refseq (test_SeqIO_features.TestWriteRead)
Write and read back protein_refseq.gb ... ok
test_protein_refseq2 (test_SeqIO_features.TestWriteRead)
Write and read back protein_refseq2.gb ... ok
----------------------------------------------------------------------
Ran 1 test in 1.182 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_index.py
test_SeqIO_index ... ok
test_ace_Ace_consed_sample_ace_get_raw (test_SeqIO_index.IndexDictTests)
Index ace file Ace/consed_sample.ace get_raw ... ok
test_ace_Ace_consed_sample_ace_keyf (test_SeqIO_index.IndexDictTests)
Index ace file Ace/consed_sample.ace with key function ... ok
test_ace_Ace_consed_sample_ace_simple (test_SeqIO_index.IndexDictTests)
Index ace file Ace/consed_sample.ace defaults ... ok
test_ace_Ace_contig1_ace_get_raw (test_SeqIO_index.IndexDictTests)
Index ace file Ace/contig1.ace get_raw ... ok
test_ace_Ace_contig1_ace_keyf (test_SeqIO_index.IndexDictTests)
Index ace file Ace/contig1.ace with key function ... ok
test_ace_Ace_contig1_ace_simple (test_SeqIO_index.IndexDictTests)
Index ace file Ace/contig1.ace defaults ... ok
test_ace_Ace_seq_cap_ace_get_raw (test_SeqIO_index.IndexDictTests)
Index ace file Ace/seq.cap.ace get_raw ... ok
test_ace_Ace_seq_cap_ace_keyf (test_SeqIO_index.IndexDictTests)
Index ace file Ace/seq.cap.ace with key function ... ok
test_ace_Ace_seq_cap_ace_simple (test_SeqIO_index.IndexDictTests)
Index ace file Ace/seq.cap.ace defaults ... ok
test_duplicates_index (test_SeqIO_index.IndexDictTests)
Index file with duplicate identifiers with Bio.SeqIO.index() ... ok
test_duplicates_index_db (test_SeqIO_index.IndexDictTests)
Index file with duplicate identifiers with Bio.SeqIO.index_db() ... ok
test_duplicates_to_dict (test_SeqIO_index.IndexDictTests)
Index file with duplicate identifiers with Bio.SeqIO.to_dict() ... ok
test_embl_EMBL_A04195_imgt_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/A04195.imgt get_raw ... ok
test_embl_EMBL_A04195_imgt_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/A04195.imgt with key function ... ok
test_embl_EMBL_A04195_imgt_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/A04195.imgt defaults ... ok
test_embl_EMBL_AAA03323_embl_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/AAA03323.embl get_raw ... ok
test_embl_EMBL_AAA03323_embl_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/AAA03323.embl with key function ... ok
test_embl_EMBL_AAA03323_embl_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/AAA03323.embl defaults ... ok
test_embl_EMBL_TRBG361_embl_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/TRBG361.embl get_raw ... ok
test_embl_EMBL_TRBG361_embl_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/TRBG361.embl with key function ... ok
test_embl_EMBL_TRBG361_embl_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/TRBG361.embl defaults ... ok
test_embl_EMBL_U87107_embl_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/U87107.embl get_raw ... ok
test_embl_EMBL_U87107_embl_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/U87107.embl with key function ... ok
test_embl_EMBL_U87107_embl_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/U87107.embl defaults ... ok
test_embl_EMBL_epo_prt_selection_embl_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/epo_prt_selection.embl get_raw ... ok
test_embl_EMBL_epo_prt_selection_embl_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/epo_prt_selection.embl with key function ... ok
test_embl_EMBL_epo_prt_selection_embl_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/epo_prt_selection.embl defaults ... ok
test_embl_EMBL_kipo_prt_sample_embl_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/kipo_prt_sample.embl get_raw ... ok
test_embl_EMBL_kipo_prt_sample_embl_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/kipo_prt_sample.embl with key function ... ok
test_embl_EMBL_kipo_prt_sample_embl_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/kipo_prt_sample.embl defaults ... ok
test_embl_EMBL_patents_embl_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/patents.embl get_raw ... ok
test_embl_EMBL_patents_embl_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/patents.embl with key function ... ok
test_embl_EMBL_patents_embl_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/patents.embl defaults ... ok
test_fasta_GenBank_NC_000932_faa_get_raw (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_000932.faa get_raw ... ok
test_fasta_GenBank_NC_000932_faa_keyf (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_000932.faa with key function ... ok
test_fasta_GenBank_NC_000932_faa_simple (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_000932.faa defaults ... ok
test_fasta_GenBank_NC_005816_faa_get_raw (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.faa get_raw ... ok
test_fasta_GenBank_NC_005816_faa_keyf (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.faa with key function ... ok
test_fasta_GenBank_NC_005816_faa_simple (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.faa defaults ... ok
test_fasta_GenBank_NC_005816_ffn_get_raw (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.ffn get_raw ... ok
test_fasta_GenBank_NC_005816_ffn_keyf (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.ffn with key function ... ok
test_fasta_GenBank_NC_005816_ffn_simple (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.ffn defaults ... ok
test_fasta_GenBank_NC_005816_fna_get_raw (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.fna get_raw ... ok
test_fasta_GenBank_NC_005816_fna_keyf (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.fna with key function ... ok
test_fasta_GenBank_NC_005816_fna_simple (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.fna defaults ... ok
test_fasta_SwissProt_multi_ex_fasta_get_raw (test_SeqIO_index.IndexDictTests)
Index fasta file SwissProt/multi_ex.fasta get_raw ... ok
test_fasta_SwissProt_multi_ex_fasta_keyf (test_SeqIO_index.IndexDictTests)
Index fasta file SwissProt/multi_ex.fasta with key function ... ok
test_fasta_SwissProt_multi_ex_fasta_simple (test_SeqIO_index.IndexDictTests)
Index fasta file SwissProt/multi_ex.fasta defaults ... ok
test_fastq-illumina_Quality_illumina_faked_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq-illumina file Quality/illumina_faked.fastq get_raw ... ok
test_fastq-illumina_Quality_illumina_faked_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq-illumina file Quality/illumina_faked.fastq with key function ... ok
test_fastq-illumina_Quality_illumina_faked_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq-illumina file Quality/illumina_faked.fastq defaults ... ok
test_fastq-sanger_Quality_example_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/example.fastq get_raw ... ok
test_fastq-sanger_Quality_example_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/example.fastq with key function ... ok
test_fastq-sanger_Quality_example_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/example.fastq defaults ... ok
test_fastq-sanger_Quality_sanger_faked_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/sanger_faked.fastq get_raw ... ok
test_fastq-sanger_Quality_sanger_faked_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/sanger_faked.fastq with key function ... ok
test_fastq-sanger_Quality_sanger_faked_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/sanger_faked.fastq defaults ... ok
test_fastq-solexa_Quality_solexa_faked_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq-solexa file Quality/solexa_faked.fastq get_raw ... ok
test_fastq-solexa_Quality_solexa_faked_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq-solexa file Quality/solexa_faked.fastq with key function ... ok
test_fastq-solexa_Quality_solexa_faked_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq-solexa file Quality/solexa_faked.fastq defaults ... ok
test_fastq_Quality_example_dos_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example_dos.fastq get_raw ... ok
test_fastq_Quality_example_dos_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example_dos.fastq with key function ... ok
test_fastq_Quality_example_dos_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example_dos.fastq defaults ... ok
test_fastq_Quality_example_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example.fastq get_raw ... ok
test_fastq_Quality_example_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example.fastq with key function ... ok
test_fastq_Quality_example_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example.fastq defaults ... ok
test_fastq_Quality_tricky_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/tricky.fastq get_raw ... ok
test_fastq_Quality_tricky_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/tricky.fastq with key function ... ok
test_fastq_Quality_tricky_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/tricky.fastq defaults ... ok
test_fastq_Quality_wrapping_original_sanger_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/wrapping_original_sanger.fastq get_raw ... ok
test_fastq_Quality_wrapping_original_sanger_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/wrapping_original_sanger.fastq with key function ... ok
test_fastq_Quality_wrapping_original_sanger_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/wrapping_original_sanger.fastq defaults ... ok
test_fastq_Quality_zero_length_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/zero_length.fastq get_raw ... ok
test_fastq_Quality_zero_length_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/zero_length.fastq with key function ... ok
test_fastq_Quality_zero_length_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/zero_length.fastq defaults ... ok
test_gb_GenBank_NC_005816_gb_get_raw (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/NC_005816.gb get_raw ... ok
test_gb_GenBank_NC_005816_gb_keyf (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/NC_005816.gb with key function ... ok
test_gb_GenBank_NC_005816_gb_simple (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/NC_005816.gb defaults ... ok
test_gb_GenBank_empty_accession_gbk_get_raw (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/empty_accession.gbk get_raw ... ok
test_gb_GenBank_empty_accession_gbk_keyf (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/empty_accession.gbk with key function ... ok
test_gb_GenBank_empty_accession_gbk_simple (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/empty_accession.gbk defaults ... ok
test_gb_GenBank_empty_version_gbk_get_raw (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/empty_version.gbk get_raw ... ok
test_gb_GenBank_empty_version_gbk_keyf (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/empty_version.gbk with key function ... ok
test_gb_GenBank_empty_version_gbk_simple (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/empty_version.gbk defaults ... ok
test_genbank_GenBank_cor6_6_gb_get_raw (test_SeqIO_index.IndexDictTests)
Index genbank file GenBank/cor6_6.gb get_raw ... ok
test_genbank_GenBank_cor6_6_gb_keyf (test_SeqIO_index.IndexDictTests)
Index genbank file GenBank/cor6_6.gb with key function ... ok
test_genbank_GenBank_cor6_6_gb_simple (test_SeqIO_index.IndexDictTests)
Index genbank file GenBank/cor6_6.gb defaults ... ok
