Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c2a6' (ED25519) to the list of known hosts.
Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 5175150 --chroot fedora-rawhide-ppc64le --detached
Version: 0.62
PID: 13603
Logging PID: 13604
Task:
{'appstream': False,
'background': True,
'build_id': 5175150,
'buildroot_pkgs': [],
'chroot': 'fedora-rawhide-ppc64le',
'enable_net': False,
'fedora_review': False,
'git_hash': 'af214c487f0ec0f4dd938d0ce3cfbbe9dd7b74fa',
'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/python-biopython',
'isolation': 'default',
'memory_reqs': 2048,
'package_name': 'python-biopython',
'package_version': '1.80-1',
'project_dirname': 'gcc-13-test',
'project_name': 'gcc-13-test',
'project_owner': 'jakub',
'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/jakub/gcc-13-test/fedora-rawhide-ppc64le/',
'id': 'copr_base',
'name': 'Copr repository'},
{'baseurl': 'https://jakub.fedorapeople.org/fedora-gcc13-$arch/',
'id': 'https_jakub_fedorapeople_org_fedora_gcc13_arch',
'name': 'Additional repo https_jakub_fedorapeople_org_fedora_gcc13_arch'}],
'sandbox': 'jakub/gcc-13-test--jakub',
'source_json': {},
'source_type': None,
'submitter': 'jakub',
'tags': [],
'task_id': '5175150-fedora-rawhide-ppc64le',
'timeout': 115200,
'uses_devel_repo': False,
'with_opts': [],
'without_opts': []}
Running: git clone https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/python-biopython /var/lib/copr-rpmbuild/workspace/workdir-gxj1he_k/python-biopython --depth 500 --no-single-branch --recursive
cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/python-biopython', '/var/lib/copr-rpmbuild/workspace/workdir-gxj1he_k/python-biopython', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout:
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-gxj1he_k/python-biopython'...
Running: git checkout af214c487f0ec0f4dd938d0ce3cfbbe9dd7b74fa
cmd: ['git', 'checkout', 'af214c487f0ec0f4dd938d0ce3cfbbe9dd7b74fa']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-gxj1he_k/python-biopython
rc: 0
stdout:
stderr: Note: switching to 'af214c487f0ec0f4dd938d0ce3cfbbe9dd7b74fa'.
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 switching back to a branch.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:
git switch -c <new-branch-name>
Or undo this operation with:
git switch -
Turn off this advice by setting config variable advice.detachedHead to false
HEAD is now at af214c4 automatic import of python-biopython
Running: copr-distgit-client sources
cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-gxj1he_k/python-biopython
rc: 0
stdout:
stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD
INFO: Reading stdout from command: git rev-parse HEAD
INFO: Reading sources specification file: sources
INFO: Downloading biopython-1.80.tar.gz
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
INFO: Calling: curl -H Pragma: -o biopython-1.80.tar.gz --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/jakub/gcc-13-test/python-biopython/biopython-1.80.tar.gz/md5/0d1c25c9d67a29534220e03e39f69052/biopython-1.80.tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 17.0M 100 17.0M 0 0 27.5M 0 --:--:-- --:--:-- --:--:-- 27.4M
INFO: Reading stdout from command: md5sum biopython-1.80.tar.gz
Running (timeout=115200): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-gxj1he_k/python-biopython/python-biopython.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-gxj1he_k/python-biopython --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1672075344.750807 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)...
Start(bootstrap): init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish(bootstrap): init plugins
Start: init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
INFO: Signal handler active
Start: run
INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-gxj1he_k/python-biopython/python-biopython.spec) Config(fedora-rawhide-ppc64le)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1672075344.750807/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Start(bootstrap): dnf install
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Updating Subscription Management repositories.
Unable to read consumer identity
This system is not registered with an entitlement server. You can use subscription-manager to register.
Copr repository 49 MB/s | 32 MB 00:00
Additional repo https_jakub_fedorapeople_org_fe 227 kB/s | 84 kB 00:00
fedora 13 MB/s | 60 MB 00:04
Dependencies resolved.
==========================================================================================================================
Package Arch Version Repository Size
==========================================================================================================================
Installing:
dnf noarch 4.14.0-1.fc38 fedora 480 k
dnf-plugins-core noarch 4.3.1-1.fc38 fedora 34 k
Installing dependencies:
alternatives ppc64le 1.21-1.fc38 copr_base 41 k
audit-libs ppc64le 3.0.9-2.fc38 fedora 130 k
basesystem noarch 11-14.fc37 fedora 7.0 k
bash ppc64le 5.2.9-3.fc38 copr_base 1.9 M
bzip2-libs ppc64le 1.0.8-12.fc38 copr_base 48 k
ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k
coreutils ppc64le 9.1-8.fc38 copr_base 1.3 M
coreutils-common ppc64le 9.1-8.fc38 copr_base 2.0 M
crypto-policies noarch 20221215-1.gita4c31a3.fc38 fedora 90 k
curl ppc64le 7.87.0-1.fc38 copr_base 348 k
cyrus-sasl-lib ppc64le 2.1.28-8.fc38 copr_base 882 k
dbus-libs ppc64le 1:1.14.4-1.fc38 copr_base 177 k
dnf-data noarch 4.14.0-1.fc38 fedora 43 k
elfutils-default-yama-scope noarch 0.188-3.fc38 copr_base 16 k
elfutils-libelf ppc64le 0.188-3.fc38 copr_base 205 k
elfutils-libs ppc64le 0.188-3.fc38 copr_base 291 k
expat ppc64le 2.5.0-1.fc38 copr_base 117 k
fedora-gpg-keys noarch 38-0.3 fedora 125 k
fedora-release noarch 38-0.6 fedora 11 k
fedora-release-common noarch 38-0.6 fedora 21 k
fedora-release-identity-basic noarch 38-0.6 fedora 11 k
fedora-repos noarch 38-0.3 fedora 10 k
fedora-repos-rawhide noarch 38-0.3 fedora 9.7 k
file-libs ppc64le 5.42-4.fc38 copr_base 688 k
filesystem ppc64le 3.18-2.fc37 fedora 1.1 M
findutils ppc64le 1:4.9.0-2.fc38 copr_base 530 k
gawk ppc64le 5.1.1-4.fc38 copr_base 1.0 M
gdbm-libs ppc64le 1:1.23-2.fc38 copr_base 62 k
glib2 ppc64le 2.74.1-2.fc38 copr_base 2.8 M
glibc ppc64le 2.36.9000-19.fc38 fedora 2.2 M
glibc-common ppc64le 2.36.9000-19.fc38 fedora 322 k
glibc-minimal-langpack ppc64le 2.36.9000-19.fc38 fedora 30 k
gmp ppc64le 1:6.2.1-3.fc38 copr_base 304 k
gnupg2 ppc64le 2.3.8-1.fc38 copr_base 2.7 M
gnutls ppc64le 3.7.8-9.fc38 copr_base 1.1 M
gpgme ppc64le 1.17.1-3.fc38 copr_base 229 k
grep ppc64le 3.8-1.fc38 copr_base 293 k
ima-evm-utils ppc64le 1.4-6.fc38 copr_base 67 k
json-c ppc64le 0.16-3.fc38 copr_base 46 k
keyutils-libs ppc64le 1.6.1-5.fc38 copr_base 33 k
krb5-libs ppc64le 1.20.1-3.fc38 copr_base 805 k
libacl ppc64le 2.3.1-4.fc38 copr_base 26 k
libarchive ppc64le 3.6.1-3.fc38 copr_base 464 k
libassuan ppc64le 2.5.5-5.fc38 copr_base 71 k
libattr ppc64le 2.5.1-5.fc38 copr_base 19 k
libb2 ppc64le 0.98.1-7.fc38 copr_base 26 k
libblkid ppc64le 2.38.1-3.fc38 fedora 122 k
libbrotli ppc64le 1.0.9-9.fc38 copr_base 345 k
libcap ppc64le 2.48-5.fc38 copr_base 73 k
libcap-ng ppc64le 0.8.3-4.fc38 copr_base 34 k
libcom_err ppc64le 1.46.5-3.fc38 copr_base 26 k
libcomps ppc64le 0.1.18-4.fc38 copr_base 84 k
libcurl ppc64le 7.87.0-1.fc38 copr_base 334 k
libdnf ppc64le 0.68.0-1.fc38 copr_base 668 k
libevent ppc64le 2.1.12-7.fc38 copr_base 276 k
libffi ppc64le 3.4.4-1.fc38 copr_base 39 k
libfsverity ppc64le 1.4-8.fc38 copr_base 20 k
libgcc ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 88 k
libgcrypt ppc64le 1.10.1-6.fc38 copr_base 596 k
libgomp ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 314 k
libgpg-error ppc64le 1.46-1.fc38 copr_base 233 k
libidn2 ppc64le 2.3.4-1.fc38 copr_base 157 k
libksba ppc64le 1.6.3-1.fc38 copr_base 175 k
libmodulemd ppc64le 2.14.0-4.fc38 copr_base 233 k
libmount ppc64le 2.38.1-3.fc38 fedora 154 k
libnghttp2 ppc64le 1.51.0-1.fc38 copr_base 85 k
libnsl2 ppc64le 2.0.0-4.fc38 copr_base 33 k
libpsl ppc64le 0.21.1-6.fc38 copr_base 67 k
librepo ppc64le 1.15.1-1.fc38 copr_base 104 k
libreport-filesystem noarch 2.17.6-1.fc38 copr_base 14 k
libselinux ppc64le 3.4-6.fc38 copr_base 100 k
libsemanage ppc64le 3.4-6.fc38 copr_base 131 k
libsepol ppc64le 3.4-4.fc38 copr_base 355 k
libsigsegv ppc64le 2.14-3.fc38 copr_base 28 k
libsmartcols ppc64le 2.38.1-3.fc38 fedora 70 k
libsolv ppc64le 0.7.22-3.fc38 copr_base 467 k
libssh ppc64le 0.10.4-2.fc38 copr_base 236 k
libssh-config noarch 0.10.4-2.fc38 copr_base 9.2 k
libstdc++ ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 932 k
libtasn1 ppc64le 4.19.0-1.fc38 copr_base 81 k
libtirpc ppc64le 1.3.3-0.fc38 copr_base 108 k
libunistring ppc64le 1.0-2.fc38 copr_base 575 k
libuuid ppc64le 2.38.1-3.fc38 fedora 29 k
libverto ppc64le 0.3.2-4.fc38 copr_base 23 k
libxcrypt ppc64le 4.4.33-5.fc38 copr_base 133 k
libxml2 ppc64le 2.10.3-2.fc38 copr_base 780 k
libyaml ppc64le 0.2.5-8.fc38 copr_base 70 k
libzstd ppc64le 1.5.2-3.fc37 fedora 316 k
lua-libs ppc64le 5.4.4-6.fc38 copr_base 149 k
lz4-libs ppc64le 1.9.3-5.fc38 copr_base 90 k
mpdecimal ppc64le 2.5.1-4.fc38 copr_base 118 k
mpfr ppc64le 4.1.1-2.fc38 copr_base 609 k
ncurses-base noarch 6.3-5.20221126.fc38 copr_base 62 k
ncurses-libs ppc64le 6.3-5.20221126.fc38 copr_base 374 k
nettle ppc64le 3.8-2.fc38 copr_base 443 k
npth ppc64le 1.6-10.fc38 copr_base 25 k
openldap ppc64le 2.6.3-1.fc38 copr_base 288 k
openssl-libs ppc64le 1:3.0.5-6.fc38 copr_base 2.2 M
p11-kit ppc64le 0.24.1-5.fc38 copr_base 359 k
p11-kit-trust ppc64le 0.24.1-5.fc38 copr_base 150 k
pcre2 ppc64le 10.40-1.fc38.1 copr_base 242 k
pcre2-syntax noarch 10.40-1.fc38.1 copr_base 143 k
popt ppc64le 1.19-1.fc38 copr_base 64 k
publicsuffix-list-dafsa noarch 20221208-1.fc38 fedora 59 k
python-pip-wheel noarch 22.3.1-1.fc38 fedora 1.4 M
python-setuptools-wheel noarch 65.5.1-1.fc38 fedora 715 k
python3 ppc64le 3.11.1-1.fc38 fedora 27 k
python3-dateutil noarch 1:2.8.2-4.fc37 fedora 361 k
python3-dbus ppc64le 1.3.2-1.fc38 copr_base 152 k
python3-distro noarch 1.8.0-1.fc38 fedora 49 k
python3-dnf noarch 4.14.0-1.fc38 fedora 607 k
python3-dnf-plugins-core noarch 4.3.1-1.fc38 fedora 277 k
python3-gpg ppc64le 1.17.1-3.fc38 copr_base 285 k
python3-hawkey ppc64le 0.68.0-1.fc38 copr_base 109 k
python3-libcomps ppc64le 0.1.18-4.fc38 copr_base 53 k
python3-libdnf ppc64le 0.68.0-1.fc38 copr_base 815 k
python3-libs ppc64le 3.11.1-1.fc38 fedora 9.7 M
python3-rpm ppc64le 4.18.0-8.fc38 fedora 101 k
python3-six noarch 1.16.0-8.fc37 fedora 42 k
readline ppc64le 8.2-2.fc38 fedora 228 k
rpm ppc64le 4.18.0-8.fc38 fedora 568 k
rpm-build-libs ppc64le 4.18.0-8.fc38 fedora 103 k
rpm-libs ppc64le 4.18.0-8.fc38 fedora 355 k
rpm-sequoia ppc64le 1.2.0-1.fc38 fedora 1.4 M
rpm-sign-libs ppc64le 4.18.0-8.fc38 fedora 27 k
sed ppc64le 4.8-11.fc37 fedora 313 k
setup noarch 2.14.3-1.fc38 fedora 152 k
shadow-utils ppc64le 2:4.13-3.fc38 fedora 1.3 M
sqlite-libs ppc64le 3.40.0-1.fc38 fedora 776 k
systemd-libs ppc64le 252.4-598.fc38 fedora 666 k
tpm2-tss ppc64le 4.0.0-0.1.rc2.fc38 fedora 631 k
tzdata noarch 2022g-1.fc38 fedora 716 k
xz-libs ppc64le 5.2.9-1.fc38 fedora 104 k
zchunk-libs ppc64le 1.2.3-1.fc38 fedora 55 k
zlib ppc64le 1.2.13-1.fc38 fedora 100 k
Transaction Summary
==========================================================================================================================
Install 137 Packages
Total download size: 60 M
Installed size: 284 M
Downloading Packages:
(1/137): alternatives-1.21-1.fc38.ppc64le.rpm 207 kB/s | 41 kB 00:00
(2/137): bzip2-libs-1.0.8-12.fc38.ppc64le.rpm 233 kB/s | 48 kB 00:00
(3/137): bash-5.2.9-3.fc38.ppc64le.rpm 7.3 MB/s | 1.9 MB 00:00
(4/137): coreutils-9.1-8.fc38.ppc64le.rpm 20 MB/s | 1.3 MB 00:00
(5/137): coreutils-common-9.1-8.fc38.ppc64le.rp 25 MB/s | 2.0 MB 00:00
(6/137): curl-7.87.0-1.fc38.ppc64le.rpm 8.9 MB/s | 348 kB 00:00
(7/137): cyrus-sasl-lib-2.1.28-8.fc38.ppc64le.r 26 MB/s | 882 kB 00:00
(8/137): dbus-libs-1.14.4-1.fc38.ppc64le.rpm 13 MB/s | 177 kB 00:00
(9/137): elfutils-default-yama-scope-0.188-3.fc 1.7 MB/s | 16 kB 00:00
(10/137): elfutils-libelf-0.188-3.fc38.ppc64le. 17 MB/s | 205 kB 00:00
(11/137): elfutils-libs-0.188-3.fc38.ppc64le.rp 22 MB/s | 291 kB 00:00
(12/137): expat-2.5.0-1.fc38.ppc64le.rpm 11 MB/s | 117 kB 00:00
(13/137): file-libs-5.42-4.fc38.ppc64le.rpm 36 MB/s | 688 kB 00:00
(14/137): findutils-4.9.0-2.fc38.ppc64le.rpm 29 MB/s | 530 kB 00:00
(15/137): gawk-5.1.1-4.fc38.ppc64le.rpm 34 MB/s | 1.0 MB 00:00
(16/137): gdbm-libs-1.23-2.fc38.ppc64le.rpm 3.2 MB/s | 62 kB 00:00
(17/137): glib2-2.74.1-2.fc38.ppc64le.rpm 38 MB/s | 2.8 MB 00:00
(18/137): gmp-6.2.1-3.fc38.ppc64le.rpm 4.6 MB/s | 304 kB 00:00
(19/137): gnupg2-2.3.8-1.fc38.ppc64le.rpm 32 MB/s | 2.7 MB 00:00
(20/137): gpgme-1.17.1-3.fc38.ppc64le.rpm 10 MB/s | 229 kB 00:00
(21/137): gnutls-3.7.8-9.fc38.ppc64le.rpm 37 MB/s | 1.1 MB 00:00
(22/137): grep-3.8-1.fc38.ppc64le.rpm 20 MB/s | 293 kB 00:00
(23/137): ima-evm-utils-1.4-6.fc38.ppc64le.rpm 5.8 MB/s | 67 kB 00:00
(24/137): json-c-0.16-3.fc38.ppc64le.rpm 5.0 MB/s | 46 kB 00:00
(25/137): keyutils-libs-1.6.1-5.fc38.ppc64le.rp 3.4 MB/s | 33 kB 00:00
(26/137): krb5-libs-1.20.1-3.fc38.ppc64le.rpm 38 MB/s | 805 kB 00:00
(27/137): libacl-2.3.1-4.fc38.ppc64le.rpm 1.4 MB/s | 26 kB 00:00
(28/137): libarchive-3.6.1-3.fc38.ppc64le.rpm 29 MB/s | 464 kB 00:00
(29/137): libassuan-2.5.5-5.fc38.ppc64le.rpm 6.4 MB/s | 71 kB 00:00
(30/137): libattr-2.5.1-5.fc38.ppc64le.rpm 1.7 MB/s | 19 kB 00:00
(31/137): libb2-0.98.1-7.fc38.ppc64le.rpm 2.6 MB/s | 26 kB 00:00
(32/137): libbrotli-1.0.9-9.fc38.ppc64le.rpm 23 MB/s | 345 kB 00:00
(33/137): libcap-2.48-5.fc38.ppc64le.rpm 4.4 MB/s | 73 kB 00:00
(34/137): libcap-ng-0.8.3-4.fc38.ppc64le.rpm 2.2 MB/s | 34 kB 00:00
(35/137): libcom_err-1.46.5-3.fc38.ppc64le.rpm 2.5 MB/s | 26 kB 00:00
(36/137): libcomps-0.1.18-4.fc38.ppc64le.rpm 6.8 MB/s | 84 kB 00:00
(37/137): libcurl-7.87.0-1.fc38.ppc64le.rpm 20 MB/s | 334 kB 00:00
(38/137): libdnf-0.68.0-1.fc38.ppc64le.rpm 34 MB/s | 668 kB 00:00
(39/137): libevent-2.1.12-7.fc38.ppc64le.rpm 15 MB/s | 276 kB 00:00
(40/137): libffi-3.4.4-1.fc38.ppc64le.rpm 2.5 MB/s | 39 kB 00:00
(41/137): libfsverity-1.4-8.fc38.ppc64le.rpm 1.9 MB/s | 20 kB 00:00
(42/137): libgcrypt-1.10.1-6.fc38.ppc64le.rpm 30 MB/s | 596 kB 00:00
(43/137): libgpg-error-1.46-1.fc38.ppc64le.rpm 10 MB/s | 233 kB 00:00
(44/137): libidn2-2.3.4-1.fc38.ppc64le.rpm 10 MB/s | 157 kB 00:00
(45/137): libksba-1.6.3-1.fc38.ppc64le.rpm 14 MB/s | 175 kB 00:00
(46/137): libmodulemd-2.14.0-4.fc38.ppc64le.rpm 16 MB/s | 233 kB 00:00
(47/137): libnghttp2-1.51.0-1.fc38.ppc64le.rpm 5.3 MB/s | 85 kB 00:00
(48/137): libnsl2-2.0.0-4.fc38.ppc64le.rpm 3.3 MB/s | 33 kB 00:00
(49/137): libpsl-0.21.1-6.fc38.ppc64le.rpm 5.8 MB/s | 67 kB 00:00
(50/137): librepo-1.15.1-1.fc38.ppc64le.rpm 8.6 MB/s | 104 kB 00:00
(51/137): libreport-filesystem-2.17.6-1.fc38.no 1.3 MB/s | 14 kB 00:00
(52/137): libselinux-3.4-6.fc38.ppc64le.rpm 9.5 MB/s | 100 kB 00:00
(53/137): libsemanage-3.4-6.fc38.ppc64le.rpm 12 MB/s | 131 kB 00:00
(54/137): libsepol-3.4-4.fc38.ppc64le.rpm 25 MB/s | 355 kB 00:00
(55/137): libsigsegv-2.14-3.fc38.ppc64le.rpm 2.9 MB/s | 28 kB 00:00
(56/137): libsolv-0.7.22-3.fc38.ppc64le.rpm 29 MB/s | 467 kB 00:00
(57/137): libssh-0.10.4-2.fc38.ppc64le.rpm 17 MB/s | 236 kB 00:00
(58/137): libssh-config-0.10.4-2.fc38.noarch.rp 874 kB/s | 9.2 kB 00:00
(59/137): libtasn1-4.19.0-1.fc38.ppc64le.rpm 7.7 MB/s | 81 kB 00:00
(60/137): libtirpc-1.3.3-0.fc38.ppc64le.rpm 9.5 MB/s | 108 kB 00:00
(61/137): libunistring-1.0-2.fc38.ppc64le.rpm 29 MB/s | 575 kB 00:00
(62/137): libverto-0.3.2-4.fc38.ppc64le.rpm 1.9 MB/s | 23 kB 00:00
(63/137): libxcrypt-4.4.33-5.fc38.ppc64le.rpm 12 MB/s | 133 kB 00:00
(64/137): libxml2-2.10.3-2.fc38.ppc64le.rpm 37 MB/s | 780 kB 00:00
(65/137): libyaml-0.2.5-8.fc38.ppc64le.rpm 3.2 MB/s | 70 kB 00:00
(66/137): lua-libs-5.4.4-6.fc38.ppc64le.rpm 7.1 MB/s | 149 kB 00:00
(67/137): lz4-libs-1.9.3-5.fc38.ppc64le.rpm 8.4 MB/s | 90 kB 00:00
(68/137): mpdecimal-2.5.1-4.fc38.ppc64le.rpm 11 MB/s | 118 kB 00:00
(69/137): mpfr-4.1.1-2.fc38.ppc64le.rpm 32 MB/s | 609 kB 00:00
(70/137): ncurses-base-6.3-5.20221126.fc38.noar 5.4 MB/s | 62 kB 00:00
(71/137): ncurses-libs-6.3-5.20221126.fc38.ppc6 25 MB/s | 374 kB 00:00
(72/137): nettle-3.8-2.fc38.ppc64le.rpm 27 MB/s | 443 kB 00:00
(73/137): npth-1.6-10.fc38.ppc64le.rpm 1.6 MB/s | 25 kB 00:00
(74/137): openldap-2.6.3-1.fc38.ppc64le.rpm 18 MB/s | 288 kB 00:00
(75/137): openssl-libs-3.0.5-6.fc38.ppc64le.rpm 39 MB/s | 2.2 MB 00:00
(76/137): p11-kit-0.24.1-5.fc38.ppc64le.rpm 5.7 MB/s | 359 kB 00:00
(77/137): p11-kit-trust-0.24.1-5.fc38.ppc64le.r 2.6 MB/s | 150 kB 00:00
(78/137): pcre2-10.40-1.fc38.1.ppc64le.rpm 16 MB/s | 242 kB 00:00
(79/137): pcre2-syntax-10.40-1.fc38.1.noarch.rp 10 MB/s | 143 kB 00:00
(80/137): popt-1.19-1.fc38.ppc64le.rpm 4.4 MB/s | 64 kB 00:00
(81/137): python3-dbus-1.3.2-1.fc38.ppc64le.rpm 12 MB/s | 152 kB 00:00
(82/137): python3-gpg-1.17.1-3.fc38.ppc64le.rpm 16 MB/s | 285 kB 00:00
(83/137): python3-hawkey-0.68.0-1.fc38.ppc64le. 5.9 MB/s | 109 kB 00:00
(84/137): python3-libcomps-0.1.18-4.fc38.ppc64l 5.4 MB/s | 53 kB 00:00
(85/137): python3-libdnf-0.68.0-1.fc38.ppc64le. 5.8 MB/s | 815 kB 00:00
(86/137): libgomp-13.0.0-0.4.fc38.ppc64le.rpm 1.2 MB/s | 314 kB 00:00
(87/137): libgcc-13.0.0-0.4.fc38.ppc64le.rpm 333 kB/s | 88 kB 00:00
(88/137): libstdc++-13.0.0-0.4.fc38.ppc64le.rpm 4.1 MB/s | 932 kB 00:00
(89/137): basesystem-11-14.fc37.noarch.rpm 48 kB/s | 7.0 kB 00:00
(90/137): crypto-policies-20221215-1.gita4c31a3 367 kB/s | 90 kB 00:00
(91/137): audit-libs-3.0.9-2.fc38.ppc64le.rpm 328 kB/s | 130 kB 00:00
(92/137): dnf-data-4.14.0-1.fc38.noarch.rpm 485 kB/s | 43 kB 00:00
(93/137): dnf-plugins-core-4.3.1-1.fc38.noarch. 406 kB/s | 34 kB 00:00
(94/137): dnf-4.14.0-1.fc38.noarch.rpm 1.7 MB/s | 480 kB 00:00
(95/137): ca-certificates-2022.2.54-5.fc37.noar 1.4 MB/s | 829 kB 00:00
(96/137): fedora-gpg-keys-38-0.3.noarch.rpm 1.0 MB/s | 125 kB 00:00
(97/137): fedora-release-38-0.6.noarch.rpm 145 kB/s | 11 kB 00:00
(98/137): fedora-release-identity-basic-38-0.6. 159 kB/s | 11 kB 00:00
(99/137): fedora-release-common-38-0.6.noarch.r 275 kB/s | 21 kB 00:00
(100/137): fedora-repos-38-0.3.noarch.rpm 137 kB/s | 10 kB 00:00
(101/137): fedora-repos-rawhide-38-0.3.noarch.r 133 kB/s | 9.7 kB 00:00
(102/137): glibc-common-2.36.9000-19.fc38.ppc64 3.4 MB/s | 322 kB 00:00
(103/137): glibc-minimal-langpack-2.36.9000-19. 416 kB/s | 30 kB 00:00
(104/137): filesystem-3.18-2.fc37.ppc64le.rpm 3.6 MB/s | 1.1 MB 00:00
(105/137): glibc-2.36.9000-19.fc38.ppc64le.rpm 8.0 MB/s | 2.2 MB 00:00
(106/137): libblkid-2.38.1-3.fc38.ppc64le.rpm 1.4 MB/s | 122 kB 00:00
(107/137): libmount-2.38.1-3.fc38.ppc64le.rpm 1.9 MB/s | 154 kB 00:00
(108/137): libsmartcols-2.38.1-3.fc38.ppc64le.r 944 kB/s | 70 kB 00:00
(109/137): libuuid-2.38.1-3.fc38.ppc64le.rpm 393 kB/s | 29 kB 00:00
(110/137): libzstd-1.5.2-3.fc37.ppc64le.rpm 3.6 MB/s | 316 kB 00:00
(111/137): publicsuffix-list-dafsa-20221208-1.f 774 kB/s | 59 kB 00:00
(112/137): python3-3.11.1-1.fc38.ppc64le.rpm 375 kB/s | 27 kB 00:00
(113/137): python-pip-wheel-22.3.1-1.fc38.noarc 8.5 MB/s | 1.4 MB 00:00
(114/137): python-setuptools-wheel-65.5.1-1.fc3 6.7 MB/s | 715 kB 00:00
(115/137): python3-dateutil-2.8.2-4.fc37.noarch 4.3 MB/s | 361 kB 00:00
(116/137): python3-distro-1.8.0-1.fc38.noarch.r 685 kB/s | 49 kB 00:00
(117/137): python3-dnf-4.14.0-1.fc38.noarch.rpm 6.0 MB/s | 607 kB 00:00
(118/137): python3-dnf-plugins-core-4.3.1-1.fc3 3.4 MB/s | 277 kB 00:00
(119/137): python3-rpm-4.18.0-8.fc38.ppc64le.rp 1.3 MB/s | 101 kB 00:00
(120/137): python3-six-1.16.0-8.fc37.noarch.rpm 566 kB/s | 42 kB 00:00
(121/137): readline-8.2-2.fc38.ppc64le.rpm 2.7 MB/s | 228 kB 00:00
(122/137): rpm-4.18.0-8.fc38.ppc64le.rpm 6.4 MB/s | 568 kB 00:00
(123/137): rpm-build-libs-4.18.0-8.fc38.ppc64le 1.3 MB/s | 103 kB 00:00
(124/137): rpm-libs-4.18.0-8.fc38.ppc64le.rpm 4.2 MB/s | 355 kB 00:00
(125/137): python3-libs-3.11.1-1.fc38.ppc64le.r 25 MB/s | 9.7 MB 00:00
(126/137): rpm-sign-libs-4.18.0-8.fc38.ppc64le. 370 kB/s | 27 kB 00:00
(127/137): rpm-sequoia-1.2.0-1.fc38.ppc64le.rpm 10 MB/s | 1.4 MB 00:00
(128/137): sed-4.8-11.fc37.ppc64le.rpm 4.0 MB/s | 313 kB 00:00
(129/137): setup-2.14.3-1.fc38.noarch.rpm 2.0 MB/s | 152 kB 00:00
(130/137): shadow-utils-4.13-3.fc38.ppc64le.rpm 11 MB/s | 1.3 MB 00:00
(131/137): sqlite-libs-3.40.0-1.fc38.ppc64le.rp 9.1 MB/s | 776 kB 00:00
(132/137): systemd-libs-252.4-598.fc38.ppc64le. 7.2 MB/s | 666 kB 00:00
(133/137): tpm2-tss-4.0.0-0.1.rc2.fc38.ppc64le. 6.5 MB/s | 631 kB 00:00
(134/137): tzdata-2022g-1.fc38.noarch.rpm 8.0 MB/s | 716 kB 00:00
(135/137): xz-libs-5.2.9-1.fc38.ppc64le.rpm 1.3 MB/s | 104 kB 00:00
(136/137): zchunk-libs-1.2.3-1.fc38.ppc64le.rpm 750 kB/s | 55 kB 00:00
(137/137): zlib-1.2.13-1.fc38.ppc64le.rpm 1.3 MB/s | 100 kB 00:00
--------------------------------------------------------------------------------
Total 18 MB/s | 60 MB 00:03
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0xEB10B464:
Userid : "Fedora (38) <fedora-38-primary@fedoraproject.org>"
Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary
Key imported successfully
fedora 1.6 MB/s | 1.6 kB 00:00
GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary (0xEB10B464) is already installed
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0x5323552A:
Userid : "Fedora (37) <fedora-37-primary@fedoraproject.org>"
Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Running scriptlet: filesystem-3.18-2.fc37.ppc64le 1/1
Preparing : 1/1
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Running scriptlet: crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/137
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Installing : glibc-minimal-langpack-2.36.9000-19.fc38.ppc64le 21/137
Installing : zlib-1.2.13-1.fc38.ppc64le 22/137
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Installing : libzstd-1.5.2-3.fc37.ppc64le 25/137
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warning: /etc/dnf/dnf.conf created as /etc/dnf/dnf.conf.rpmnew
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useradd: Warning: missing or non-executable shell '/usr/sbin/nologin'
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Verifying : gpgme-1.17.1-3.fc38.ppc64le 21/137
Verifying : grep-3.8-1.fc38.ppc64le 22/137
Verifying : ima-evm-utils-1.4-6.fc38.ppc64le 23/137
Verifying : json-c-0.16-3.fc38.ppc64le 24/137
Verifying : keyutils-libs-1.6.1-5.fc38.ppc64le 25/137
Verifying : krb5-libs-1.20.1-3.fc38.ppc64le 26/137
Verifying : libacl-2.3.1-4.fc38.ppc64le 27/137
Verifying : libarchive-3.6.1-3.fc38.ppc64le 28/137
Verifying : libassuan-2.5.5-5.fc38.ppc64le 29/137
Verifying : libattr-2.5.1-5.fc38.ppc64le 30/137
Verifying : libb2-0.98.1-7.fc38.ppc64le 31/137
Verifying : libbrotli-1.0.9-9.fc38.ppc64le 32/137
Verifying : libcap-2.48-5.fc38.ppc64le 33/137
Verifying : libcap-ng-0.8.3-4.fc38.ppc64le 34/137
Verifying : libcom_err-1.46.5-3.fc38.ppc64le 35/137
Verifying : libcomps-0.1.18-4.fc38.ppc64le 36/137
Verifying : libcurl-7.87.0-1.fc38.ppc64le 37/137
Verifying : libdnf-0.68.0-1.fc38.ppc64le 38/137
Verifying : libevent-2.1.12-7.fc38.ppc64le 39/137
Verifying : libffi-3.4.4-1.fc38.ppc64le 40/137
Verifying : libfsverity-1.4-8.fc38.ppc64le 41/137
Verifying : libgcrypt-1.10.1-6.fc38.ppc64le 42/137
Verifying : libgpg-error-1.46-1.fc38.ppc64le 43/137
Verifying : libidn2-2.3.4-1.fc38.ppc64le 44/137
Verifying : libksba-1.6.3-1.fc38.ppc64le 45/137
Verifying : libmodulemd-2.14.0-4.fc38.ppc64le 46/137
Verifying : libnghttp2-1.51.0-1.fc38.ppc64le 47/137
Verifying : libnsl2-2.0.0-4.fc38.ppc64le 48/137
Verifying : libpsl-0.21.1-6.fc38.ppc64le 49/137
Verifying : librepo-1.15.1-1.fc38.ppc64le 50/137
Verifying : libreport-filesystem-2.17.6-1.fc38.noarch 51/137
Verifying : libselinux-3.4-6.fc38.ppc64le 52/137
Verifying : libsemanage-3.4-6.fc38.ppc64le 53/137
Verifying : libsepol-3.4-4.fc38.ppc64le 54/137
Verifying : libsigsegv-2.14-3.fc38.ppc64le 55/137
Verifying : libsolv-0.7.22-3.fc38.ppc64le 56/137
Verifying : libssh-0.10.4-2.fc38.ppc64le 57/137
Verifying : libssh-config-0.10.4-2.fc38.noarch 58/137
Verifying : libtasn1-4.19.0-1.fc38.ppc64le 59/137
Verifying : libtirpc-1.3.3-0.fc38.ppc64le 60/137
Verifying : libunistring-1.0-2.fc38.ppc64le 61/137
Verifying : libverto-0.3.2-4.fc38.ppc64le 62/137
Verifying : libxcrypt-4.4.33-5.fc38.ppc64le 63/137
Verifying : libxml2-2.10.3-2.fc38.ppc64le 64/137
Verifying : libyaml-0.2.5-8.fc38.ppc64le 65/137
Verifying : lua-libs-5.4.4-6.fc38.ppc64le 66/137
Verifying : lz4-libs-1.9.3-5.fc38.ppc64le 67/137
Verifying : mpdecimal-2.5.1-4.fc38.ppc64le 68/137
Verifying : mpfr-4.1.1-2.fc38.ppc64le 69/137
Verifying : ncurses-base-6.3-5.20221126.fc38.noarch 70/137
Verifying : ncurses-libs-6.3-5.20221126.fc38.ppc64le 71/137
Verifying : nettle-3.8-2.fc38.ppc64le 72/137
Verifying : npth-1.6-10.fc38.ppc64le 73/137
Verifying : openldap-2.6.3-1.fc38.ppc64le 74/137
Verifying : openssl-libs-1:3.0.5-6.fc38.ppc64le 75/137
Verifying : p11-kit-0.24.1-5.fc38.ppc64le 76/137
Verifying : p11-kit-trust-0.24.1-5.fc38.ppc64le 77/137
Verifying : pcre2-10.40-1.fc38.1.ppc64le 78/137
Verifying : pcre2-syntax-10.40-1.fc38.1.noarch 79/137
Verifying : popt-1.19-1.fc38.ppc64le 80/137
Verifying : python3-dbus-1.3.2-1.fc38.ppc64le 81/137
Verifying : python3-gpg-1.17.1-3.fc38.ppc64le 82/137
Verifying : python3-hawkey-0.68.0-1.fc38.ppc64le 83/137
Verifying : python3-libcomps-0.1.18-4.fc38.ppc64le 84/137
Verifying : python3-libdnf-0.68.0-1.fc38.ppc64le 85/137
Verifying : libgcc-13.0.0-0.4.fc38.ppc64le 86/137
Verifying : libgomp-13.0.0-0.4.fc38.ppc64le 87/137
Verifying : libstdc++-13.0.0-0.4.fc38.ppc64le 88/137
Verifying : audit-libs-3.0.9-2.fc38.ppc64le 89/137
Verifying : basesystem-11-14.fc37.noarch 90/137
Verifying : ca-certificates-2022.2.54-5.fc37.noarch 91/137
Verifying : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 92/137
Verifying : dnf-4.14.0-1.fc38.noarch 93/137
Verifying : dnf-data-4.14.0-1.fc38.noarch 94/137
Verifying : dnf-plugins-core-4.3.1-1.fc38.noarch 95/137
Verifying : fedora-gpg-keys-38-0.3.noarch 96/137
Verifying : fedora-release-38-0.6.noarch 97/137
Verifying : fedora-release-common-38-0.6.noarch 98/137
Verifying : fedora-release-identity-basic-38-0.6.noarch 99/137
Verifying : fedora-repos-38-0.3.noarch 100/137
Verifying : fedora-repos-rawhide-38-0.3.noarch 101/137
Verifying : filesystem-3.18-2.fc37.ppc64le 102/137
Verifying : glibc-2.36.9000-19.fc38.ppc64le 103/137
Verifying : glibc-common-2.36.9000-19.fc38.ppc64le 104/137
Verifying : glibc-minimal-langpack-2.36.9000-19.fc38.ppc64le 105/137
Verifying : libblkid-2.38.1-3.fc38.ppc64le 106/137
Verifying : libmount-2.38.1-3.fc38.ppc64le 107/137
Verifying : libsmartcols-2.38.1-3.fc38.ppc64le 108/137
Verifying : libuuid-2.38.1-3.fc38.ppc64le 109/137
Verifying : libzstd-1.5.2-3.fc37.ppc64le 110/137
Verifying : publicsuffix-list-dafsa-20221208-1.fc38.noarch 111/137
Verifying : python-pip-wheel-22.3.1-1.fc38.noarch 112/137
Verifying : python-setuptools-wheel-65.5.1-1.fc38.noarch 113/137
Verifying : python3-3.11.1-1.fc38.ppc64le 114/137
Verifying : python3-dateutil-1:2.8.2-4.fc37.noarch 115/137
Verifying : python3-distro-1.8.0-1.fc38.noarch 116/137
Verifying : python3-dnf-4.14.0-1.fc38.noarch 117/137
Verifying : python3-dnf-plugins-core-4.3.1-1.fc38.noarch 118/137
Verifying : python3-libs-3.11.1-1.fc38.ppc64le 119/137
Verifying : python3-rpm-4.18.0-8.fc38.ppc64le 120/137
Verifying : python3-six-1.16.0-8.fc37.noarch 121/137
Verifying : readline-8.2-2.fc38.ppc64le 122/137
Verifying : rpm-4.18.0-8.fc38.ppc64le 123/137
Verifying : rpm-build-libs-4.18.0-8.fc38.ppc64le 124/137
Verifying : rpm-libs-4.18.0-8.fc38.ppc64le 125/137
Verifying : rpm-sequoia-1.2.0-1.fc38.ppc64le 126/137
Verifying : rpm-sign-libs-4.18.0-8.fc38.ppc64le 127/137
Verifying : sed-4.8-11.fc37.ppc64le 128/137
Verifying : setup-2.14.3-1.fc38.noarch 129/137
Verifying : shadow-utils-2:4.13-3.fc38.ppc64le 130/137
Verifying : sqlite-libs-3.40.0-1.fc38.ppc64le 131/137
Verifying : systemd-libs-252.4-598.fc38.ppc64le 132/137
Verifying : tpm2-tss-4.0.0-0.1.rc2.fc38.ppc64le 133/137
Verifying : tzdata-2022g-1.fc38.noarch 134/137
Verifying : xz-libs-5.2.9-1.fc38.ppc64le 135/137
Verifying : zchunk-libs-1.2.3-1.fc38.ppc64le 136/137
Verifying : zlib-1.2.13-1.fc38.ppc64le 137/137
Installed products updated.
Installed:
alternatives-1.21-1.fc38.ppc64le
audit-libs-3.0.9-2.fc38.ppc64le
basesystem-11-14.fc37.noarch
bash-5.2.9-3.fc38.ppc64le
bzip2-libs-1.0.8-12.fc38.ppc64le
ca-certificates-2022.2.54-5.fc37.noarch
coreutils-9.1-8.fc38.ppc64le
coreutils-common-9.1-8.fc38.ppc64le
crypto-policies-20221215-1.gita4c31a3.fc38.noarch
curl-7.87.0-1.fc38.ppc64le
cyrus-sasl-lib-2.1.28-8.fc38.ppc64le
dbus-libs-1:1.14.4-1.fc38.ppc64le
dnf-4.14.0-1.fc38.noarch
dnf-data-4.14.0-1.fc38.noarch
dnf-plugins-core-4.3.1-1.fc38.noarch
elfutils-default-yama-scope-0.188-3.fc38.noarch
elfutils-libelf-0.188-3.fc38.ppc64le
elfutils-libs-0.188-3.fc38.ppc64le
expat-2.5.0-1.fc38.ppc64le
fedora-gpg-keys-38-0.3.noarch
fedora-release-38-0.6.noarch
fedora-release-common-38-0.6.noarch
fedora-release-identity-basic-38-0.6.noarch
fedora-repos-38-0.3.noarch
fedora-repos-rawhide-38-0.3.noarch
file-libs-5.42-4.fc38.ppc64le
filesystem-3.18-2.fc37.ppc64le
findutils-1:4.9.0-2.fc38.ppc64le
gawk-5.1.1-4.fc38.ppc64le
gdbm-libs-1:1.23-2.fc38.ppc64le
glib2-2.74.1-2.fc38.ppc64le
glibc-2.36.9000-19.fc38.ppc64le
glibc-common-2.36.9000-19.fc38.ppc64le
glibc-minimal-langpack-2.36.9000-19.fc38.ppc64le
gmp-1:6.2.1-3.fc38.ppc64le
gnupg2-2.3.8-1.fc38.ppc64le
gnutls-3.7.8-9.fc38.ppc64le
gpgme-1.17.1-3.fc38.ppc64le
grep-3.8-1.fc38.ppc64le
ima-evm-utils-1.4-6.fc38.ppc64le
json-c-0.16-3.fc38.ppc64le
keyutils-libs-1.6.1-5.fc38.ppc64le
krb5-libs-1.20.1-3.fc38.ppc64le
libacl-2.3.1-4.fc38.ppc64le
libarchive-3.6.1-3.fc38.ppc64le
libassuan-2.5.5-5.fc38.ppc64le
libattr-2.5.1-5.fc38.ppc64le
libb2-0.98.1-7.fc38.ppc64le
libblkid-2.38.1-3.fc38.ppc64le
libbrotli-1.0.9-9.fc38.ppc64le
libcap-2.48-5.fc38.ppc64le
libcap-ng-0.8.3-4.fc38.ppc64le
libcom_err-1.46.5-3.fc38.ppc64le
libcomps-0.1.18-4.fc38.ppc64le
libcurl-7.87.0-1.fc38.ppc64le
libdnf-0.68.0-1.fc38.ppc64le
libevent-2.1.12-7.fc38.ppc64le
libffi-3.4.4-1.fc38.ppc64le
libfsverity-1.4-8.fc38.ppc64le
libgcc-13.0.0-0.4.fc38.ppc64le
libgcrypt-1.10.1-6.fc38.ppc64le
libgomp-13.0.0-0.4.fc38.ppc64le
libgpg-error-1.46-1.fc38.ppc64le
libidn2-2.3.4-1.fc38.ppc64le
libksba-1.6.3-1.fc38.ppc64le
libmodulemd-2.14.0-4.fc38.ppc64le
libmount-2.38.1-3.fc38.ppc64le
libnghttp2-1.51.0-1.fc38.ppc64le
libnsl2-2.0.0-4.fc38.ppc64le
libpsl-0.21.1-6.fc38.ppc64le
librepo-1.15.1-1.fc38.ppc64le
libreport-filesystem-2.17.6-1.fc38.noarch
libselinux-3.4-6.fc38.ppc64le
libsemanage-3.4-6.fc38.ppc64le
libsepol-3.4-4.fc38.ppc64le
libsigsegv-2.14-3.fc38.ppc64le
libsmartcols-2.38.1-3.fc38.ppc64le
libsolv-0.7.22-3.fc38.ppc64le
libssh-0.10.4-2.fc38.ppc64le
libssh-config-0.10.4-2.fc38.noarch
libstdc++-13.0.0-0.4.fc38.ppc64le
libtasn1-4.19.0-1.fc38.ppc64le
libtirpc-1.3.3-0.fc38.ppc64le
libunistring-1.0-2.fc38.ppc64le
libuuid-2.38.1-3.fc38.ppc64le
libverto-0.3.2-4.fc38.ppc64le
libxcrypt-4.4.33-5.fc38.ppc64le
libxml2-2.10.3-2.fc38.ppc64le
libyaml-0.2.5-8.fc38.ppc64le
libzstd-1.5.2-3.fc37.ppc64le
lua-libs-5.4.4-6.fc38.ppc64le
lz4-libs-1.9.3-5.fc38.ppc64le
mpdecimal-2.5.1-4.fc38.ppc64le
mpfr-4.1.1-2.fc38.ppc64le
ncurses-base-6.3-5.20221126.fc38.noarch
ncurses-libs-6.3-5.20221126.fc38.ppc64le
nettle-3.8-2.fc38.ppc64le
npth-1.6-10.fc38.ppc64le
openldap-2.6.3-1.fc38.ppc64le
openssl-libs-1:3.0.5-6.fc38.ppc64le
p11-kit-0.24.1-5.fc38.ppc64le
p11-kit-trust-0.24.1-5.fc38.ppc64le
pcre2-10.40-1.fc38.1.ppc64le
pcre2-syntax-10.40-1.fc38.1.noarch
popt-1.19-1.fc38.ppc64le
publicsuffix-list-dafsa-20221208-1.fc38.noarch
python-pip-wheel-22.3.1-1.fc38.noarch
python-setuptools-wheel-65.5.1-1.fc38.noarch
python3-3.11.1-1.fc38.ppc64le
python3-dateutil-1:2.8.2-4.fc37.noarch
python3-dbus-1.3.2-1.fc38.ppc64le
python3-distro-1.8.0-1.fc38.noarch
python3-dnf-4.14.0-1.fc38.noarch
python3-dnf-plugins-core-4.3.1-1.fc38.noarch
python3-gpg-1.17.1-3.fc38.ppc64le
python3-hawkey-0.68.0-1.fc38.ppc64le
python3-libcomps-0.1.18-4.fc38.ppc64le
python3-libdnf-0.68.0-1.fc38.ppc64le
python3-libs-3.11.1-1.fc38.ppc64le
python3-rpm-4.18.0-8.fc38.ppc64le
python3-six-1.16.0-8.fc37.noarch
readline-8.2-2.fc38.ppc64le
rpm-4.18.0-8.fc38.ppc64le
rpm-build-libs-4.18.0-8.fc38.ppc64le
rpm-libs-4.18.0-8.fc38.ppc64le
rpm-sequoia-1.2.0-1.fc38.ppc64le
rpm-sign-libs-4.18.0-8.fc38.ppc64le
sed-4.8-11.fc37.ppc64le
setup-2.14.3-1.fc38.noarch
shadow-utils-2:4.13-3.fc38.ppc64le
sqlite-libs-3.40.0-1.fc38.ppc64le
systemd-libs-252.4-598.fc38.ppc64le
tpm2-tss-4.0.0-0.1.rc2.fc38.ppc64le
tzdata-2022g-1.fc38.noarch
xz-libs-5.2.9-1.fc38.ppc64le
zchunk-libs-1.2.3-1.fc38.ppc64le
zlib-1.2.13-1.fc38.ppc64le
Complete!
Finish(bootstrap): dnf install
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-1672075344.750807/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Start: dnf install
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 10 kB/s | 3.0 kB 00:00
Copr repository 27 MB/s | 32 MB 00:01
Additional repo https_jakub_fedorapeople_org_fe 8.8 kB/s | 3.0 kB 00:00
fedora 74 kB/s | 6.7 kB 00:00
Dependencies resolved.
==========================================================================================================================
Package Arch Version Repository Size
==========================================================================================================================
Installing group/module packages:
bash ppc64le 5.2.9-3.fc38 copr_base 1.9 M
bzip2 ppc64le 1.0.8-12.fc38 copr_base 54 k
coreutils ppc64le 9.1-8.fc38 copr_base 1.3 M
cpio ppc64le 2.13-13.fc38 copr_base 277 k
diffutils ppc64le 3.8-3.fc38 copr_base 381 k
fedora-release-common noarch 38-0.6 fedora 21 k
findutils ppc64le 1:4.9.0-2.fc38 copr_base 530 k
gawk ppc64le 5.1.1-4.fc38 copr_base 1.0 M
glibc-minimal-langpack ppc64le 2.36.9000-19.fc38 fedora 30 k
grep ppc64le 3.8-1.fc38 copr_base 293 k
gzip ppc64le 1.12-2.fc38 copr_base 163 k
info ppc64le 7.0.1-1.fc38 fedora 199 k
patch ppc64le 2.7.6-17.fc38 copr_base 136 k
redhat-rpm-config noarch 235-1.fc38 fedora 80 k
rpm-build ppc64le 4.18.0-8.fc38 fedora 78 k
sed ppc64le 4.8-11.fc37 fedora 313 k
shadow-utils ppc64le 2:4.13-3.fc38 fedora 1.3 M
tar ppc64le 2:1.34-5.fc38 fedora 914 k
unzip ppc64le 6.0-58.fc38 fedora 188 k
util-linux ppc64le 2.38.1-3.fc38 fedora 2.4 M
which ppc64le 2.21-36.fc38 fedora 42 k
xz ppc64le 5.2.9-1.fc38 fedora 310 k
Installing dependencies:
alternatives ppc64le 1.21-1.fc38 copr_base 41 k
ansible-srpm-macros noarch 1-8.1.fc38 fedora 8.6 k
audit-libs ppc64le 3.0.9-2.fc38 fedora 130 k
authselect ppc64le 1.4.2-1.fc38 copr_base 141 k
authselect-libs ppc64le 1.4.2-1.fc38 copr_base 241 k
basesystem noarch 11-14.fc37 fedora 7.0 k
binutils ppc64le 2.39-6.fc38 copr_base 6.2 M
binutils-gold ppc64le 2.39-6.fc38 copr_base 1.1 M
bzip2-libs ppc64le 1.0.8-12.fc38 copr_base 48 k
ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k
coreutils-common ppc64le 9.1-8.fc38 copr_base 2.0 M
cracklib ppc64le 2.9.7-30.fc38 copr_base 84 k
crypto-policies noarch 20221215-1.gita4c31a3.fc38 fedora 90 k
curl ppc64le 7.87.0-1.fc38 copr_base 348 k
cyrus-sasl-lib ppc64le 2.1.28-8.fc38 copr_base 882 k
debugedit ppc64le 5.0-5.fc37 fedora 80 k
dwz ppc64le 0.15-1.fc38 copr_base 143 k
ed ppc64le 1.18-2.fc38 copr_base 82 k
efi-srpm-macros noarch 5-6.fc37 fedora 22 k
elfutils ppc64le 0.188-3.fc38 copr_base 555 k
elfutils-debuginfod-client ppc64le 0.188-3.fc38 copr_base 42 k
elfutils-default-yama-scope noarch 0.188-3.fc38 copr_base 16 k
elfutils-libelf ppc64le 0.188-3.fc38 copr_base 205 k
elfutils-libs ppc64le 0.188-3.fc38 copr_base 291 k
fedora-gpg-keys noarch 38-0.3 fedora 125 k
fedora-release noarch 38-0.6 fedora 11 k
fedora-release-identity-basic noarch 38-0.6 fedora 11 k
fedora-repos noarch 38-0.3 fedora 10 k
fedora-repos-rawhide noarch 38-0.3 fedora 9.7 k
file ppc64le 5.42-4.fc38 copr_base 50 k
file-libs ppc64le 5.42-4.fc38 copr_base 688 k
filesystem ppc64le 3.18-2.fc37 fedora 1.1 M
fonts-srpm-macros noarch 1:2.0.5-10.fc38 fedora 26 k
fpc-srpm-macros noarch 1.3-6.fc37 fedora 7.7 k
gdb-minimal ppc64le 12.1-10.fc38 fedora 3.7 M
gdbm-libs ppc64le 1:1.23-2.fc38 copr_base 62 k
ghc-srpm-macros noarch 1.5.0-7.fc37 fedora 7.8 k
glibc ppc64le 2.36.9000-19.fc38 fedora 2.2 M
glibc-common ppc64le 2.36.9000-19.fc38 fedora 322 k
glibc-gconv-extra ppc64le 2.36.9000-19.fc38 fedora 1.9 M
gmp ppc64le 1:6.2.1-3.fc38 copr_base 304 k
gnat-srpm-macros noarch 4-16.fc37 fedora 8.3 k
go-srpm-macros noarch 3.2.0-1.fc38 fedora 27 k
jansson ppc64le 2.13.1-5.fc38 copr_base 50 k
kernel-srpm-macros noarch 1.0-15.fc37 fedora 9.4 k
keyutils-libs ppc64le 1.6.1-5.fc38 copr_base 33 k
krb5-libs ppc64le 1.20.1-3.fc38 copr_base 805 k
libacl ppc64le 2.3.1-4.fc38 copr_base 26 k
libarchive ppc64le 3.6.1-3.fc38 copr_base 464 k
libattr ppc64le 2.5.1-5.fc38 copr_base 19 k
libblkid ppc64le 2.38.1-3.fc38 fedora 122 k
libbrotli ppc64le 1.0.9-9.fc38 copr_base 345 k
libcap ppc64le 2.48-5.fc38 copr_base 73 k
libcap-ng ppc64le 0.8.3-4.fc38 copr_base 34 k
libcom_err ppc64le 1.46.5-3.fc38 copr_base 26 k
libcurl ppc64le 7.87.0-1.fc38 copr_base 334 k
libdb ppc64le 5.3.28-54.fc38 copr_base 842 k
libeconf ppc64le 0.4.0-4.fc38 copr_base 31 k
libevent ppc64le 2.1.12-7.fc38 copr_base 276 k
libfdisk ppc64le 2.38.1-3.fc38 fedora 176 k
libffi ppc64le 3.4.4-1.fc38 copr_base 39 k
libgcc ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 88 k
libgomp ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 314 k
libidn2 ppc64le 2.3.4-1.fc38 copr_base 157 k
libmount ppc64le 2.38.1-3.fc38 fedora 154 k
libnghttp2 ppc64le 1.51.0-1.fc38 copr_base 85 k
libnsl2 ppc64le 2.0.0-4.fc38 copr_base 33 k
libpkgconf ppc64le 1.8.0-3.fc38 copr_base 40 k
libpsl ppc64le 0.21.1-6.fc38 copr_base 67 k
libpwquality ppc64le 1.4.5-1.fc38 fedora 122 k
librtas ppc64le 2.0.3-1.fc38 copr_base 68 k
libselinux ppc64le 3.4-6.fc38 copr_base 100 k
libsemanage ppc64le 3.4-6.fc38 copr_base 131 k
libsepol ppc64le 3.4-4.fc38 copr_base 355 k
libsigsegv ppc64le 2.14-3.fc38 copr_base 28 k
libsmartcols ppc64le 2.38.1-3.fc38 fedora 70 k
libssh ppc64le 0.10.4-2.fc38 copr_base 236 k
libssh-config noarch 0.10.4-2.fc38 copr_base 9.2 k
libstdc++ ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 932 k
libtasn1 ppc64le 4.19.0-1.fc38 copr_base 81 k
libtirpc ppc64le 1.3.3-0.fc38 copr_base 108 k
libunistring ppc64le 1.0-2.fc38 copr_base 575 k
libutempter ppc64le 1.2.1-7.fc38 copr_base 27 k
libuuid ppc64le 2.38.1-3.fc38 fedora 29 k
libverto ppc64le 0.3.2-4.fc38 copr_base 23 k
libxcrypt ppc64le 4.4.33-5.fc38 copr_base 133 k
libxml2 ppc64le 2.10.3-2.fc38 copr_base 780 k
libzstd ppc64le 1.5.2-3.fc37 fedora 316 k
lua-libs ppc64le 5.4.4-6.fc38 copr_base 149 k
lua-srpm-macros noarch 1-7.fc37 fedora 8.8 k
lz4-libs ppc64le 1.9.3-5.fc38 copr_base 90 k
mpfr ppc64le 4.1.1-2.fc38 copr_base 609 k
ncurses-base noarch 6.3-5.20221126.fc38 copr_base 62 k
ncurses-libs ppc64le 6.3-5.20221126.fc38 copr_base 374 k
nettle ppc64le 3.8-2.fc38 copr_base 443 k
nim-srpm-macros noarch 3-7.fc37 fedora 8.4 k
ocaml-srpm-macros noarch 7-2.fc37 fedora 13 k
openblas-srpm-macros noarch 2-12.fc37 fedora 7.5 k
openldap ppc64le 2.6.3-1.fc38 copr_base 288 k
openssl-libs ppc64le 1:3.0.5-6.fc38 copr_base 2.2 M
p11-kit ppc64le 0.24.1-5.fc38 copr_base 359 k
p11-kit-trust ppc64le 0.24.1-5.fc38 copr_base 150 k
package-notes-srpm-macros noarch 0.5-6.fc38 fedora 11 k
pam ppc64le 1.5.2-15.fc38 copr_base 569 k
pam-libs ppc64le 1.5.2-15.fc38 copr_base 64 k
pcre2 ppc64le 10.40-1.fc38.1 copr_base 242 k
pcre2-syntax noarch 10.40-1.fc38.1 copr_base 143 k
perl-srpm-macros noarch 1-47.fc38 fedora 8.2 k
pkgconf ppc64le 1.8.0-3.fc38 copr_base 43 k
pkgconf-m4 noarch 1.8.0-3.fc38 copr_base 15 k
pkgconf-pkg-config ppc64le 1.8.0-3.fc38 copr_base 11 k
popt ppc64le 1.19-1.fc38 copr_base 64 k
publicsuffix-list-dafsa noarch 20221208-1.fc38 fedora 59 k
python-srpm-macros noarch 3.11-6.fc38 fedora 25 k
qt5-srpm-macros noarch 5.15.7-1.fc38 fedora 7.9 k
readline ppc64le 8.2-2.fc38 fedora 228 k
rpm ppc64le 4.18.0-8.fc38 fedora 568 k
rpm-build-libs ppc64le 4.18.0-8.fc38 fedora 103 k
rpm-libs ppc64le 4.18.0-8.fc38 fedora 355 k
rpm-sequoia ppc64le 1.2.0-1.fc38 fedora 1.4 M
rpmautospec-rpm-macros noarch 0.3.1-1.fc38 fedora 8.8 k
rust-srpm-macros noarch 23-1.fc38 fedora 9.4 k
setup noarch 2.14.3-1.fc38 fedora 152 k
sqlite-libs ppc64le 3.40.0-1.fc38 fedora 776 k
systemd-libs ppc64le 252.4-598.fc38 fedora 666 k
tzdata noarch 2022g-1.fc38 fedora 716 k
util-linux-core ppc64le 2.38.1-3.fc38 fedora 515 k
xxhash-libs ppc64le 0.8.1-3.fc37 fedora 38 k
xz-libs ppc64le 5.2.9-1.fc38 fedora 104 k
zip ppc64le 3.0-35.fc38 fedora 267 k
zlib ppc64le 1.2.13-1.fc38 fedora 100 k
zstd ppc64le 1.5.2-3.fc37 fedora 466 k
Installing Groups:
Buildsystem building group
Transaction Summary
==========================================================================================================================
Install 154 Packages
Total size: 57 M
Installed size: 328 M
Downloading Packages:
[SKIPPED] alternatives-1.21-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] authselect-1.4.2-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] authselect-libs-1.4.2-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] bash-5.2.9-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] binutils-2.39-6.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] binutils-gold-2.39-6.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] bzip2-1.0.8-12.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] bzip2-libs-1.0.8-12.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] coreutils-9.1-8.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] coreutils-common-9.1-8.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] cpio-2.13-13.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] cracklib-2.9.7-30.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] curl-7.87.0-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] cyrus-sasl-lib-2.1.28-8.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] diffutils-3.8-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] dwz-0.15-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] ed-1.18-2.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] elfutils-0.188-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] elfutils-debuginfod-client-0.188-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] elfutils-default-yama-scope-0.188-3.fc38.noarch.rpm: Already downloaded
[SKIPPED] elfutils-libelf-0.188-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] elfutils-libs-0.188-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] file-5.42-4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] file-libs-5.42-4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] findutils-4.9.0-2.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] gawk-5.1.1-4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] gdbm-libs-1.23-2.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] gmp-6.2.1-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] grep-3.8-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] gzip-1.12-2.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] jansson-2.13.1-5.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] keyutils-libs-1.6.1-5.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] krb5-libs-1.20.1-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libacl-2.3.1-4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libarchive-3.6.1-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libattr-2.5.1-5.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libbrotli-1.0.9-9.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libcap-2.48-5.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libcap-ng-0.8.3-4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libcom_err-1.46.5-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libcurl-7.87.0-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libdb-5.3.28-54.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libeconf-0.4.0-4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libevent-2.1.12-7.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libffi-3.4.4-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libidn2-2.3.4-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libnghttp2-1.51.0-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libnsl2-2.0.0-4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libpkgconf-1.8.0-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libpsl-0.21.1-6.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] librtas-2.0.3-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libselinux-3.4-6.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libsemanage-3.4-6.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libsepol-3.4-4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libsigsegv-2.14-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libssh-0.10.4-2.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libssh-config-0.10.4-2.fc38.noarch.rpm: Already downloaded
[SKIPPED] libtasn1-4.19.0-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libtirpc-1.3.3-0.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libunistring-1.0-2.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libutempter-1.2.1-7.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libverto-0.3.2-4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libxcrypt-4.4.33-5.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libxml2-2.10.3-2.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] lua-libs-5.4.4-6.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] lz4-libs-1.9.3-5.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] mpfr-4.1.1-2.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] ncurses-base-6.3-5.20221126.fc38.noarch.rpm: Already downloaded
[SKIPPED] ncurses-libs-6.3-5.20221126.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] nettle-3.8-2.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] openldap-2.6.3-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] openssl-libs-3.0.5-6.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] p11-kit-0.24.1-5.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] p11-kit-trust-0.24.1-5.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] pam-1.5.2-15.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] pam-libs-1.5.2-15.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] patch-2.7.6-17.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] pcre2-10.40-1.fc38.1.ppc64le.rpm: Already downloaded
[SKIPPED] pcre2-syntax-10.40-1.fc38.1.noarch.rpm: Already downloaded
[SKIPPED] pkgconf-1.8.0-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] pkgconf-m4-1.8.0-3.fc38.noarch.rpm: Already downloaded
[SKIPPED] pkgconf-pkg-config-1.8.0-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] popt-1.19-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libgcc-13.0.0-0.4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libgomp-13.0.0-0.4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libstdc++-13.0.0-0.4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] ansible-srpm-macros-1-8.1.fc38.noarch.rpm: Already downloaded
[SKIPPED] audit-libs-3.0.9-2.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] basesystem-11-14.fc37.noarch.rpm: Already downloaded
[SKIPPED] ca-certificates-2022.2.54-5.fc37.noarch.rpm: Already downloaded
[SKIPPED] crypto-policies-20221215-1.gita4c31a3.fc38.noarch.rpm: Already downloaded
[SKIPPED] debugedit-5.0-5.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] efi-srpm-macros-5-6.fc37.noarch.rpm: Already downloaded
[SKIPPED] fedora-gpg-keys-38-0.3.noarch.rpm: Already downloaded
[SKIPPED] fedora-release-38-0.6.noarch.rpm: Already downloaded
[SKIPPED] fedora-release-common-38-0.6.noarch.rpm: Already downloaded
[SKIPPED] fedora-release-identity-basic-38-0.6.noarch.rpm: Already downloaded