test_ig_IntelliGenetics_TAT_mase_nuc_txt_get_raw (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/TAT_mase_nuc.txt get_raw ... ok
test_ig_IntelliGenetics_TAT_mase_nuc_txt_keyf (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/TAT_mase_nuc.txt with key function ... ok
test_ig_IntelliGenetics_TAT_mase_nuc_txt_simple (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/TAT_mase_nuc.txt defaults ... ok
test_ig_IntelliGenetics_VIF_mase-pro_txt_get_raw (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/VIF_mase-pro.txt get_raw ... ok
test_ig_IntelliGenetics_VIF_mase-pro_txt_keyf (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/VIF_mase-pro.txt with key function ... ok
test_ig_IntelliGenetics_VIF_mase-pro_txt_simple (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/VIF_mase-pro.txt defaults ... ok
test_ig_IntelliGenetics_vpu_nucaligned_txt_get_raw (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/vpu_nucaligned.txt get_raw ... ok
test_ig_IntelliGenetics_vpu_nucaligned_txt_keyf (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/vpu_nucaligned.txt with key function ... ok
test_ig_IntelliGenetics_vpu_nucaligned_txt_simple (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/vpu_nucaligned.txt defaults ... ok
test_imgt_EMBL_A04195_imgt_get_raw (test_SeqIO_index.IndexDictTests)
Index imgt file EMBL/A04195.imgt get_raw ... ok
test_imgt_EMBL_A04195_imgt_keyf (test_SeqIO_index.IndexDictTests)
Index imgt file EMBL/A04195.imgt with key function ... ok
test_imgt_EMBL_A04195_imgt_simple (test_SeqIO_index.IndexDictTests)
Index imgt file EMBL/A04195.imgt defaults ... ok
test_imgt_EMBL_hla_3260_sample_imgt_get_raw (test_SeqIO_index.IndexDictTests)
Index imgt file EMBL/hla_3260_sample.imgt get_raw ... ok
test_imgt_EMBL_hla_3260_sample_imgt_keyf (test_SeqIO_index.IndexDictTests)
Index imgt file EMBL/hla_3260_sample.imgt with key function ... ok
test_imgt_EMBL_hla_3260_sample_imgt_simple (test_SeqIO_index.IndexDictTests)
Index imgt file EMBL/hla_3260_sample.imgt defaults ... ok
test_phd_Phd_phd1_get_raw (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd1 get_raw ... ok
test_phd_Phd_phd1_keyf (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd1 with key function ... ok
test_phd_Phd_phd1_simple (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd1 defaults ... ok
test_phd_Phd_phd2_get_raw (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd2 get_raw ... ok
test_phd_Phd_phd2_keyf (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd2 with key function ... ok
test_phd_Phd_phd2_simple (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd2 defaults ... ok
test_phd_Phd_phd_454_get_raw (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd_454 get_raw ... ok
test_phd_Phd_phd_454_keyf (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd_454 with key function ... ok
test_phd_Phd_phd_454_simple (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd_454 defaults ... ok
test_phd_Phd_phd_solexa_get_raw (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd_solexa get_raw ... ok
test_phd_Phd_phd_solexa_keyf (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd_solexa with key function ... ok
test_phd_Phd_phd_solexa_simple (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd_solexa defaults ... ok
test_pir_NBRF_B_nuc_pir_get_raw (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/B_nuc.pir get_raw ... ok
test_pir_NBRF_B_nuc_pir_keyf (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/B_nuc.pir with key function ... ok
test_pir_NBRF_B_nuc_pir_simple (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/B_nuc.pir defaults ... ok
test_pir_NBRF_Cw_prot_pir_get_raw (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/Cw_prot.pir get_raw ... ok
test_pir_NBRF_Cw_prot_pir_keyf (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/Cw_prot.pir with key function ... ok
test_pir_NBRF_Cw_prot_pir_simple (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/Cw_prot.pir defaults ... ok
test_pir_NBRF_clustalw_pir_get_raw (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/clustalw.pir get_raw ... ok
test_pir_NBRF_clustalw_pir_keyf (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/clustalw.pir with key function ... ok
test_pir_NBRF_clustalw_pir_simple (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/clustalw.pir defaults ... ok
test_sff-trim_Roche_E3MFGYR02_random_10_reads_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/E3MFGYR02_random_10_reads.sff get_raw ... ok
test_sff-trim_Roche_E3MFGYR02_random_10_reads_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/E3MFGYR02_random_10_reads.sff with key function ... ok
test_sff-trim_Roche_E3MFGYR02_random_10_reads_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/E3MFGYR02_random_10_reads.sff defaults ... ok
test_sff-trim_Roche_greek_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/greek.sff get_raw ... ok
test_sff-trim_Roche_greek_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/greek.sff with key function ... ok
test_sff-trim_Roche_greek_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/greek.sff defaults ... ok
test_sff-trim_Roche_paired_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/paired.sff get_raw ... ok
test_sff-trim_Roche_paired_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/paired.sff with key function ... ok
test_sff-trim_Roche_paired_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/paired.sff defaults ... ok
test_sff_Roche_E3MFGYR02_alt_index_at_end_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_at_end.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_alt_index_at_end_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_at_end.sff with key function ... ok
test_sff_Roche_E3MFGYR02_alt_index_at_end_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_at_end.sff defaults ... ok
test_sff_Roche_E3MFGYR02_alt_index_at_start_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_at_start.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_alt_index_at_start_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_at_start.sff with key function ... ok
test_sff_Roche_E3MFGYR02_alt_index_at_start_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_at_start.sff defaults ... ok
test_sff_Roche_E3MFGYR02_alt_index_in_middle_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_in_middle.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_alt_index_in_middle_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_in_middle.sff with key function ... ok
test_sff_Roche_E3MFGYR02_alt_index_in_middle_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_in_middle.sff defaults ... ok
test_sff_Roche_E3MFGYR02_index_at_start_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_index_at_start.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_index_at_start_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_index_at_start.sff with key function ... ok
test_sff_Roche_E3MFGYR02_index_at_start_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_index_at_start.sff defaults ... ok
test_sff_Roche_E3MFGYR02_index_in_middle_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_index_in_middle.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_index_in_middle_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_index_in_middle.sff with key function ... ok
test_sff_Roche_E3MFGYR02_index_in_middle_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_index_in_middle.sff defaults ... ok
test_sff_Roche_E3MFGYR02_no_manifest_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_no_manifest.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_no_manifest_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_no_manifest.sff with key function ... ok
test_sff_Roche_E3MFGYR02_no_manifest_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_no_manifest.sff defaults ... ok
test_sff_Roche_E3MFGYR02_random_10_reads_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_random_10_reads.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_random_10_reads_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_random_10_reads.sff with key function ... ok
test_sff_Roche_E3MFGYR02_random_10_reads_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_random_10_reads.sff defaults ... ok
test_sff_Roche_greek_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/greek.sff get_raw ... ok
test_sff_Roche_greek_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/greek.sff with key function ... ok
test_sff_Roche_greek_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/greek.sff defaults ... ok
test_sff_Roche_paired_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/paired.sff get_raw ... ok
test_sff_Roche_paired_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/paired.sff with key function ... ok
test_sff_Roche_paired_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/paired.sff defaults ... ok
test_swiss_SwissProt_multi_ex_txt_get_raw (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/multi_ex.txt get_raw ... ok
test_swiss_SwissProt_multi_ex_txt_keyf (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/multi_ex.txt with key function ... ok
test_swiss_SwissProt_multi_ex_txt_simple (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/multi_ex.txt defaults ... ok
test_swiss_SwissProt_sp001_get_raw (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp001 get_raw ... ok
test_swiss_SwissProt_sp001_keyf (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp001 with key function ... ok
test_swiss_SwissProt_sp001_simple (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp001 defaults ... ok
test_swiss_SwissProt_sp010_get_raw (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp010 get_raw ... ok
test_swiss_SwissProt_sp010_keyf (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp010 with key function ... ok
test_swiss_SwissProt_sp010_simple (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp010 defaults ... ok
test_swiss_SwissProt_sp016_get_raw (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp016 get_raw ... ok
test_swiss_SwissProt_sp016_keyf (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp016 with key function ... ok
test_swiss_SwissProt_sp016_simple (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp016 defaults ... ok
test_tab_GenBank_NC_005816_tsv_get_raw (test_SeqIO_index.IndexDictTests)
Index tab file GenBank/NC_005816.tsv get_raw ... ok
test_tab_GenBank_NC_005816_tsv_keyf (test_SeqIO_index.IndexDictTests)
Index tab file GenBank/NC_005816.tsv with key function ... ok
test_tab_GenBank_NC_005816_tsv_simple (test_SeqIO_index.IndexDictTests)
Index tab file GenBank/NC_005816.tsv defaults ... ok
test_uniprot-xml_SwissProt_multi_ex_xml_get_raw (test_SeqIO_index.IndexDictTests)
Index uniprot-xml file SwissProt/multi_ex.xml get_raw ... ok
test_uniprot-xml_SwissProt_multi_ex_xml_keyf (test_SeqIO_index.IndexDictTests)
Index uniprot-xml file SwissProt/multi_ex.xml with key function ... ok
test_uniprot-xml_SwissProt_multi_ex_xml_simple (test_SeqIO_index.IndexDictTests)
Index uniprot-xml file SwissProt/multi_ex.xml defaults ... ok
test_order_index_db (test_SeqIO_index.IndexOrderingManyFiles)
Check index_db preserves order in multiple indexed files. ... ok
test_order_index (test_SeqIO_index.IndexOrderingSingleFile)
Check index preserves order in indexed file. ... ok
test_order_index_db (test_SeqIO_index.IndexOrderingSingleFile)
Check index_db preserves ordering indexed file. ... ok
test_order_to_dict (test_SeqIO_index.IndexOrderingSingleFile)
Check to_dict preserves order in indexed file. ... ok
test_child_folder_rel (test_SeqIO_index.NewIndexTest)
Check relative links to child folder. ... ok
test_same_folder (test_SeqIO_index.NewIndexTest)
Check relative links in same folder. ... ok
test_some_abs (test_SeqIO_index.NewIndexTest)
Check absolute filenames in index. ... ok
test_old (test_SeqIO_index.OldIndexTest)
Load existing index with no options (from parent directory). ... ok
test_old_contents (test_SeqIO_index.OldIndexTest)
Check actual filenames in existing indexes. ... ok
test_old_files (test_SeqIO_index.OldIndexTest)
Load existing index with correct files (from parent directory). ... ok
test_old_files_same_dir (test_SeqIO_index.OldIndexTest)
Load existing index with correct files (from same directory). ... ok
test_old_files_wrong (test_SeqIO_index.OldIndexTest)
Load existing index with wrong files. ... ok
test_old_files_wrong2 (test_SeqIO_index.OldIndexTest)
Load existing index with wrong number of files. ... ok
test_old_format (test_SeqIO_index.OldIndexTest)
Load existing index with correct format. ... ok
test_old_format_wrong (test_SeqIO_index.OldIndexTest)
Load existing index with wrong format. ... ok
test_old_rel (test_SeqIO_index.OldIndexTest)
Load existing index (with relative paths) with no options (from parent directory). ... ok
test_old_same_dir (test_SeqIO_index.OldIndexTest)
Load existing index with no options (from same directory). ... ok
test_old_same_dir_rel (test_SeqIO_index.OldIndexTest)
Load existing index (with relative paths) with no options (from same directory). ... ok
----------------------------------------------------------------------
Ran 1 test in 15.590 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_online.py
22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7test_SeqIO_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.010 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_write.py
test_SeqIO_write ... ok
test_bad_handle (test_SeqIO_write.WriterTests) ... ok
test_clustal_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
clustal for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_clustal_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
clustal for alignment with repeated record ... ok
test_clustal_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
clustal for three DNA sequence alignment ... ok
test_clustal_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
clustal for three peptides of different lengths ... ok
test_clustal_three_proteins_alignment (test_SeqIO_write.WriterTests)
clustal for three proteins alignment ... ok
test_clustal_zero_records (test_SeqIO_write.WriterTests)
clustal for zero records ... ok
test_embl_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
embl for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_embl_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
embl for alignment with repeated record ... ok
test_embl_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
embl for three DNA sequence alignment ... ok
test_embl_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
embl for three peptides of different lengths ... ok
test_embl_three_proteins_alignment (test_SeqIO_write.WriterTests)
embl for three proteins alignment ... ok
test_embl_zero_records (test_SeqIO_write.WriterTests)
embl for zero records ... ok
test_fasta-2line_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
fasta-2line for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_fasta-2line_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
fasta-2line for alignment with repeated record ... ok
test_fasta-2line_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
fasta-2line for three DNA sequence alignment ... ok
test_fasta-2line_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
fasta-2line for three peptides of different lengths ... ok
test_fasta-2line_three_proteins_alignment (test_SeqIO_write.WriterTests)
fasta-2line for three proteins alignment ... ok
test_fasta-2line_zero_records (test_SeqIO_write.WriterTests)
fasta-2line for zero records ... ok
test_fasta_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
fasta for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_fasta_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
fasta for alignment with repeated record ... ok
test_fasta_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
fasta for three DNA sequence alignment ... ok
test_fasta_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
fasta for three peptides of different lengths ... ok
test_fasta_three_proteins_alignment (test_SeqIO_write.WriterTests)
fasta for three proteins alignment ... ok
test_fasta_zero_records (test_SeqIO_write.WriterTests)
fasta for zero records ... ok
test_fastq-illumina_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
fastq-illumina for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_fastq-illumina_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
fastq-illumina for alignment with repeated record ... ok
test_fastq-illumina_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
fastq-illumina for three DNA sequence alignment ... ok
test_fastq-illumina_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
fastq-illumina for three peptides of different lengths ... ok
test_fastq-illumina_three_proteins_alignment (test_SeqIO_write.WriterTests)
fastq-illumina for three proteins alignment ... ok
test_fastq-illumina_zero_records (test_SeqIO_write.WriterTests)
fastq-illumina for zero records ... ok
test_fastq-solexa_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
fastq-solexa for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_fastq-solexa_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
fastq-solexa for alignment with repeated record ... ok
test_fastq-solexa_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
fastq-solexa for three DNA sequence alignment ... ok
test_fastq-solexa_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
fastq-solexa for three peptides of different lengths ... ok
test_fastq-solexa_three_proteins_alignment (test_SeqIO_write.WriterTests)
fastq-solexa for three proteins alignment ... ok
test_fastq-solexa_zero_records (test_SeqIO_write.WriterTests)
fastq-solexa for zero records ... ok
test_fastq_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
fastq for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_fastq_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
fastq for alignment with repeated record ... ok
test_fastq_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
fastq for three DNA sequence alignment ... ok
test_fastq_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
fastq for three peptides of different lengths ... ok
test_fastq_three_proteins_alignment (test_SeqIO_write.WriterTests)
fastq for three proteins alignment ... ok
test_fastq_zero_records (test_SeqIO_write.WriterTests)
fastq for zero records ... ok
test_genbank_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
genbank for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_genbank_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
genbank for alignment with repeated record ... ok
test_genbank_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
genbank for three DNA sequence alignment ... ok
test_genbank_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
genbank for three peptides of different lengths ... ok
test_genbank_three_proteins_alignment (test_SeqIO_write.WriterTests)
genbank for three proteins alignment ... ok
test_genbank_zero_records (test_SeqIO_write.WriterTests)
genbank for zero records ... ok
test_imgt_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
imgt for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_imgt_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
imgt for alignment with repeated record ... ok
test_imgt_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
imgt for three DNA sequence alignment ... ok
test_imgt_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
imgt for three peptides of different lengths ... ok
test_imgt_three_proteins_alignment (test_SeqIO_write.WriterTests)
imgt for three proteins alignment ... ok
test_imgt_zero_records (test_SeqIO_write.WriterTests)
imgt for zero records ... ok
test_maf_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
maf for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_maf_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
maf for alignment with repeated record ... ok
test_maf_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
maf for three DNA sequence alignment ... ok
test_maf_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
maf for three peptides of different lengths ... ok
test_maf_three_proteins_alignment (test_SeqIO_write.WriterTests)
maf for three proteins alignment ... ok
test_maf_zero_records (test_SeqIO_write.WriterTests)
maf for zero records ... ok
test_mauve_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
mauve for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_mauve_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
mauve for alignment with repeated record ... ok
test_mauve_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
mauve for three DNA sequence alignment ... ok
test_mauve_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
mauve for three peptides of different lengths ... ok
test_mauve_three_proteins_alignment (test_SeqIO_write.WriterTests)
mauve for three proteins alignment ... ok
test_mauve_zero_records (test_SeqIO_write.WriterTests)
mauve for zero records ... ok
test_nexus_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
nexus for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_nexus_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
nexus for alignment with repeated record ... ok
test_nexus_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
nexus for three DNA sequence alignment ... ok
test_nexus_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
nexus for three peptides of different lengths ... ok
test_nexus_three_proteins_alignment (test_SeqIO_write.WriterTests)
nexus for three proteins alignment ... ok
test_nexus_zero_records (test_SeqIO_write.WriterTests)
nexus for zero records ... ok
test_phd_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
phd for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_phd_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
phd for alignment with repeated record ... ok
test_phd_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
phd for three DNA sequence alignment ... ok
test_phd_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
phd for three peptides of different lengths ... ok
test_phd_three_proteins_alignment (test_SeqIO_write.WriterTests)
phd for three proteins alignment ... ok
test_phd_zero_records (test_SeqIO_write.WriterTests)
phd for zero records ... ok
test_phylip-relaxed_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