[SKIPPED] fedora-repos-38-0.3.noarch.rpm: Already downloaded
[SKIPPED] fedora-repos-rawhide-38-0.3.noarch.rpm: Already downloaded
[SKIPPED] filesystem-3.18-2.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] fonts-srpm-macros-2.0.5-10.fc38.noarch.rpm: Already downloaded
[SKIPPED] fpc-srpm-macros-1.3-6.fc37.noarch.rpm: Already downloaded
[SKIPPED] gdb-minimal-12.1-10.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] ghc-srpm-macros-1.5.0-7.fc37.noarch.rpm: Already downloaded
[SKIPPED] glibc-2.36.9000-19.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] glibc-common-2.36.9000-19.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] glibc-gconv-extra-2.36.9000-19.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] glibc-minimal-langpack-2.36.9000-19.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] gnat-srpm-macros-4-16.fc37.noarch.rpm: Already downloaded
[SKIPPED] go-srpm-macros-3.2.0-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] info-7.0.1-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] kernel-srpm-macros-1.0-15.fc37.noarch.rpm: Already downloaded
[SKIPPED] libblkid-2.38.1-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libfdisk-2.38.1-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libmount-2.38.1-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libpwquality-1.4.5-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libsmartcols-2.38.1-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libuuid-2.38.1-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libzstd-1.5.2-3.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] lua-srpm-macros-1-7.fc37.noarch.rpm: Already downloaded
[SKIPPED] nim-srpm-macros-3-7.fc37.noarch.rpm: Already downloaded
[SKIPPED] ocaml-srpm-macros-7-2.fc37.noarch.rpm: Already downloaded
[SKIPPED] openblas-srpm-macros-2-12.fc37.noarch.rpm: Already downloaded
[SKIPPED] package-notes-srpm-macros-0.5-6.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-srpm-macros-1-47.fc38.noarch.rpm: Already downloaded
[SKIPPED] publicsuffix-list-dafsa-20221208-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] python-srpm-macros-3.11-6.fc38.noarch.rpm: Already downloaded
[SKIPPED] qt5-srpm-macros-5.15.7-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] readline-8.2-2.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] redhat-rpm-config-235-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] rpm-4.18.0-8.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] rpm-build-4.18.0-8.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] rpm-build-libs-4.18.0-8.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] rpm-libs-4.18.0-8.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] rpm-sequoia-1.2.0-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] rpmautospec-rpm-macros-0.3.1-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] rust-srpm-macros-23-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] sed-4.8-11.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] setup-2.14.3-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] shadow-utils-4.13-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] sqlite-libs-3.40.0-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] systemd-libs-252.4-598.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] tar-1.34-5.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] tzdata-2022g-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] unzip-6.0-58.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] util-linux-2.38.1-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] util-linux-core-2.38.1-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] which-2.21-36.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] xxhash-libs-0.8.1-3.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] xz-5.2.9-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] xz-libs-5.2.9-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] zip-3.0-35.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] zlib-1.2.13-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] zstd-1.5.2-3.fc37.ppc64le.rpm: Already downloaded
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0xEB10B464:
Userid : "Fedora (38) <fedora-38-primary@fedoraproject.org>"
Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary
Key imported successfully
fedora 1.6 MB/s | 1.6 kB 00:00
GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary (0xEB10B464) is already installed
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0x5323552A:
Userid : "Fedora (37) <fedora-37-primary@fedoraproject.org>"
Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Running scriptlet: filesystem-3.18-2.fc37.ppc64le 1/1
Preparing : 1/1
Installing : libgcc-13.0.0-0.4.fc38.ppc64le 1/154
Running scriptlet: libgcc-13.0.0-0.4.fc38.ppc64le 1/154
Installing : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/154
Running scriptlet: crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/154
Installing : fedora-release-identity-basic-38-0.6.noarch 3/154
Installing : tzdata-2022g-1.fc38.noarch 4/154
Installing : rust-srpm-macros-23-1.fc38.noarch 5/154
Installing : qt5-srpm-macros-5.15.7-1.fc38.noarch 6/154
Installing : publicsuffix-list-dafsa-20221208-1.fc38.noarch 7/154
Installing : perl-srpm-macros-1-47.fc38.noarch 8/154
Installing : package-notes-srpm-macros-0.5-6.fc38.noarch 9/154
Installing : openblas-srpm-macros-2-12.fc37.noarch 10/154
Installing : ocaml-srpm-macros-7-2.fc37.noarch 11/154
Installing : nim-srpm-macros-3-7.fc37.noarch 12/154
Installing : kernel-srpm-macros-1.0-15.fc37.noarch 13/154
Installing : gnat-srpm-macros-4-16.fc37.noarch 14/154
Installing : ghc-srpm-macros-1.5.0-7.fc37.noarch 15/154
Installing : fpc-srpm-macros-1.3-6.fc37.noarch 16/154
Installing : fedora-gpg-keys-38-0.3.noarch 17/154
Installing : fedora-release-38-0.6.noarch 18/154
Installing : fedora-release-common-38-0.6.noarch 19/154
Installing : fedora-repos-rawhide-38-0.3.noarch 20/154
Installing : fedora-repos-38-0.3.noarch 21/154
Installing : setup-2.14.3-1.fc38.noarch 22/154
warning: /etc/hosts created as /etc/hosts.rpmnew
Running scriptlet: setup-2.14.3-1.fc38.noarch 22/154
Installing : filesystem-3.18-2.fc37.ppc64le 23/154
Installing : basesystem-11-14.fc37.noarch 24/154
Installing : ansible-srpm-macros-1-8.1.fc38.noarch 25/154
Installing : pkgconf-m4-1.8.0-3.fc38.noarch 26/154
Installing : pcre2-syntax-10.40-1.fc38.1.noarch 27/154
Installing : ncurses-base-6.3-5.20221126.fc38.noarch 28/154
Installing : ncurses-libs-6.3-5.20221126.fc38.ppc64le 29/154
Installing : glibc-gconv-extra-2.36.9000-19.fc38.ppc64le 30/154
Running scriptlet: glibc-gconv-extra-2.36.9000-19.fc38.ppc64le 30/154
Running scriptlet: glibc-2.36.9000-19.fc38.ppc64le 31/154
Installing : glibc-2.36.9000-19.fc38.ppc64le 31/154
Running scriptlet: glibc-2.36.9000-19.fc38.ppc64le 31/154
Installing : bash-5.2.9-3.fc38.ppc64le 32/154
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Installing : info-7.0.1-1.fc38.ppc64le 154/154
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Running scriptlet: rpm-4.18.0-8.fc38.ppc64le 154/154
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Installed:
alternatives-1.21-1.fc38.ppc64le
ansible-srpm-macros-1-8.1.fc38.noarch
audit-libs-3.0.9-2.fc38.ppc64le
authselect-1.4.2-1.fc38.ppc64le
authselect-libs-1.4.2-1.fc38.ppc64le
basesystem-11-14.fc37.noarch
bash-5.2.9-3.fc38.ppc64le
binutils-2.39-6.fc38.ppc64le
binutils-gold-2.39-6.fc38.ppc64le
bzip2-1.0.8-12.fc38.ppc64le
bzip2-libs-1.0.8-12.fc38.ppc64le
ca-certificates-2022.2.54-5.fc37.noarch
coreutils-9.1-8.fc38.ppc64le
coreutils-common-9.1-8.fc38.ppc64le
cpio-2.13-13.fc38.ppc64le
cracklib-2.9.7-30.fc38.ppc64le
crypto-policies-20221215-1.gita4c31a3.fc38.noarch
curl-7.87.0-1.fc38.ppc64le
cyrus-sasl-lib-2.1.28-8.fc38.ppc64le
debugedit-5.0-5.fc37.ppc64le
diffutils-3.8-3.fc38.ppc64le
dwz-0.15-1.fc38.ppc64le
ed-1.18-2.fc38.ppc64le
efi-srpm-macros-5-6.fc37.noarch
elfutils-0.188-3.fc38.ppc64le
elfutils-debuginfod-client-0.188-3.fc38.ppc64le
elfutils-default-yama-scope-0.188-3.fc38.noarch
elfutils-libelf-0.188-3.fc38.ppc64le
elfutils-libs-0.188-3.fc38.ppc64le
fedora-gpg-keys-38-0.3.noarch
fedora-release-38-0.6.noarch
fedora-release-common-38-0.6.noarch
fedora-release-identity-basic-38-0.6.noarch
fedora-repos-38-0.3.noarch
fedora-repos-rawhide-38-0.3.noarch
file-5.42-4.fc38.ppc64le
file-libs-5.42-4.fc38.ppc64le
filesystem-3.18-2.fc37.ppc64le
findutils-1:4.9.0-2.fc38.ppc64le
fonts-srpm-macros-1:2.0.5-10.fc38.noarch
fpc-srpm-macros-1.3-6.fc37.noarch
gawk-5.1.1-4.fc38.ppc64le
gdb-minimal-12.1-10.fc38.ppc64le
gdbm-libs-1:1.23-2.fc38.ppc64le
ghc-srpm-macros-1.5.0-7.fc37.noarch
glibc-2.36.9000-19.fc38.ppc64le
glibc-common-2.36.9000-19.fc38.ppc64le
glibc-gconv-extra-2.36.9000-19.fc38.ppc64le
glibc-minimal-langpack-2.36.9000-19.fc38.ppc64le
gmp-1:6.2.1-3.fc38.ppc64le
gnat-srpm-macros-4-16.fc37.noarch
go-srpm-macros-3.2.0-1.fc38.noarch
grep-3.8-1.fc38.ppc64le
gzip-1.12-2.fc38.ppc64le
info-7.0.1-1.fc38.ppc64le
jansson-2.13.1-5.fc38.ppc64le
kernel-srpm-macros-1.0-15.fc37.noarch
keyutils-libs-1.6.1-5.fc38.ppc64le
krb5-libs-1.20.1-3.fc38.ppc64le
libacl-2.3.1-4.fc38.ppc64le
libarchive-3.6.1-3.fc38.ppc64le
libattr-2.5.1-5.fc38.ppc64le
libblkid-2.38.1-3.fc38.ppc64le
libbrotli-1.0.9-9.fc38.ppc64le
libcap-2.48-5.fc38.ppc64le
libcap-ng-0.8.3-4.fc38.ppc64le
libcom_err-1.46.5-3.fc38.ppc64le
libcurl-7.87.0-1.fc38.ppc64le
libdb-5.3.28-54.fc38.ppc64le
libeconf-0.4.0-4.fc38.ppc64le
libevent-2.1.12-7.fc38.ppc64le
libfdisk-2.38.1-3.fc38.ppc64le
libffi-3.4.4-1.fc38.ppc64le
libgcc-13.0.0-0.4.fc38.ppc64le
libgomp-13.0.0-0.4.fc38.ppc64le
libidn2-2.3.4-1.fc38.ppc64le
libmount-2.38.1-3.fc38.ppc64le
libnghttp2-1.51.0-1.fc38.ppc64le
libnsl2-2.0.0-4.fc38.ppc64le
libpkgconf-1.8.0-3.fc38.ppc64le
libpsl-0.21.1-6.fc38.ppc64le
libpwquality-1.4.5-1.fc38.ppc64le
librtas-2.0.3-1.fc38.ppc64le
libselinux-3.4-6.fc38.ppc64le
libsemanage-3.4-6.fc38.ppc64le
libsepol-3.4-4.fc38.ppc64le
libsigsegv-2.14-3.fc38.ppc64le
libsmartcols-2.38.1-3.fc38.ppc64le
libssh-0.10.4-2.fc38.ppc64le
libssh-config-0.10.4-2.fc38.noarch
libstdc++-13.0.0-0.4.fc38.ppc64le
libtasn1-4.19.0-1.fc38.ppc64le
libtirpc-1.3.3-0.fc38.ppc64le
libunistring-1.0-2.fc38.ppc64le
libutempter-1.2.1-7.fc38.ppc64le
libuuid-2.38.1-3.fc38.ppc64le
libverto-0.3.2-4.fc38.ppc64le
libxcrypt-4.4.33-5.fc38.ppc64le
libxml2-2.10.3-2.fc38.ppc64le
libzstd-1.5.2-3.fc37.ppc64le
lua-libs-5.4.4-6.fc38.ppc64le
lua-srpm-macros-1-7.fc37.noarch
lz4-libs-1.9.3-5.fc38.ppc64le
mpfr-4.1.1-2.fc38.ppc64le
ncurses-base-6.3-5.20221126.fc38.noarch
ncurses-libs-6.3-5.20221126.fc38.ppc64le
nettle-3.8-2.fc38.ppc64le
nim-srpm-macros-3-7.fc37.noarch
ocaml-srpm-macros-7-2.fc37.noarch
openblas-srpm-macros-2-12.fc37.noarch
openldap-2.6.3-1.fc38.ppc64le
openssl-libs-1:3.0.5-6.fc38.ppc64le
p11-kit-0.24.1-5.fc38.ppc64le
p11-kit-trust-0.24.1-5.fc38.ppc64le
package-notes-srpm-macros-0.5-6.fc38.noarch
pam-1.5.2-15.fc38.ppc64le
pam-libs-1.5.2-15.fc38.ppc64le
patch-2.7.6-17.fc38.ppc64le
pcre2-10.40-1.fc38.1.ppc64le
pcre2-syntax-10.40-1.fc38.1.noarch
perl-srpm-macros-1-47.fc38.noarch
pkgconf-1.8.0-3.fc38.ppc64le
pkgconf-m4-1.8.0-3.fc38.noarch
pkgconf-pkg-config-1.8.0-3.fc38.ppc64le
popt-1.19-1.fc38.ppc64le
publicsuffix-list-dafsa-20221208-1.fc38.noarch
python-srpm-macros-3.11-6.fc38.noarch
qt5-srpm-macros-5.15.7-1.fc38.noarch
readline-8.2-2.fc38.ppc64le
redhat-rpm-config-235-1.fc38.noarch
rpm-4.18.0-8.fc38.ppc64le
rpm-build-4.18.0-8.fc38.ppc64le
rpm-build-libs-4.18.0-8.fc38.ppc64le
rpm-libs-4.18.0-8.fc38.ppc64le
rpm-sequoia-1.2.0-1.fc38.ppc64le
rpmautospec-rpm-macros-0.3.1-1.fc38.noarch
rust-srpm-macros-23-1.fc38.noarch
sed-4.8-11.fc37.ppc64le
setup-2.14.3-1.fc38.noarch
shadow-utils-2:4.13-3.fc38.ppc64le
sqlite-libs-3.40.0-1.fc38.ppc64le
systemd-libs-252.4-598.fc38.ppc64le
tar-2:1.34-5.fc38.ppc64le
tzdata-2022g-1.fc38.noarch
unzip-6.0-58.fc38.ppc64le
util-linux-2.38.1-3.fc38.ppc64le
util-linux-core-2.38.1-3.fc38.ppc64le
which-2.21-36.fc38.ppc64le
xxhash-libs-0.8.1-3.fc37.ppc64le
xz-5.2.9-1.fc38.ppc64le
xz-libs-5.2.9-1.fc38.ppc64le
zip-3.0-35.fc38.ppc64le
zlib-1.2.13-1.fc38.ppc64le
zstd-1.5.2-3.fc37.ppc64le
Complete!
Finish: dnf install
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: libdb-5.3.28-54.fc38.ppc64le
nim-srpm-macros-3-7.fc37.noarch
glibc-gconv-extra-2.36.9000-19.fc38.ppc64le
ncurses-libs-6.3-5.20221126.fc38.ppc64le
glibc-common-2.36.9000-19.fc38.ppc64le
libfdisk-2.38.1-3.fc38.ppc64le
fpc-srpm-macros-1.3-6.fc37.noarch
go-srpm-macros-3.2.0-1.fc38.noarch
libsemanage-3.4-6.fc38.ppc64le
redhat-rpm-config-235-1.fc38.noarch
fonts-srpm-macros-2.0.5-10.fc38.noarch
krb5-libs-1.20.1-3.fc38.ppc64le
libbrotli-1.0.9-9.fc38.ppc64le
cracklib-2.9.7-30.fc38.ppc64le
elfutils-libelf-0.188-3.fc38.ppc64le
libselinux-3.4-6.fc38.ppc64le
libpkgconf-1.8.0-3.fc38.ppc64le
rpm-4.18.0-8.fc38.ppc64le
gpg-pubkey-eb10b464-6202d9c6
qt5-srpm-macros-5.15.7-1.fc38.noarch
sqlite-libs-3.40.0-1.fc38.ppc64le
libarchive-3.6.1-3.fc38.ppc64le
elfutils-default-yama-scope-0.188-3.fc38.noarch
libgomp-13.0.0-0.4.fc38.ppc64le
fedora-release-common-38-0.6.noarch
ocaml-srpm-macros-7-2.fc37.noarch
nettle-3.8-2.fc38.ppc64le
rpm-build-libs-4.18.0-8.fc38.ppc64le
package-notes-srpm-macros-0.5-6.fc38.noarch
openssl-libs-3.0.5-6.fc38.ppc64le
authselect-libs-1.4.2-1.fc38.ppc64le
libcap-ng-0.8.3-4.fc38.ppc64le
libzstd-1.5.2-3.fc37.ppc64le
grep-3.8-1.fc38.ppc64le
lua-srpm-macros-1-7.fc37.noarch
tzdata-2022g-1.fc38.noarch
libtasn1-4.19.0-1.fc38.ppc64le
glibc-minimal-langpack-2.36.9000-19.fc38.ppc64le
zlib-1.2.13-1.fc38.ppc64le
dwz-0.15-1.fc38.ppc64le
cpio-2.13-13.fc38.ppc64le
rpm-build-4.18.0-8.fc38.ppc64le
bzip2-1.0.8-12.fc38.ppc64le
diffutils-3.8-3.fc38.ppc64le
bash-5.2.9-3.fc38.ppc64le
libstdc++-13.0.0-0.4.fc38.ppc64le
popt-1.19-1.fc38.ppc64le
rpmautospec-rpm-macros-0.3.1-1.fc38.noarch
audit-libs-3.0.9-2.fc38.ppc64le
readline-8.2-2.fc38.ppc64le
libidn2-2.3.4-1.fc38.ppc64le
fedora-repos-38-0.3.noarch
fedora-gpg-keys-38-0.3.noarch
ca-certificates-2022.2.54-5.fc37.noarch
rpm-libs-4.18.0-8.fc38.ppc64le
gawk-5.1.1-4.fc38.ppc64le
systemd-libs-252.4-598.fc38.ppc64le
elfutils-libs-0.188-3.fc38.ppc64le
sed-4.8-11.fc37.ppc64le
libcom_err-1.46.5-3.fc38.ppc64le
openblas-srpm-macros-2-12.fc37.noarch
authselect-1.4.2-1.fc38.ppc64le
perl-srpm-macros-1-47.fc38.noarch
ed-1.18-2.fc38.ppc64le
libsmartcols-2.38.1-3.fc38.ppc64le
debugedit-5.0-5.fc37.ppc64le
libpsl-0.21.1-6.fc38.ppc64le
libmount-2.38.1-3.fc38.ppc64le
jansson-2.13.1-5.fc38.ppc64le
pam-1.5.2-15.fc38.ppc64le
efi-srpm-macros-5-6.fc37.noarch
gzip-1.12-2.fc38.ppc64le
libuuid-2.38.1-3.fc38.ppc64le
libblkid-2.38.1-3.fc38.ppc64le
gdb-minimal-12.1-10.fc38.ppc64le
xz-libs-5.2.9-1.fc38.ppc64le
fedora-repos-rawhide-38-0.3.noarch
setup-2.14.3-1.fc38.noarch
alternatives-1.21-1.fc38.ppc64le
librtas-2.0.3-1.fc38.ppc64le
pcre2-syntax-10.40-1.fc38.1.noarch
rust-srpm-macros-23-1.fc38.noarch
rpm-sequoia-1.2.0-1.fc38.ppc64le
libeconf-0.4.0-4.fc38.ppc64le
pkgconf-1.8.0-3.fc38.ppc64le
publicsuffix-list-dafsa-20221208-1.fc38.noarch
libcap-2.48-5.fc38.ppc64le
ghc-srpm-macros-1.5.0-7.fc37.noarch
p11-kit-trust-0.24.1-5.fc38.ppc64le
unzip-6.0-58.fc38.ppc64le
libcurl-7.87.0-1.fc38.ppc64le
pam-libs-1.5.2-15.fc38.ppc64le
libpwquality-1.4.5-1.fc38.ppc64le
zstd-1.5.2-3.fc37.ppc64le
python-srpm-macros-3.11-6.fc38.noarch
util-linux-core-2.38.1-3.fc38.ppc64le
basesystem-11-14.fc37.noarch
fedora-release-identity-basic-38-0.6.noarch
ansible-srpm-macros-1-8.1.fc38.noarch
findutils-4.9.0-2.fc38.ppc64le
glibc-2.36.9000-19.fc38.ppc64le
crypto-policies-20221215-1.gita4c31a3.fc38.noarch
binutils-gold-2.39-6.fc38.ppc64le
bzip2-libs-1.0.8-12.fc38.ppc64le
util-linux-2.38.1-3.fc38.ppc64le
cyrus-sasl-lib-2.1.28-8.fc38.ppc64le
libutempter-1.2.1-7.fc38.ppc64le
lz4-libs-1.9.3-5.fc38.ppc64le
info-7.0.1-1.fc38.ppc64le
libacl-2.3.1-4.fc38.ppc64le
elfutils-debuginfod-client-0.188-3.fc38.ppc64le
xz-5.2.9-1.fc38.ppc64le
libattr-2.5.1-5.fc38.ppc64le
file-5.42-4.fc38.ppc64le
libssh-0.10.4-2.fc38.ppc64le
curl-7.87.0-1.fc38.ppc64le
libevent-2.1.12-7.fc38.ppc64le
lua-libs-5.4.4-6.fc38.ppc64le
gpg-pubkey-5323552a-6112bcdc
file-libs-5.42-4.fc38.ppc64le
libxml2-2.10.3-2.fc38.ppc64le
openldap-2.6.3-1.fc38.ppc64le
binutils-2.39-6.fc38.ppc64le
shadow-utils-4.13-3.fc38.ppc64le
libunistring-1.0-2.fc38.ppc64le
p11-kit-0.24.1-5.fc38.ppc64le
libxcrypt-4.4.33-5.fc38.ppc64le
pkgconf-m4-1.8.0-3.fc38.noarch
gdbm-libs-1.23-2.fc38.ppc64le
gnat-srpm-macros-4-16.fc37.noarch
libverto-0.3.2-4.fc38.ppc64le
zip-3.0-35.fc38.ppc64le
coreutils-9.1-8.fc38.ppc64le
gmp-6.2.1-3.fc38.ppc64le
xxhash-libs-0.8.1-3.fc37.ppc64le
kernel-srpm-macros-1.0-15.fc37.noarch
ncurses-base-6.3-5.20221126.fc38.noarch
mpfr-4.1.1-2.fc38.ppc64le
libsepol-3.4-4.fc38.ppc64le
coreutils-common-9.1-8.fc38.ppc64le
libgcc-13.0.0-0.4.fc38.ppc64le
pkgconf-pkg-config-1.8.0-3.fc38.ppc64le
pcre2-10.40-1.fc38.1.ppc64le
tar-1.34-5.fc38.ppc64le
keyutils-libs-1.6.1-5.fc38.ppc64le
filesystem-3.18-2.fc37.ppc64le
libnghttp2-1.51.0-1.fc38.ppc64le
libtirpc-1.3.3-0.fc38.ppc64le
libnsl2-2.0.0-4.fc38.ppc64le
libsigsegv-2.14-3.fc38.ppc64le
patch-2.7.6-17.fc38.ppc64le
libssh-config-0.10.4-2.fc38.noarch
libffi-3.4.4-1.fc38.ppc64le
elfutils-0.188-3.fc38.ppc64le
which-2.21-36.fc38.ppc64le
fedora-release-38-0.6.noarch
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1669248000
Wrote: /builddir/build/SRPMS/python-biopython-1.80-1.fc38.src.rpm
Finish: rpmbuild -bs
cp: ‘var/lib/mock/fedora-rawhide-ppc64le-1672075344.750807/root/var/log’: No such file or directory
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-ppc64le-1672075344.750807/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-ppc64le-1672075344.750807/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-ppc64le-1672075344.750807/root/var/log/dnf.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-gxj1he_k/python-biopython/python-biopython.spec) Config(child) 1 minutes 34 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=115200): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/python-biopython-1.80-1.fc38.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1672075344.750807 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)...
Start(bootstrap): init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish(bootstrap): init plugins
Start: init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
INFO: Signal handler active
Start: run
INFO: Start(/var/lib/copr-rpmbuild/results/python-biopython-1.80-1.fc38.src.rpm) Config(fedora-rawhide-ppc64le)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1672075344.750807/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1672075344.750807/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-1672075344.750807/root.
INFO: calling preinit hooks
INFO: enabled root cache
Start: unpacking root cache
Finish: unpacking root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Start: dnf update
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 10 kB/s | 3.0 kB 00:00
Copr repository 27 MB/s | 32 MB 00:01
Additional repo https_jakub_fedorapeople_org_fe 8.3 kB/s | 3.0 kB 00:00
fedora 25 kB/s | 6.7 kB 00:00
Dependencies resolved.
Nothing to do.
Complete!
Finish: dnf update
Finish: chroot init
Start: build phase for python-biopython-1.80-1.fc38.src.rpm
Start: build setup for python-biopython-1.80-1.fc38.src.rpm
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1669248000
Wrote: /builddir/build/SRPMS/python-biopython-1.80-1.fc38.src.rpm
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 11 kB/s | 3.0 kB 00:00
Additional repo https_jakub_fedorapeople_org_fe 8.8 kB/s | 3.0 kB 00:00
fedora 23 kB/s | 6.7 kB 00:00
Dependencies resolved.
==============================================================================================================
Package Arch Version Repository Size
==============================================================================================================
Installing:
gcc ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 30 M
mysql-connector-python3 noarch 8.0.21-7.fc37 fedora 590 k
python3-devel ppc64le 3.11.1-1.fc38 fedora 269 k
python3-mysqlclient ppc64le 2.1.1-2.fc38 fedora 108 k
python3-numpy ppc64le 1:1.23.5-1.fc38 copr_base 7.3 M
python3-psycopg2 ppc64le 2.9.3-6.fc37 fedora 218 k
python3-rdflib noarch 6.2.0-1.fc38 fedora 965 k
python3-reportlab ppc64le 3.6.12-1.fc38 fedora 3.5 M
python3-setuptools noarch 65.5.1-1.fc38 fedora 1.7 M
Installing dependencies:
annobin-docs noarch 10.99-1.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 93 k
annobin-plugin-gcc ppc64le 10.99-1.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 890 k
cpp ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 9.8 M
dejavu-sans-fonts noarch 2.37-19.fc37 fedora 1.3 M
expat ppc64le 2.5.0-1.fc38 copr_base 117 k
flexiblas ppc64le 3.2.1-3.fc38 fedora 32 k
flexiblas-netlib ppc64le 3.2.1-3.fc38 fedora 2.7 M
flexiblas-openblas-openmp ppc64le 3.2.1-3.fc38 fedora 16 k
fonts-filesystem noarch 1:2.0.5-10.fc38 fedora 8.0 k
freetype ppc64le 2.12.1-3.fc38 copr_base 471 k
fribidi ppc64le 1.0.12-2.fc38 copr_base 93 k
gc ppc64le 8.2.2-1.fc38 copr_base 122 k
gcc-plugin-annobin ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 32 k
glib2 ppc64le 2.74.1-2.fc38 copr_base 2.8 M
glibc-devel ppc64le 2.36.9000-19.fc38 fedora 546 k
gnutls ppc64le 3.7.8-9.fc38 copr_base 1.1 M
graphite2 ppc64le 1.3.14-10.fc38 copr_base 105 k
guile22 ppc64le 2.2.7-6.fc38 copr_base 6.5 M
harfbuzz ppc64le 6.0.0-1.fc38 copr_base 897 k
jbigkit-libs ppc64le 2.1-24.fc38 copr_base 57 k
kernel-headers ppc64le 6.1.0-1.fc38 fedora 1.5 M
lcms2 ppc64le 2.14-1.fc38 copr_base 205 k
libXau ppc64le 1.0.11-1.fc38 copr_base 33 k
libart_lgpl ppc64le 2.3.21-28.fc38 copr_base 79 k
libasan ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 477 k
libatomic ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 19 k
libb2 ppc64le 0.98.1-7.fc38 copr_base 26 k
libgfortran ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 597 k
libimagequant ppc64le 2.17.0-3.fc38 copr_base 70 k
libjpeg-turbo ppc64le 2.1.4-1.fc38 copr_base 209 k
libmpc ppc64le 1.2.1-5.fc38 copr_base 85 k
libpng ppc64le 2:1.6.37-13.fc38 copr_base 139 k
libpq ppc64le 15.0-2.fc38 copr_base 227 k
libquadmath ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 195 k
libraqm ppc64le 0.8.0-2.fc38 copr_base 22 k
libtiff ppc64le 4.4.0-4.fc38 copr_base 233 k
libtool-ltdl ppc64le 2.4.7-3.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 41 k
libubsan ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 234 k
libwebp ppc64le 1.2.4-2.fc38 copr_base 260 k
libxcb ppc64le 1.13.1-10.fc38 copr_base 244 k
libxcrypt-devel ppc64le 4.4.33-5.fc38 copr_base 31 k
make ppc64le 1:4.3-11.fc38 copr_base 549 k
mariadb-connector-c ppc64le 3.2.7-2.fc38 copr_base 218 k
mariadb-connector-c-config noarch 3.2.7-2.fc38 copr_base 10 k
mpdecimal ppc64le 2.5.1-4.fc38 copr_base 118 k
openblas ppc64le 0.3.21-4.fc38 fedora 35 k
openblas-openmp ppc64le 0.3.21-4.fc38 fedora 4.4 M
openjpeg2 ppc64le 2.5.0-2.fc38 copr_base 204 k
protobuf ppc64le 3.19.6-1.fc38 copr_base 1.0 M
pyproject-rpm-macros noarch 1.5.0-1.fc38 fedora 40 k
python-pip-wheel noarch 22.3.1-1.fc38 fedora 1.4 M
python-rpm-macros noarch 3.11-6.fc38 fedora 19 k
python-setuptools-wheel noarch 65.5.1-1.fc38 fedora 715 k
python3 ppc64le 3.11.1-1.fc38 fedora 27 k
python3-isodate noarch 0.6.1-5.fc37 fedora 79 k
python3-libs ppc64le 3.11.1-1.fc38 fedora 9.7 M
python3-olefile noarch 0.46-18.fc37 fedora 67 k
python3-packaging noarch 21.3-7.fc38 fedora 98 k
python3-pillow ppc64le 9.3.0-2.fc38 fedora 959 k
python3-protobuf ppc64le 3.19.6-1.fc38 copr_base 402 k
python3-pyparsing noarch 3.0.9-2.fc37 fedora 262 k
python3-rpm-generators noarch 13-2.fc37 fedora 30 k
python3-rpm-macros noarch 3.11-6.fc38 fedora 15 k
python3-six noarch 1.16.0-8.fc37 fedora 42 k
Transaction Summary
==============================================================================================================
Install 73 Packages
Total size: 98 M
Total download size: 32 M
Installed size: 408 M
Downloading Packages:
[SKIPPED] expat-2.5.0-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] gc-8.2.2-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] guile22-2.2.7-6.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libb2-0.98.1-7.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libmpc-1.2.1-5.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libxcrypt-devel-4.4.33-5.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] make-4.3-11.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] mpdecimal-2.5.1-4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] annobin-docs-10.99-1.0.1.fc38.noarch.rpm: Already downloaded
[SKIPPED] annobin-plugin-gcc-10.99-1.0.1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] cpp-13.0.0-0.4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] gcc-13.0.0-0.4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] gcc-plugin-annobin-13.0.0-0.4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libasan-13.0.0-0.4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libatomic-13.0.0-0.4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libtool-ltdl-2.4.7-3.0.1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libubsan-13.0.0-0.4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] fonts-filesystem-2.0.5-10.fc38.noarch.rpm: Already downloaded
[SKIPPED] glibc-devel-2.36.9000-19.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] kernel-headers-6.1.0-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] pyproject-rpm-macros-1.5.0-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] python-pip-wheel-22.3.1-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] python-rpm-macros-3.11-6.fc38.noarch.rpm: Already downloaded
[SKIPPED] python-setuptools-wheel-65.5.1-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] python3-3.11.1-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] python3-devel-3.11.1-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] python3-isodate-0.6.1-5.fc37.noarch.rpm: Already downloaded
[SKIPPED] python3-libs-3.11.1-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] python3-packaging-21.3-7.fc38.noarch.rpm: Already downloaded
[SKIPPED] python3-pyparsing-3.0.9-2.fc37.noarch.rpm: Already downloaded
[SKIPPED] python3-rpm-generators-13-2.fc37.noarch.rpm: Already downloaded
[SKIPPED] python3-rpm-macros-3.11-6.fc38.noarch.rpm: Already downloaded
[SKIPPED] python3-setuptools-65.5.1-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] python3-six-1.16.0-8.fc37.noarch.rpm: Already downloaded
(35/73): fribidi-1.0.12-2.fc38.ppc64le.rpm 298 kB/s | 93 kB 00:00
(36/73): freetype-2.12.1-3.fc38.ppc64le.rpm 1.4 MB/s | 471 kB 00:00
(37/73): gnutls-3.7.8-9.fc38.ppc64le.rpm 31 MB/s | 1.1 MB 00:00
(38/73): graphite2-1.3.14-10.fc38.ppc64le.rpm 5.0 MB/s | 105 kB 00:00
(39/73): glib2-2.74.1-2.fc38.ppc64le.rpm 7.3 MB/s | 2.8 MB 00:00
(40/73): harfbuzz-6.0.0-1.fc38.ppc64le.rpm 19 MB/s | 897 kB 00:00
(41/73): jbigkit-libs-2.1-24.fc38.ppc64le.rpm 1.2 MB/s | 57 kB 00:00
(42/73): lcms2-2.14-1.fc38.ppc64le.rpm 15 MB/s | 205 kB 00:00
(43/73): libart_lgpl-2.3.21-28.fc38.ppc64le.rpm 4.9 MB/s | 79 kB 00:00
(44/73): libXau-1.0.11-1.fc38.ppc64le.rpm 1.9 MB/s | 33 kB 00:00
(45/73): libimagequant-2.17.0-3.fc38.ppc64le.rp 5.2 MB/s | 70 kB 00:00
(46/73): libjpeg-turbo-2.1.4-1.fc38.ppc64le.rpm 14 MB/s | 209 kB 00:00
(47/73): libpng-1.6.37-13.fc38.ppc64le.rpm 8.4 MB/s | 139 kB 00:00
(48/73): libpq-15.0-2.fc38.ppc64le.rpm 15 MB/s | 227 kB 00:00
(49/73): libraqm-0.8.0-2.fc38.ppc64le.rpm 1.4 MB/s | 22 kB 00:00
(50/73): libwebp-1.2.4-2.fc38.ppc64le.rpm 16 MB/s | 260 kB 00:00
(51/73): libtiff-4.4.0-4.fc38.ppc64le.rpm 11 MB/s | 233 kB 00:00
(52/73): libxcb-1.13.1-10.fc38.ppc64le.rpm 18 MB/s | 244 kB 00:00
(53/73): mariadb-connector-c-3.2.7-2.fc38.ppc64 11 MB/s | 218 kB 00:00
(54/73): mariadb-connector-c-config-3.2.7-2.fc3 563 kB/s | 10 kB 00:00
(55/73): openjpeg2-2.5.0-2.fc38.ppc64le.rpm 15 MB/s | 204 kB 00:00
(56/73): python3-protobuf-3.19.6-1.fc38.ppc64le 12 MB/s | 402 kB 00:00
(57/73): python3-numpy-1.23.5-1.fc38.ppc64le.rp 50 MB/s | 7.3 MB 00:00
(58/73): protobuf-3.19.6-1.fc38.ppc64le.rpm 6.3 MB/s | 1.0 MB 00:00
(59/73): libquadmath-13.0.0-0.4.fc38.ppc64le.rp 1.5 MB/s | 195 kB 00:00
(60/73): libgfortran-13.0.0-0.4.fc38.ppc64le.rp 2.3 MB/s | 597 kB 00:00
(61/73): flexiblas-3.2.1-3.fc38.ppc64le.rpm 131 kB/s | 32 kB 00:00
(62/73): flexiblas-openblas-openmp-3.2.1-3.fc38 175 kB/s | 16 kB 00:00
(63/73): dejavu-sans-fonts-2.37-19.fc37.noarch. 2.0 MB/s | 1.3 MB 00:00
(64/73): openblas-0.3.21-4.fc38.ppc64le.rpm 470 kB/s | 35 kB 00:00
(65/73): flexiblas-netlib-3.2.1-3.fc38.ppc64le. 3.8 MB/s | 2.7 MB 00:00
(66/73): mysql-connector-python3-8.0.21-7.fc37. 1.4 MB/s | 590 kB 00:00
(67/73): openblas-openmp-0.3.21-4.fc38.ppc64le. 17 MB/s | 4.4 MB 00:00
(68/73): python3-olefile-0.46-18.fc37.noarch.rp 412 kB/s | 67 kB 00:00
(69/73): python3-mysqlclient-2.1.1-2.fc38.ppc64 576 kB/s | 108 kB 00:00
(70/73): python3-rdflib-6.2.0-1.fc38.noarch.rpm 10 MB/s | 965 kB 00:00
(71/73): python3-pillow-9.3.0-2.fc38.ppc64le.rp 6.9 MB/s | 959 kB 00:00
(72/73): python3-psycopg2-2.9.3-6.fc37.ppc64le. 1.7 MB/s | 218 kB 00:00
(73/73): python3-reportlab-3.6.12-1.fc38.ppc64l 18 MB/s | 3.5 MB 00:00
--------------------------------------------------------------------------------
Total 12 MB/s | 32 MB 00:02
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Preparing : 1/1
Installing : python-rpm-macros-3.11-6.fc38.noarch 1/73
Installing : python3-rpm-macros-3.11-6.fc38.noarch 2/73
Installing : flexiblas-3.2.1-3.fc38.ppc64le 3/73
Installing : libquadmath-13.0.0-0.4.fc38.ppc64le 4/73
Installing : libgfortran-13.0.0-0.4.fc38.ppc64le 5/73
Installing : libwebp-1.2.4-2.fc38.ppc64le 6/73
Installing : libmpc-1.2.1-5.fc38.ppc64le 7/73
Installing : libjpeg-turbo-2.1.4-1.fc38.ppc64le 8/73
Installing : cpp-13.0.0-0.4.fc38.ppc64le 9/73
Installing : pyproject-rpm-macros-1.5.0-1.fc38.noarch 10/73
Installing : python-setuptools-wheel-65.5.1-1.fc38.noarch 11/73
Installing : python-pip-wheel-22.3.1-1.fc38.noarch 12/73
Installing : openblas-0.3.21-4.fc38.ppc64le 13/73
Installing : openblas-openmp-0.3.21-4.fc38.ppc64le 14/73
Installing : flexiblas-netlib-3.2.1-3.fc38.ppc64le 15/73
Installing : flexiblas-openblas-openmp-3.2.1-3.fc38.ppc64le 16/73
Installing : kernel-headers-6.1.0-1.fc38.ppc64le 17/73
Installing : glibc-devel-2.36.9000-19.fc38.ppc64le 18/73
Installing : libxcrypt-devel-4.4.33-5.fc38.ppc64le 19/73
Installing : fonts-filesystem-1:2.0.5-10.fc38.noarch 20/73
Installing : dejavu-sans-fonts-2.37-19.fc37.noarch 21/73
Installing : libubsan-13.0.0-0.4.fc38.ppc64le 22/73
Installing : libtool-ltdl-2.4.7-3.0.1.fc38.ppc64le 23/73
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Installing : libasan-13.0.0-0.4.fc38.ppc64le 25/73
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Installing : protobuf-3.19.6-1.fc38.ppc64le 27/73
Installing : openjpeg2-2.5.0-2.fc38.ppc64le 28/73
Installing : mpdecimal-2.5.1-4.fc38.ppc64le 29/73
Installing : mariadb-connector-c-config-3.2.7-2.fc38.noarch 30/73
Installing : mariadb-connector-c-3.2.7-2.fc38.ppc64le 31/73
Installing : libpq-15.0-2.fc38.ppc64le 32/73
Installing : libpng-2:1.6.37-13.fc38.ppc64le 33/73
Installing : libimagequant-2.17.0-3.fc38.ppc64le 34/73
Installing : libb2-0.98.1-7.fc38.ppc64le 35/73
Installing : libart_lgpl-2.3.21-28.fc38.ppc64le 36/73
Installing : libXau-1.0.11-1.fc38.ppc64le 37/73
Installing : libxcb-1.13.1-10.fc38.ppc64le 38/73
Installing : lcms2-2.14-1.fc38.ppc64le 39/73
Installing : jbigkit-libs-2.1-24.fc38.ppc64le 40/73
Installing : libtiff-4.4.0-4.fc38.ppc64le 41/73
Installing : graphite2-1.3.14-10.fc38.ppc64le 42/73
Installing : gnutls-3.7.8-9.fc38.ppc64le 43/73
Installing : glib2-2.74.1-2.fc38.ppc64le 44/73
Installing : harfbuzz-6.0.0-1.fc38.ppc64le 45/73
Installing : freetype-2.12.1-3.fc38.ppc64le 46/73
Installing : gc-8.2.2-1.fc38.ppc64le 47/73
Installing : guile22-2.2.7-6.fc38.ppc64le 48/73
Installing : make-1:4.3-11.fc38.ppc64le 49/73
Installing : gcc-13.0.0-0.4.fc38.ppc64le 50/73
Running scriptlet: gcc-13.0.0-0.4.fc38.ppc64le 50/73
Installing : fribidi-1.0.12-2.fc38.ppc64le 51/73
Installing : libraqm-0.8.0-2.fc38.ppc64le 52/73
Installing : expat-2.5.0-1.fc38.ppc64le 53/73
Installing : python3-3.11.1-1.fc38.ppc64le 54/73
Installing : python3-libs-3.11.1-1.fc38.ppc64le 55/73
Installing : python3-pyparsing-3.0.9-2.fc37.noarch 56/73
Installing : python3-packaging-21.3-7.fc38.noarch 57/73
Installing : python3-rpm-generators-13-2.fc37.noarch 58/73
Installing : python3-protobuf-3.19.6-1.fc38.ppc64le 59/73
Installing : python3-olefile-0.46-18.fc37.noarch 60/73
Installing : python3-pillow-9.3.0-2.fc38.ppc64le 61/73
Installing : python3-setuptools-65.5.1-1.fc38.noarch 62/73
Installing : python3-six-1.16.0-8.fc37.noarch 63/73
Installing : python3-isodate-0.6.1-5.fc37.noarch 64/73
Installing : python3-rdflib-6.2.0-1.fc38.noarch 65/73
Installing : python3-reportlab-3.6.12-1.fc38.ppc64le 66/73
Installing : mysql-connector-python3-8.0.21-7.fc37.noarch 67/73
Installing : python3-devel-3.11.1-1.fc38.ppc64le 68/73
Installing : python3-numpy-1:1.23.5-1.fc38.ppc64le 69/73
Installing : python3-mysqlclient-2.1.1-2.fc38.ppc64le 70/73
Installing : python3-psycopg2-2.9.3-6.fc37.ppc64le 71/73
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Installing : gcc-plugin-annobin-13.0.0-0.4.fc38.ppc64le 73/73
Running scriptlet: gcc-plugin-annobin-13.0.0-0.4.fc38.ppc64le 73/73
Verifying : expat-2.5.0-1.fc38.ppc64le 1/73
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Verifying : libwebp-1.2.4-2.fc38.ppc64le 22/73
Verifying : libxcb-1.13.1-10.fc38.ppc64le 23/73
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Verifying : python3-packaging-21.3-7.fc38.noarch 64/73
Verifying : python3-pillow-9.3.0-2.fc38.ppc64le 65/73
Verifying : python3-psycopg2-2.9.3-6.fc37.ppc64le 66/73
Verifying : python3-pyparsing-3.0.9-2.fc37.noarch 67/73
Verifying : python3-rdflib-6.2.0-1.fc38.noarch 68/73
Verifying : python3-reportlab-3.6.12-1.fc38.ppc64le 69/73
Verifying : python3-rpm-generators-13-2.fc37.noarch 70/73
Verifying : python3-rpm-macros-3.11-6.fc38.noarch 71/73
Verifying : python3-setuptools-65.5.1-1.fc38.noarch 72/73
Verifying : python3-six-1.16.0-8.fc37.noarch 73/73
Installed:
annobin-docs-10.99-1.0.1.fc38.noarch
annobin-plugin-gcc-10.99-1.0.1.fc38.ppc64le
cpp-13.0.0-0.4.fc38.ppc64le
dejavu-sans-fonts-2.37-19.fc37.noarch
expat-2.5.0-1.fc38.ppc64le
flexiblas-3.2.1-3.fc38.ppc64le
flexiblas-netlib-3.2.1-3.fc38.ppc64le
flexiblas-openblas-openmp-3.2.1-3.fc38.ppc64le
fonts-filesystem-1:2.0.5-10.fc38.noarch
freetype-2.12.1-3.fc38.ppc64le
fribidi-1.0.12-2.fc38.ppc64le
gc-8.2.2-1.fc38.ppc64le
gcc-13.0.0-0.4.fc38.ppc64le
gcc-plugin-annobin-13.0.0-0.4.fc38.ppc64le
glib2-2.74.1-2.fc38.ppc64le
glibc-devel-2.36.9000-19.fc38.ppc64le
gnutls-3.7.8-9.fc38.ppc64le
graphite2-1.3.14-10.fc38.ppc64le
guile22-2.2.7-6.fc38.ppc64le
harfbuzz-6.0.0-1.fc38.ppc64le
jbigkit-libs-2.1-24.fc38.ppc64le
kernel-headers-6.1.0-1.fc38.ppc64le
lcms2-2.14-1.fc38.ppc64le
libXau-1.0.11-1.fc38.ppc64le
libart_lgpl-2.3.21-28.fc38.ppc64le
libasan-13.0.0-0.4.fc38.ppc64le
libatomic-13.0.0-0.4.fc38.ppc64le
libb2-0.98.1-7.fc38.ppc64le
libgfortran-13.0.0-0.4.fc38.ppc64le
libimagequant-2.17.0-3.fc38.ppc64le
libjpeg-turbo-2.1.4-1.fc38.ppc64le
libmpc-1.2.1-5.fc38.ppc64le
libpng-2:1.6.37-13.fc38.ppc64le
libpq-15.0-2.fc38.ppc64le
libquadmath-13.0.0-0.4.fc38.ppc64le
libraqm-0.8.0-2.fc38.ppc64le
libtiff-4.4.0-4.fc38.ppc64le
libtool-ltdl-2.4.7-3.0.1.fc38.ppc64le
libubsan-13.0.0-0.4.fc38.ppc64le
libwebp-1.2.4-2.fc38.ppc64le
libxcb-1.13.1-10.fc38.ppc64le
libxcrypt-devel-4.4.33-5.fc38.ppc64le
make-1:4.3-11.fc38.ppc64le
mariadb-connector-c-3.2.7-2.fc38.ppc64le
mariadb-connector-c-config-3.2.7-2.fc38.noarch
mpdecimal-2.5.1-4.fc38.ppc64le
mysql-connector-python3-8.0.21-7.fc37.noarch
openblas-0.3.21-4.fc38.ppc64le
openblas-openmp-0.3.21-4.fc38.ppc64le
openjpeg2-2.5.0-2.fc38.ppc64le
protobuf-3.19.6-1.fc38.ppc64le
pyproject-rpm-macros-1.5.0-1.fc38.noarch
python-pip-wheel-22.3.1-1.fc38.noarch
python-rpm-macros-3.11-6.fc38.noarch
python-setuptools-wheel-65.5.1-1.fc38.noarch
python3-3.11.1-1.fc38.ppc64le
python3-devel-3.11.1-1.fc38.ppc64le
python3-isodate-0.6.1-5.fc37.noarch
python3-libs-3.11.1-1.fc38.ppc64le
python3-mysqlclient-2.1.1-2.fc38.ppc64le
python3-numpy-1:1.23.5-1.fc38.ppc64le
python3-olefile-0.46-18.fc37.noarch
python3-packaging-21.3-7.fc38.noarch
python3-pillow-9.3.0-2.fc38.ppc64le
python3-protobuf-3.19.6-1.fc38.ppc64le
python3-psycopg2-2.9.3-6.fc37.ppc64le
python3-pyparsing-3.0.9-2.fc37.noarch
python3-rdflib-6.2.0-1.fc38.noarch
python3-reportlab-3.6.12-1.fc38.ppc64le
python3-rpm-generators-13-2.fc37.noarch
python3-rpm-macros-3.11-6.fc38.noarch
python3-setuptools-65.5.1-1.fc38.noarch
python3-six-1.16.0-8.fc37.noarch
Complete!
Finish: build setup for python-biopython-1.80-1.fc38.src.rpm
Start: rpmbuild python-biopython-1.80-1.fc38.src.rpm
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1669248000
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.FIsFXs
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf python-biopython-1.80
+ /usr/bin/mkdir -p python-biopython-1.80
+ cd python-biopython-1.80
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/biopython-1.80.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ pushd biopython-1.80
~/build/BUILD/python-biopython-1.80/biopython-1.80 ~/build/BUILD/python-biopython-1.80
+ 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' '{}' ';'
~/build/BUILD/python-biopython-1.80
+ popd
+ cp -a biopython-1.80 python3
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.mNff9C
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
~/build/BUILD/python-biopython-1.80/python3 ~/build/BUILD/python-biopython-1.80
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd python-biopython-1.80
+ pushd python3
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -sP'
running build
running build_py
creating build
creating build/lib.linux-ppc64le-cpython-311
creating build/lib.linux-ppc64le-cpython-311/Bio
copying Bio/File.py -> build/lib.linux-ppc64le-cpython-311/Bio
copying Bio/LogisticRegression.py -> build/lib.linux-ppc64le-cpython-311/Bio
copying Bio/MarkovModel.py -> build/lib.linux-ppc64le-cpython-311/Bio
copying Bio/MaxEntropy.py -> build/lib.linux-ppc64le-cpython-311/Bio
copying Bio/NaiveBayes.py -> build/lib.linux-ppc64le-cpython-311/Bio
copying Bio/Seq.py -> build/lib.linux-ppc64le-cpython-311/Bio
copying Bio/SeqFeature.py -> build/lib.linux-ppc64le-cpython-311/Bio
copying Bio/SeqRecord.py -> build/lib.linux-ppc64le-cpython-311/Bio
copying Bio/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio
copying Bio/_utils.py -> build/lib.linux-ppc64le-cpython-311/Bio
copying Bio/bgzf.py -> build/lib.linux-ppc64le-cpython-311/Bio
copying Bio/kNN.py -> build/lib.linux-ppc64le-cpython-311/Bio
copying Bio/pairwise2.py -> build/lib.linux-ppc64le-cpython-311/Bio
creating build/lib.linux-ppc64le-cpython-311/Bio/Affy
copying Bio/Affy/CelFile.py -> build/lib.linux-ppc64le-cpython-311/Bio/Affy
copying Bio/Affy/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Affy
creating build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/AlignInfo.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/a2m.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/bed.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/bigbed.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/bigmaf.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/bigpsl.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/clustal.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/emboss.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/exonerate.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/fasta.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/hhr.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/interfaces.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/maf.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/mauve.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/msf.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/nexus.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/phylip.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/psl.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/sam.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/stockholm.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
copying Bio/Align/tabular.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align
creating build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/_ClustalOmega.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/_Clustalw.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/_Dialign.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/_MSAProbs.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/_Mafft.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/_Muscle.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/_Prank.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/_Probcons.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/_TCoffee.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications
creating build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices
copying Bio/Align/substitution_matrices/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices
creating build/lib.linux-ppc64le-cpython-311/Bio/AlignIO
copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/AlignIO
copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/AlignIO
copying Bio/AlignIO/FastaIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/AlignIO
copying Bio/AlignIO/Interfaces.py -> build/lib.linux-ppc64le-cpython-311/Bio/AlignIO
copying Bio/AlignIO/MafIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/AlignIO
copying Bio/AlignIO/MauveIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/AlignIO
copying Bio/AlignIO/MsfIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/AlignIO
copying Bio/AlignIO/NexusIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/AlignIO
copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/AlignIO
copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/AlignIO
copying Bio/AlignIO/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/AlignIO
creating build/lib.linux-ppc64le-cpython-311/Bio/Alphabet
copying Bio/Alphabet/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Alphabet
creating build/lib.linux-ppc64le-cpython-311/Bio/Application
copying Bio/Application/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Application
creating build/lib.linux-ppc64le-cpython-311/Bio/Blast
copying Bio/Blast/Applications.py -> build/lib.linux-ppc64le-cpython-311/Bio/Blast
copying Bio/Blast/NCBIWWW.py -> build/lib.linux-ppc64le-cpython-311/Bio/Blast
copying Bio/Blast/NCBIXML.py -> build/lib.linux-ppc64le-cpython-311/Bio/Blast
copying Bio/Blast/ParseBlastTable.py -> build/lib.linux-ppc64le-cpython-311/Bio/Blast
copying Bio/Blast/Record.py -> build/lib.linux-ppc64le-cpython-311/Bio/Blast
copying Bio/Blast/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Blast
creating build/lib.linux-ppc64le-cpython-311/Bio/CAPS
copying Bio/CAPS/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/CAPS
creating build/lib.linux-ppc64le-cpython-311/Bio/Cluster
copying Bio/Cluster/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Cluster
creating build/lib.linux-ppc64le-cpython-311/Bio/codonalign
copying Bio/codonalign/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/codonalign
copying Bio/codonalign/codonalignment.py -> build/lib.linux-ppc64le-cpython-311/Bio/codonalign
copying Bio/codonalign/codonseq.py -> build/lib.linux-ppc64le-cpython-311/Bio/codonalign
creating build/lib.linux-ppc64le-cpython-311/Bio/Compass
copying Bio/Compass/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Compass
creating build/lib.linux-ppc64le-cpython-311/Bio/Data
copying Bio/Data/CodonTable.py -> build/lib.linux-ppc64le-cpython-311/Bio/Data
copying Bio/Data/IUPACData.py -> build/lib.linux-ppc64le-cpython-311/Bio/Data
copying Bio/Data/PDBData.py -> build/lib.linux-ppc64le-cpython-311/Bio/Data
copying Bio/Data/SCOPData.py -> build/lib.linux-ppc64le-cpython-311/Bio/Data
copying Bio/Data/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Data
creating build/lib.linux-ppc64le-cpython-311/Bio/Emboss
copying Bio/Emboss/Applications.py -> build/lib.linux-ppc64le-cpython-311/Bio/Emboss
copying Bio/Emboss/Primer3.py -> build/lib.linux-ppc64le-cpython-311/Bio/Emboss
copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-ppc64le-cpython-311/Bio/Emboss
copying Bio/Emboss/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Emboss
creating build/lib.linux-ppc64le-cpython-311/Bio/Entrez
copying Bio/Entrez/Parser.py -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez
copying Bio/Entrez/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez
creating build/lib.linux-ppc64le-cpython-311/Bio/ExPASy
copying Bio/ExPASy/Enzyme.py -> build/lib.linux-ppc64le-cpython-311/Bio/ExPASy
copying Bio/ExPASy/Prodoc.py -> build/lib.linux-ppc64le-cpython-311/Bio/ExPASy
copying Bio/ExPASy/Prosite.py -> build/lib.linux-ppc64le-cpython-311/Bio/ExPASy
copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-ppc64le-cpython-311/Bio/ExPASy
copying Bio/ExPASy/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/ExPASy
copying Bio/ExPASy/cellosaurus.py -> build/lib.linux-ppc64le-cpython-311/Bio/ExPASy
creating build/lib.linux-ppc64le-cpython-311/Bio/GenBank
copying Bio/GenBank/Record.py -> build/lib.linux-ppc64le-cpython-311/Bio/GenBank
copying Bio/GenBank/Scanner.py -> build/lib.linux-ppc64le-cpython-311/Bio/GenBank
copying Bio/GenBank/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/GenBank
copying Bio/GenBank/utils.py -> build/lib.linux-ppc64le-cpython-311/Bio/GenBank
creating build/lib.linux-ppc64le-cpython-311/Bio/Geo
copying Bio/Geo/Record.py -> build/lib.linux-ppc64le-cpython-311/Bio/Geo
copying Bio/Geo/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Geo
creating build/lib.linux-ppc64le-cpython-311/Bio/Graphics
copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-ppc64le-cpython-311/Bio/Graphics
copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-ppc64le-cpython-311/Bio/Graphics
copying Bio/Graphics/Comparative.py -> build/lib.linux-ppc64le-cpython-311/Bio/Graphics
copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-ppc64le-cpython-311/Bio/Graphics
copying Bio/Graphics/Distribution.py -> build/lib.linux-ppc64le-cpython-311/Bio/Graphics
copying Bio/Graphics/KGML_vis.py -> build/lib.linux-ppc64le-cpython-311/Bio/Graphics
copying Bio/Graphics/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Graphics
creating build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram
creating build/lib.linux-ppc64le-cpython-311/Bio/HMM
copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-ppc64le-cpython-311/Bio/HMM
copying Bio/HMM/MarkovModel.py -> build/lib.linux-ppc64le-cpython-311/Bio/HMM
copying Bio/HMM/Trainer.py -> build/lib.linux-ppc64le-cpython-311/Bio/HMM
copying Bio/HMM/Utilities.py -> build/lib.linux-ppc64le-cpython-311/Bio/HMM
copying Bio/HMM/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/HMM
creating build/lib.linux-ppc64le-cpython-311/Bio/KEGG
copying Bio/KEGG/REST.py -> build/lib.linux-ppc64le-cpython-311/Bio/KEGG
copying Bio/KEGG/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/KEGG
creating build/lib.linux-ppc64le-cpython-311/Bio/KEGG/Compound
copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/KEGG/Compound
creating build/lib.linux-ppc64le-cpython-311/Bio/KEGG/Enzyme
copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/KEGG/Enzyme
creating build/lib.linux-ppc64le-cpython-311/Bio/KEGG/Gene
copying Bio/KEGG/Gene/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/KEGG/Gene
creating build/lib.linux-ppc64le-cpython-311/Bio/KEGG/Map
copying Bio/KEGG/Map/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/KEGG/Map
creating build/lib.linux-ppc64le-cpython-311/Bio/PDB
creating build/lib.linux-ppc64le-cpython-311/Bio/PDB/mmtf
copying Bio/PDB/mmtf/DefaultParser.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB/mmtf
copying Bio/PDB/mmtf/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB/mmtf
copying Bio/PDB/mmtf/mmtfio.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB/mmtf
creating build/lib.linux-ppc64le-cpython-311/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-ppc64le-cpython-311/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-ppc64le-cpython-311/Bio/KEGG/KGML
copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/KEGG/KGML
creating build/lib.linux-ppc64le-cpython-311/Bio/Medline
copying Bio/Medline/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Medline
creating build/lib.linux-ppc64le-cpython-311/Bio/motifs
copying Bio/motifs/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/motifs
copying Bio/motifs/alignace.py -> build/lib.linux-ppc64le-cpython-311/Bio/motifs
copying Bio/motifs/clusterbuster.py -> build/lib.linux-ppc64le-cpython-311/Bio/motifs
copying Bio/motifs/mast.py -> build/lib.linux-ppc64le-cpython-311/Bio/motifs
copying Bio/motifs/matrix.py -> build/lib.linux-ppc64le-cpython-311/Bio/motifs
copying Bio/motifs/meme.py -> build/lib.linux-ppc64le-cpython-311/Bio/motifs
copying Bio/motifs/minimal.py -> build/lib.linux-ppc64le-cpython-311/Bio/motifs
copying Bio/motifs/pfm.py -> build/lib.linux-ppc64le-cpython-311/Bio/motifs
copying Bio/motifs/thresholds.py -> build/lib.linux-ppc64le-cpython-311/Bio/motifs
copying Bio/motifs/transfac.py -> build/lib.linux-ppc64le-cpython-311/Bio/motifs
copying Bio/motifs/xms.py -> build/lib.linux-ppc64le-cpython-311/Bio/motifs
creating build/lib.linux-ppc64le-cpython-311/Bio/motifs/applications
copying Bio/motifs/applications/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/motifs/applications
copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-ppc64le-cpython-311/Bio/motifs/applications
creating build/lib.linux-ppc64le-cpython-311/Bio/motifs/jaspar
copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/motifs/jaspar
copying Bio/motifs/jaspar/db.py -> build/lib.linux-ppc64le-cpython-311/Bio/motifs/jaspar
creating build/lib.linux-ppc64le-cpython-311/Bio/Nexus
copying Bio/Nexus/Nexus.py -> build/lib.linux-ppc64le-cpython-311/Bio/Nexus
copying Bio/Nexus/Nodes.py -> build/lib.linux-ppc64le-cpython-311/Bio/Nexus
copying Bio/Nexus/StandardData.py -> build/lib.linux-ppc64le-cpython-311/Bio/Nexus
copying Bio/Nexus/Trees.py -> build/lib.linux-ppc64le-cpython-311/Bio/Nexus
copying Bio/Nexus/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Nexus
creating build/lib.linux-ppc64le-cpython-311/Bio/NMR
copying Bio/NMR/NOEtools.py -> build/lib.linux-ppc64le-cpython-311/Bio/NMR
copying Bio/NMR/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/NMR
copying Bio/NMR/xpktools.py -> build/lib.linux-ppc64le-cpython-311/Bio/NMR
creating build/lib.linux-ppc64le-cpython-311/Bio/Pathway
copying Bio/Pathway/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Pathway
creating build/lib.linux-ppc64le-cpython-311/Bio/Pathway/Rep
copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-ppc64le-cpython-311/Bio/Pathway/Rep
copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-ppc64le-cpython-311/Bio/Pathway/Rep
copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Pathway/Rep
copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/Atom.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/Chain.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/DSSP.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/Dice.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/Entity.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/FragmentMapper.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/HSExposure.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/MMCIFParser.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/Model.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/NACCESS.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/NeighborSearch.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/PDBExceptions.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/PDBIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/PDBList.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/PDBParser.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/PICIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/PSEA.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/Polypeptide.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/Residue.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/ResidueDepth.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/SASA.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/SCADIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/Selection.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/Structure.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/StructureAlignment.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/StructureBuilder.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/Superimposer.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/cealign.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/ic_data.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/ic_rebuild.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/internal_coords.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/mmcifio.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/qcprot.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/vectors.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
creating build/lib.linux-ppc64le-cpython-311/Bio/phenotype
copying Bio/phenotype/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/phenotype
copying Bio/phenotype/phen_micro.py -> build/lib.linux-ppc64le-cpython-311/Bio/phenotype
copying Bio/phenotype/pm_fitting.py -> build/lib.linux-ppc64le-cpython-311/Bio/phenotype
creating build/lib.linux-ppc64le-cpython-311/Bio/PopGen
copying Bio/PopGen/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/PopGen
creating build/lib.linux-ppc64le-cpython-311/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/Controller.py -> build/lib.linux-ppc64le-cpython-311/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/EasyController.py -> build/lib.linux-ppc64le-cpython-311/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-ppc64le-cpython-311/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-ppc64le-cpython-311/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/PopGen/GenePop
creating build/lib.linux-ppc64le-cpython-311/Bio/Restriction
copying Bio/Restriction/PrintFormat.py -> build/lib.linux-ppc64le-cpython-311/Bio/Restriction
copying Bio/Restriction/Restriction.py -> build/lib.linux-ppc64le-cpython-311/Bio/Restriction
copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-ppc64le-cpython-311/Bio/Restriction
copying Bio/Restriction/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Restriction
creating build/lib.linux-ppc64le-cpython-311/Bio/SCOP
copying Bio/SCOP/Cla.py -> build/lib.linux-ppc64le-cpython-311/Bio/SCOP
copying Bio/SCOP/Des.py -> build/lib.linux-ppc64le-cpython-311/Bio/SCOP
copying Bio/SCOP/Dom.py -> build/lib.linux-ppc64le-cpython-311/Bio/SCOP
copying Bio/SCOP/Hie.py -> build/lib.linux-ppc64le-cpython-311/Bio/SCOP
copying Bio/SCOP/Raf.py -> build/lib.linux-ppc64le-cpython-311/Bio/SCOP
copying Bio/SCOP/Residues.py -> build/lib.linux-ppc64le-cpython-311/Bio/SCOP
copying Bio/SCOP/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/SCOP
creating build/lib.linux-ppc64le-cpython-311/Bio/SearchIO
copying Bio/SearchIO/BlatIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO
copying Bio/SearchIO/FastaIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO
copying Bio/SearchIO/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO
copying Bio/SearchIO/_index.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO
copying Bio/SearchIO/_utils.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO
creating build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/NCBIStandalone.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/ParserSupport.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_legacy
creating build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_model
copying Bio/SearchIO/_model/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_model
copying Bio/SearchIO/_model/_base.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hit.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hsp.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_model
copying Bio/SearchIO/_model/query.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_model
creating build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_text.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/BlastIO
creating build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/HHsuiteIO
copying Bio/SearchIO/HHsuiteIO/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/HHsuiteIO
copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/HHsuiteIO
creating build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/HmmerIO
creating build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/ExonerateIO
creating build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/InterproscanIO
creating build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/AbiIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/AceIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/FastaIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/GckIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/IgIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/Interfaces.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/NibIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/PdbIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/PhdIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/PirIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/QualityIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/SffIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/SnapGeneIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/SwissIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/TabIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/TwoBitIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/XdnaIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/SeqIO/_index.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
creating build/lib.linux-ppc64le-cpython-311/Bio/SeqUtils
copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsage.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsageIndices.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqUtils
copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqUtils
copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqUtils
copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqUtils
copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqUtils
copying Bio/SeqUtils/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqUtils
copying Bio/SeqUtils/lcc.py -> build/lib.linux-ppc64le-cpython-311/Bio/SeqUtils
creating build/lib.linux-ppc64le-cpython-311/Bio/Sequencing
copying Bio/Sequencing/Ace.py -> build/lib.linux-ppc64le-cpython-311/Bio/Sequencing
copying Bio/Sequencing/Phd.py -> build/lib.linux-ppc64le-cpython-311/Bio/Sequencing
copying Bio/Sequencing/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Sequencing
creating build/lib.linux-ppc64le-cpython-311/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_Novoalign.py -> build/lib.linux-ppc64le-cpython-311/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_bwa.py -> build/lib.linux-ppc64le-cpython-311/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_samtools.py -> build/lib.linux-ppc64le-cpython-311/Bio/Sequencing/Applications
creating build/lib.linux-ppc64le-cpython-311/Bio/SVDSuperimposer
copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/SVDSuperimposer
creating build/lib.linux-ppc64le-cpython-311/Bio/PDB/QCPSuperimposer
copying Bio/PDB/QCPSuperimposer/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/PDB/QCPSuperimposer
creating build/lib.linux-ppc64le-cpython-311/Bio/SwissProt
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copying Bio/SwissProt/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/SwissProt
creating build/lib.linux-ppc64le-cpython-311/Bio/TogoWS
copying Bio/TogoWS/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/TogoWS
creating build/lib.linux-ppc64le-cpython-311/Bio/Phylo
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copying Bio/Phylo/CDAO.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo
copying Bio/Phylo/CDAOIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo
copying Bio/Phylo/Consensus.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo
copying Bio/Phylo/NeXML.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo
copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo
copying Bio/Phylo/Newick.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo
copying Bio/Phylo/NewickIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo
copying Bio/Phylo/NexusIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo
copying Bio/Phylo/PhyloXML.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo
copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo
copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo
copying Bio/Phylo/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo
copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo
copying Bio/Phylo/_io.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo
copying Bio/Phylo/_utils.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo
creating build/lib.linux-ppc64le-cpython-311/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Fasttree.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Phyml.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Raxml.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo/Applications
copying Bio/Phylo/Applications/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo/Applications
creating build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PAML
copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PAML
copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PAML
copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PAML
copying Bio/Phylo/PAML/codeml.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PAML
copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PAML
creating build/lib.linux-ppc64le-cpython-311/Bio/UniGene
copying Bio/UniGene/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/UniGene
creating build/lib.linux-ppc64le-cpython-311/Bio/UniProt
copying Bio/UniProt/GOA.py -> build/lib.linux-ppc64le-cpython-311/Bio/UniProt
copying Bio/UniProt/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/UniProt
creating build/lib.linux-ppc64le-cpython-311/Bio/Wise
copying Bio/Wise/__init__.py -> build/lib.linux-ppc64le-cpython-311/Bio/Wise
copying Bio/Wise/dnal.py -> build/lib.linux-ppc64le-cpython-311/Bio/Wise
copying Bio/Wise/psw.py -> build/lib.linux-ppc64le-cpython-311/Bio/Wise
creating build/lib.linux-ppc64le-cpython-311/BioSQL
copying BioSQL/__init__.py -> build/lib.linux-ppc64le-cpython-311/BioSQL
copying BioSQL/Loader.py -> build/lib.linux-ppc64le-cpython-311/BioSQL
copying BioSQL/DBUtils.py -> build/lib.linux-ppc64le-cpython-311/BioSQL
copying BioSQL/BioSeqDatabase.py -> build/lib.linux-ppc64le-cpython-311/BioSQL
copying BioSQL/BioSeq.py -> build/lib.linux-ppc64le-cpython-311/BioSQL
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'
warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
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
adding license file 'LICENSE'
adding license file 'LICENSE.rst'
warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt'
writing manifest file 'biopython.egg-info/SOURCES.txt'
/usr/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'Bio.Align.substitution_matrices.data' as data is deprecated, please list it in `packages`.