phylip-relaxed for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_phylip-relaxed_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
phylip-relaxed for alignment with repeated record ... ok
test_phylip-relaxed_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
phylip-relaxed for three DNA sequence alignment ... ok
test_phylip-relaxed_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
phylip-relaxed for three peptides of different lengths ... ok
test_phylip-relaxed_three_proteins_alignment (test_SeqIO_write.WriterTests)
phylip-relaxed for three proteins alignment ... ok
test_phylip-relaxed_zero_records (test_SeqIO_write.WriterTests)
phylip-relaxed for zero records ... ok
test_phylip-sequential_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
phylip-sequential for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_phylip-sequential_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
phylip-sequential for alignment with repeated record ... ok
test_phylip-sequential_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
phylip-sequential for three DNA sequence alignment ... ok
test_phylip-sequential_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
phylip-sequential for three peptides of different lengths ... ok
test_phylip-sequential_three_proteins_alignment (test_SeqIO_write.WriterTests)
phylip-sequential for three proteins alignment ... ok
test_phylip-sequential_zero_records (test_SeqIO_write.WriterTests)
phylip-sequential for zero records ... ok
test_phylip_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
phylip for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_phylip_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
phylip for alignment with repeated record ... ok
test_phylip_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
phylip for three DNA sequence alignment ... ok
test_phylip_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
phylip for three peptides of different lengths ... ok
test_phylip_three_proteins_alignment (test_SeqIO_write.WriterTests)
phylip for three proteins alignment ... ok
test_phylip_zero_records (test_SeqIO_write.WriterTests)
phylip for zero records ... ok
test_pir_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
pir for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_pir_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
pir for alignment with repeated record ... ok
test_pir_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
pir for three DNA sequence alignment ... ok
test_pir_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
pir for three peptides of different lengths ... ok
test_pir_three_proteins_alignment (test_SeqIO_write.WriterTests)
pir for three proteins alignment ... ok
test_pir_zero_records (test_SeqIO_write.WriterTests)
pir for zero records ... ok
test_qual_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
qual for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_qual_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
qual for alignment with repeated record ... ok
test_qual_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
qual for three DNA sequence alignment ... ok
test_qual_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
qual for three peptides of different lengths ... ok
test_qual_three_proteins_alignment (test_SeqIO_write.WriterTests)
qual for three proteins alignment ... ok
test_qual_zero_records (test_SeqIO_write.WriterTests)
qual for zero records ... ok
test_seqxml_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
seqxml for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_seqxml_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
seqxml for alignment with repeated record ... ok
test_seqxml_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
seqxml for three DNA sequence alignment ... ok
test_seqxml_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
seqxml for three peptides of different lengths ... ok
test_seqxml_three_proteins_alignment (test_SeqIO_write.WriterTests)
seqxml for three proteins alignment ... ok
test_seqxml_zero_records (test_SeqIO_write.WriterTests)
seqxml for zero records ... ok
test_sff_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
sff for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_sff_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
sff for alignment with repeated record ... ok
test_sff_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
sff for three DNA sequence alignment ... ok
test_sff_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
sff for three peptides of different lengths ... ok
test_sff_three_proteins_alignment (test_SeqIO_write.WriterTests)
sff for three proteins alignment ... ok
test_sff_zero_records (test_SeqIO_write.WriterTests)
sff for zero records ... ok
test_stockholm_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
stockholm for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_stockholm_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
stockholm for alignment with repeated record ... ok
test_stockholm_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
stockholm for three DNA sequence alignment ... ok
test_stockholm_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
stockholm for three peptides of different lengths ... ok
test_stockholm_three_proteins_alignment (test_SeqIO_write.WriterTests)
stockholm for three proteins alignment ... ok
test_stockholm_zero_records (test_SeqIO_write.WriterTests)
stockholm for zero records ... ok
test_tab_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
tab for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_tab_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
tab for alignment with repeated record ... ok
test_tab_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
tab for three DNA sequence alignment ... ok
test_tab_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
tab for three peptides of different lengths ... ok
test_tab_three_proteins_alignment (test_SeqIO_write.WriterTests)
tab for three proteins alignment ... ok
test_tab_zero_records (test_SeqIO_write.WriterTests)
tab for zero records ... ok
----------------------------------------------------------------------
Ran 1 test in 0.157 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqRecord.py
test_SeqRecord ... ok
test_annotations (test_SeqRecord.SeqRecordCreation)
Pass in annotations to SeqRecords ... ok
test_letter_annotations (test_SeqRecord.SeqRecordCreation)
Pass in letter annotations to SeqRecords ... ok
test_replacing_seq (test_SeqRecord.SeqRecordCreation)
Replacing .seq if .letter_annotation present. ... ok
test_valid_annotations (test_SeqRecord.SeqRecordCreation) ... ok
test_valid_dbxrefs (test_SeqRecord.SeqRecordCreation) ... ok
test_valid_description (test_SeqRecord.SeqRecordCreation) ... ok
test_valid_features (test_SeqRecord.SeqRecordCreation) ... ok
test_valid_id (test_SeqRecord.SeqRecordCreation) ... ok
test_valid_name (test_SeqRecord.SeqRecordCreation) ... ok
test_add_seq (test_SeqRecord.SeqRecordMethods)
Simple addition of Seq or string ... ok
test_add_seq_left (test_SeqRecord.SeqRecordMethods)
Simple left addition of Seq or string ... ok
test_add_seqrecord (test_SeqRecord.SeqRecordMethods)
Simple left addition of SeqRecord from genbank file. ... ok
test_add_simple (test_SeqRecord.SeqRecordMethods)
Simple addition ... ok
test_contains (test_SeqRecord.SeqRecordMethods) ... ok
test_format (test_SeqRecord.SeqRecordMethods) ... ok
test_iter (test_SeqRecord.SeqRecordMethods) ... ok
test_lower (test_SeqRecord.SeqRecordMethods) ... ok
test_repr (test_SeqRecord.SeqRecordMethods) ... ok
test_slice_add_shift (test_SeqRecord.SeqRecordMethods)
Simple slice and add to shift ... ok
test_slice_add_simple (test_SeqRecord.SeqRecordMethods)
Simple slice and add ... ok
test_slice_simple (test_SeqRecord.SeqRecordMethods)
Simple slice ... ok
test_slice_variants (test_SeqRecord.SeqRecordMethods)
Simple slices using different start/end values ... ok
test_slice_zero (test_SeqRecord.SeqRecordMethods)
Zero slice ... ok
test_slicing (test_SeqRecord.SeqRecordMethods) ... ok
test_str (test_SeqRecord.SeqRecordMethods) ... ok
test_upper (test_SeqRecord.SeqRecordMethods) ... ok
test_eq_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_ge_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_gt_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_hash_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_le_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_lt_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_ne_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_reverse_complement_mutable_seq (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_reverse_complement_seq (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_translate (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_defaults (test_SeqRecord.TestTranslation) ... ok
test_new_annot (test_SeqRecord.TestTranslation) ... ok
test_preserve (test_SeqRecord.TestTranslation) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.283 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqUtils.py
test_SeqUtils ... ok
test_GC (test_SeqUtils.SeqUtilsTests) ... ok
test_GC_skew (test_SeqUtils.SeqUtilsTests) ... ok
test_checksum1 (test_SeqUtils.SeqUtilsTests) ... ok
test_checksum2 (test_SeqUtils.SeqUtilsTests) ... ok
test_checksum3 (test_SeqUtils.SeqUtilsTests) ... ok
test_codon_usage_custom (test_SeqUtils.SeqUtilsTests)
Test Codon Adaptation Index (CAI) using FASTA file for background. ... ok
test_codon_usage_ecoli (test_SeqUtils.SeqUtilsTests)
Test Codon Adaptation Index (CAI) using default E. coli data. ... ok
test_crc_checksum_collision (test_SeqUtils.SeqUtilsTests) ... ok
test_seq1_seq3 (test_SeqUtils.SeqUtilsTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.128 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Seq_objs.py
test_Seq_objs ... ok
test_unknown_seq_ungap (test_Seq_objs.FileBasedTests)
Test ungap() works properly on UnknownSeq instances. ... ok
test_count_overlap_start_end_GG (test_Seq_objs.StringMethodTests)
Check our count_overlap method using GG with variable ends and starts. ... ok
test_count_overlap_start_end_NN (test_Seq_objs.StringMethodTests)
Check our count_overlap method using NN with variable ends and starts. ... ok
test_init_typeerror (test_Seq_objs.StringMethodTests)
Check Seq __init__ gives TypeError exceptions. ... ok
test_str_comparison (test_Seq_objs.StringMethodTests) ... ok
test_str_count (test_Seq_objs.StringMethodTests)
Check matches the python string count method. ... ok
test_str_count_overlap_GG (test_Seq_objs.StringMethodTests)
Check our count_overlap method using GG. ... ok
test_str_count_overlap_NN (test_Seq_objs.StringMethodTests)
Check our count_overlap method using NN. ... ok
test_str_endswith (test_Seq_objs.StringMethodTests)
Check matches the python string endswith method. ... ok
test_str_find (test_Seq_objs.StringMethodTests)
Check matches the python string find method. ... ok
test_str_getitem (test_Seq_objs.StringMethodTests)
Check slicing and indexing works like a string. ... ok
test_str_hash (test_Seq_objs.StringMethodTests) ... ok
test_str_length (test_Seq_objs.StringMethodTests)
Check matches the python string __len__ method. ... ok
test_str_lower (test_Seq_objs.StringMethodTests)
Check matches the python string lower method. ... ok
test_str_lsplit (test_Seq_objs.StringMethodTests)
Check matches the python string rstrip method. ... ok
test_str_rfind (test_Seq_objs.StringMethodTests)
Check matches the python string rfind method. ... ok
test_str_rsplit (test_Seq_objs.StringMethodTests)
Check matches the python string rstrip method. ... ok
test_str_rstrip (test_Seq_objs.StringMethodTests)
Check matches the python string rstrip method. ... ok
test_str_split (test_Seq_objs.StringMethodTests)
Check matches the python string rstrip method. ... ok
test_str_startswith (test_Seq_objs.StringMethodTests)
Check matches the python string startswith method. ... ok
test_str_strip (test_Seq_objs.StringMethodTests)
Check matches the python string strip method. ... ok
test_str_upper (test_Seq_objs.StringMethodTests)
Check matches the python string upper method. ... ok
test_the_back_transcription (test_Seq_objs.StringMethodTests)
Check obj.back_transcribe() method. ... ok
test_the_complement (test_Seq_objs.StringMethodTests)
Check obj.complement() method. ... ok
test_the_reverse_complement (test_Seq_objs.StringMethodTests)
Check obj.reverse_complement() method. ... ok
test_the_transcription (test_Seq_objs.StringMethodTests)
Check obj.transcribe() method. ... ok
test_the_translate (test_Seq_objs.StringMethodTests)
Check obj.translate() method. ... ok
test_the_translation_of_ambig_codons (test_Seq_objs.StringMethodTests)
Check obj.translate() method with ambiguous codons. ... ok
test_the_translation_of_invalid_codons (test_Seq_objs.StringMethodTests)
Check obj.translate() method with invalid codons. ... ok
test_the_translation_of_stops (test_Seq_objs.StringMethodTests)
Check obj.translate() method with stop codons. ... ok
test_tomutable (test_Seq_objs.StringMethodTests)
Check obj.tomutable() method. ... ok
test_toseq (test_Seq_objs.StringMethodTests)
Check obj.toseq() method. ... ok
----------------------------------------------------------------------
Ran 1 test in 4.383 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SffIO.py
test_SffIO ... ok
test_alt_index_at_end (test_SffIO.TestAlternativeIndexes) ... ok
test_alt_index_at_start (test_SffIO.TestAlternativeIndexes) ... ok
test_alt_index_in_middle (test_SffIO.TestAlternativeIndexes) ... ok
test_index_at_start (test_SffIO.TestAlternativeIndexes) ... ok
test_index_in_middle (test_SffIO.TestAlternativeIndexes) ... ok
test_trim (test_SffIO.TestAlternativeIndexes) ... ok
test_index1 (test_SffIO.TestConcatenated) ... ok
test_index2 (test_SffIO.TestConcatenated) ... ok
test_parse1 (test_SffIO.TestConcatenated) ... ok
test_parse2 (test_SffIO.TestConcatenated) ... ok
test_parses_gzipped_stream (test_SffIO.TestConcatenated) ... ok
test_30bytes (test_SffIO.TestErrors) ... ok
test_31bytes (test_SffIO.TestErrors) ... ok
test_31bytes_bad_flowgram (test_SffIO.TestErrors) ... ok
test_31bytes_bad_ver (test_SffIO.TestErrors) ... ok
test_31bytes_index_header (test_SffIO.TestErrors) ... ok
test_bad_index_eof (test_SffIO.TestErrors) ... ok
test_bad_index_length (test_SffIO.TestErrors) ... ok
test_bad_index_offset (test_SffIO.TestErrors) ... ok
test_empty (test_SffIO.TestErrors) ... ok
test_index_lengths (test_SffIO.TestErrors) ... ok
test_index_mft_data_size (test_SffIO.TestErrors) ... ok
test_index_mft_version (test_SffIO.TestErrors) ... ok
test_index_name_no_null (test_SffIO.TestErrors) ... ok
test_no_index (test_SffIO.TestErrors) ... ok
test_no_manifest_xml (test_SffIO.TestErrors) ... ok
test_premature_end_of_index (test_SffIO.TestErrors) ... ok
test_unknown_index (test_SffIO.TestErrors) ... ok
test_both_ways (test_SffIO.TestIndex) ... ok
test_manifest (test_SffIO.TestIndex) ... ok
test_index (test_SffIO.TestSelf) ... ok
test_read (test_SffIO.TestSelf) ... ok
test_read_wrong (test_SffIO.TestSelf) ... ok
test_write (test_SffIO.TestSelf) ... ok
test_coords (test_SffIO.TestUAN) ... ok
test_region (test_SffIO.TestUAN) ... ok
test_time (test_SffIO.TestUAN) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.154 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SubsMat.py
test_SubsMat ... ok
runTest (__main__.ComparisonTestCase)
test_SubsMat ... ok
----------------------------------------------------------------------
Ran 1 test in 0.043 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SwissProt.py
test_SwissProt ... ok
test_sp001 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp001. ... ok
test_sp002 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp002. ... ok
test_sp003 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp003. ... ok
test_sp004 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp004. ... ok
test_sp005 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp005. ... ok
test_sp006 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp006. ... ok
test_sp007 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp007. ... ok
test_sp008 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp008. ... ok
test_sp009 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp009. ... ok
test_sp010 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp010. ... ok
test_sp011 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp011. ... ok
test_sp012 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp012. ... ok
test_sp013 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp013. ... ok
test_sp014 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp014. ... ok
test_sp015 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp015. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.180 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_TCoffee_tool.py
test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.117 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_TogoWS.py
test_TogoWS ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.009 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_TreeConstruction.py
test_TreeConstruction ... ok
test_known_matrices (test_TreeConstruction.DistanceCalculatorTest) ... ok
test_nonmatching_seqs (test_TreeConstruction.DistanceCalculatorTest) ... ok
test_bad_construction (test_TreeConstruction.DistanceMatrixTest) ... ok
test_bad_manipulation (test_TreeConstruction.DistanceMatrixTest) ... ok
test_format_phylip (test_TreeConstruction.DistanceMatrixTest) ... ok
test_good_construction (test_TreeConstruction.DistanceMatrixTest) ... ok
test_good_manipulation (test_TreeConstruction.DistanceMatrixTest) ... ok
test_built_tree (test_TreeConstruction.DistanceTreeConstructorTest) ... ok
test_nj (test_TreeConstruction.DistanceTreeConstructorTest) ... ok
test_upgma (test_TreeConstruction.DistanceTreeConstructorTest) ... ok
test_get_neighbors (test_TreeConstruction.NNITreeSearcherTest) ... ok
test_get_score (test_TreeConstruction.ParsimonyScorerTest) ... ok
test_build_tree (test_TreeConstruction.ParsimonyTreeConstructorTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.678 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_UniGene.py
test_UniGene ... ok
test_parse (test_UniGene.TestUniGene) ... ok
test_read (test_UniGene.TestUniGene) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.032 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Uniprot.py
test_Uniprot ... ok
test_F2CXE6 (test_Uniprot.TestUniprot)
Compare SwissProt text and uniprot XML versions of F2CXE6. ... ok
test_H2CNN8 (test_Uniprot.TestUniprot)
Compare SwissProt text and uniprot XML versions of H2CNN8. ... ok
test_P84001 (test_Uniprot.TestUniprot)
Parse mass spec structured comment with unknown loc ... ok
test_Q13639 (test_Uniprot.TestUniprot)
Compare SwissProt text and uniprot XML versions of Q13639. ... ok
test_multi_ex (test_Uniprot.TestUniprot)
Compare SwissProt text and uniprot XML versions of several examples. ... ok
test_multi_ex_index (test_Uniprot.TestUniprot)
Index SwissProt text and uniprot XML versions of several examples. ... ok
test_sp002 (test_Uniprot.TestUniprot)
Parsing SwissProt file sp002 ... ok
test_sp016 (test_Uniprot.TestUniprot)
Parsing SwissProt file sp016 ... ok
test_submittedName_allowed (test_Uniprot.TestUniprot)
Checks if parser supports new XML Element (submittedName). ... ok
test_uni001 (test_Uniprot.TestUniprot)
Parsing Uniprot file uni001 ... ok
test_uni003 (test_Uniprot.TestUniprot)
Parsing Uniprot file uni003 ... ok
----------------------------------------------------------------------
Ran 1 test in 0.288 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Wise.py
test_Wise ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
----------------------------------------------------------------------
Ran 1 test in 0.010 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_XXmotif_tool.py
test_XXmotif_tool ... skipping. Install XXmotif if you want to use XXmotif from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.117 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_align.py
test_align ... ok
runTest (__main__.ComparisonTestCase)
test_align ... ok
----------------------------------------------------------------------
Ran 1 test in 0.222 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_cellosaurus.py
test_cellosaurus ... ok
test__str__ (test_cellosaurus.TestCellosaurus)
Test string function ... ok
test_parse (test_cellosaurus.TestCellosaurus)
Test parsing function ... ok
test_read (test_cellosaurus.TestCellosaurus)
Test read function ... ok
----------------------------------------------------------------------
Ran 1 test in 0.009 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_codonalign.py
test_codonalign ... /builddir/build/BUILD/python-biopython-1.73/python3/build/lib.linux-i686-3.7/Bio/Seq.py:2589: BiopythonWarning: This table contains 6 codon(s) which code(s) for both STOP and an amino acid (e.g. 'TAA' -> 'stop' or STOP). Such codons will be translated as amino acid.
BiopythonWarning)
ok
test_IO (test_codonalign.TestBuildAndIO) ... ok
test_align (test_codonalign.TestCodonAlignment) ... ok
test_seq (test_codonalign.TestCodonSeq) ... ok
test_mk (test_codonalign.Test_MK) ... ok
test_build (test_codonalign.Test_build) ... ok
test_dn_ds (test_codonalign.Test_dn_ds) ... ok
test_dn_ds_matrix (test_codonalign.Test_dn_ds) ... ok
----------------------------------------------------------------------
Ran 1 test in 7.286 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_geo.py
test_geo ... ok
runTest (__main__.ComparisonTestCase)
test_geo ... ok
----------------------------------------------------------------------
Ran 1 test in 0.023 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_kNN.py
test_kNN ... ok
test_calculate_model (test_kNN.TestKNN) ... ok
test_calculate_probability (test_kNN.TestKNN) ... ok
test_classify (test_kNN.TestKNN) ... ok
test_leave_one_out (test_kNN.TestKNN) ... ok
test_model_accuracy (test_kNN.TestKNN) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.015 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_lowess.py
test_lowess ... ok
test_Precomputed (test_lowess.test_lowess) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.009 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_mmtf.py
test_mmtf ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)
----------------------------------------------------------------------
Ran 1 test in 0.082 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_mmtf_online.py