!!
############################
# Package would be ignored #
############################
Python recognizes 'Bio.Align.substitution_matrices.data' as an importable package,
but it is not listed in the `packages` configuration of setuptools.
'Bio.Align.substitution_matrices.data' has been automatically added to the distribution only
because it may contain data files, but this behavior is likely to change
in future versions of setuptools (and therefore is considered deprecated).
Please make sure that 'Bio.Align.substitution_matrices.data' is included as a package by using
the `packages` configuration field or the proper discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" and "data files" on setuptools
documentation page.
!!
check.warn(importable)
/usr/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'Bio.Entrez.DTDs' as data is deprecated, please list it in `packages`.
!!
############################
# Package would be ignored #
############################
Python recognizes 'Bio.Entrez.DTDs' as an importable package,
but it is not listed in the `packages` configuration of setuptools.
'Bio.Entrez.DTDs' has been automatically added to the distribution only
because it may contain data files, but this behavior is likely to change
in future versions of setuptools (and therefore is considered deprecated).
Please make sure that 'Bio.Entrez.DTDs' is included as a package by using
the `packages` configuration field or the proper discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" and "data files" on setuptools
documentation page.
!!
check.warn(importable)
/usr/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'Bio.Entrez.XSDs' as data is deprecated, please list it in `packages`.
!!
############################
# Package would be ignored #
############################
Python recognizes 'Bio.Entrez.XSDs' as an importable package,
but it is not listed in the `packages` configuration of setuptools.
'Bio.Entrez.XSDs' has been automatically added to the distribution only
because it may contain data files, but this behavior is likely to change
in future versions of setuptools (and therefore is considered deprecated).
Please make sure that 'Bio.Entrez.XSDs' is included as a package by using
the `packages` configuration field or the proper discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" and "data files" on setuptools
documentation page.
!!
check.warn(importable)
copying Bio/cpairwise2module.c -> build/lib.linux-ppc64le-cpython-311/Bio
copying Bio/Align/_aligners.c -> build/lib.linux-ppc64le-cpython-311/Bio/Align
creating build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER22 -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER6 -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER74 -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLASTN -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLASTP -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM45 -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM50 -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM62 -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM80 -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM90 -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/DAYHOFF -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/FENG -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/GENETIC -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/GONNET1992 -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/HOXD70 -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/JOHNSON -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/JONES -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/LEVIN -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MCLACHLAN -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MDM78 -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MEGABLAST -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/NUC.4.4 -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM250 -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM30 -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM70 -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/RAO -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/RISLER -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/SCHNEIDER -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/STR -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/TRANS -> build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Cluster/cluster.c -> build/lib.linux-ppc64le-cpython-311/Bio/Cluster
copying Bio/Cluster/cluster.h -> build/lib.linux-ppc64le-cpython-311/Bio/Cluster
copying Bio/Cluster/clustermodule.c -> build/lib.linux-ppc64le-cpython-311/Bio/Cluster
creating build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/BITS-embedded-index2.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/BITS-question-answer2.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-chars1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-common1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-display1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-format1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-funding1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-link1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-list1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-math1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-modules1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-notat1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-para1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-phrase1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-references1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-related-object1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-section1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Features.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Access.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_General.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
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copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/xhtml-table-1.mod -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs
creating build/lib.linux-ppc64le-cpython-311/Bio/Entrez/XSDs
copying Bio/Entrez/XSDs/IPGReportSet.xsd -> build/lib.linux-ppc64le-cpython-311/Bio/Entrez/XSDs
copying Bio/motifs/_pwm.c -> build/lib.linux-ppc64le-cpython-311/Bio/motifs
copying Bio/Nexus/cnexus.c -> build/lib.linux-ppc64le-cpython-311/Bio/Nexus
copying Bio/PDB/ccealignmodule.c -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/PDB/kdtrees.c -> build/lib.linux-ppc64le-cpython-311/Bio/PDB
copying Bio/SeqIO/_twoBitIO.c -> build/lib.linux-ppc64le-cpython-311/Bio/SeqIO
copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> build/lib.linux-ppc64le-cpython-311/Bio/PDB/QCPSuperimposer
running build_ext
building 'Bio.Align._aligners' extension
creating build/temp.linux-ppc64le-cpython-311
creating build/temp.linux-ppc64le-cpython-311/Bio
creating build/temp.linux-ppc64le-cpython-311/Bio/Align
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/Align/_aligners.c -o build/temp.linux-ppc64le-cpython-311/Bio/Align/_aligners.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-ppc64le-cpython-311/Bio/Align/_aligners.o -L/usr/lib64 -o build/lib.linux-ppc64le-cpython-311/Bio/Align/_aligners.cpython-311-powerpc64le-linux-gnu.so
building 'Bio.cpairwise2' extension
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/cpairwise2module.c -o build/temp.linux-ppc64le-cpython-311/Bio/cpairwise2module.o
Bio/cpairwise2module.c: In function ‘_get_match_score’:
Bio/cpairwise2module.c:60:5: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations]
60 | if(!(py_result = PyEval_CallObject(py_match_fn, py_arglist)))
| ^~
In file included from /usr/include/python3.11/Python.h:95,
from Bio/cpairwise2module.c:16:
/usr/include/python3.11/ceval.h:27:43: note: declared here
27 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-ppc64le-cpython-311/Bio/cpairwise2module.o -L/usr/lib64 -o build/lib.linux-ppc64le-cpython-311/Bio/cpairwise2.cpython-311-powerpc64le-linux-gnu.so
building 'Bio.Nexus.cnexus' extension
creating build/temp.linux-ppc64le-cpython-311/Bio/Nexus
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/Nexus/cnexus.c -o build/temp.linux-ppc64le-cpython-311/Bio/Nexus/cnexus.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-ppc64le-cpython-311/Bio/Nexus/cnexus.o -L/usr/lib64 -o build/lib.linux-ppc64le-cpython-311/Bio/Nexus/cnexus.cpython-311-powerpc64le-linux-gnu.so
building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension
creating build/temp.linux-ppc64le-cpython-311/Bio/PDB
creating build/temp.linux-ppc64le-cpython-311/Bio/PDB/QCPSuperimposer
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-ppc64le-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-ppc64le-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.o -L/usr/lib64 -o build/lib.linux-ppc64le-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-powerpc64le-linux-gnu.so
building 'Bio.motifs._pwm' extension
creating build/temp.linux-ppc64le-cpython-311/Bio/motifs
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/motifs/_pwm.c -o build/temp.linux-ppc64le-cpython-311/Bio/motifs/_pwm.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-ppc64le-cpython-311/Bio/motifs/_pwm.o -L/usr/lib64 -o build/lib.linux-ppc64le-cpython-311/Bio/motifs/_pwm.cpython-311-powerpc64le-linux-gnu.so
building 'Bio.Cluster._cluster' extension
creating build/temp.linux-ppc64le-cpython-311/Bio/Cluster
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/Cluster/cluster.c -o build/temp.linux-ppc64le-cpython-311/Bio/Cluster/cluster.o
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/Cluster/clustermodule.c -o build/temp.linux-ppc64le-cpython-311/Bio/Cluster/clustermodule.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-ppc64le-cpython-311/Bio/Cluster/cluster.o build/temp.linux-ppc64le-cpython-311/Bio/Cluster/clustermodule.o -L/usr/lib64 -o build/lib.linux-ppc64le-cpython-311/Bio/Cluster/_cluster.cpython-311-powerpc64le-linux-gnu.so
building 'Bio.PDB.kdtrees' extension
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/PDB/kdtrees.c -o build/temp.linux-ppc64le-cpython-311/Bio/PDB/kdtrees.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-ppc64le-cpython-311/Bio/PDB/kdtrees.o -L/usr/lib64 -o build/lib.linux-ppc64le-cpython-311/Bio/PDB/kdtrees.cpython-311-powerpc64le-linux-gnu.so
building 'Bio.PDB.ccealign' extension
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-ppc64le-cpython-311/Bio/PDB/ccealignmodule.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-ppc64le-cpython-311/Bio/PDB/ccealignmodule.o -L/usr/lib64 -o build/lib.linux-ppc64le-cpython-311/Bio/PDB/ccealign.cpython-311-powerpc64le-linux-gnu.so
building 'Bio.SeqIO._twoBitIO' extension
creating build/temp.linux-ppc64le-cpython-311/Bio/SeqIO
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-ppc64le-cpython-311/Bio/SeqIO/_twoBitIO.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-ppc64le-cpython-311/Bio/SeqIO/_twoBitIO.o -L/usr/lib64 -o build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/_twoBitIO.cpython-311-powerpc64le-linux-gnu.so
+ popd
+ RPM_EC=0
~/build/BUILD/python-biopython-1.80
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.PehUSy
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le
++ dirname /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
~/build/BUILD/python-biopython-1.80/python3 ~/build/BUILD/python-biopython-1.80
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd python-biopython-1.80
+ pushd python3
+ /usr/bin/python3 setup.py install -O1 --skip-build --root=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le --install-data=/usr/share/python-biopython
running install
/usr/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running install_lib
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/BioSQL
copying build/lib.linux-ppc64le-cpython-311/BioSQL/BioSeq.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/BioSQL
copying build/lib.linux-ppc64le-cpython-311/BioSQL/BioSeqDatabase.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/BioSQL
copying build/lib.linux-ppc64le-cpython-311/BioSQL/DBUtils.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/BioSQL
copying build/lib.linux-ppc64le-cpython-311/BioSQL/Loader.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/BioSQL
copying build/lib.linux-ppc64le-cpython-311/BioSQL/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/BioSQL
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio
copying build/lib.linux-ppc64le-cpython-311/Bio/cpairwise2.cpython-311-powerpc64le-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio
copying build/lib.linux-ppc64le-cpython-311/Bio/cpairwise2module.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Wise
copying build/lib.linux-ppc64le-cpython-311/Bio/Wise/psw.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Wise
copying build/lib.linux-ppc64le-cpython-311/Bio/Wise/dnal.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Wise
copying build/lib.linux-ppc64le-cpython-311/Bio/Wise/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Wise
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/UniProt
copying build/lib.linux-ppc64le-cpython-311/Bio/UniProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/UniProt
copying build/lib.linux-ppc64le-cpython-311/Bio/UniProt/GOA.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/UniProt
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/UniGene
copying build/lib.linux-ppc64le-cpython-311/Bio/UniGene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/UniGene
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PAML/yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PAML/codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PAML/chi2.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PAML/baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PAML/_parse_yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PAML/_parse_codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PAML/_parse_baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PAML/_paml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PAML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/Applications/_Raxml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/Applications/_Phyml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/Applications/_Fasttree.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/_io.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/_cdao_owl.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/TreeConstruction.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PhyloXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/PhyloXML.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/NewickIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/Newick.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/NeXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/NeXML.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/Consensus.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/CDAOIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/CDAO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-ppc64le-cpython-311/Bio/Phylo/BaseTree.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/TogoWS
copying build/lib.linux-ppc64le-cpython-311/Bio/TogoWS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/TogoWS
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SwissProt
copying build/lib.linux-ppc64le-cpython-311/Bio/SwissProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SwissProt
copying build/lib.linux-ppc64le-cpython-311/Bio/SwissProt/KeyWList.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SwissProt
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SVDSuperimposer
copying build/lib.linux-ppc64le-cpython-311/Bio/SVDSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SVDSuperimposer
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Sequencing
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Sequencing/Applications/_samtools.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Sequencing/Applications/_bwa.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Sequencing/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Sequencing/Applications/_Novoalign.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Sequencing/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Sequencing
copying build/lib.linux-ppc64le-cpython-311/Bio/Sequencing/Phd.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Sequencing
copying build/lib.linux-ppc64le-cpython-311/Bio/Sequencing/Ace.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Sequencing
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqUtils
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqUtils/lcc.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqUtils
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqUtils/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqUtils
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqUtils/ProtParamData.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqUtils
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqUtils/ProtParam.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqUtils
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqUtils/MeltingTemp.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqUtils
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqUtils/IsoelectricPoint.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqUtils
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqUtils/CodonUsageIndices.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqUtils
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqUtils/CodonUsage.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqUtils
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqUtils/CheckSum.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqUtils
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/_twoBitIO.cpython-311-powerpc64le-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/_twoBitIO.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/XdnaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/UniprotIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/TwoBitIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/TabIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/SwissIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/SnapGeneIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/SffIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/SeqXmlIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/QualityIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/PirIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/PhdIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/PdbIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/NibIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/InsdcIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/IgIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/GckIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/AceIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqIO/AbiIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/InterproscanIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/InterproscanIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/InterproscanIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/InterproscanIO
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/ExonerateIO/exonerate_text.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/ExonerateIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/ExonerateIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/HmmerIO/hmmer3_text.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/HmmerIO/hmmer2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/HmmerIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/HmmerIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/HHsuiteIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/HHsuiteIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/HHsuiteIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/HHsuiteIO
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/BlastIO/blast_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/BlastIO/blast_text.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/BlastIO/blast_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/BlastIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_model/query.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_model/hsp.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_model/hit.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_model/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_model/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_legacy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_legacy/ParserSupport.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_legacy/NCBIStandalone.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO
copying build/lib.linux-ppc64le-cpython-311/Bio/SearchIO/BlatIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SCOP
copying build/lib.linux-ppc64le-cpython-311/Bio/SCOP/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SCOP
copying build/lib.linux-ppc64le-cpython-311/Bio/SCOP/Residues.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SCOP
copying build/lib.linux-ppc64le-cpython-311/Bio/SCOP/Raf.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SCOP
copying build/lib.linux-ppc64le-cpython-311/Bio/SCOP/Hie.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SCOP
copying build/lib.linux-ppc64le-cpython-311/Bio/SCOP/Dom.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SCOP
copying build/lib.linux-ppc64le-cpython-311/Bio/SCOP/Des.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SCOP
copying build/lib.linux-ppc64le-cpython-311/Bio/SCOP/Cla.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SCOP
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Restriction
copying build/lib.linux-ppc64le-cpython-311/Bio/Restriction/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Restriction
copying build/lib.linux-ppc64le-cpython-311/Bio/Restriction/Restriction_Dictionary.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Restriction
copying build/lib.linux-ppc64le-cpython-311/Bio/Restriction/Restriction.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Restriction
copying build/lib.linux-ppc64le-cpython-311/Bio/Restriction/PrintFormat.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Restriction
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PopGen
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-ppc64le-cpython-311/Bio/PopGen/GenePop/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-ppc64le-cpython-311/Bio/PopGen/GenePop/LargeFileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-ppc64le-cpython-311/Bio/PopGen/GenePop/FileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-ppc64le-cpython-311/Bio/PopGen/GenePop/EasyController.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-ppc64le-cpython-311/Bio/PopGen/GenePop/Controller.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-ppc64le-cpython-311/Bio/PopGen/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PopGen
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/phenotype
copying build/lib.linux-ppc64le-cpython-311/Bio/phenotype/pm_fitting.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/phenotype
copying build/lib.linux-ppc64le-cpython-311/Bio/phenotype/phen_micro.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/phenotype
copying build/lib.linux-ppc64le-cpython-311/Bio/phenotype/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/phenotype
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Pathway
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep
copying build/lib.linux-ppc64le-cpython-311/Bio/Pathway/Rep/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep
copying build/lib.linux-ppc64le-cpython-311/Bio/Pathway/Rep/MultiGraph.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep
copying build/lib.linux-ppc64le-cpython-311/Bio/Pathway/Rep/Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep
copying build/lib.linux-ppc64le-cpython-311/Bio/Pathway/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Pathway
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/NMR
copying build/lib.linux-ppc64le-cpython-311/Bio/NMR/xpktools.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/NMR
copying build/lib.linux-ppc64le-cpython-311/Bio/NMR/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/NMR
copying build/lib.linux-ppc64le-cpython-311/Bio/NMR/NOEtools.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/NMR
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Nexus
copying build/lib.linux-ppc64le-cpython-311/Bio/Nexus/cnexus.cpython-311-powerpc64le-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Nexus
copying build/lib.linux-ppc64le-cpython-311/Bio/Nexus/cnexus.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Nexus
copying build/lib.linux-ppc64le-cpython-311/Bio/Nexus/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Nexus
copying build/lib.linux-ppc64le-cpython-311/Bio/Nexus/Trees.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Nexus
copying build/lib.linux-ppc64le-cpython-311/Bio/Nexus/StandardData.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Nexus
copying build/lib.linux-ppc64le-cpython-311/Bio/Nexus/Nodes.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Nexus
copying build/lib.linux-ppc64le-cpython-311/Bio/Nexus/Nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Nexus
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs
copying build/lib.linux-ppc64le-cpython-311/Bio/motifs/_pwm.cpython-311-powerpc64le-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs
copying build/lib.linux-ppc64le-cpython-311/Bio/motifs/_pwm.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs/jaspar
copying build/lib.linux-ppc64le-cpython-311/Bio/motifs/jaspar/db.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs/jaspar
copying build/lib.linux-ppc64le-cpython-311/Bio/motifs/jaspar/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs/jaspar
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs/applications
copying build/lib.linux-ppc64le-cpython-311/Bio/motifs/applications/_xxmotif.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs/applications
copying build/lib.linux-ppc64le-cpython-311/Bio/motifs/applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs/applications
copying build/lib.linux-ppc64le-cpython-311/Bio/motifs/xms.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs
copying build/lib.linux-ppc64le-cpython-311/Bio/motifs/transfac.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs
copying build/lib.linux-ppc64le-cpython-311/Bio/motifs/thresholds.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs
copying build/lib.linux-ppc64le-cpython-311/Bio/motifs/pfm.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs
copying build/lib.linux-ppc64le-cpython-311/Bio/motifs/minimal.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs
copying build/lib.linux-ppc64le-cpython-311/Bio/motifs/meme.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs
copying build/lib.linux-ppc64le-cpython-311/Bio/motifs/matrix.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs
copying build/lib.linux-ppc64le-cpython-311/Bio/motifs/mast.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs
copying build/lib.linux-ppc64le-cpython-311/Bio/motifs/clusterbuster.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs
copying build/lib.linux-ppc64le-cpython-311/Bio/motifs/alignace.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs
copying build/lib.linux-ppc64le-cpython-311/Bio/motifs/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Medline
copying build/lib.linux-ppc64le-cpython-311/Bio/Medline/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Medline
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/ccealign.cpython-311-powerpc64le-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/kdtrees.cpython-311-powerpc64le-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/kdtrees.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/ccealignmodule.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-powerpc64le-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/QCPSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/vectors.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/qcprot.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/parse_pdb_header.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/mmcifio.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/internal_coords.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/ic_rebuild.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/ic_data.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/cealign.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/Superimposer.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/StructureBuilder.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/StructureAlignment.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/Structure.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/Selection.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/SCADIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/SASA.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/ResidueDepth.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/Residue.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/Polypeptide.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/PSEA.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/PICIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/PDBParser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/PDBList.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/PDBIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/PDBExceptions.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/NeighborSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/NACCESS.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/Model.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/MMCIFParser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/MMCIF2Dict.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/HSExposure.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/FragmentMapper.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/Entity.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/Dice.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/DSSP.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/Chain.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/Atom.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/AbstractPropertyMap.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/mmtf/mmtfio.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/mmtf/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf
copying build/lib.linux-ppc64le-cpython-311/Bio/PDB/mmtf/DefaultParser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/KEGG
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML
copying build/lib.linux-ppc64le-cpython-311/Bio/KEGG/KGML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML
copying build/lib.linux-ppc64le-cpython-311/Bio/KEGG/KGML/KGML_pathway.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML
copying build/lib.linux-ppc64le-cpython-311/Bio/KEGG/KGML/KGML_parser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/KEGG/Map
copying build/lib.linux-ppc64le-cpython-311/Bio/KEGG/Map/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/KEGG/Map
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/KEGG/Gene
copying build/lib.linux-ppc64le-cpython-311/Bio/KEGG/Gene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/KEGG/Gene
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/KEGG/Enzyme
copying build/lib.linux-ppc64le-cpython-311/Bio/KEGG/Enzyme/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/KEGG/Enzyme
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/KEGG/Compound
copying build/lib.linux-ppc64le-cpython-311/Bio/KEGG/Compound/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/KEGG/Compound
copying build/lib.linux-ppc64le-cpython-311/Bio/KEGG/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/KEGG
copying build/lib.linux-ppc64le-cpython-311/Bio/KEGG/REST.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/KEGG
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/HMM
copying build/lib.linux-ppc64le-cpython-311/Bio/HMM/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/HMM
copying build/lib.linux-ppc64le-cpython-311/Bio/HMM/Utilities.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/HMM
copying build/lib.linux-ppc64le-cpython-311/Bio/HMM/Trainer.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/HMM
copying build/lib.linux-ppc64le-cpython-311/Bio/HMM/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/HMM
copying build/lib.linux-ppc64le-cpython-311/Bio/HMM/DynamicProgramming.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/HMM
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram/_Track.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram/_GraphSet.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram/_Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram/_Feature.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram/_Diagram.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram/_CrossLink.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram/_Colors.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-ppc64le-cpython-311/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-ppc64le-cpython-311/Bio/Graphics/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics
copying build/lib.linux-ppc64le-cpython-311/Bio/Graphics/KGML_vis.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics
copying build/lib.linux-ppc64le-cpython-311/Bio/Graphics/Distribution.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics
copying build/lib.linux-ppc64le-cpython-311/Bio/Graphics/DisplayRepresentation.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics
copying build/lib.linux-ppc64le-cpython-311/Bio/Graphics/Comparative.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics
copying build/lib.linux-ppc64le-cpython-311/Bio/Graphics/ColorSpiral.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics
copying build/lib.linux-ppc64le-cpython-311/Bio/Graphics/BasicChromosome.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Graphics
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Geo
copying build/lib.linux-ppc64le-cpython-311/Bio/Geo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Geo
copying build/lib.linux-ppc64le-cpython-311/Bio/Geo/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Geo
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/GenBank
copying build/lib.linux-ppc64le-cpython-311/Bio/GenBank/utils.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/GenBank
copying build/lib.linux-ppc64le-cpython-311/Bio/GenBank/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/GenBank
copying build/lib.linux-ppc64le-cpython-311/Bio/GenBank/Scanner.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/GenBank
copying build/lib.linux-ppc64le-cpython-311/Bio/GenBank/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/GenBank
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/ExPASy
copying build/lib.linux-ppc64le-cpython-311/Bio/ExPASy/cellosaurus.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/ExPASy
copying build/lib.linux-ppc64le-cpython-311/Bio/ExPASy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/ExPASy
copying build/lib.linux-ppc64le-cpython-311/Bio/ExPASy/ScanProsite.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/ExPASy
copying build/lib.linux-ppc64le-cpython-311/Bio/ExPASy/Prosite.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/ExPASy
copying build/lib.linux-ppc64le-cpython-311/Bio/ExPASy/Prodoc.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/ExPASy
copying build/lib.linux-ppc64le-cpython-311/Bio/ExPASy/Enzyme.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/ExPASy
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/XSDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/XSDs/IPGReportSet.xsd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/XSDs
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/xmlspecchars.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/xhtml-table-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/taxon.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/section.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/references.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/pubmed_190101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/pubmed_180601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/pubmed_180101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/pubmed_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/pubmed_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/pubmed_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/pubmed_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/pubmed_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/pubmed_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/pubmed_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/pubmed_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/pubmed_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/pubmed_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/pubmed_020114.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/pmc-1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/phrase.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/para.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/notat.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmserials_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmserials_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/mmlextra.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/mmlalias.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/mathmlsetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/mathml3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/mathml3-qname1.mod -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/mathml2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/mathml2-qname-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/math.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/list.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/link.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/journalmeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isotech.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isopub.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isonum.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isomscr.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isomopf.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isomfrk.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isolat2.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isolat1.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isogrk4.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isogrk3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isogrk2.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isogrk1.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isodia.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isocyr2.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isocyr1.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isobox.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isoamsr.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isoamso.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isoamsn.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isoamsc.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isoamsb.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/isoamsa.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/htmltable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/format.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/esummary-v1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/esearch.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/elink_020122.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/einfo.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/egquery.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/eSummary_041029.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/eSpell.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/eSearch_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/ePost_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/eLink_101123.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/eLink_090910.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/eInfo_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/display.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/default-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/default-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/common.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/chars.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/bookdoc_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/bookdoc_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/bookdoc_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/bookdoc_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/bookdoc_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/bookdoc_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/backmatter.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/articlemeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/archivecustom-modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/archivecustom-models.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/archivecustom-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/archivecustom-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/archivearticle.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/SP_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/SP_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/PRF_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/PRF_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/PIR_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/PIR_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/PDB_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/PDB_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/OMSSA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/OMSSA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NSE.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NSE.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_all.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Variation.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Systems.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Submit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Remap.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_RNA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Pub.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Protein.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Project.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Organism.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Mime.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Mim.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Medline.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Gene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/NCBI_Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/MMDB_Features.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/MMDB.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/MMDB.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-section1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-related-object1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-references1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-phrase1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-para1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-notat1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-math1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-list1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-link1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-funding1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-format1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-display1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-common1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-chars1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/HomoloGene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/GenBank_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/EMBL_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/Docsum_3_4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/Docsum_3_3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/Docsum_3_2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/Docsum_3_1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/Docsum_3_0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/BITS-question-answer2.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/DTDs/BITS-embedded-index2.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez
copying build/lib.linux-ppc64le-cpython-311/Bio/Entrez/Parser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Emboss
copying build/lib.linux-ppc64le-cpython-311/Bio/Emboss/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Emboss
copying build/lib.linux-ppc64le-cpython-311/Bio/Emboss/PrimerSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Emboss
copying build/lib.linux-ppc64le-cpython-311/Bio/Emboss/Primer3.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Emboss
copying build/lib.linux-ppc64le-cpython-311/Bio/Emboss/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Emboss
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Data
copying build/lib.linux-ppc64le-cpython-311/Bio/Data/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Data
copying build/lib.linux-ppc64le-cpython-311/Bio/Data/SCOPData.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Data
copying build/lib.linux-ppc64le-cpython-311/Bio/Data/PDBData.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Data
copying build/lib.linux-ppc64le-cpython-311/Bio/Data/IUPACData.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Data
copying build/lib.linux-ppc64le-cpython-311/Bio/Data/CodonTable.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Data
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Compass
copying build/lib.linux-ppc64le-cpython-311/Bio/Compass/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Compass
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/codonalign
copying build/lib.linux-ppc64le-cpython-311/Bio/codonalign/codonseq.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/codonalign
copying build/lib.linux-ppc64le-cpython-311/Bio/codonalign/codonalignment.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/codonalign
copying build/lib.linux-ppc64le-cpython-311/Bio/codonalign/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/codonalign
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Cluster
copying build/lib.linux-ppc64le-cpython-311/Bio/Cluster/_cluster.cpython-311-powerpc64le-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Cluster
copying build/lib.linux-ppc64le-cpython-311/Bio/Cluster/clustermodule.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Cluster
copying build/lib.linux-ppc64le-cpython-311/Bio/Cluster/cluster.h -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Cluster
copying build/lib.linux-ppc64le-cpython-311/Bio/Cluster/cluster.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Cluster
copying build/lib.linux-ppc64le-cpython-311/Bio/Cluster/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Cluster
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/CAPS
copying build/lib.linux-ppc64le-cpython-311/Bio/CAPS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/CAPS
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Blast
copying build/lib.linux-ppc64le-cpython-311/Bio/Blast/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Blast
copying build/lib.linux-ppc64le-cpython-311/Bio/Blast/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Blast
copying build/lib.linux-ppc64le-cpython-311/Bio/Blast/ParseBlastTable.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Blast
copying build/lib.linux-ppc64le-cpython-311/Bio/Blast/NCBIXML.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Blast
copying build/lib.linux-ppc64le-cpython-311/Bio/Blast/NCBIWWW.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Blast
copying build/lib.linux-ppc64le-cpython-311/Bio/Blast/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Blast
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Application
copying build/lib.linux-ppc64le-cpython-311/Bio/Application/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Application
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Alphabet
copying build/lib.linux-ppc64le-cpython-311/Bio/Alphabet/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Alphabet
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-ppc64le-cpython-311/Bio/AlignIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-ppc64le-cpython-311/Bio/AlignIO/StockholmIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-ppc64le-cpython-311/Bio/AlignIO/PhylipIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-ppc64le-cpython-311/Bio/AlignIO/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-ppc64le-cpython-311/Bio/AlignIO/MsfIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-ppc64le-cpython-311/Bio/AlignIO/MauveIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-ppc64le-cpython-311/Bio/AlignIO/MafIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-ppc64le-cpython-311/Bio/AlignIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-ppc64le-cpython-311/Bio/AlignIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-ppc64le-cpython-311/Bio/AlignIO/EmbossIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-ppc64le-cpython-311/Bio/AlignIO/ClustalIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/AlignIO
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/_aligners.cpython-311-powerpc64le-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/_aligners.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/TRANS -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/STR -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/SCHNEIDER -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/RISLER -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/RAO -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/PAM70 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/PAM30 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/PAM250 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/NUC.4.4 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/MEGABLAST -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/MDM78 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/MCLACHLAN -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/LEVIN -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/JONES -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/JOHNSON -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/HOXD70 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/GONNET1992 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/GENETIC -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/FENG -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/DAYHOFF -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM90 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM80 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM62 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM50 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM45 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/BLASTP -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/BLASTN -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/BENNER74 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/BENNER6 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/data/BENNER22 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/substitution_matrices/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications/_TCoffee.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications/_Probcons.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications/_Prank.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications/_Muscle.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications/_Mafft.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications/_MSAProbs.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications/_Dialign.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications/_Clustalw.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/Applications/_ClustalOmega.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/tabular.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/stockholm.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/sam.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/psl.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/phylip.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/msf.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/mauve.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/maf.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/hhr.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/fasta.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/exonerate.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/emboss.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/clustal.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/bigpsl.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/bigmaf.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/bigbed.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/bed.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/a2m.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
copying build/lib.linux-ppc64le-cpython-311/Bio/Align/AlignInfo.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Affy
copying build/lib.linux-ppc64le-cpython-311/Bio/Affy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Affy
copying build/lib.linux-ppc64le-cpython-311/Bio/Affy/CelFile.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Affy
copying build/lib.linux-ppc64le-cpython-311/Bio/pairwise2.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio
copying build/lib.linux-ppc64le-cpython-311/Bio/kNN.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio
copying build/lib.linux-ppc64le-cpython-311/Bio/bgzf.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio
copying build/lib.linux-ppc64le-cpython-311/Bio/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio
copying build/lib.linux-ppc64le-cpython-311/Bio/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqRecord.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio
copying build/lib.linux-ppc64le-cpython-311/Bio/SeqFeature.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio
copying build/lib.linux-ppc64le-cpython-311/Bio/Seq.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio
copying build/lib.linux-ppc64le-cpython-311/Bio/NaiveBayes.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio
copying build/lib.linux-ppc64le-cpython-311/Bio/MaxEntropy.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio
copying build/lib.linux-ppc64le-cpython-311/Bio/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio
copying build/lib.linux-ppc64le-cpython-311/Bio/LogisticRegression.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio
copying build/lib.linux-ppc64le-cpython-311/Bio/File.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/BioSQL/BioSeq.py to BioSeq.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/BioSQL/BioSeqDatabase.py to BioSeqDatabase.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/BioSQL/DBUtils.py to DBUtils.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/BioSQL/Loader.py to Loader.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/BioSQL/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Wise/psw.py to psw.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Wise/dnal.py to dnal.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Wise/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/UniProt/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/UniProt/GOA.py to GOA.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/UniGene/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/yn00.py to yn00.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/codeml.py to codeml.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/chi2.py to chi2.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/baseml.py to baseml.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/_parse_yn00.py to _parse_yn00.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/_parse_codeml.py to _parse_codeml.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/_parse_baseml.py to _parse_baseml.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/_paml.py to _paml.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications/_Raxml.py to _Raxml.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications/_Phyml.py to _Phyml.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications/_Fasttree.py to _Fasttree.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/_utils.py to _utils.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/_io.py to _io.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/_cdao_owl.py to _cdao_owl.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/TreeConstruction.py to TreeConstruction.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PhyloXMLIO.py to PhyloXMLIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/PhyloXML.py to PhyloXML.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/NexusIO.py to NexusIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/NewickIO.py to NewickIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/Newick.py to Newick.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/NeXMLIO.py to NeXMLIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/NeXML.py to NeXML.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/Consensus.py to Consensus.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/CDAOIO.py to CDAOIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/CDAO.py to CDAO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Phylo/BaseTree.py to BaseTree.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/TogoWS/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SwissProt/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SwissProt/KeyWList.py to KeyWList.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SVDSuperimposer/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications/_samtools.py to _samtools.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications/_bwa.py to _bwa.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications/_Novoalign.py to _Novoalign.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Sequencing/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Sequencing/Phd.py to Phd.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Sequencing/Ace.py to Ace.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqUtils/lcc.py to lcc.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqUtils/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqUtils/ProtParamData.py to ProtParamData.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqUtils/ProtParam.py to ProtParam.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqUtils/MeltingTemp.py to MeltingTemp.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqUtils/IsoelectricPoint.py to IsoelectricPoint.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqUtils/CodonUsageIndices.py to CodonUsageIndices.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqUtils/CodonUsage.py to CodonUsage.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqUtils/CheckSum.py to CheckSum.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/_index.py to _index.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/XdnaIO.py to XdnaIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/UniprotIO.py to UniprotIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/TwoBitIO.py to TwoBitIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/TabIO.py to TabIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/SwissIO.py to SwissIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/SnapGeneIO.py to SnapGeneIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/SffIO.py to SffIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/SeqXmlIO.py to SeqXmlIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/QualityIO.py to QualityIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/PirIO.py to PirIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/PhdIO.py to PhdIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/PdbIO.py to PdbIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/NibIO.py to NibIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/Interfaces.py to Interfaces.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py to InsdcIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/IgIO.py to IgIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/GckIO.py to GckIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/FastaIO.py to FastaIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/AceIO.py to AceIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/AbiIO.py to AbiIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/InterproscanIO/interproscan_xml.py to interproscan_xml.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/InterproscanIO/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py to exonerate_vulgar.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO/exonerate_text.py to exonerate_text.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO/exonerate_cigar.py to exonerate_cigar.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO/_base.py to _base.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO/hmmer3_text.py to hmmer3_text.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO/hmmer3_tab.py to hmmer3_tab.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO/hmmer3_domtab.py to hmmer3_domtab.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO/hmmer2_text.py to hmmer2_text.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO/_base.py to _base.cpython-311.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/bigpsl.py to bigpsl.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/bigmaf.py to bigmaf.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/bigbed.py to bigbed.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/bed.py to bed.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/a2m.py to a2m.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/AlignInfo.py to AlignInfo.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Affy/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Affy/CelFile.py to CelFile.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/pairwise2.py to pairwise2.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/kNN.py to kNN.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/bgzf.py to bgzf.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/_utils.py to _utils.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqRecord.py to SeqRecord.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqFeature.py to SeqFeature.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Seq.py to Seq.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/NaiveBayes.py to NaiveBayes.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/MaxEntropy.py to MaxEntropy.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/MarkovModel.py to MarkovModel.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/LogisticRegression.py to LogisticRegression.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/File.py to File.cpython-311.pyc
writing byte-compilation script '/tmp/tmpmdtjd_ca.py'
/usr/bin/python3 /tmp/tmpmdtjd_ca.py
removing /tmp/tmpmdtjd_ca.py
running install_egg_info
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'
warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
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
warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt'
adding license file 'LICENSE'
adding license file 'LICENSE.rst'
writing manifest file 'biopython.egg-info/SOURCES.txt'
Copying biopython.egg-info to /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/biopython-1.80-py3.11.egg-info
running install_scripts
+ find Scripts -name '*.py'
+ xargs /usr/bin/python3 /usr/lib/rpm/redhat/pathfix.py -pn -i /usr/bin/python3
Scripts/xbbtools/xbbtools.py: updating
Scripts/xbbtools/xbb_widget.py: updating
Scripts/xbbtools/xbb_utils.py: updating
Scripts/xbbtools/xbb_translations.py: updating
Scripts/xbbtools/xbb_search.py: updating
Scripts/xbbtools/xbb_help.py: updating
Scripts/xbbtools/xbb_blastbg.py: updating
Scripts/xbbtools/xbb_blast.py: updating
Scripts/xbbtools/nextorf.py: updating
Scripts/update_ncbi_codon_table.py: no change
Scripts/scop_pdb.py: updating
Scripts/query_pubmed.py: updating
Scripts/SeqGui/SeqGui.py: no change
Scripts/Restriction/rebase_update.py: updating
Scripts/Restriction/ranacompiler.py: updating
Scripts/Performance/biosql_performance_read.py: updating
Scripts/Performance/biosql_performance_load.py: updating
Scripts/PDB/hsexpo.py: updating
Scripts/PDB/generate_three_to_one_dict.py: no change
Scripts/GenBank/check_output_simple.py: updating
Scripts/GenBank/check_output.py: updating
~/build/BUILD/python-biopython-1.80
+ popd
+ /usr/bin/find-debuginfo -j5 --strict-build-id -m -i --build-id-seed 1.80-1.fc38 --unique-debug-suffix -1.80-1.fc38.ppc64le --unique-debug-src-base python-biopython-1.80-1.fc38.ppc64le --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/python-biopython-1.80
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Align/_aligners.cpython-311-powerpc64le-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Cluster/_cluster.cpython-311-powerpc64le-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Nexus/cnexus.cpython-311-powerpc64le-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB/ccealign.cpython-311-powerpc64le-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-powerpc64le-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/PDB/kdtrees.cpython-311-powerpc64le-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/_twoBitIO.cpython-311-powerpc64le-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/cpairwise2.cpython-311-powerpc64le-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/motifs/_pwm.cpython-311-powerpc64le-linux-gnu.so
original debug info size: 1344kB, size after compression: 1344kB
/usr/bin/sepdebugcrcfix: Updated 9 CRC32s, 0 CRC32s did match.