test_mmtf_online ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)
----------------------------------------------------------------------
Ran 1 test in 0.083 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_motifs.py
test_motifs ... ok
test_mixed_alphabets (test_motifs.MotifTestPWM)
Test creating motif with mixed alphabets. ... ok
test_simple (test_motifs.MotifTestPWM)
Test if Bio.motifs PWM scoring works. ... ok
test_with_alt_alphabet (test_motifs.MotifTestPWM)
Test motif search using alternative instance of alphabet. ... ok
test_with_bad_char (test_motifs.MotifTestPWM)
Test if Bio.motifs PWM scoring works with unexpected letters like N. ... ok
test_with_mixed_case (test_motifs.MotifTestPWM)
Test if Bio.motifs PWM scoring works with mixed case. ... ok
test_TFoutput (test_motifs.MotifTestsBasic)
Ensure that we can write proper TransFac output files. ... ok
test_alignace_parsing (test_motifs.MotifTestsBasic)
Test if Bio.motifs can parse AlignAce output files. ... ok
test_format (test_motifs.MotifTestsBasic) ... ok
test_pfm_parsing (test_motifs.MotifTestsBasic)
Test if Bio.motifs can parse JASPAR-style pfm files. ... ok
test_sites_parsing (test_motifs.MotifTestsBasic)
Test if Bio.motifs can parse JASPAR-style sites files. ... ok
test_mast_parser_1 (test_motifs.TestMAST)
Parse motifs/mast.dna.oops.txt file. ... ok
test_mast_parser_2 (test_motifs.TestMAST)
Parse motifs/mast.protein.oops.txt file. ... ok
test_mast_parser_3 (test_motifs.TestMAST)
Parse motifs/mast.protein.tcm.txt file. ... ok
test_meme_parser_1 (test_motifs.TestMEME)
Parsing motifs/meme.out file. ... ok
test_meme_parser_2 (test_motifs.TestMEME)
Parse motifs/meme.dna.oops.txt file. ... ok
test_meme_parser_3 (test_motifs.TestMEME)
Parse motifs/meme.protein.oops.txt file. ... ok
test_meme_parser_4 (test_motifs.TestMEME)
Parse motifs/meme.protein.tcm.txt file. ... ok
test_meme_parser_4_11_4 (test_motifs.TestMEME)
Parse motifs/meme_v_4_11_4.txt file. ... ok
test_meme_parser_rna (test_motifs.TestMEME)
Test if Bio.motifs can parse MEME output files using RNA. ... ok
test_minimal_meme_parser (test_motifs.TestMEME)
Parse motifs/minimal_test.meme file. ... ok
test_transfac_parser (test_motifs.TestTransfac)
Parse motifs/transfac.dat file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.142 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_motifs_online.py
test_motifs_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.062 seconds
.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring int+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_pairwise2.py
test_pairwise2 ... ok
test_clean_alignments (test_pairwise2.TestOtherFunctions)
``_clean_alignments`` removes redundant alignments. ... ok
test_print_matrix (test_pairwise2.TestOtherFunctions)
``print_matrix`` prints nested lists as nice matrices. ... ok
test_function_name (test_pairwise2.TestPairwiseErrorConditions)
Test for wrong function names. ... ok
test_function_parameters (test_pairwise2.TestPairwiseErrorConditions)
Test for number of parameters. ... ok
test_warnings (test_pairwise2.TestPairwiseErrorConditions)
Test for warnings. ... ok
test_extend_penalty1 (test_pairwise2.TestPairwiseExtendPenalty) ... ok
test_extend_penalty2 (test_pairwise2.TestPairwiseExtendPenalty) ... ok
test_globalxx_simple (test_pairwise2.TestPairwiseGlobal) ... ok
test_globalxx_simple2 (test_pairwise2.TestPairwiseGlobal)
Do the same test with sequence order reversed. ... ok
test_list_input (test_pairwise2.TestPairwiseGlobal)
Do a global aligment with sequences supplied as lists. ... ok
test_blosum62 (test_pairwise2.TestPairwiseLocal)
Test localds with blosum62. ... ok
test_localms (test_pairwise2.TestPairwiseLocal)
Two different local alignments. ... ok
test_localxs (test_pairwise2.TestPairwiseLocal) ... ok
test_match_dictionary1 (test_pairwise2.TestPairwiseMatchDictionary) ... ok
test_match_dictionary2 (test_pairwise2.TestPairwiseMatchDictionary) ... ok
test_match_dictionary3 (test_pairwise2.TestPairwiseMatchDictionary) ... ok
test_align_one_char1 (test_pairwise2.TestPairwiseOneCharacter) ... ok
test_align_one_char2 (test_pairwise2.TestPairwiseOneCharacter) ... ok
test_align_one_char3 (test_pairwise2.TestPairwiseOneCharacter) ... ok
test_match_score_open_penalty1 (test_pairwise2.TestPairwiseOpenPenalty) ... ok
test_match_score_open_penalty2 (test_pairwise2.TestPairwiseOpenPenalty) ... ok
test_match_score_open_penalty3 (test_pairwise2.TestPairwiseOpenPenalty) ... ok
test_match_score_open_penalty4 (test_pairwise2.TestPairwiseOpenPenalty) ... ok
test_penalize_end_gaps (test_pairwise2.TestPairwisePenalizeEndgaps) ... ok
test_penalize_end_gaps2 (test_pairwise2.TestPairwisePenalizeEndgaps)
Do the same, but use the generic method (with the same result). ... ok
test_separate_penalize_end_gaps (test_pairwise2.TestPairwisePenalizeEndgaps)
Test alignment where end-gaps are differently penalized. ... ok
test_penalize_extend_when_opening (test_pairwise2.TestPairwisePenalizeExtendWhenOpening) ... ok
test_separate_gap_penalties1 (test_pairwise2.TestPairwiseSeparateGapPenalties) ... ok
test_separate_gap_penalties2 (test_pairwise2.TestPairwiseSeparateGapPenalties) ... ok
test_separate_gap_penalties_with_extension (test_pairwise2.TestPairwiseSeparateGapPenaltiesWithExtension) ... ok
test_gap_here_only_1 (test_pairwise2.TestPersiteGapPenalties) ... ok
test_gap_here_only_2 (test_pairwise2.TestPersiteGapPenalties)
Force a bad alignment. ... ok
test_score_only_global (test_pairwise2.TestScoreOnly)
Test ``score_only`` in a global alignment. ... ok
test_score_only_local (test_pairwise2.TestScoreOnly)
Test ``score_only`` in a local alignment. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.076 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_pairwise_aligner.py
test_pairwise_aligner ... ok
test_aligner_property_epsilon (test_pairwise_aligner.TestAlignerProperties) ... ok
test_aligner_property_gapscores (test_pairwise_aligner.TestAlignerProperties) ... ok
test_aligner_property_match_mismatch (test_pairwise_aligner.TestAlignerProperties) ... ok
test_aligner_property_mode (test_pairwise_aligner.TestAlignerProperties) ... ok
test_extend_penalty1 (test_pairwise_aligner.TestPairwiseExtendPenalty) ... ok
test_extend_penalty2 (test_pairwise_aligner.TestPairwiseExtendPenalty) ... ok
test_align_affine1_score (test_pairwise_aligner.TestPairwiseGlobal) ... ok
test_needlemanwunsch_simple1 (test_pairwise_aligner.TestPairwiseGlobal) ... ok
test_gotoh_local (test_pairwise_aligner.TestPairwiseLocal) ... ok
test_smithwaterman (test_pairwise_aligner.TestPairwiseLocal) ... ok
test_match_dictionary1 (test_pairwise_aligner.TestPairwiseMatchDictionary) ... ok
test_match_dictionary2 (test_pairwise_aligner.TestPairwiseMatchDictionary) ... ok
test_match_dictionary3 (test_pairwise_aligner.TestPairwiseMatchDictionary) ... ok
test_align_one_char1 (test_pairwise_aligner.TestPairwiseOneCharacter) ... ok
test_align_one_char2 (test_pairwise_aligner.TestPairwiseOneCharacter) ... ok
test_align_one_char3 (test_pairwise_aligner.TestPairwiseOneCharacter) ... ok
test_align_one_char_score3 (test_pairwise_aligner.TestPairwiseOneCharacter) ... ok
test_match_score_open_penalty1 (test_pairwise_aligner.TestPairwiseOpenPenalty) ... ok
test_match_score_open_penalty2 (test_pairwise_aligner.TestPairwiseOpenPenalty) ... ok
test_match_score_open_penalty3 (test_pairwise_aligner.TestPairwiseOpenPenalty) ... ok
test_match_score_open_penalty4 (test_pairwise_aligner.TestPairwiseOpenPenalty) ... ok
test_penalize_end_gaps (test_pairwise_aligner.TestPairwisePenalizeEndgaps) ... ok
test_penalize_extend_when_opening (test_pairwise_aligner.TestPairwisePenalizeExtendWhenOpening) ... ok
test_separate_gap_penalties1 (test_pairwise_aligner.TestPairwiseSeparateGapPenalties) ... ok
test_separate_gap_penalties2 (test_pairwise_aligner.TestPairwiseSeparateGapPenalties) ... ok
test_separate_gap_penalties_with_extension (test_pairwise_aligner.TestPairwiseSeparateGapPenaltiesWithExtension) ... ok
test_broken_gap_function (test_pairwise_aligner.TestPerSiteGapPenalties) ... ok
test_gap_here_only_1 (test_pairwise_aligner.TestPerSiteGapPenalties) ... ok
test_gap_here_only_2 (test_pairwise_aligner.TestPerSiteGapPenalties) ... ok
test_gap_here_only_3 (test_pairwise_aligner.TestPerSiteGapPenalties) ... ok
test_gap_here_only_local_1 (test_pairwise_aligner.TestPerSiteGapPenalties) ... ok
test_gap_here_only_local_2 (test_pairwise_aligner.TestPerSiteGapPenalties) ... ok
test_gap_here_only_local_3 (test_pairwise_aligner.TestPerSiteGapPenalties) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.138 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_phenotype.py
test_phenotype ... ok
test_PlateRecord (test_phenotype.TestPhenoMicro)
Test basic functionalities of PlateRecord objects ... ok
test_PlateRecord_errors (test_phenotype.TestPhenoMicro)
Test bad arguments with PlateRecord objects ... ok
test_WellRecord (test_phenotype.TestPhenoMicro)
Test basic functionalities of WellRecord objects ... ok
test_bad_fit_args (test_phenotype.TestPhenoMicro)
Test error handling of the fit method. ... ok
test_phenotype_IO (test_phenotype.TestPhenoMicro)
Test basic functionalities of phenotype IO methods ... ok
test_phenotype_IO_errors (test_phenotype.TestPhenoMicro)
Test bad arguments to phenotype IO methods ... ok
----------------------------------------------------------------------
Ran 1 test in 13.756 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_phenotype_fit.py
test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality.
----------------------------------------------------------------------
Ran 1 test in 0.010 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_phyml_tool.py
test_phyml_tool ... skipping. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.222 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_prodoc.py
test_prodoc ... ok
test_parse_pdoc (test_prodoc.TestProdocParse)
Parsing an excerpt of prosite.doc ... ok
test_read_pdoc00100 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00100 ... ok
test_read_pdoc00113 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00113 ... ok
test_read_pdoc00144 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00144 ... ok
test_read_pdoc00149 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00149 ... ok
test_read_pdoc00340 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00340 ... ok
test_read_pdoc00424 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00424 ... ok
test_read_pdoc00472 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00472 ... ok
test_read_pdoc00640 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00640 ... ok
test_read_pdoc00787 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00787 ... ok
test_read_pdoc0933 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00933 ... ok
----------------------------------------------------------------------
Ran 1 test in 0.018 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_prosite1.py
test_prosite1 ... ok
test_read1 (test_prosite1.TestPrositeRead)
Parsing Prosite record ps00107.txt ... ok
test_read2 (test_prosite1.TestPrositeRead)
Parsing Prosite record ps00159.txt ... ok
test_read3 (test_prosite1.TestPrositeRead)
Parsing Prosite record ps00165.txt ... ok
----------------------------------------------------------------------
Ran 1 test in 0.074 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_prosite2.py
test_prosite2 ... ok
test_read4 (test_prosite2.TestPrositeRead)
Parsing Prosite record ps00432.txt ... ok
test_read5 (test_prosite2.TestPrositeRead)
Parsing Prosite record ps00488.txt ... ok
test_read6 (test_prosite2.TestPrositeRead)
Parsing Prosite record ps00546.txt ... ok
----------------------------------------------------------------------
Ran 1 test in 0.025 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_psw.py
test_psw ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
----------------------------------------------------------------------
Ran 1 test in 0.010 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_raxml_tool.py
test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.209 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_samtools_tool.py
test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program
if you want to use it from Biopython
----------------------------------------------------------------------
Ran 1 test in 0.020 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_seq.py
test_seq ... ok
test_ambiguous_values (test_seq.TestAmbiguousComplements)
Test that other tests do not introduce characters to our values ... ok
test_complement_ambiguous_dna_values (test_seq.TestComplement) ... ok
test_complement_ambiguous_rna_values (test_seq.TestComplement) ... ok
test_complement_incompatible_alphabets (test_seq.TestComplement) ... ok
test_complement_of_dna (test_seq.TestComplement) ... ok
test_complement_of_mixed_dna_rna (test_seq.TestComplement) ... ok
test_complement_of_rna (test_seq.TestComplement) ... ok
test_complement_on_proteins (test_seq.TestComplement)
Test complement shouldn't work on a protein! ... ok
test_reverse_complements (test_seq.TestDoubleReverseComplement)
Test double reverse complement preserves the sequence ... ok
test_add_method (test_seq.TestMutableSeq)
Test adding wrong type to MutableSeq ... ok
test_appending (test_seq.TestMutableSeq) ... ok
test_as_string (test_seq.TestMutableSeq) ... ok
test_complement (test_seq.TestMutableSeq) ... ok
test_complement_dna_string (test_seq.TestMutableSeq) ... ok
test_complement_mixed_aphabets (test_seq.TestMutableSeq) ... ok
test_complement_rna (test_seq.TestMutableSeq) ... ok
test_complement_rna_string (test_seq.TestMutableSeq) ... ok
test_converting_to_immutable (test_seq.TestMutableSeq) ... ok
test_count (test_seq.TestMutableSeq) ... ok
test_delete_stride_slice (test_seq.TestMutableSeq) ... ok
test_deleting_item (test_seq.TestMutableSeq) ... ok
test_deleting_slice (test_seq.TestMutableSeq) ... ok
test_equal_comparison (test_seq.TestMutableSeq)
Test __eq__ comparison method ... ok
test_equal_comparison_of_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
test_extend_method (test_seq.TestMutableSeq) ... ok
test_extend_with_mutable_seq (test_seq.TestMutableSeq) ... ok
test_extract_third_nucleotide (test_seq.TestMutableSeq)
Test extracting every third nucleotide (slicing with stride 3) ... ok
test_first_nucleotide (test_seq.TestMutableSeq) ... ok
test_greater_than_comparison (test_seq.TestMutableSeq)
Test __gt__ comparison method ... ok
test_greater_than_comparison_of_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
test_greater_than_comparison_of_incompatible_types (test_seq.TestMutableSeq) ... ok
test_greater_than_comparison_without_alphabet (test_seq.TestMutableSeq) ... ok
test_greater_than_or_equal_comparison (test_seq.TestMutableSeq)
Test __ge__ comparison method ... ok
test_greater_than_or_equal_comparison_of_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq) ... ok
test_greater_than_or_equal_comparison_without_alphabet (test_seq.TestMutableSeq) ... ok
test_index (test_seq.TestMutableSeq) ... ok
test_inserting (test_seq.TestMutableSeq) ... ok
test_length (test_seq.TestMutableSeq) ... ok
test_less_than_comparison (test_seq.TestMutableSeq)
Test __lt__ comparison method ... ok
test_less_than_comparison_of_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
test_less_than_comparison_of_incompatible_types (test_seq.TestMutableSeq) ... ok
test_less_than_comparison_without_alphabet (test_seq.TestMutableSeq) ... ok
test_less_than_or_equal_comparison (test_seq.TestMutableSeq)
Test __le__ comparison method ... ok
test_less_than_or_equal_comparison_of_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq) ... ok
test_less_than_or_equal_comparison_without_alphabet (test_seq.TestMutableSeq) ... ok
test_mutableseq_creation (test_seq.TestMutableSeq)
Test creating MutableSeqs in multiple ways ... ok
test_not_equal_comparison (test_seq.TestMutableSeq)
Test __ne__ comparison method ... ok
test_popping_last_item (test_seq.TestMutableSeq) ... ok
test_radd_method (test_seq.TestMutableSeq) ... ok
test_radd_method_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
test_radd_method_using_seq_object (test_seq.TestMutableSeq) ... ok
test_radd_method_wrong_type (test_seq.TestMutableSeq) ... ok
test_remove_items (test_seq.TestMutableSeq) ... ok
test_repr (test_seq.TestMutableSeq) ... ok
test_reverse (test_seq.TestMutableSeq)
Test using reverse method ... ok
test_reverse_complement (test_seq.TestMutableSeq) ... ok
test_reverse_complement_of_protein (test_seq.TestMutableSeq) ... ok
test_reverse_with_stride (test_seq.TestMutableSeq)
Test reverse using -1 stride ... ok
test_set_wobble_codon_to_n (test_seq.TestMutableSeq)
Test setting wobble codon to N (set slice with stride 3) ... ok
test_setting_item (test_seq.TestMutableSeq) ... ok
test_setting_slices (test_seq.TestMutableSeq) ... ok
test_truncated_repr (test_seq.TestMutableSeq) ... ok
test_reverse_complement (test_seq.TestReverseComplement) ... ok
test_reverse_complement_of_dna (test_seq.TestReverseComplement) ... ok
test_reverse_complement_of_mixed_dna_rna (test_seq.TestReverseComplement) ... ok
test_reverse_complement_of_rna (test_seq.TestReverseComplement) ... ok
test_reverse_complement_on_proteins (test_seq.TestReverseComplement)
Test reverse complement shouldn't work on a protein! ... ok
test_alphabet (test_seq.TestSeq)
Test alphabet of derived Seq object ... ok
test_alphabet_letters (test_seq.TestSeq)
Test nucleotides in DNA Seq ... ok
test_as_string (test_seq.TestSeq)
Test converting Seq to string ... ok
test_concatenation_error (test_seq.TestSeq)
DNA Seq objects cannot be concatenated with Protein Seq objects. ... ok
test_concatenation_of_ambiguous_and_unambiguous_dna (test_seq.TestSeq)
Concatenate Seq object with ambiguous and unambiguous DNA returns ambiguous Seq. ... ok
test_concatenation_of_seq (test_seq.TestSeq) ... ok
test_construction_using_a_seq_object (test_seq.TestSeq)
Test using a Seq object to initialize another Seq object ... ok
test_extract_third_nucleotide (test_seq.TestSeq)
Test extracting every third nucleotide (slicing with stride 3) ... ok
test_first_nucleotide (test_seq.TestSeq)
Test getting first nucleotide of Seq ... ok
test_last_nucleotide (test_seq.TestSeq)
Test getting last nucleotide of Seq ... ok
test_length (test_seq.TestSeq)
Test len method on Seq object ... ok
test_length_concatenated_unambiguous_seq (test_seq.TestSeq)
Test length of concatenated Seq object with unambiguous DNA ... ok
test_repr (test_seq.TestSeq)
Test representation of Seq object ... ok
test_reverse (test_seq.TestSeq)
Test reverse using -1 stride ... ok
test_slicing (test_seq.TestSeq)
Test slicing of Seq ... ok
test_truncated_repr (test_seq.TestSeq) ... ok
test_ungap (test_seq.TestSeq) ... ok
test_adding_generic_nucleotide_with_other_nucleotides (test_seq.TestSeqAddition) ... ok
test_adding_generic_nucleotide_with_other_nucleotides_inplace (test_seq.TestSeqAddition) ... ok
test_addition_dna_rna_with_generic_nucleotides (test_seq.TestSeqAddition) ... ok
test_addition_dna_rna_with_generic_nucleotides_inplace (test_seq.TestSeqAddition) ... ok
test_addition_dna_with_dna (test_seq.TestSeqAddition) ... ok
test_addition_dna_with_dna_inplace (test_seq.TestSeqAddition) ... ok
test_addition_dna_with_rna (test_seq.TestSeqAddition) ... ok
test_addition_proteins (test_seq.TestSeqAddition) ... ok
test_addition_proteins_inplace (test_seq.TestSeqAddition) ... ok
test_addition_rna_with_rna (test_seq.TestSeqAddition) ... ok
test_addition_rna_with_rna_inplace (test_seq.TestSeqAddition) ... ok
test_exception_when_added_protein_has_more_than_one_gap_type (test_seq.TestSeqAddition)
Test resulting protein has gap types '-' and '.' ... ok
test_exception_when_added_protein_has_several_stop_codon_types (test_seq.TestSeqAddition)
Test resulting protein has stop codon types '*' and '@' ... ok
test_exception_when_added_rna_has_more_than_one_gap_type (test_seq.TestSeqAddition)
Test resulting sequence has gap types '-' and '.' ... ok
test_exception_when_adding_protein_with_nucleotides (test_seq.TestSeqAddition) ... ok
test_imul_method (test_seq.TestSeqMultiplication)
Test imul method; relies on addition and mull methods ... ok
test_imul_method_exceptions (test_seq.TestSeqMultiplication)
Test imul method exceptions ... ok
test_mul_method (test_seq.TestSeqMultiplication)
Test mul method; relies on addition method ... ok
test_mul_method_exceptions (test_seq.TestSeqMultiplication)
Test mul method exceptions ... ok
test_rmul_method (test_seq.TestSeqMultiplication)
Test rmul method; relies on addition method ... ok
test_rmul_method_exceptions (test_seq.TestSeqMultiplication)
Test rmul method exceptions ... ok
test_add_method_using_wrong_object (test_seq.TestSeqStringMethods) ... ok
test_append_nucleotides (test_seq.TestSeqStringMethods) ... ok
test_append_proteins (test_seq.TestSeqStringMethods) ... ok
test_contains_method (test_seq.TestSeqStringMethods) ... ok
test_counting_characters (test_seq.TestSeqStringMethods) ... ok
test_endswith (test_seq.TestSeqStringMethods) ... ok
test_equal_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
Test __eq__ comparison method ... ok
test_exception_when_clashing_alphabets (test_seq.TestSeqStringMethods)
Test by setting up clashing alphabet sequences ... ok
test_finding_characters (test_seq.TestSeqStringMethods) ... ok
test_greater_than_comparison (test_seq.TestSeqStringMethods)
Test __gt__ comparison method ... ok
test_greater_than_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
Test incompatible alphabet __gt__ comparison method ... ok
test_greater_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods)
Test incompatible types __gt__ comparison method ... ok
test_greater_than_or_equal_comparison (test_seq.TestSeqStringMethods)
Test __ge__ comparison method ... ok
test_greater_than_or_equal_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
Test incompatible alphabet __ge__ comparison method ... ok
test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods)
Test incompatible types __ge__ comparison method ... ok
test_hash (test_seq.TestSeqStringMethods) ... ok
test_less_than_comparison (test_seq.TestSeqStringMethods)
Test __lt__ comparison method ... ok
test_less_than_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
Test incompatible alphabet __lt__ comparison method ... ok
test_less_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods)
Test incompatible types __lt__ comparison method ... ok