1192 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0
Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib/debug/usr/lib64/python3.11 using python3.11
Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11 using python3.11
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.dlI0bI
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd python-biopython-1.80
+ pushd python3/Tests
~/build/BUILD/python-biopython-1.80/python3/Tests ~/build/BUILD/python-biopython-1.80
+ find . -name run_tests.py
+ xargs /usr/bin/python3 /usr/lib/rpm/redhat/pathfix.py -pn -i /usr/bin/python3
./run_tests.py: updating
+ find ../ -name __init__.py
+ xargs rm -f
++ grep -v Nexus
++ grep -v Phylo
++ grep -v Tutorial
++ grep -v SearchIO_blast
++ 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_Align_Alignment.py test_Align_a2m.py test_Align_bed.py test_Align_bigbed.py test_Align_bigmaf.py test_Align_bigpsl.py test_Align_clustal.py test_Align_emboss.py test_Align_exonerate.py test_Align_fasta.py test_Align_hhr.py test_Align_maf.py test_Align_mauve.py test_Align_msf.py test_Align_nexus.py test_Align_phylip.py test_Align_psl.py test_Align_sam.py test_Align_stockholm.py test_Align_tabular.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_Blast_Record.py test_CAPS.py test_Chi2.py test_ClustalOmega_tool.py test_Clustalw_tool.py test_Cluster.py test_CodonTable.py test_ColorSpiral.py test_Compass.py test_Consensus.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_Fasttree_tool.py test_File.py test_GenBank.py test_GenomeDiagram.py test_GraphicsBitmaps.py test_GraphicsChromosome.py test_GraphicsDistribution.py test_GraphicsGeneral.py test_HMMCasino.py test_HMMGeneral.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_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_NCBITextParser.py test_NCBIXML.py test_NCBI_BLAST_tools.py test_NMR.py test_NaiveBayes.py test_Nexus.py test_PAML_baseml.py test_PAML_codeml.py test_PAML_tools.py test_PAML_yn00.py test_PDBList.py test_PDB_CEAligner.py test_PDB_DSSP.py test_PDB_Dice.py test_PDB_Disordered.py test_PDB_Exposure.py test_PDB_FragmentMapper.py test_PDB_KDTree.py test_PDB_MMCIF2Dict.py test_PDB_MMCIFIO.py test_PDB_MMCIFParser.py test_PDB_NACCESS.py test_PDB_PDBIO.py test_PDB_PDBParser.py test_PDB_PSEA.py test_PDB_Polypeptide.py test_PDB_QCSuperimposer.py test_PDB_ResidueDepth.py test_PDB_SASA.py test_PDB_SMCRA.py test_PDB_Selection.py test_PDB_StructureAlignment.py test_PDB_Superimposer.py test_PDB_internal_coords.py test_PDB_parse_pdb_header.py test_PDB_vectors.py test_PQR.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_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_hhsuite2_text.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_Gck.py test_SeqIO_Insdc.py test_SeqIO_NibIO.py test_SeqIO_PdbIO.py test_SeqIO_QualityIO.py test_SeqIO_SeqXML.py test_SeqIO_SnapGene.py test_SeqIO_TwoBitIO.py test_SeqIO_Xdna.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_SwissProt.py test_TCoffee_tool.py test_TogoWS.py test_TreeConstruction.py test_Tutorial.py test_UniGene.py test_UniProt_GOA.py test_Uniprot.py test_Wise.py test_XXmotif_tool.py test_align.py test_align_substitution_matrices.py test_bgzf.py test_cellosaurus.py test_codonalign.py test_geo.py test_kNN.py test_mmtf.py test_mmtf_online.py test_motifs.py test_motifs_online.py test_pairwise2.py test_pairwise2_no_C.py test_pairwise_aligner.py test_pairwise_alignment_map.py test_phenotype.py test_phenotype_fit.py test_phyml_tool.py test_prodoc.py test_prosite.py test_raxml_tool.py test_samtools_tool.py test_seq.py test_translate.py
++ grep -v SubsMat
++ grep -v bgzf
++ grep -v pairwise_aligner
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Ace.py
test_Ace ... ok
test_check_ACEParser (test_Ace.AceTestOne.test_check_ACEParser)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestOne.test_check_record_parser)
Test to check that contig parser parses each contig into a contig. ... ok
test_check_ACEParser (test_Ace.AceTestThree.test_check_ACEParser)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestThree.test_check_record_parser)
Test to check that record parser parses each contig into a record. ... ok
test_check_ACEParser (test_Ace.AceTestTwo.test_check_ACEParser)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestTwo.test_check_record_parser)
Test to check that record parser parses each contig into a record. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.056 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Affy.py
test_Affy ... ok
testAffy3 (test_Affy.AffyTest.testAffy3) ... ok
testAffy4 (test_Affy.AffyTest.testAffy4) ... ok
testAffyBadHeader (test_Affy.AffyTest.testAffyBadHeader) ... ok
testAffyWrongModeReadV3 (test_Affy.AffyTest.testAffyWrongModeReadV3) ... ok
testAffyWrongModeReadV4 (test_Affy.AffyTest.testAffyWrongModeReadV4) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.018 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO.py
test_AlignIO ... ok
test_parsing_empty_files (test_AlignIO.TestAlignIO_exceptions.test_parsing_empty_files)
Check that parsing an empty file returns an empty list. ... ok
test_phylip_reject_duplicate (test_AlignIO.TestAlignIO_exceptions.test_phylip_reject_duplicate)
Check that writing duplicated IDs after truncation fails for PHYLIP. ... ok
test_writing_empty_files (test_AlignIO.TestAlignIO_exceptions.test_writing_empty_files)
Check that writers can cope with no alignments. ... ok
test_writing_not_alignments (test_AlignIO.TestAlignIO_exceptions.test_writing_not_alignments)
Check that writers reject records that are not alignments. ... ok
test_reading_alignments_clustal1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal1) ... ok
test_reading_alignments_clustal2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal2) ... ok
test_reading_alignments_clustal3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal3) ... ok
test_reading_alignments_clustal4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal4) ... ok
test_reading_alignments_clustal5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal5) ... ok
test_reading_alignments_clustal6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal6) ... ok
test_reading_alignments_emboss1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss1) ... ok
test_reading_alignments_emboss2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss2) ... ok
test_reading_alignments_emboss3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss3) ... ok
test_reading_alignments_emboss4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss4) ... ok
test_reading_alignments_emboss5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss5) ... ok
test_reading_alignments_emboss6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss6) ... ok
test_reading_alignments_emboss7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss7) ... ok
test_reading_alignments_emboss8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss8) ... ok
test_reading_alignments_fasta (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta) ... ok
test_reading_alignments_fasta_m10_1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_1) ... ok
test_reading_alignments_fasta_m10_2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_2) ... ok
test_reading_alignments_fasta_m10_3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_3) ... ok
test_reading_alignments_fasta_m10_4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_4) ... ok
test_reading_alignments_fasta_m10_5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_5) ... ok
test_reading_alignments_fasta_m10_6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_6) ... ok
test_reading_alignments_fasta_m10_7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_7) ... ok
test_reading_alignments_fasta_m10_8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_8) ... ok
test_reading_alignments_ig (test_AlignIO.TestAlignIO_reading.test_reading_alignments_ig) ... ok
test_reading_alignments_maf1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf1) ... ok
test_reading_alignments_maf2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf2) ... ok
test_reading_alignments_maf3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf3) ... ok
test_reading_alignments_maf4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf4) ... ok
test_reading_alignments_mauve (test_AlignIO.TestAlignIO_reading.test_reading_alignments_mauve) ... ok
test_reading_alignments_msf1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_msf1) ... ok
test_reading_alignments_msf2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_msf2) ... ok
test_reading_alignments_nexus1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_nexus1) ... ok
test_reading_alignments_nexus2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_nexus2) ... ok
test_reading_alignments_phylip1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip1) ... ok
test_reading_alignments_phylip10 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip10) ... ok
test_reading_alignments_phylip2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip2) ... ok
test_reading_alignments_phylip3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip3) ... ok
test_reading_alignments_phylip4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip4) ... ok
test_reading_alignments_phylip5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip5) ... ok
test_reading_alignments_phylip6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip6) ... ok
test_reading_alignments_phylip7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip7) ... ok
test_reading_alignments_phylip8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip8) ... ok
test_reading_alignments_phylip9 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip9) ... ok
test_reading_alignments_pir (test_AlignIO.TestAlignIO_reading.test_reading_alignments_pir) ... ok
test_reading_alignments_stockholm1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_stockholm1) ... ok
test_reading_alignments_stockholm2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_stockholm2) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.748 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_ClustalIO.py
test_AlignIO_ClustalIO ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_biopython_header (test_AlignIO_ClustalIO.TestClustalIO.test_biopython_header)
Make sure we can parse the Biopython header. ... ok
test_cat_one_two (test_AlignIO_ClustalIO.TestClustalIO.test_cat_one_two) ... ok
test_empy (test_AlignIO_ClustalIO.TestClustalIO.test_empy)
Checking empty file. ... ok
test_kalign_header (test_AlignIO_ClustalIO.TestClustalIO.test_kalign_header)
Make sure we can parse the Kalign header. ... ok
test_one (test_AlignIO_ClustalIO.TestClustalIO.test_one) ... ok
test_three (test_AlignIO_ClustalIO.TestClustalIO.test_three) ... ok
test_two (test_AlignIO_ClustalIO.TestClustalIO.test_two) ... ok
test_write_read (test_AlignIO_ClustalIO.TestClustalIO.test_write_read)
Checking write/read. ... ok
test_write_read_single (test_AlignIO_ClustalIO.TestClustalIO.test_write_read_single)
Testing write/read when there is only one sequence. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.068 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_EmbossIO.py
test_AlignIO_EmbossIO ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_pair_example (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example) ... ok
test_pair_example2 (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example2) ... ok
test_pair_example3 (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example3) ... ok
test_pair_plus_simple (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_plus_simple) ... ok
test_simple_example (test_AlignIO_EmbossIO.TestEmbossIO.test_simple_example) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.072 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_FastaIO.py
test_AlignIO_FastaIO ... ok
test_output001 (test_AlignIO_FastaIO.FastaIOTests.test_output001)
Check output001.m10 file. ... ok
test_output002 (test_AlignIO_FastaIO.FastaIOTests.test_output002)
Check output002.m10 file. ... ok
test_output003 (test_AlignIO_FastaIO.FastaIOTests.test_output003)
Check output003.m10 file. ... ok
test_output004 (test_AlignIO_FastaIO.FastaIOTests.test_output004)
Check output004.m10 file. ... ok
test_output005 (test_AlignIO_FastaIO.FastaIOTests.test_output005)
Check output005.m10 file. ... ok
test_output006 (test_AlignIO_FastaIO.FastaIOTests.test_output006)
Check output006.m10 file. ... ok
test_output007 (test_AlignIO_FastaIO.FastaIOTests.test_output007)
Check output007.m10 file. ... ok
test_output008 (test_AlignIO_FastaIO.FastaIOTests.test_output008)
Check output008.m10 file. ... ok
test_output009 (test_AlignIO_FastaIO.FastaIOTests.test_output009)
Check output009.m10 file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.083 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_MauveIO.py
test_AlignIO_MauveIO ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_one (test_AlignIO_MauveIO.TestMauveIO.test_one) ... ok
test_sequence_positions (test_AlignIO_MauveIO.TestMauveIO.test_sequence_positions) ... ok
test_write_read (test_AlignIO_MauveIO.TestMauveIO.test_write_read) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.093 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_PhylipIO.py
test_AlignIO_PhylipIO ... ok
test_concatenation (test_AlignIO_PhylipIO.TestPhylipIO.test_concatenation) ... ok
test_five (test_AlignIO_PhylipIO.TestPhylipIO.test_five) ... ok
test_four (test_AlignIO_PhylipIO.TestPhylipIO.test_four) ... ok
test_one (test_AlignIO_PhylipIO.TestPhylipIO.test_one) ... ok
test_six (test_AlignIO_PhylipIO.TestPhylipIO.test_six) ... ok
test_two_and_three (test_AlignIO_PhylipIO.TestPhylipIO.test_two_and_three) ... ok
test_write_read (test_AlignIO_PhylipIO.TestPhylipIO.test_write_read) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.070 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_convert.py
test_AlignIO_convert ... ok
test_clustal_to_nexus_with_mol_type (test_AlignIO_convert.ConvertTests.test_clustal_to_nexus_with_mol_type)
Converting Clustal to NEXUS with a molecule type. ... ok
test_clustal_to_nexus_without_mol_type (test_AlignIO_convert.ConvertTests.test_clustal_to_nexus_without_mol_type)
Converting Clustal to NEXUS without a molecule type. ... ok
test_convert (test_AlignIO_convert.ConvertTests.test_convert) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.260 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignInfo.py
test_AlignInfo ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_nucleotides (test_AlignInfo.AlignInfoTests.test_nucleotides) ... ok
test_proteins (test_AlignInfo.AlignInfoTests.test_proteins) ... ok
test_pseudo_count (test_AlignInfo.AlignInfoTests.test_pseudo_count) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.091 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_Alignment.py
test_Align_Alignment ... ok
test_a2m (test_Align_Alignment.TestAlignment_format.test_a2m) ... ok
test_bed (test_Align_Alignment.TestAlignment_format.test_bed) ... ok
test_bigbed (test_Align_Alignment.TestAlignment_format.test_bigbed) ... ok
test_bigmaf (test_Align_Alignment.TestAlignment_format.test_bigmaf) ... ok
test_bigpsl (test_Align_Alignment.TestAlignment_format.test_bigpsl) ... ok
test_clustal (test_Align_Alignment.TestAlignment_format.test_clustal) ... ok
test_emboss (test_Align_Alignment.TestAlignment_format.test_emboss) ... ok
test_exonerate (test_Align_Alignment.TestAlignment_format.test_exonerate) ... ok
test_fasta (test_Align_Alignment.TestAlignment_format.test_fasta) ... ok
test_hhr (test_Align_Alignment.TestAlignment_format.test_hhr) ... ok
test_maf (test_Align_Alignment.TestAlignment_format.test_maf) ... ok
test_mauve (test_Align_Alignment.TestAlignment_format.test_mauve) ... ok
test_msf (test_Align_Alignment.TestAlignment_format.test_msf) ... ok
test_nexus (test_Align_Alignment.TestAlignment_format.test_nexus) ... ok
test_phylip (test_Align_Alignment.TestAlignment_format.test_phylip) ... ok
test_psl (test_Align_Alignment.TestAlignment_format.test_psl) ... ok
test_sam (test_Align_Alignment.TestAlignment_format.test_sam) ... ok
test_stockholm (test_Align_Alignment.TestAlignment_format.test_stockholm) ... ok
test_tabular (test_Align_Alignment.TestAlignment_format.test_tabular) ... ok
test_comparison (test_Align_Alignment.TestMultipleAlignment.test_comparison) ... ok
test_indexing_slicing (test_Align_Alignment.TestMultipleAlignment.test_indexing_slicing) ... ok
test_sort (test_Align_Alignment.TestMultipleAlignment.test_sort) ... ok
test_substitutions (test_Align_Alignment.TestMultipleAlignment.test_substitutions) ... ok
test_target_query_properties (test_Align_Alignment.TestMultipleAlignment.test_target_query_properties) ... ok
test_aligned_indices (test_Align_Alignment.TestPairwiseAlignment.test_aligned_indices) ... ok
test_indexing_slicing (test_Align_Alignment.TestPairwiseAlignment.test_indexing_slicing) ... ok
test_sort (test_Align_Alignment.TestPairwiseAlignment.test_sort) ... ok
test_substitutions (test_Align_Alignment.TestPairwiseAlignment.test_substitutions) ... ok
test_target_query_properties (test_Align_Alignment.TestPairwiseAlignment.test_target_query_properties) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.279 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_a2m.py
test_Align_a2m ... ok
test_clustalw (test_Align_a2m.TestA2MReadingWriting.test_clustalw) ... ok
test_empty (test_Align_a2m.TestA2MReadingWriting.test_empty)
Checking empty file. ... ok
test_kalign (test_Align_a2m.TestA2MReadingWriting.test_kalign) ... ok
test_msaprobs (test_Align_a2m.TestA2MReadingWriting.test_msaprobs) ... ok
test_muscle (test_Align_a2m.TestA2MReadingWriting.test_muscle) ... ok
test_probcons (test_Align_a2m.TestA2MReadingWriting.test_probcons) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.089 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_bed.py
test_Align_bed ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_reading (test_Align_bed.TestAlign_bed12.test_reading)
Test parsing alignments in file formats BED3 through BED12. ... ok
test_writing (test_Align_bed.TestAlign_bed12.test_writing)
Test writing the alignments in bed12.bed as BED3 through BED12. ... ok
test_reading_psl_34_001 (test_Align_bed.TestAlign_dna.test_reading_psl_34_001)
Test parsing psl_34_001.bed. ... ok
test_reading_psl_34_003 (test_Align_bed.TestAlign_dna.test_reading_psl_34_003)
Test parsing psl_34_003.bed. ... ok
test_reading_psl_34_004 (test_Align_bed.TestAlign_dna.test_reading_psl_34_004)
Test parsing psl_34_004.bed. ... ok
test_reading_psl_34_005 (test_Align_bed.TestAlign_dna.test_reading_psl_34_005)
Test parsing psl_34_005.bed. ... ok
test_writing_psl_34_001 (test_Align_bed.TestAlign_dna.test_writing_psl_34_001)
Test writing the alignments in psl_34_001.bed. ... ok
test_writing_psl_34_003 (test_Align_bed.TestAlign_dna.test_writing_psl_34_003)
Test writing the alignments in psl_34_003.bed. ... ok
test_writing_psl_34_004 (test_Align_bed.TestAlign_dna.test_writing_psl_34_004)
Test writing the alignments in psl_34_004.bed. ... ok
test_writing_psl_34_005 (test_Align_bed.TestAlign_dna.test_writing_psl_34_005)
Test writing the alignments in psl_34_005.bed. ... ok
test_reading (test_Align_bed.TestAlign_dna_rna.test_reading)
Test parsing dna_rna.bed. ... ok
test_writing (test_Align_bed.TestAlign_dna_rna.test_writing)
Test writing the alignments in dna_rna.bed. ... ok
test_reading_psl_35_001 (test_Align_bed.TestAlign_dnax_prot.test_reading_psl_35_001)
Test parsing psl_35_001.bed. ... ok
test_reading_psl_35_002 (test_Align_bed.TestAlign_dnax_prot.test_reading_psl_35_002)
Test parsing psl_35_002.bed. ... ok
test_writing_psl_35_001 (test_Align_bed.TestAlign_dnax_prot.test_writing_psl_35_001)
Test writing the alignments in psl_35_001.bed. ... ok
test_writing_psl_35_002 (test_Align_bed.TestAlign_dnax_prot.test_writing_psl_35_002)
Test writing the alignments in psl_35_002.bed. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.137 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_bigbed.py
test_Align_bigbed ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_reading (test_Align_bigbed.TestAlign_bed12.test_reading)
Test parsing alignments in file formats BED3 through BED12. ... ok
test_reading_psl_34_001 (test_Align_bigbed.TestAlign_dna.test_reading_psl_34_001)
Test parsing psl_34_001.bb. ... ok
test_reading_psl_34_003 (test_Align_bigbed.TestAlign_dna.test_reading_psl_34_003)
Test parsing psl_34_003.bb. ... ok
test_reading_psl_34_004 (test_Align_bigbed.TestAlign_dna.test_reading_psl_34_004)
Test parsing psl_34_004.bb. ... ok
test_reading_psl_34_005 (test_Align_bigbed.TestAlign_dna.test_reading_psl_34_005)
Test parsing psl_34_005.bb. ... ok
test_reading (test_Align_bigbed.TestAlign_dna_rna.test_reading)
Test parsing dna_rna.bb. ... ok
test_reading_psl_35_001 (test_Align_bigbed.TestAlign_dnax_prot.test_reading_psl_35_001)
Test parsing psl_35_001.bb. ... ok
test_reading (test_Align_bigbed.TestAlign_extended_bed.test_reading)
Test parsing bigbed_extended.bb. ... ok
test_search_chromosome (test_Align_bigbed.TestAlign_searching.test_search_chromosome) ... ok
test_search_position (test_Align_bigbed.TestAlign_searching.test_search_position) ... ok
test_search_region (test_Align_bigbed.TestAlign_searching.test_search_region) ... ok
test_three_iterators (test_Align_bigbed.TestAlign_searching.test_three_iterators)
Create three iterators and use them concurrently. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.139 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_bigmaf.py
test_Align_bigmaf ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_reading_bundle_without_target (test_Align_bigmaf.TestAlign_reading.test_reading_bundle_without_target)
Test parsing bundle_without_target.bb. ... ok
test_reading_ucsc_mm9_chr10 (test_Align_bigmaf.TestAlign_reading.test_reading_ucsc_mm9_chr10)
Test parsing MAF file ucsc_mm9_chr10.bb. ... ok
test_reading_ucsc_test (test_Align_bigmaf.TestAlign_reading.test_reading_ucsc_test)
Test parsing ucsc_test.bb. ... ok
test_search_chromosome (test_Align_bigmaf.TestAlign_searching.test_search_chromosome) ... ok
test_search_position (test_Align_bigmaf.TestAlign_searching.test_search_position) ... ok
test_search_region (test_Align_bigmaf.TestAlign_searching.test_search_region) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.268 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_bigpsl.py
test_Align_bigpsl ... ok
test_reading_bigpsl (test_Align_bigpsl.TestAlign_bigpsl.test_reading_bigpsl)
Test parsing bigPsl.bb. ... ok
test_reading_psl_34_001 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_001)
Test parsing psl_34_001.psl.bb. ... ok
test_reading_psl_34_003 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_003)
Test parsing psl_34_003.psl.bb. ... ok
test_reading_psl_34_004 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_004)
Test parsing psl_34_004.psl.bb. ... ok
test_reading_psl_34_005 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_005)
Test parsing psl_34_005.psl.bb. ... ok
test_reading (test_Align_bigpsl.TestAlign_dna_rna.test_reading)
Test parsing dna_rna.psl.bb. ... ok
test_reading_psl_35_001 (test_Align_bigpsl.TestAlign_dnax_prot.test_reading_psl_35_001)
Test parsing psl_35_001.psl.bb. ... ok
test_reading_psl_35_002 (test_Align_bigpsl.TestAlign_dnax_prot.test_reading_psl_35_002)
Test parsing psl_35_002.psl.bb. ... ok
test_search_chromosome (test_Align_bigpsl.TestAlign_searching.test_search_chromosome) ... ok
test_search_position (test_Align_bigpsl.TestAlign_searching.test_search_position) ... ok
test_search_region (test_Align_bigpsl.TestAlign_searching.test_search_region) ... ok
test_three_iterators (test_Align_bigpsl.TestAlign_searching.test_three_iterators)
Create three iterators and use them concurrently. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.291 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_clustal.py
test_Align_clustal ... ok
test_clustalw (test_Align_clustal.TestClustalReadingWriting.test_clustalw) ... ok
test_empty (test_Align_clustal.TestClustalReadingWriting.test_empty)
Checking empty file. ... ok
test_kalign (test_Align_clustal.TestClustalReadingWriting.test_kalign)
Make sure we can parse the Kalign header. ... ok
test_msaprobs (test_Align_clustal.TestClustalReadingWriting.test_msaprobs) ... ok
test_muscle (test_Align_clustal.TestClustalReadingWriting.test_muscle) ... ok
test_probcons (test_Align_clustal.TestClustalReadingWriting.test_probcons) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.086 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_emboss.py
test_Align_emboss ... ok
test_local_water2 (test_Align_emboss.TestEmboss.test_local_water2)
Test parsing a local alignment. ... ok
test_matcher_pair (test_Align_emboss.TestEmboss.test_matcher_pair) ... ok
test_matcher_simple (test_Align_emboss.TestEmboss.test_matcher_simple) ... ok
test_needle_asis (test_Align_emboss.TestEmboss.test_needle_asis) ... ok
test_pair_aln_full_blank_line (test_Align_emboss.TestEmboss.test_pair_aln_full_blank_line) ... ok
test_pair_example (test_Align_emboss.TestEmboss.test_pair_example) ... ok
test_pair_example2 (test_Align_emboss.TestEmboss.test_pair_example2) ... ok
test_pair_example3 (test_Align_emboss.TestEmboss.test_pair_example3) ... ok
test_pair_example_nobrief (test_Align_emboss.TestEmboss.test_pair_example_nobrief) ... ok
test_water_reverse1 (test_Align_emboss.TestEmboss.test_water_reverse1) ... ok
test_water_reverse2 (test_Align_emboss.TestEmboss.test_water_reverse2) ... ok
test_water_reverse3 (test_Align_emboss.TestEmboss.test_water_reverse3) ... ok
test_water_reverse4 (test_Align_emboss.TestEmboss.test_water_reverse4) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.116 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_exonerate.py
test_Align_exonerate ... ok
test_exn_22_m_affine_local_cigar (test_Align_exonerate.Exonerate_affine_local.test_exn_22_m_affine_local_cigar)
Test parsing exn_22_m_affine_local_cigar.exn. ... ok
test_exn_22_m_affine_local_vulgar (test_Align_exonerate.Exonerate_affine_local.test_exn_22_m_affine_local_vulgar)
Test parsing exn_22_m_affine_local_vulgar.exn. ... ok
test_exn_22_m_cdna2genome_cigar (test_Align_exonerate.Exonerate_cdna2genome.test_exn_22_m_cdna2genome_cigar)
Test parsing exn_22_m_cdna2genome_cigar.exn. ... ok
test_exn_22_m_cdna2genome_vulgar (test_Align_exonerate.Exonerate_cdna2genome.test_exn_22_m_cdna2genome_vulgar)
Test parsing exn_22_m_cdna2genome_vulgar.exn. ... ok
test_exn_22_m_coding2coding_cigar (test_Align_exonerate.Exonerate_coding2coding.test_exn_22_m_coding2coding_cigar)
Test parsing exn_22_m_coding2coding_cigar.exn. ... ok
test_exn_22_m_coding2coding_vulgar (test_Align_exonerate.Exonerate_coding2coding.test_exn_22_m_coding2coding_vulgar)
Test parsing exn_22_m_coding2coding_vulgar.exn. ... ok
test_exn_22_m_coding2coding_fshifts_cigar (test_Align_exonerate.Exonerate_coding2coding_fshifts.test_exn_22_m_coding2coding_fshifts_cigar)
Test parsing exn_22_m_cigar_fshifts.exn). ... ok
test_exn_22_m_coding2coding_fshifts_vulgar (test_Align_exonerate.Exonerate_coding2coding_fshifts.test_exn_22_m_coding2coding_fshifts_vulgar)
Test parsing exn_22_o_vulgar_fshifts.exn. ... ok
test_exn_22_m_coding2genome_cigar (test_Align_exonerate.Exonerate_coding2genome.test_exn_22_m_coding2genome_cigar)
Test parsing exn_22_m_coding2genome_cigar.exn. ... ok
test_exn_22_m_coding2genome_vulgar (test_Align_exonerate.Exonerate_coding2genome.test_exn_22_m_coding2genome_vulgar)
Test parsing exn_22_m_coding2genome_vulgar.exn. ... ok
test_exn_22_m_dna2protein_cigar (test_Align_exonerate.Exonerate_dna2protein.test_exn_22_m_dna2protein_cigar)
Test parsing exn_22_m_dna2protein_cigar.exn. ... ok
test_exn_22_m_dna2protein_vulgar (test_Align_exonerate.Exonerate_dna2protein.test_exn_22_m_dna2protein_vulgar)
Test parsing exn_22_m_dna2protein_vulgar.exn. ... ok
test_exn_22_m_est2genome_cigar (test_Align_exonerate.Exonerate_est2genome.test_exn_22_m_est2genome_cigar)
Test parsing exn_22_m_est2genome_cigar.exn. ... ok
test_exn_22_m_est2genome_vulgar (test_Align_exonerate.Exonerate_est2genome.test_exn_22_m_est2genome_vulgar)
Test parsing exn_22_m_est2genome_vulgar.exn. ... ok
test_exn_22_m_genome2genome_cigar (test_Align_exonerate.Exonerate_genome2genome.test_exn_22_m_genome2genome_cigar)
Test parsing exn_22_o_vulgar_cigar.exn. ... ok
test_exn_22_m_genome2genome_vulgar (test_Align_exonerate.Exonerate_genome2genome.test_exn_22_m_genome2genome_vulgar)