test_less_than_or_equal_comparison (test_seq.TestSeqStringMethods)
Test __le__ comparison method ... ok
test_less_than_or_equal_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
Test incompatible alphabet __le__ comparison method ... ok
test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods)
Test incompatible types __le__ comparison method ... ok
test_not_equal_comparsion (test_seq.TestSeqStringMethods)
Test __ne__ comparison method ... ok
test_radd_method (test_seq.TestSeqStringMethods) ... ok
test_radd_method_using_incompatible_alphabets (test_seq.TestSeqStringMethods) ... ok
test_radd_method_using_wrong_object (test_seq.TestSeqStringMethods) ... ok
test_splits (test_seq.TestSeqStringMethods) ... ok
test_startswith (test_seq.TestSeqStringMethods) ... ok
test_string_methods (test_seq.TestSeqStringMethods) ... ok
test_stripping_characters (test_seq.TestSeqStringMethods) ... ok
test_sequence_alphabets (test_seq.TestSequenceAlphabets)
Sanity test on the test sequence alphabets. ... ok
test_stops (test_seq.TestStopCodons) ... ok
test_translation_of_stops (test_seq.TestStopCodons) ... ok
test_back_transcribe_rna_into_dna (test_seq.TestTranscription) ... ok
test_back_transcribe_rna_string_into_dna (test_seq.TestTranscription) ... ok
test_back_transcription_of_dna (test_seq.TestTranscription)
Test back-transcription shouldn't work on DNA! ... ok
test_back_transcription_of_proteins (test_seq.TestTranscription)
Test back-transcription shouldn't work on a protein! ... ok
test_seq_object_back_transcription_method (test_seq.TestTranscription) ... ok
test_seq_object_transcription_method (test_seq.TestTranscription) ... ok
test_transcription_dna_into_rna (test_seq.TestTranscription) ... ok
test_transcription_dna_string_into_rna (test_seq.TestTranscription) ... ok
test_transcription_of_proteins (test_seq.TestTranscription)
Test transcription shouldn't work on a protein! ... ok
test_transcription_of_rna (test_seq.TestTranscription)
Test transcription shouldn't work on RNA! ... ok
test_alphabet_of_translated_gapped_seq (test_seq.TestTranslating) ... ok
test_alphabets_of_translated_seqs (test_seq.TestTranslating) ... ok
test_gapped_seq_no_gap_char_given (test_seq.TestTranslating) ... ok
test_gapped_seq_no_gap_char_given_and_inferred_from_alphabet (test_seq.TestTranslating) ... ok
test_gapped_seq_with_gap_char_given (test_seq.TestTranslating) ... ok
test_gapped_seq_with_gap_char_given_and_inferred_from_alphabet (test_seq.TestTranslating) ... ok
test_gapped_seq_with_gap_char_given_and_inferred_from_alphabet2 (test_seq.TestTranslating)
Test using stop codon in sequence ... ok
test_gapped_seq_with_stop_codon_and_gap_char_given (test_seq.TestTranslating) ... ok
test_translation (test_seq.TestTranslating) ... ok
test_translation_extra_stop_codon (test_seq.TestTranslating) ... ok
test_translation_incomplete_codon (test_seq.TestTranslating) ... ok
test_translation_of_asparagine (test_seq.TestTranslating) ... ok
test_translation_of_gapped_string_no_gap_char_given (test_seq.TestTranslating) ... ok
test_translation_of_gapped_string_with_gap_char_given (test_seq.TestTranslating) ... ok
test_translation_of_glutamine (test_seq.TestTranslating) ... ok
test_translation_of_invalid_codon (test_seq.TestTranslating) ... ok
test_translation_of_leucine (test_seq.TestTranslating) ... ok
test_translation_of_string (test_seq.TestTranslating) ... ok
test_translation_on_proteins (test_seq.TestTranslating)
Test translation shouldn't work on a protein! ... ok
test_translation_to_stop (test_seq.TestTranslating) ... ok
test_translation_using_cds (test_seq.TestTranslating) ... ok
test_translation_using_tables_with_ambiguous_stop_codons (test_seq.TestTranslating)
Check for error and warning messages. ... ok
test_translation_with_bad_table_argument (test_seq.TestTranslating) ... ok
test_translation_with_codon_table_as_table_argument (test_seq.TestTranslating) ... ok
test_translation_wrong_type (test_seq.TestTranslating)
Test translation table cannot be CodonTable ... ok
test_add_method (test_seq.TestUnknownSeq) ... ok
test_back_transcribe (test_seq.TestUnknownSeq) ... ok
test_complement (test_seq.TestUnknownSeq) ... ok
test_complement_of_protein (test_seq.TestUnknownSeq)
Test reverse complement shouldn't work on a protein! ... ok
test_construction (test_seq.TestUnknownSeq) ... ok
test_count (test_seq.TestUnknownSeq) ... ok
test_getitem_method (test_seq.TestUnknownSeq) ... ok
test_length (test_seq.TestUnknownSeq) ... ok
test_lower (test_seq.TestUnknownSeq) ... ok
test_repr (test_seq.TestUnknownSeq) ... ok
test_reverse_complement (test_seq.TestUnknownSeq) ... ok
test_reverse_complement_of_protein (test_seq.TestUnknownSeq) ... ok
test_transcribe (test_seq.TestUnknownSeq) ... ok
test_translation (test_seq.TestUnknownSeq) ... ok
test_translation_of_proteins (test_seq.TestUnknownSeq) ... ok
test_ungap (test_seq.TestUnknownSeq) ... ok
test_upper (test_seq.TestUnknownSeq) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.139 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_translate.py
test_translate ... ok
runTest (__main__.ComparisonTestCase)
test_translate ... ok
----------------------------------------------------------------------
Ran 1 test in 0.063 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_trie.py
test_trie ... ok
test_get_approximate (test_trie.TestTrie) ... ok
test_get_set (test_trie.TestTrie) ... ok
test_large_save_load (test_trie.TestTrie)
Generate random key/val pairs in three length categories. ... ok
test_prefix (test_trie.TestTrie) ... ok
test_save (test_trie.TestTrie) ... ok
test_with_prefix (test_trie.TestTrie) ... ok
test_find (test_trie.TestTrieFind) ... ok
----------------------------------------------------------------------
Ran 1 test in 31.765 seconds
+ popd
+ RPM_EC=0
++ jobs -p
+ exit 0
ernet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Jul 15 2019, 17:02:22)
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
~/build/BUILD/python-biopython-1.73
Processing files: python3-biopython-1.73-5.fc31.i686
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.cRA3tv
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.73
+ DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/share/doc/python3-biopython
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/share/doc/python3-biopython
+ cp -pr python3/Scripts /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/share/doc/python3-biopython
+ cp -pr python3/CONTRIB.rst /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/share/doc/python3-biopython
+ cp -pr python3/DEPRECATED.rst /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/share/doc/python3-biopython
+ cp -pr python3/NEWS.rst /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/share/doc/python3-biopython
+ cp -pr python3/README.rst /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/share/doc/python3-biopython
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.U73DBw
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.73
+ LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/share/licenses/python3-biopython
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/share/licenses/python3-biopython
+ cp -pr python3/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/share/licenses/python3-biopython
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: python-biopython = 1.73-5.fc31 python3-biopython = 1.73-5.fc31 python3-biopython(x86-32) = 1.73-5.fc31 python3.7dist(biopython) = 1.73 python3dist(biopython) = 1.73
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.4) libpython3.7m.so.1.0 python(abi) = 3.7 python3.7dist(numpy) rtld(GNU_HASH)
Obsoletes: python-biopython < 1.73-5.fc31
Processing files: python-biopython-doc-1.73-5.fc31.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.gJ3M6s
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.73
+ DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/share/doc/python-biopython-doc
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/share/doc/python-biopython-doc
+ cp -pr biopython-1.73/Doc /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/share/doc/python-biopython-doc
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.2qmbNu
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.73
+ LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/share/licenses/python-biopython-doc
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/share/licenses/python-biopython-doc
+ cp -pr biopython-1.73/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386/usr/share/licenses/python-biopython-doc
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: python-biopython-doc = 1.73-5.fc31
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python-biopython-debugsource-1.73-5.fc31.i686
Provides: python-biopython-debugsource = 1.73-5.fc31 python-biopython-debugsource(x86-32) = 1.73-5.fc31
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python3-biopython-debuginfo-1.73-5.fc31.i686
Provides: debuginfo(build-id) = 1be9517b2e748d9528b7542190e70e9dbe5f41d4 debuginfo(build-id) = 1cefa59260518fee0df92338c71e1fcbc0da20f6 debuginfo(build-id) = 4c99e88ed66d598c1838f1303f372cee863882bb debuginfo(build-id) = 53fa5b8a3ed67d6c3e0168380d3c0e64c6296a0a debuginfo(build-id) = 7001596135094cc22168feba7d9bd27dd1dfc554 debuginfo(build-id) = b726cf9561583c06d2ef37e6d02c8d60431dfa66 debuginfo(build-id) = bde4b2f6bcfc9d19ffba1927d67635c6e1933c98 debuginfo(build-id) = c39fd33dede806dd1279031718b1f95bd100e0ae debuginfo(build-id) = e02e5bf00bf6e23412cb8b5639eb193b2426c74e python3-biopython-debuginfo = 1.73-5.fc31 python3-biopython-debuginfo(x86-32) = 1.73-5.fc31
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: python-biopython-debugsource(x86-32) = 1.73-5.fc31
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386
Wrote: /builddir/build/RPMS/python-biopython-doc-1.73-5.fc31.noarch.rpm
Wrote: /builddir/build/RPMS/python-biopython-debugsource-1.73-5.fc31.i686.rpm
Wrote: /builddir/build/RPMS/python3-biopython-debuginfo-1.73-5.fc31.i686.rpm
Wrote: /builddir/build/RPMS/python3-biopython-1.73-5.fc31.i686.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.oUsmcv
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.73
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/python-biopython-1.73-5.fc31.i386
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild python-biopython-1.73-5.fc31.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/974971-fedora-rawhide-i386-1563453628.674863/root/var/log/dnf.log
/var/lib/mock/974971-fedora-rawhide-i386-1563453628.674863/root/var/log/dnf.librepo.log
/var/lib/mock/974971-fedora-rawhide-i386-1563453628.674863/root/var/log/dnf.rpm.log
Finish: build phase for python-biopython-1.73-5.fc31.src.rpm
INFO: Done(/var/lib/copr-rpmbuild/results/python-biopython-1.73-5.fc31.src.rpm) Config(child) 5 minutes 40 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
WARNING: Could not find required logging config file: /var/lib/copr-rpmbuild/results/configs/logging.ini. Using default...
INFO: mock.py version 1.4.16 starting (python version = 3.7.3)...
Start: init plugins
INFO: tmpfs initialized
INFO: selinux disabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
Start: run
Start: scrub ['cache']
INFO: scrubbing cache for child
Finish: scrub ['cache']
Finish: run