Test parsing exn_22_o_vulgar.exn. ... ok
test_exn_22_q_multiple_cigar (test_Align_exonerate.Exonerate_multiple.test_exn_22_q_multiple_cigar)
Test parsing exn_22_q_multiple_cigar.exn. ... ok
test_exn_22_q_multiple_vulgar (test_Align_exonerate.Exonerate_multiple.test_exn_22_q_multiple_vulgar)
Test parsing exn_22_q_multiple_vulgar.exn. ... ok
test_exn_22_m_ner_cigar (test_Align_exonerate.Exonerate_ner.test_exn_22_m_ner_cigar)
Test parsing exonerate output (exn_22_m_ner_cigar.exn). ... ok
test_exn_22_m_ner_vulgar (test_Align_exonerate.Exonerate_ner.test_exn_22_m_ner_vulgar)
Test parsing exonerate output (exn_22_m_ner_vulgar.exn). ... ok
test_exn_22_q_none (test_Align_exonerate.Exonerate_none.test_exn_22_q_none)
Test parsing exonerate output (exn_22_q_none.exn). ... ok
test_exn_22_m_protein2dna_cigar (test_Align_exonerate.Exonerate_protein2dna.test_exn_22_m_protein2dna_cigar)
Test parsing exonerate output (exn_22_m_protein2dna_cigar.exn). ... ok
test_exn_22_m_protein2dna_vulgar (test_Align_exonerate.Exonerate_protein2dna.test_exn_22_m_protein2dna_vulgar)
Test parsing exonerate output (exn_22_m_protein2dna_vulgar.exn). ... ok
test_exn_22_m_protein2dna_fshifts_cigar (test_Align_exonerate.Exonerate_protein2dna_fshifts.test_exn_22_m_protein2dna_fshifts_cigar)
Test parsing exonerate output (exn_22_o_cigar_fshifts2.exn). ... ok
test_exn_22_m_protein2dna_fshifts_vulgar (test_Align_exonerate.Exonerate_protein2dna_fshifts.test_exn_22_m_protein2dna_fshifts_vulgar)
Test parsing exonerate output (exn_22_o_vulgar_fshifts2.exn). ... ok
test_exn_22_m_protein2genome_cigar (test_Align_exonerate.Exonerate_protein2genome.test_exn_22_m_protein2genome_cigar)
Test parsing exn_22_m_protein2genome_cigar.exn. ... ok
test_exn_22_m_protein2genome_vulgar (test_Align_exonerate.Exonerate_protein2genome.test_exn_22_m_protein2genome_vulgar)
Test parsing exn_22_m_protein2genome_vulgar.exn. ... ok
test_exn_24_protein2genome_met_intron_cigar (test_Align_exonerate.Exonerate_protein2genome_met_intron.test_exn_24_protein2genome_met_intron_cigar)
Test parsing exn_24_m_protein2genome_met_intron_cigar.exn. ... ok
test_exn_24_protein2genome_met_intron_vulgar (test_Align_exonerate.Exonerate_protein2genome_met_intron.test_exn_24_protein2genome_met_intron_vulgar)
Test parsing exn_24_m_protein2genome_met_intron_vulgar.exn. ... ok
test_exn_24_m_protein2genome_revcomp_fshifts_cigar (test_Align_exonerate.Exonerate_protein2genome_revcomp_fshifts.test_exn_24_m_protein2genome_revcomp_fshifts_cigar)
Test parsing exn_24_m_protein2genome_revcomp_fshifts_cigar.exn. ... ok
test_exn_24_m_protein2genome_revcomp_fshifts_vulgar (test_Align_exonerate.Exonerate_protein2genome_revcomp_fshifts.test_exn_24_m_protein2genome_revcomp_fshifts_vulgar)
Test parsing exn_24_m_protein2genome_revcomp_fshifts_vulgar.exn. ... ok
test_exn_22_m_ungapped_cigar (test_Align_exonerate.Exonerate_ungapped.test_exn_22_m_ungapped_cigar)
Test parsing exn_22_m_ungapped_cigar.exn. ... ok
test_exn_22_m_ungapped_vulgar (test_Align_exonerate.Exonerate_ungapped.test_exn_22_m_ungapped_vulgar)
Test parsing exn_22_m_ungapped_vulgar.exn. ... ok
test_exn_22_m_ungapped_trans_cigar (test_Align_exonerate.Exonerate_ungapped_trans.test_exn_22_m_ungapped_trans_cigar)
Test parsing exn_22_m_ungapped_trans_cigar.exn. ... ok
test_exn_22_m_ungapped_trans_vulgar (test_Align_exonerate.Exonerate_ungapped_trans.test_exn_22_m_ungapped_trans_vulgar)
Test parsing exn_22_m_ungapped_trans_vulgar.exn. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.195 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_fasta.py
test_Align_fasta ... ok
test_clustalw (test_Align_fasta.TestFASTAReadingWriting.test_clustalw) ... ok
test_empty (test_Align_fasta.TestFASTAReadingWriting.test_empty)
Checking empty file. ... ok
test_kalign (test_Align_fasta.TestFASTAReadingWriting.test_kalign) ... ok
test_msaprobs (test_Align_fasta.TestFASTAReadingWriting.test_msaprobs) ... ok
test_muscle (test_Align_fasta.TestFASTAReadingWriting.test_muscle) ... ok
test_probcons (test_Align_fasta.TestFASTAReadingWriting.test_probcons) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.096 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_hhr.py
test_Align_hhr ... ok
test_length (test_Align_hhr.Align_hhr_2uvo_hhblits.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_2uvo_hhblits_emptytable.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits_emptytable.test_reading) ... ok
test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits_onlyheader.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_2uvo_hhsearch.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_2uvo_hhsearch.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_4p79_hhsearch_server_NOssm.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_4p79_hhsearch_server_NOssm.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_4y9h_hhsearch_server_NOssm.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_4y9h_hhsearch_server_NOssm.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_allx.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_allx.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_hhpred_9590198.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_hhpred_9590198.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.test_reading) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.292 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_maf.py
test_Align_maf ... ok
test_reading_bug2453 (test_Align_maf.TestAlign_reading.test_reading_bug2453)
Test parsing bug2453.maf. ... ok
test_reading_bundle_without_target (test_Align_maf.TestAlign_reading.test_reading_bundle_without_target)
Test parsing bundle_without_target.maf. ... ok
test_reading_length_coords_mismatch (test_Align_maf.TestAlign_reading.test_reading_length_coords_mismatch)
Test parsing inconsistent MAF file length_coords_mismatch.maf. ... ok
test_reading_missing_signature (test_Align_maf.TestAlign_reading.test_reading_missing_signature)
Test parsing MAF file ucsc_mm9_chr10_big.maf with missing signature. ... ok
test_reading_ucsc_mm9_chr10 (test_Align_maf.TestAlign_reading.test_reading_ucsc_mm9_chr10)
Test parsing MAF file ucsc_mm9_chr10.maf. ... ok
test_reading_ucsc_mm9_chr10_bad (test_Align_maf.TestAlign_reading.test_reading_ucsc_mm9_chr10_bad)
Test parsing MAF file ucsc_mm9_chr10_bad.maf with incorrect sequence size. ... ok
test_reading_ucsc_test (test_Align_maf.TestAlign_reading.test_reading_ucsc_test)
Test parsing ucsc_test.maf. ... ok
test_writing_bug2453 (test_Align_maf.TestAlign_writing.test_writing_bug2453)
Test reading and writing bug2453.maf. ... ok
test_writing_bundle_without_target (test_Align_maf.TestAlign_writing.test_writing_bundle_without_target)
Test reading and writing bundle_without_target.maf. ... ok
test_writing_ucsc_mm9_chr10 (test_Align_maf.TestAlign_writing.test_writing_ucsc_mm9_chr10)
Test reading and writing ucsc_mm9_chr10.maf. ... ok
test_writing_ucsc_test (test_Align_maf.TestAlign_writing.test_writing_ucsc_test)
Test reading and writing ucsc_test.maf. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.410 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_mauve.py
test_Align_mauve ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_parse (test_Align_mauve.TestCombinedFile.test_parse) ... ok
test_write_read (test_Align_mauve.TestCombinedFile.test_write_read) ... ok
test_parse (test_Align_mauve.TestDSeparateFiles.test_parse) ... ok
test_write_read (test_Align_mauve.TestDSeparateFiles.test_write_read) ... ok
test_empty (test_Align_mauve.TestMauveBasic.test_empty) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.105 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_msf.py
test_Align_msf ... ok
test_protein1 (test_Align_msf.TestMSF.test_protein1) ... ok
test_protein2 (test_Align_msf.TestMSF.test_protein2) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.076 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_nexus.py
test_Align_nexus ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_empty (test_Align_nexus.TestNexusBasic.test_empty) ... ok
test_nexus1 (test_Align_nexus.TestNexusReading.test_nexus1) ... ok
test_nexus2 (test_Align_nexus.TestNexusReading.test_nexus2) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.092 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_phylip.py
test_Align_phylip ... ok
test_five_and_six (test_Align_phylip.TestPhylipReading.test_five_and_six) ... ok
test_four (test_Align_phylip.TestPhylipReading.test_four) ... ok
test_one (test_Align_phylip.TestPhylipReading.test_one) ... ok
test_two_and_three (test_Align_phylip.TestPhylipReading.test_two_and_three) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.093 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_psl.py
test_Align_psl ... ok
test_reading_psl_34_001 (test_Align_psl.TestAlign_dna.test_reading_psl_34_001)
Test parsing psl_34_001.psl and pslx_34_001.pslx. ... ok
test_reading_psl_34_002 (test_Align_psl.TestAlign_dna.test_reading_psl_34_002)
Test parsing psl_34_002.psl and pslx_34_002.pslx. ... ok
test_reading_psl_34_003 (test_Align_psl.TestAlign_dna.test_reading_psl_34_003)
Test parsing psl_34_003.psl and pslx_34_003.pslx. ... ok
test_reading_psl_34_004 (test_Align_psl.TestAlign_dna.test_reading_psl_34_004)
Test parsing psl_34_004.psl and pslx_34_004.pslx. ... ok
test_reading_psl_34_005 (test_Align_psl.TestAlign_dna.test_reading_psl_34_005)
Test parsing psl_34_005.psl and pslx_34_005.pslx. ... ok
test_writing_psl_34_001 (test_Align_psl.TestAlign_dna.test_writing_psl_34_001)
Test writing the alignments in psl_34_001.psl. ... ok
test_writing_psl_34_002 (test_Align_psl.TestAlign_dna.test_writing_psl_34_002)
Test writing the alignments in psl_34_002.psl. ... ok
test_writing_psl_34_003 (test_Align_psl.TestAlign_dna.test_writing_psl_34_003)
Test writing the alignments in psl_34_003.psl. ... ok
test_writing_psl_34_004 (test_Align_psl.TestAlign_dna.test_writing_psl_34_004)
Test writing the alignments in psl_34_004.psl. ... ok
test_writing_psl_34_005 (test_Align_psl.TestAlign_dna.test_writing_psl_34_005)
Test writing the alignments in psl_34_005.psl. ... ok
test_reading (test_Align_psl.TestAlign_dna_rna.test_reading)
Test parsing dna_rna.psl. ... ok
test_writing (test_Align_psl.TestAlign_dna_rna.test_writing)
Test writing the alignments in dna_rna.psl. ... ok
test_reading_psl_35_001 (test_Align_psl.TestAlign_dnax_prot.test_reading_psl_35_001)
Test parsing psl_35_001.psl and pslx_35_001.pslx. ... ok
test_reading_psl_35_002 (test_Align_psl.TestAlign_dnax_prot.test_reading_psl_35_002)
Test parsing psl_35_002.psl. ... ok
test_writing_psl_35_001 (test_Align_psl.TestAlign_dnax_prot.test_writing_psl_35_001)
Test writing the alignments in psl_35_001.psl. ... ok
test_writing_psl_35_002 (test_Align_psl.TestAlign_dnax_prot.test_writing_psl_35_002)
Test writing the alignments in psl_35_002.psl. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.344 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_sam.py
test_Align_sam ... ok
test_4D8I6M (test_Align_sam.TestAlign_clippping.test_4D8I6M)
Test alignment starting with deletion followed by insertion. ... ok
test_4I8D6M (test_Align_sam.TestAlign_clippping.test_4I8D6M)
Test alignment starting with insertion followed by deletion. ... ok
test_4S6M (test_Align_sam.TestAlign_clippping.test_4S6M)
Test alignment starting with soft clip at non-zero position. ... ok
test_4S8D6M (test_Align_sam.TestAlign_clippping.test_4S8D6M)
Test alignment starting with soft clip followed by deletion. ... ok
test_4S8I6M (test_Align_sam.TestAlign_clippping.test_4S8I6M)
Test alignment starting with soft clip followed by insertion. ... ok
test_6M (test_Align_sam.TestAlign_clippping.test_6M)
Test alignment starting at non-zero position. ... ok
test_8D6M_ex1 (test_Align_sam.TestAlign_clippping.test_8D6M_ex1)
Test alignment starting with deletion. ... ok
test_8D6M_ex2 (test_Align_sam.TestAlign_clippping.test_8D6M_ex2)
Test alignment starting with deletion at non-zero position. ... ok
test_8I6M_ex1 (test_Align_sam.TestAlign_clippping.test_8I6M_ex1)
Test alignment starting with insertion. ... ok
test_8I6M_ex2 (test_Align_sam.TestAlign_clippping.test_8I6M_ex2)
Test alignment starting with insertion at non-zero position. ... ok
test_8S6M (test_Align_sam.TestAlign_clippping.test_8S6M)
Test alignment starting with soft clip. ... ok
test_reading_psl_34_001 (test_Align_sam.TestAlign_dna.test_reading_psl_34_001)
Test parsing psl_34_001.sam. ... ok
test_reading_psl_34_003 (test_Align_sam.TestAlign_dna.test_reading_psl_34_003)
Test parsing psl_34_003.sam. ... ok
test_reading_psl_34_004 (test_Align_sam.TestAlign_dna.test_reading_psl_34_004)
Test parsing psl_34_004.sam. ... ok
test_reading_psl_34_005 (test_Align_sam.TestAlign_dna.test_reading_psl_34_005)
Test parsing psl_34_005.sam. ... ok
test_writing_psl_34_001 (test_Align_sam.TestAlign_dna.test_writing_psl_34_001)
Test writing the alignments in psl_34_001.sam. ... ok
test_writing_psl_34_003 (test_Align_sam.TestAlign_dna.test_writing_psl_34_003)
Test writing the alignments in psl_34_003.sam. ... ok
test_writing_psl_34_004 (test_Align_sam.TestAlign_dna.test_writing_psl_34_004)
Test writing the alignments in psl_34_004.sam. ... ok
test_writing_psl_34_005 (test_Align_sam.TestAlign_dna.test_writing_psl_34_005)
Test writing the alignments in psl_34_005.sam. ... ok
test_reading (test_Align_sam.TestAlign_dna_rna.test_reading)
Test parsing dna_rna.sam. ... ok
test_reading_psl_comparison (test_Align_sam.TestAlign_dna_rna.test_reading_psl_comparison)
Test parsing dna_rna.sam and comparing to dna_rna.psl. ... ok
test_writing (test_Align_sam.TestAlign_dna_rna.test_writing)
Test writing the alignments in dna_rna.sam. ... ok
test_ex1 (test_Align_sam.TestAlign_sambam.test_ex1) ... ok
test_ex1_header (test_Align_sam.TestAlign_sambam.test_ex1_header) ... ok
test_sam1 (test_Align_sam.TestAlign_sambam.test_sam1) ... ok
test_sam2 (test_Align_sam.TestAlign_sambam.test_sam2) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.409 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_stockholm.py
test_Align_stockholm ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_reading_alignments_cath1 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath1)
Test parsing CATH record 3.30.160.60/FF/004774. ... ok
test_reading_alignments_cath2 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath2)
Test parsing CATH record 2.105.10.10/FF/000002. ... ok
test_reading_alignments_cath3 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath3)
Test parsing CATH record 1.10.275.10/FF/000026. ... ok
test_reading_example (test_Align_stockholm.TestStockholm_reading.test_reading_example)
Test parsing Pfam record HAT as the docstring example. ... ok
test_reading_writing_alignments_globins45 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_globins45)
Test parsing hmmalign output. ... ok
test_reading_writing_alignments_pfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam1)
Test parsing Pfam record 120_Rick_ant. ... ok
test_reading_writing_alignments_pfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam2)
Test parsing Pfam record 7kD_DNA_binding. ... ok
test_reading_writing_alignments_pfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam3)
Test parsing Pfam record 12TM_1. ... ok
test_reading_writing_alignments_pfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam4)
Test parsing Pfam record 3Beta_HSD. ... ok
test_reading_writing_alignments_pfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam5)
Test parsing Pfam record ArsP_1. ... ok
test_reading_writing_alignments_pfam6 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam6)
Test parsing Pfam record COX2_TM. ... ok
test_reading_writing_alignments_pfam7 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam7)
Test parsing Pfam record Alpha_E1_glycop. ... ok
test_reading_writing_alignments_pfam8 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam8)
Test parsing Pfam record Cyclin_N. ... ok
test_reading_writing_alignments_pfam9 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam9)
Test parsing Pfam record SH3_11. ... ok
test_reading_writing_alignments_rfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam1)
Test parsing Rfam record BTnc005. ... ok
test_reading_writing_alignments_rfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam2)
Test parsing Rfam record SraC_RyeA. ... ok
test_reading_writing_alignments_rfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam3)
Test parsing Rfam record McaS. ... ok
test_reading_writing_alignments_rfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam4)
Test parsing Rfam record IRES_KSHV. ... ok
test_reading_writing_alignments_rfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam5)
Test parsing Rfam record BMV3_UPD-PK3. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.329 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_tabular.py
test_Align_tabular ... ok
test_2226_tblastn_001 (test_Align_tabular.TestBlast.test_2226_tblastn_001) ... ok
test_2226_tblastn_002 (test_Align_tabular.TestBlast.test_2226_tblastn_002) ... ok
test_2226_tblastn_003 (test_Align_tabular.TestBlast.test_2226_tblastn_003) ... ok
test_2226_tblastn_004 (test_Align_tabular.TestBlast.test_2226_tblastn_004) ... ok
test_2226_tblastn_005 (test_Align_tabular.TestBlast.test_2226_tblastn_005) ... ok
test_2226_tblastn_007 (test_Align_tabular.TestBlast.test_2226_tblastn_007) ... ok
test_2226_tblastn_008 (test_Align_tabular.TestBlast.test_2226_tblastn_008) ... ok
test_2226_tblastn_009 (test_Align_tabular.TestBlast.test_2226_tblastn_009) ... ok
test_2226_tblastn_010 (test_Align_tabular.TestBlast.test_2226_tblastn_010) ... ok
test_2226_tblastn_011 (test_Align_tabular.TestBlast.test_2226_tblastn_011) ... ok
test_2226_tblastn_012 (test_Align_tabular.TestBlast.test_2226_tblastn_012) ... ok
test_2228_tblastn_001 (test_Align_tabular.TestBlast.test_2228_tblastn_001) ... ok
test_2228_tblastx_001 (test_Align_tabular.TestBlast.test_2228_tblastx_001) ... ok
test_empty (test_Align_tabular.TestFastaBasic.test_empty) ... ok
test_m8CB (test_Align_tabular.TestFastaNucleotide.test_m8CB) ... ok
test_m8CC (test_Align_tabular.TestFastaNucleotide.test_m8CC) ... ok
test_m8CB (test_Align_tabular.TestFastaProtein.test_m8CB) ... ok
test_m8CC (test_Align_tabular.TestFastaProtein.test_m8CC) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.476 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Application.py
test_Application ... ok
test_echo (test_Application.TestApp.test_echo) ... ok
test_echo_capture_both (test_Application.TestApp.test_echo_capture_both) ... ok
test_echo_capture_neither (test_Application.TestApp.test_echo_capture_neither) ... ok
test_echo_capture_stderr (test_Application.TestApp.test_echo_capture_stderr) ... ok
test_echo_capture_stdout (test_Application.TestApp.test_echo_capture_stdout) ... ok
test_echo_file_both (test_Application.TestApp.test_echo_file_both) ... ok
test_echo_file_same (test_Application.TestApp.test_echo_file_same) ... ok
test_echo_file_stderr (test_Application.TestApp.test_echo_file_stderr) ... ok
test_echo_file_stdout (test_Application.TestApp.test_echo_file_stdout) ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.023 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.023 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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)
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.147 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.122 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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)
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.102 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.118 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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)
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.113 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.120 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_sqlite3.py
test_BioSQL_sqlite3 ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_SeqIO_loading (common_BioSQL.AutoSeqIOTests.test_SeqIO_loading) ... ok
test_backwards_compatibility (test_BioSQL_sqlite3.BackwardsCompatibilityTest.test_backwards_compatibility)
Check can re-use an old BioSQL SQLite3 database. ... ok
test_NC_000932 (common_BioSQL.ClosedLoopTest.test_NC_000932)
From GenBank file to BioSQL and back to a GenBank file, NC_000932. ... ok
test_NC_005816 (common_BioSQL.ClosedLoopTest.test_NC_005816)
From GenBank file to BioSQL and back to a GenBank file, NC_005816. ... ok
test_NT_019265 (common_BioSQL.ClosedLoopTest.test_NT_019265)
From GenBank file to BioSQL and back to a GenBank file, NT_019265. ... ok
test_arab1 (common_BioSQL.ClosedLoopTest.test_arab1)
From GenBank file to BioSQL and back to a GenBank file, arab1. ... ok
test_cor6_6 (common_BioSQL.ClosedLoopTest.test_cor6_6)
From GenBank file to BioSQL and back to a GenBank file, cor6_6. ... ok
test_no_ref (common_BioSQL.ClosedLoopTest.test_no_ref)
From GenBank file to BioSQL and back to a GenBank file, noref. ... ok
test_one_of (common_BioSQL.ClosedLoopTest.test_one_of)
From GenBank file to BioSQL and back to a GenBank file, one_of. ... ok
test_protein_refseq2 (common_BioSQL.ClosedLoopTest.test_protein_refseq2)
From GenBank file to BioSQL and back to a GenBank file, protein_refseq2. ... ok
test_del_db_items (common_BioSQL.DeleteTest.test_del_db_items)
Check all associated data is deleted from an item. ... ok
test_server (common_BioSQL.DeleteTest.test_server)
Check BioSeqDatabase methods. ... ok
test_duplicate_id_load (common_BioSQL.DupLoadTest.test_duplicate_id_load)
Make sure can't import records with same ID (in one go). ... ok
test_duplicate_load (common_BioSQL.DupLoadTest.test_duplicate_load)
Make sure can't import a single record twice (in one go). ... ok
test_duplicate_load2 (common_BioSQL.DupLoadTest.test_duplicate_load2)
Make sure can't import a single record twice (in steps). ... ok
test_record_loading (common_BioSQL.InDepthLoadTest.test_record_loading)
Make sure all records are correctly loaded. ... ok
test_reload (common_BioSQL.InDepthLoadTest.test_reload)
Make sure can't reimport existing records. ... ok
test_seq_feature (common_BioSQL.InDepthLoadTest.test_seq_feature)
In depth check that SeqFeatures are transmitted through the db. ... ok
test_transfer (common_BioSQL.InDepthLoadTest.test_transfer)
Make sure can load record into another namespace. ... ok
test_load_database (common_BioSQL.LoaderTest.test_load_database)
Load SeqRecord objects into a BioSQL database. ... ok
test_cross_retrieval_of_items (common_BioSQL.MultiReadTest.test_cross_retrieval_of_items)
Test that valid ids can't be retrieved between namespaces. ... ok
test_get_db_items (common_BioSQL.MultiReadTest.test_get_db_items)
Check list, keys, length etc. ... ok
test_server (common_BioSQL.MultiReadTest.test_server)
Check BioSeqDatabase methods. ... ok
test_get_db_items (common_BioSQL.ReadTest.test_get_db_items)
Check list, keys, length etc. ... ok
test_lookup_items (common_BioSQL.ReadTest.test_lookup_items)
Test retrieval of items using various ids. ... ok
test_server (common_BioSQL.ReadTest.test_server)
Check BioSeqDatabase methods. ... ok
test_addition (common_BioSQL.SeqInterfaceTest.test_addition)
Check can add Seq objects from BioSQL together. ... ok
test_convert (common_BioSQL.SeqInterfaceTest.test_convert)
Check can turn a Seq object from BioSQL into a Seq or MutableSeq. ... ok
test_eq (common_BioSQL.SeqInterfaceTest.test_eq) ... ok
test_ge (common_BioSQL.SeqInterfaceTest.test_ge) ... ok
test_gt (common_BioSQL.SeqInterfaceTest.test_gt) ... ok
test_le (common_BioSQL.SeqInterfaceTest.test_le) ... ok
test_lt (common_BioSQL.SeqInterfaceTest.test_lt) ... ok
test_multiplication (common_BioSQL.SeqInterfaceTest.test_multiplication)
Check can multiply Seq objects from BioSQL by integers. ... ok
test_ne (common_BioSQL.SeqInterfaceTest.test_ne) ... ok
test_record_slicing (common_BioSQL.SeqInterfaceTest.test_record_slicing)
Check that slices of DBSeqRecord are retrieved properly. ... ok
test_seq (common_BioSQL.SeqInterfaceTest.test_seq)
Make sure Seqs from BioSQL implement the right interface. ... ok
test_seq_features (common_BioSQL.SeqInterfaceTest.test_seq_features)
Check SeqFeatures of a sequence. ... ok
test_seq_record (common_BioSQL.SeqInterfaceTest.test_seq_record)
Make sure SeqRecords from BioSQL implement the right interface. ... ok
test_seq_slicing (common_BioSQL.SeqInterfaceTest.test_seq_slicing)
Check that slices of sequences are retrieved properly. ... ok
test_ambiguous_location (common_BioSQL.SwissProtUnknownPositionTest.test_ambiguous_location)
Loaded uniprot-xml with ambiguous location in BioSQL. ... ok
test_add (common_BioSQL.TestBaseClassMethods.test_add) ... ok
test_bytes (common_BioSQL.TestBaseClassMethods.test_bytes) ... ok
test_contains (common_BioSQL.TestBaseClassMethods.test_contains) ... ok
test_count (common_BioSQL.TestBaseClassMethods.test_count) ... ok
test_endswith (common_BioSQL.TestBaseClassMethods.test_endswith) ... ok
test_find (common_BioSQL.TestBaseClassMethods.test_find) ... ok
test_hash (common_BioSQL.TestBaseClassMethods.test_hash) ... ok
test_index (common_BioSQL.TestBaseClassMethods.test_index) ... ok
test_lower (common_BioSQL.TestBaseClassMethods.test_lower) ... ok
test_lstrip (common_BioSQL.TestBaseClassMethods.test_lstrip) ... ok
test_mul (common_BioSQL.TestBaseClassMethods.test_mul) ... ok
test_radd (common_BioSQL.TestBaseClassMethods.test_radd) ... ok
test_replace (common_BioSQL.TestBaseClassMethods.test_replace) ... ok
test_repr (common_BioSQL.TestBaseClassMethods.test_repr) ... ok
test_rfind (common_BioSQL.TestBaseClassMethods.test_rfind) ... ok
test_rindex (common_BioSQL.TestBaseClassMethods.test_rindex) ... ok
test_rsplit (common_BioSQL.TestBaseClassMethods.test_rsplit) ... ok
test_rstrip (common_BioSQL.TestBaseClassMethods.test_rstrip) ... ok
test_split (common_BioSQL.TestBaseClassMethods.test_split) ... ok
test_startswith (common_BioSQL.TestBaseClassMethods.test_startswith) ... ok
test_str (common_BioSQL.TestBaseClassMethods.test_str) ... ok
test_strip (common_BioSQL.TestBaseClassMethods.test_strip) ... ok
test_translate (common_BioSQL.TestBaseClassMethods.test_translate) ... ok
test_upper (common_BioSQL.TestBaseClassMethods.test_upper) ... ok
test_NC_000932 (common_BioSQL.TransferTest.test_NC_000932)
From GenBank file to BioSQL, then again to a new namespace, NC_000932. ... ok
test_NC_005816 (common_BioSQL.TransferTest.test_NC_005816)
From GenBank file to BioSQL, then again to a new namespace, NC_005816. ... ok
test_NT_019265 (common_BioSQL.TransferTest.test_NT_019265)
From GenBank file to BioSQL, then again to a new namespace, NT_019265. ... ok
test_arab1 (common_BioSQL.TransferTest.test_arab1)
From GenBank file to BioSQL, then again to a new namespace, arab1. ... ok
test_cor6_6 (common_BioSQL.TransferTest.test_cor6_6)
From GenBank file to BioSQL, then again to a new namespace, cor6_6. ... ok
test_no_ref (common_BioSQL.TransferTest.test_no_ref)
From GenBank file to BioSQL, then again to a new namespace, noref. ... ok
test_one_of (common_BioSQL.TransferTest.test_one_of)
From GenBank file to BioSQL, then again to a new namespace, one_of. ... ok
test_protein_refseq2 (common_BioSQL.TransferTest.test_protein_refseq2)
From GenBank file to BioSQL, then again to a new namespace, protein_refseq2. ... ok
----------------------------------------------------------------------
Ran 1 test in 6.350 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.113 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Blast_Record.py
test_Blast_Record ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_str (test_Blast_Record.TestHsp.test_str) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.063 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_CAPS.py
test_CAPS ... ok
test (test_CAPS.TestCAPS.test) ... ok
testNoCAPS (test_CAPS.TestCAPS.testNoCAPS) ... ok
test_trivial (test_CAPS.TestCAPS.test_trivial) ... ok
test_uneven (test_CAPS.TestCAPS.test_uneven) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.213 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Chi2.py
test_Chi2 ... ok
test_cdf_chi2 (test_Chi2.ModTest.test_cdf_chi2) ... ok
test_incomplete_gamma (test_Chi2.ModTest.test_incomplete_gamma) ... ok
test_ln_gamma (test_Chi2.ModTest.test_ln_gamma) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.115 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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.
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.090 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.093 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Cluster.py
test_Cluster ... ok
test_clusterdistance (test_Cluster.TestCluster.test_clusterdistance) ... ok
test_clusterdistance_arguments (test_Cluster.TestCluster.test_clusterdistance_arguments) ... ok
test_distancematrix_arguments (test_Cluster.TestCluster.test_distancematrix_arguments) ... ok
test_distancematrix_kmedoids (test_Cluster.TestCluster.test_distancematrix_kmedoids) ... ok
test_kcluster (test_Cluster.TestCluster.test_kcluster) ... ok
test_kcluster_arguments (test_Cluster.TestCluster.test_kcluster_arguments) ... ok
test_kmedoids_arguments (test_Cluster.TestCluster.test_kmedoids_arguments) ... ok
test_mask_parse (test_Cluster.TestCluster.test_mask_parse) ... ok
test_matrix_parse (test_Cluster.TestCluster.test_matrix_parse) ... ok
test_pca (test_Cluster.TestCluster.test_pca) ... ok
test_pca_arguments (test_Cluster.TestCluster.test_pca_arguments) ... ok
test_somcluster (test_Cluster.TestCluster.test_somcluster) ... ok
test_somcluster_arguments (test_Cluster.TestCluster.test_somcluster_arguments) ... ok
test_tree (test_Cluster.TestCluster.test_tree) ... ok
test_tree_arguments (test_Cluster.TestCluster.test_tree_arguments) ... ok
test_treecluster (test_Cluster.TestCluster.test_treecluster) ... ok
test_treecluster_arguments (test_Cluster.TestCluster.test_treecluster_arguments) ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.053 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_CodonTable.py
test_CodonTable ... ok
test_coding (test_CodonTable.AmbiguousCodonsTests.test_coding)
Check a few ambiguous codons for correct coding. ... ok
test_list_ambiguous_codons (test_CodonTable.AmbiguousCodonsTests.test_list_ambiguous_codons)
Check if stop codons are properly extended. ... ok
test_start_codons (test_CodonTable.AmbiguousCodonsTests.test_start_codons)
Test various ambiguous codons as start codon. ... ok
test_stop_codons (test_CodonTable.AmbiguousCodonsTests.test_stop_codons)
Test various ambiguous codons as stop codon. ... ok
test_ambiguous_tables (test_CodonTable.BasicSanityTests.test_ambiguous_tables)
Check if all IDs and all names are present in ambiguous tables. ... ok
test_complete_tables (test_CodonTable.BasicSanityTests.test_complete_tables)
Check if all unambiguous codon tables have all entries. ... ok
test_number_of_tables (test_CodonTable.BasicSanityTests.test_number_of_tables)
Check if we have the same number of tables for each type. ... ok
test_ambiguous_forward_table (test_CodonTable.ErrorConditions.test_ambiguous_forward_table)
Raise errors in AmbiguousForwardTable. ... ok
test_list_possible_proteins (test_CodonTable.ErrorConditions.test_list_possible_proteins)
Raise errors in list_possible proteins. ... ok
test_print_table (test_CodonTable.PrintTable.test_print_table)
Test output of __str__ function. ... ok
test_table01 (test_CodonTable.SingleTableTests.test_table01)
Check table 1: Standard. ... ok
test_table02 (test_CodonTable.SingleTableTests.test_table02)
Check table 2: Vertebrate Mitochondrial. ... ok
test_table03 (test_CodonTable.SingleTableTests.test_table03)
Check table 3: Yeast Mitochondrial. ... ok
test_table04 (test_CodonTable.SingleTableTests.test_table04)
Check table 4: Mold Mitochondrial and others. ... ok
test_table05 (test_CodonTable.SingleTableTests.test_table05)
Check table 5: Invertebrate Mitochondrial. ... ok
test_table06 (test_CodonTable.SingleTableTests.test_table06)
Check table 6: Ciliate and Other Nuclear. ... ok
test_table09 (test_CodonTable.SingleTableTests.test_table09)
Check table 9: Echinoderm and Flatworm Mitochondrial. ... ok
test_table10 (test_CodonTable.SingleTableTests.test_table10)
Check table 10: Euplotid Nuclear. ... ok
test_table11 (test_CodonTable.SingleTableTests.test_table11)
Check table 11: Bacterial, Archaeal and Plant Plastid. ... ok
test_table12 (test_CodonTable.SingleTableTests.test_table12)
Check table 12: Alternative Yeast Nuclear. ... ok
test_table13 (test_CodonTable.SingleTableTests.test_table13)
Check table 13: Ascidian Mitochondrial. ... ok
test_table14 (test_CodonTable.SingleTableTests.test_table14)
Check table 14: Alternative Flatworm Mitochondrial. ... ok
test_table16 (test_CodonTable.SingleTableTests.test_table16)
Check table 16: Chlorophycean Mitochondrial. ... ok
test_table21 (test_CodonTable.SingleTableTests.test_table21)
Check table 21: Trematode Mitochondrial. ... ok
test_table22 (test_CodonTable.SingleTableTests.test_table22)
Check table 22: Scenedesmus obliquus Mitochondrial. ... ok
test_table23 (test_CodonTable.SingleTableTests.test_table23)
Check table 9: Thraustochytrium Mitochondrial. ... ok
test_table24 (test_CodonTable.SingleTableTests.test_table24)
Check table 24: Pterobranchia Mitochondrial. ... ok
test_table25 (test_CodonTable.SingleTableTests.test_table25)
Check table 25: Candidate Division SR1 and Gracilibacteria. ... ok
test_table26 (test_CodonTable.SingleTableTests.test_table26)
Check table 26: Pachysolen tannophilus Nuclear. ... ok
test_table27 (test_CodonTable.SingleTableTests.test_table27)
Check table 27: Karyorelict Nuclear. ... ok
test_table28 (test_CodonTable.SingleTableTests.test_table28)
Check table 28: Condylostoma Nuclear. ... ok
test_table29 (test_CodonTable.SingleTableTests.test_table29)
Check table 29: Mesodinium Nuclear. ... ok
test_table30 (test_CodonTable.SingleTableTests.test_table30)
Check table 30: Peritrich Nuclear. ... ok
test_table31 (test_CodonTable.SingleTableTests.test_table31)
Check table 31: Blastocrithidia Nuclear. ... ok
test_table32 (test_CodonTable.SingleTableTests.test_table32)
Check table 32: Balanophoraceae Plastid. ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.099 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ColorSpiral.py
test_ColorSpiral ... ok
test_dict (test_ColorSpiral.DictTest.test_dict)
get_color_dict() for classes A-D, no jitter. ... ok
test_colorlist (test_ColorSpiral.SpiralTest.test_colorlist)
Get set of eight colours, no jitter, using ColorSpiral. ... ok
test_colorspiral (test_ColorSpiral.SpiralTest.test_colorspiral)
Get set of 16 colours, no jitter, using ColorSpiral. ... ok
test_colorspiral (test_ColorSpiral.SquareTest.test_colorspiral)
Set of 625 colours, with jitter, using get_colors(). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.064 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Compass.py
test_Compass ... ok
testAlignmentParsingOne (test_Compass.CompassTest.testAlignmentParsingOne) ... ok
testAlignmentParsingTwo (test_Compass.CompassTest.testAlignmentParsingTwo) ... ok
testCompassIteratorEasy (test_Compass.CompassTest.testCompassIteratorEasy) ... ok
testCompassIteratorHard (test_Compass.CompassTest.testCompassIteratorHard) ... ok
testCompassParser (test_Compass.CompassTest.testCompassParser) ... ok
testCompassScanAndConsume (test_Compass.CompassTest.testCompassScanAndConsume) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.013 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Consensus.py
test_Consensus ... ok
test_bitstring (test_Consensus.BitStringTest.test_bitstring) ... ok
test_bootstrap (test_Consensus.BootstrapTest.test_bootstrap) ... ok
test_bootstrap_consensus (test_Consensus.BootstrapTest.test_bootstrap_consensus) ... ok
test_bootstrap_trees (test_Consensus.BootstrapTest.test_bootstrap_trees) ... ok
test_adam_consensus (test_Consensus.ConsensusTest.test_adam_consensus) ... ok
test_count_clades (test_Consensus.ConsensusTest.test_count_clades) ... ok
test_get_support (test_Consensus.ConsensusTest.test_get_support) ... ok
test_majority_consensus (test_Consensus.ConsensusTest.test_majority_consensus) ... ok
test_strict_consensus (test_Consensus.ConsensusTest.test_strict_consensus) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.215 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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.
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.067 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_EMBL_unittest.py
test_EMBL_unittest ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_embl_0_line (test_EMBL_unittest.EMBLTests.test_embl_0_line)
Test SQ line with 0 length sequence. ... ok
test_embl_content_after_co (test_EMBL_unittest.EMBLTests.test_embl_content_after_co)
Test a ValueError is thrown by content after a CO line. ... ok
test_embl_no_coords (test_EMBL_unittest.EMBLTests.test_embl_no_coords)
Test sequence lines without coordinates. ... ok
test_embl_wrong_dr_line (test_EMBL_unittest.EMBLTests.test_embl_wrong_dr_line)
Test files with wrong DR lines. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.092 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.106 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.105 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_EmbossPrimer.py
test_EmbossPrimer ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_in_depth_single_parse (test_EmbossPrimer.Primer3ParseTest.test_in_depth_single_parse)
Make sure we get info right from a single primer find. ... ok
test_indepth_regular_parse (test_EmbossPrimer.Primer3ParseTest.test_indepth_regular_parse)
Make sure we get the data from normal primer3 files okay. ... ok
test_internal_oligo_single_parse (test_EmbossPrimer.Primer3ParseTest.test_internal_oligo_single_parse)
Make sure we can parse an internal oligo file correctly. ... ok
test_multi_record_full (test_EmbossPrimer.Primer3ParseTest.test_multi_record_full)
Test parsing multiple primer sets (NirK full). ... ok
test_multi_record_fwd (test_EmbossPrimer.Primer3ParseTest.test_multi_record_fwd)
Test parsing multiple primer sets (NirK forward). ... ok
test_simple_parse (test_EmbossPrimer.Primer3ParseTest.test_simple_parse)
Make sure that we can use all single target primer3 files. ... ok
test_primer_representation (test_EmbossPrimer.PrimerSearchInputTest.test_primer_representation)
Make sure we can output primer information correctly. ... ok
test_in_depth_normal_parse (test_EmbossPrimer.PrimersearchParseTest.test_in_depth_normal_parse)
Make sure the output from a simple primersearch file is correct. ... ok
test_simple_parse (test_EmbossPrimer.PrimersearchParseTest.test_simple_parse)
Make sure that we can parse all primersearch files. ... ok
----------------------------------------------------------------------
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Entrez.py
test_Entrez ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Entrez/__init__.py:686: UserWarning:
Email address is not specified.
To make use of NCBI's E-utilities, NCBI requires you to specify your
email address with each request. As an example, if your email address
is A.N.Other@example.com, you can specify it as follows:
from Bio import Entrez
Entrez.email = 'A.N.Other@example.com'
In case of excessive usage of the E-utilities, NCBI will attempt to contact
a user at the email address provided before blocking access to the
E-utilities.
warnings.warn(
ok
test_custom_directory (test_Entrez.CustomDirectoryTest.test_custom_directory) ... ok
test_construct_cgi_ecitmatch (test_Entrez.TestURLConstruction.test_construct_cgi_ecitmatch) ... ok
test_construct_cgi_efetch (test_Entrez.TestURLConstruction.test_construct_cgi_efetch) ... ok
test_construct_cgi_einfo (test_Entrez.TestURLConstruction.test_construct_cgi_einfo)
Test constructed url for request to Entrez. ... ok
test_construct_cgi_elink1 (test_Entrez.TestURLConstruction.test_construct_cgi_elink1) ... ok
test_construct_cgi_elink2 (test_Entrez.TestURLConstruction.test_construct_cgi_elink2)
Commas: Link from protein to gene. ... ok
test_construct_cgi_elink3 (test_Entrez.TestURLConstruction.test_construct_cgi_elink3)
Multiple ID entries: Find one-to-one links from protein to gene. ... ok
test_construct_cgi_epost1 (test_Entrez.TestURLConstruction.test_construct_cgi_epost1) ... ok
test_construct_cgi_epost2 (test_Entrez.TestURLConstruction.test_construct_cgi_epost2) ... ok
test_default_params (test_Entrez.TestURLConstruction.test_default_params)
Test overriding default values for the "email", "api_key", and "tool" parameters. ... ok
test_email_warning (test_Entrez.TestURLConstruction.test_email_warning)
Test issuing warning when user does not specify email address. ... ok
test_format_ids (test_Entrez.TestURLConstruction.test_format_ids) ... ok
test_has_api_key (test_Entrez.TestURLConstruction.test_has_api_key)
Test checking whether a Request object specifies an API key. ... ok
----------------------------------------------------------------------
Ran 1 test in 4.162 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.079 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_efetch_schemas)
Test parsing XML using Schemas. ... ok
test_fasta (test_Entrez_parser.EFetchTest.test_fasta)
Test error handling when presented with Fasta non-XML data. ... ok
test_genbank (test_Entrez_parser.EFetchTest.test_genbank)
Test error handling when presented with GenBank non-XML data. ... ok
test_nucleotide1 (test_Entrez_parser.EFetchTest.test_nucleotide1)
Test parsing XML returned by EFetch, Nucleotide database (first test). ... ok
test_nucleotide2 (test_Entrez_parser.EFetchTest.test_nucleotide2)
Test parsing XML returned by EFetch, Nucleotide database (second test). ... ok
test_omim (test_Entrez_parser.EFetchTest.test_omim)
Test parsing XML returned by EFetch, OMIM database. ... ok
test_pmc (test_Entrez_parser.EFetchTest.test_pmc)
Test parsing XML returned by EFetch from PubMed Central. ... ok
test_protein (test_Entrez_parser.EFetchTest.test_protein)
Test parsing XML returned by EFetch, Protein database. ... ok
test_pubmed1 (test_Entrez_parser.EFetchTest.test_pubmed1)
Test parsing XML returned by EFetch, PubMed database (first test). ... ok
test_pubmed2 (test_Entrez_parser.EFetchTest.test_pubmed2)
Test parsing XML returned by EFetch, PubMed database (second test). ... ok
test_pubmed_html (test_Entrez_parser.EFetchTest.test_pubmed_html)
Test error handling when presented with HTML (so XML-like) data. ... ok
test_pubmed_html_escaping (test_Entrez_parser.EFetchTest.test_pubmed_html_escaping)
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_pubmed_html_mathml_tags)
Test parsing XML returned by EFetch, PubMed database, with both HTML and MathML tags. ... ok
test_pubmed_html_tags (test_Entrez_parser.EFetchTest.test_pubmed_html_tags)
Test parsing XML returned by EFetch, PubMed database with HTML tags. ... ok
test_pubmed_mathml_tags (test_Entrez_parser.EFetchTest.test_pubmed_mathml_tags)
Test parsing XML returned by EFetch, PubMed database, with extensive MathML tags. ... ok
test_taxonomy (test_Entrez_parser.EFetchTest.test_taxonomy)
Test parsing XML returned by EFetch, Taxonomy database. ... ok
test_truncated_xml (test_Entrez_parser.EFetchTest.test_truncated_xml)
Test error handling for a truncated XML declaration. ... ok
test_xml_without_declaration (test_Entrez_parser.EFetchTest.test_xml_without_declaration)
Test error handling for a missing XML declaration. ... ok
test_xml_without_definition (test_Entrez_parser.EFetchTest.test_xml_without_definition)
Test error handling for a missing DTD or XML Schema. ... ok
test_egquery1 (test_Entrez_parser.EGQueryTest.test_egquery1)
Test parsing XML output returned by EGQuery (first test). ... ok
test_egquery2 (test_Entrez_parser.EGQueryTest.test_egquery2)
Test parsing XML output returned by EGQuery (second test). ... ok
test_corrupted (test_Entrez_parser.EInfoTest.test_corrupted)
Test if corrupted XML is handled correctly. ... ok
test_list (test_Entrez_parser.EInfoTest.test_list)
Test parsing database list returned by EInfo. ... ok
test_pubmed1 (test_Entrez_parser.EInfoTest.test_pubmed1)
Test parsing database info returned by EInfo. ... ok
test_pubmed2 (test_Entrez_parser.EInfoTest.test_pubmed2)
Test validating the XML against the DTD. ... ok
test_pubmed3 (test_Entrez_parser.EInfoTest.test_pubmed3)
Test non-validating parser on XML with an inconsistent DTD. ... ok
test_medline (test_Entrez_parser.ELinkTest.test_medline)
Test parsing medline indexed articles returned by ELink. ... ok
test_nucleotide (test_Entrez_parser.ELinkTest.test_nucleotide)
Test parsing Nucleotide to Protein links returned by ELink. ... ok
test_pubmed1 (test_Entrez_parser.ELinkTest.test_pubmed1)
Test parsing pubmed links returned by ELink (first test). ... ok
test_pubmed2 (test_Entrez_parser.ELinkTest.test_pubmed2)
Test parsing pubmed links returned by ELink (second test). ... ok
test_pubmed3 (test_Entrez_parser.ELinkTest.test_pubmed3)
Test parsing pubmed link returned by ELink (third test). ... ok
test_pubmed4 (test_Entrez_parser.ELinkTest.test_pubmed4)
Test parsing pubmed links returned by ELink (fourth test). ... ok
test_pubmed5 (test_Entrez_parser.ELinkTest.test_pubmed5)
Test parsing pubmed links returned by ELink (fifth test). ... ok
test_pubmed6 (test_Entrez_parser.ELinkTest.test_pubmed6)
Test parsing pubmed links returned by ELink (sixth test). ... ok
test_epost (test_Entrez_parser.EPostTest.test_epost)
Test parsing XML returned by EPost. ... ok
test_invalid (test_Entrez_parser.EPostTest.test_invalid)
Test parsing XML returned by EPost with invalid id (overflow tag). ... ok
test_wrong (test_Entrez_parser.EPostTest.test_wrong)
Test parsing XML returned by EPost with incorrect arguments. ... ok
test_journals (test_Entrez_parser.ESearchTest.test_journals)
Test parsing XML returned by ESearch from the Journals database. ... ok
test_notfound (test_Entrez_parser.ESearchTest.test_notfound)
Test parsing XML returned by ESearch when no items were found. ... ok
test_nucleotide (test_Entrez_parser.ESearchTest.test_nucleotide)
Test parsing XML returned by ESearch from the Nucleotide database. ... ok
test_pmc (test_Entrez_parser.ESearchTest.test_pmc)
Test parsing XML returned by ESearch from PubMed Central. ... ok
test_protein (test_Entrez_parser.ESearchTest.test_protein)
Test parsing XML returned by ESearch from the Protein database. ... ok
test_pubmed1 (test_Entrez_parser.ESearchTest.test_pubmed1)
Test parsing XML returned by ESearch from PubMed (first test). ... ok
test_pubmed2 (test_Entrez_parser.ESearchTest.test_pubmed2)
Test parsing XML returned by ESearch from PubMed (second test). ... ok
test_pubmed3 (test_Entrez_parser.ESearchTest.test_pubmed3)
Test parsing XML returned by ESearch from PubMed (third test). ... ok
test_espell (test_Entrez_parser.ESpellTest.test_espell)
Test parsing XML output returned by ESpell. ... ok
test_integer_none (test_Entrez_parser.ESummaryTest.test_integer_none)
Test parsing ESummary XML where an Integer is not defined. ... ok
test_journals (test_Entrez_parser.ESummaryTest.test_journals)
Test parsing XML returned by ESummary from the Journals database. ... ok
test_nucleotide (test_Entrez_parser.ESummaryTest.test_nucleotide)
Test parsing XML returned by ESummary from the Nucleotide database. ... ok
test_protein (test_Entrez_parser.ESummaryTest.test_protein)
Test parsing XML returned by ESummary from the Protein database. ... ok
test_pubmed (test_Entrez_parser.ESummaryTest.test_pubmed)
Test parsing XML returned by ESummary from PubMed. ... ok
test_structure (test_Entrez_parser.ESummaryTest.test_structure)
Test parsing XML returned by ESummary from the Structure database. ... ok
test_taxonomy (test_Entrez_parser.ESummaryTest.test_taxonomy)
Test parsing XML returned by ESummary from the Taxonomy database. ... ok
test_unists (test_Entrez_parser.ESummaryTest.test_unists)
Test parsing XML returned by ESummary from the UniSTS database. ... ok
test_wrong (test_Entrez_parser.ESummaryTest.test_wrong)
Test parsing XML returned by ESummary with incorrect arguments. ... ok
test_BytesIO (test_Entrez_parser.GeneralTests.test_BytesIO)
Test parsing a BytesIO handle (bytes not string). ... ok
test_closed_handle (test_Entrez_parser.GeneralTests.test_closed_handle)
Test parsing closed handle fails gracefully. ... ok
test_parse_bytes_handle (test_Entrez_parser.GeneralTests.test_parse_bytes_handle)
Test parsing a handle opened in binary mode. ... ok
test_parse_text_handle (test_Entrez_parser.GeneralTests.test_parse_text_handle)
Test parsing a handle opened in text mode. ... ok
test_pickle (test_Entrez_parser.GeneralTests.test_pickle)
Test if records created by the parser can be pickled. ... ok
test_read_bytes_handle (test_Entrez_parser.GeneralTests.test_read_bytes_handle)
Test reading a handle opened in binary mode. ... ok
test_read_text_handle (test_Entrez_parser.GeneralTests.test_read_text_handle)
Test reading a handle opened in text mode. ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.657 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Enzyme.py
test_Enzyme ... ok
test_lactate (test_Enzyme.TestEnzyme.test_lactate)
Parsing ENZYME record for lactate racemase (5.1.2.1). ... ok
test_lipoprotein (test_Enzyme.TestEnzyme.test_lipoprotein)
Parsing ENZYME record for lipoprotein lipase (3.1.1.34). ... ok
test_parse_many (test_Enzyme.TestEnzyme.test_parse_many)
Check parse function with multiple records. ... ok
test_parse_one (test_Enzyme.TestEnzyme.test_parse_one)
Check parse function with one record. ... ok
test_parse_zero (test_Enzyme.TestEnzyme.test_parse_zero) ... ok
test_proline (test_Enzyme.TestEnzyme.test_proline)
Parsing ENZYME record for proline racemase (5.1.1.4). ... ok
test_valine (test_Enzyme.TestEnzyme.test_valine)
Parsing ENZYME record for valine decarboxylase (4.1.1.14). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.013 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ExPASy.py
test_ExPASy ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.011 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.140 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_custom_path_like_object)
Test as_handle with a custom path-like object. ... ok
test_handle (test_File.AsHandleTestCase.test_handle)
Test as_handle with a file-like object argument. ... ok
test_path_object (test_File.AsHandleTestCase.test_path_object)
Test as_handle with a pathlib.Path object. ... ok
test_string_path (test_File.AsHandleTestCase.test_string_path)
Test as_handle with a string path argument. ... ok
test_stringio (test_File.AsHandleTestCase.test_stringio)
Testing passing StringIO handles. ... ok
test_instance_exception (test_File.BaseClassTests.test_instance_exception) ... ok
test_bgzf (test_File.RandomAccess.test_bgzf)
Test BGZF compressed file. ... ok
test_gzip (test_File.RandomAccess.test_gzip)
Test gzip compressed file. ... ok
test_plain (test_File.RandomAccess.test_plain)
Test plain text file. ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.013 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GenBank.py
test_GenBank ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA
warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
ok
test_embl_cds_interaction (test_GenBank.GenBankScannerTests.test_embl_cds_interaction)
Test EMBL CDS interaction, parse CDS features on embl files. ... ok
test_embl_record_interaction (test_GenBank.GenBankScannerTests.test_embl_record_interaction)
Test EMBL Record interaction on embl files. ... ok
test_genbank_cds_interaction (test_GenBank.GenBankScannerTests.test_genbank_cds_interaction)
Test CDS interaction, parse CDS features on gb(k) files. ... ok
test_genbank_interaction (test_GenBank.GenBankScannerTests.test_genbank_interaction)
Test GenBank records interaction on gbk files. ... ok
test_000_genbank_bad_loc_wrap_warning (test_GenBank.GenBankTests.test_000_genbank_bad_loc_wrap_warning)
Feature line wrapping warning. ... ok
test_001_genbank_bad_origin_wrapping_location (test_GenBank.GenBankTests.test_001_genbank_bad_origin_wrapping_location)
Bad origin wrapping. ... ok
test_001_implicit_orign_wrap_fix (test_GenBank.GenBankTests.test_001_implicit_orign_wrap_fix)
Attempt to fix implied origin wrapping. ... ok
test_001_negative_location_warning (test_GenBank.GenBankTests.test_001_negative_location_warning)
Un-parsable feature location warning. ... ok
test_compound_complex_origin_wrap (test_GenBank.GenBankTests.test_compound_complex_origin_wrap)
Test the attempts to fix compound complex origin wrapping. ... ok
test_dbline_embl_gb (test_GenBank.GenBankTests.test_dbline_embl_gb)
Parse GenBank/EMBL paired records with PR project entry: EMBL. ... ok
test_dbline_gb_embl (test_GenBank.GenBankTests.test_dbline_gb_embl)
Parse GenBank/EMBL paired records with PR project entry: GenBank. ... ok
test_dblink (test_GenBank.GenBankTests.test_dblink)
Parse GenBank record with old DBLINK project entry. ... ok
test_dblink_two (test_GenBank.GenBankTests.test_dblink_two)
Parse GenBank record with old and new DBLINK project entries. ... ok
test_dot_lineage (test_GenBank.GenBankTests.test_dot_lineage)
Missing taxonomy lineage. ... ok
test_extremely_long_sequence (test_GenBank.GenBankTests.test_extremely_long_sequence)
Tests if extremely long sequences can be read. ... ok
test_fuzzy_origin_wrap (test_GenBank.GenBankTests.test_fuzzy_origin_wrap)
Test features that wrap an origin, and have fuzzy location. ... ok
test_genbank_bad_loc_wrap_parsing (test_GenBank.GenBankTests.test_genbank_bad_loc_wrap_parsing)
Bad location wrapping. ... ok
test_genbank_date_correct (test_GenBank.GenBankTests.test_genbank_date_correct)
Check if user provided date is inserted correctly. ... ok
test_genbank_date_datetime (test_GenBank.GenBankTests.test_genbank_date_datetime)
Check if datetime objects are handled correctly. ... ok
test_genbank_date_default (test_GenBank.GenBankTests.test_genbank_date_default)
Check if default date is handled correctly. ... ok
test_genbank_date_invalid (test_GenBank.GenBankTests.test_genbank_date_invalid)
Check if invalid dates are treated as default. ... ok
test_genbank_date_list (test_GenBank.GenBankTests.test_genbank_date_list)
Check if date lists are handled correctly. ... ok
test_genbank_read (test_GenBank.GenBankTests.test_genbank_read)
GenBank.read(...) simple test. ... ok
test_genbank_read_invalid (test_GenBank.GenBankTests.test_genbank_read_invalid)
GenBank.read(...) error on invalid file (e.g. FASTA file). ... ok
test_genbank_read_multirecord (test_GenBank.GenBankTests.test_genbank_read_multirecord)
GenBank.read(...) error on multiple record input. ... ok
test_genbank_read_no_origin_no_end (test_GenBank.GenBankTests.test_genbank_read_no_origin_no_end)
GenBank.read(...) error on malformed file. ... ok
test_implicit_orign_wrap_extract_and_translate (test_GenBank.GenBankTests.test_implicit_orign_wrap_extract_and_translate)
Test that features wrapped around origin give expected data. ... ok
test_invalid_product_line_raises_value_error (test_GenBank.GenBankTests.test_invalid_product_line_raises_value_error)
Parsing invalid product line. ... ok
test_locus_line_topogoly (test_GenBank.GenBankTests.test_locus_line_topogoly)
Test if chromosome topology is conserved. ... ok
test_long_names (test_GenBank.GenBankTests.test_long_names)
Various GenBank names which push the column based LOCUS line. ... ok
test_longer_locus_line (test_GenBank.GenBankTests.test_longer_locus_line)
Check that we can read and write files with longer locus lines. ... ok
test_malformed_structured_comment_parsing (test_GenBank.GenBankTests.test_malformed_structured_comment_parsing)
Test malformed structured comment gives warning. ... ok
test_multiline_structured_comment_parsing (test_GenBank.GenBankTests.test_multiline_structured_comment_parsing)
Multiline structured comment parsing. ... ok
test_negative_location (test_GenBank.GenBankTests.test_negative_location)
Negative feature locations. ... ok
test_qualifier_escaping_read (test_GenBank.GenBankTests.test_qualifier_escaping_read)
Check qualifier escaping is preserved when parsing. ... ok
test_qualifier_escaping_write (test_GenBank.GenBankTests.test_qualifier_escaping_write)
Check qualifier escaping is preserved when writing. ... ok
test_qualifier_order (test_GenBank.GenBankTests.test_qualifier_order)
Check the qualifier order is preserved. ... ok
test_structured_comment_parsing (test_GenBank.GenBankTests.test_structured_comment_parsing)
Structured comment parsing. ... ok
test_tsa (test_GenBank.GenBankTests.test_tsa)
Test TSA annotation parsing. ... ok
test_first_line_imgt (test_GenBank.LineOneTests.test_first_line_imgt)
Check IMGT ID line parsing. ... ok
test_topology_embl (test_GenBank.LineOneTests.test_topology_embl)
Check EMBL ID line parsing. ... ok
test_topology_genbank (test_GenBank.LineOneTests.test_topology_genbank)
Check GenBank LOCUS line parsing. ... ok
test_000_write_invalid_but_parsed_locus_line (test_GenBank.OutputTests.test_000_write_invalid_but_parsed_locus_line)
Make sure we survive writing slightly invalid LOCUS lines we could parse. ... ok
test_mad_dots (test_GenBank.OutputTests.test_mad_dots)
Writing and reading back accesssion.version variants. ... ok
test_seqrecord_default_description (test_GenBank.OutputTests.test_seqrecord_default_description)
Read in file using SeqRecord default description. ... ok
test_write_tsa_data_division (test_GenBank.OutputTests.test_write_tsa_data_division)
Make sure we don't kill the TSA data_file_division for TSA files. ... ok
test_cleaning_features (test_GenBank.TestBasics.test_cleaning_features)
Test the ability to clean up feature values. ... ok
test_ensembl_locus (test_GenBank.TestBasics.test_ensembl_locus)
Test the ENSEMBL locus line. ... ok
test_write_format (test_GenBank.TestBasics.test_write_format)
Test writing to the difference formats. ... ok
test_feature_parser_01 (test_GenBank.TestFeatureParser.test_feature_parser_01) ... ok
test_feature_parser_02 (test_GenBank.TestFeatureParser.test_feature_parser_02) ... ok
test_feature_parser_03 (test_GenBank.TestFeatureParser.test_feature_parser_03) ... ok
test_feature_parser_04 (test_GenBank.TestFeatureParser.test_feature_parser_04) ... ok
test_feature_parser_05 (test_GenBank.TestFeatureParser.test_feature_parser_05) ... ok
test_feature_parser_06 (test_GenBank.TestFeatureParser.test_feature_parser_06) ... ok
test_feature_parser_07 (test_GenBank.TestFeatureParser.test_feature_parser_07) ... ok
test_feature_parser_08 (test_GenBank.TestFeatureParser.test_feature_parser_08) ... ok
test_feature_parser_09 (test_GenBank.TestFeatureParser.test_feature_parser_09) ... ok
test_feature_parser_10 (test_GenBank.TestFeatureParser.test_feature_parser_10) ... ok
test_feature_parser_11 (test_GenBank.TestFeatureParser.test_feature_parser_11) ... ok
test_feature_parser_12 (test_GenBank.TestFeatureParser.test_feature_parser_12) ... ok
test_feature_parser_13 (test_GenBank.TestFeatureParser.test_feature_parser_13) ... ok
test_feature_parser_14 (test_GenBank.TestFeatureParser.test_feature_parser_14) ... ok
test_feature_parser_15 (test_GenBank.TestFeatureParser.test_feature_parser_15) ... ok
test_feature_parser_16 (test_GenBank.TestFeatureParser.test_feature_parser_16) ... ok
test_feature_parser_17 (test_GenBank.TestFeatureParser.test_feature_parser_17) ... ok
test_feature_parser_18 (test_GenBank.TestFeatureParser.test_feature_parser_18) ... ok
test_feature_parser_19 (test_GenBank.TestFeatureParser.test_feature_parser_19) ... ok
test_feature_parser_20 (test_GenBank.TestFeatureParser.test_feature_parser_20) ... ok
test_features_spanning_origin (test_GenBank.TestFeatureParser.test_features_spanning_origin)
Test that features that span the origin on circular DNA are included correctly for different ways of specifying the topology. ... ok
test_record_parser_01 (test_GenBank.TestRecordParser.test_record_parser_01) ... ok
test_record_parser_02 (test_GenBank.TestRecordParser.test_record_parser_02) ... ok
test_record_parser_03 (test_GenBank.TestRecordParser.test_record_parser_03) ... ok
test_record_parser_04 (test_GenBank.TestRecordParser.test_record_parser_04) ... ok
test_record_parser_05 (test_GenBank.TestRecordParser.test_record_parser_05) ... ok
test_record_parser_06 (test_GenBank.TestRecordParser.test_record_parser_06) ... ok
test_record_parser_07 (test_GenBank.TestRecordParser.test_record_parser_07) ... ok
test_record_parser_08 (test_GenBank.TestRecordParser.test_record_parser_08) ... ok
test_record_parser_09 (test_GenBank.TestRecordParser.test_record_parser_09) ... ok
test_record_parser_10 (test_GenBank.TestRecordParser.test_record_parser_10) ... ok
test_record_parser_11 (test_GenBank.TestRecordParser.test_record_parser_11) ... ok
test_record_parser_12 (test_GenBank.TestRecordParser.test_record_parser_12) ... ok
test_record_parser_13 (test_GenBank.TestRecordParser.test_record_parser_13) ... ok
test_record_parser_14 (test_GenBank.TestRecordParser.test_record_parser_14) ... ok
test_record_parser_15 (test_GenBank.TestRecordParser.test_record_parser_15) ... ok
test_record_parser_16 (test_GenBank.TestRecordParser.test_record_parser_16) ... ok
test_record_parser_17 (test_GenBank.TestRecordParser.test_record_parser_17) ... ok
test_record_parser_18 (test_GenBank.TestRecordParser.test_record_parser_18) ... ok
test_record_parser_19 (test_GenBank.TestRecordParser.test_record_parser_19) ... ok
test_record_parser_20 (test_GenBank.TestRecordParser.test_record_parser_20) ... ok
test_record_parser_tls (test_GenBank.TestRecordParser.test_record_parser_tls) ... ok
test_record_parser_tsa (test_GenBank.TestRecordParser.test_record_parser_tsa) ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.375 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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!
x_order_2: colinear!
test_GenomeDiagram ... ok
test_color_conversions (test_GenomeDiagram.ColorsTest.test_color_conversions)
Test color translations. ... ok
test_add_track (test_GenomeDiagram.DiagramTest.test_add_track)
Add track. ... ok
test_add_track_error (test_GenomeDiagram.DiagramTest.test_add_track_error)
Test adding unspecified track. ... ok
test_add_track_to_occupied_level (test_GenomeDiagram.DiagramTest.test_add_track_to_occupied_level)
Add track to occupied level. ... ok
test_del_tracks (test_GenomeDiagram.DiagramTest.test_del_tracks)
Delete track. ... ok
test_diagram_via_methods_pdf (test_GenomeDiagram.DiagramTest.test_diagram_via_methods_pdf)
Construct and draw PDF using method approach. ... ok
test_diagram_via_object_pdf (test_GenomeDiagram.DiagramTest.test_diagram_via_object_pdf)
Construct and draw PDF using object approach. ... ok
test_get_tracks (test_GenomeDiagram.DiagramTest.test_get_tracks)
Get track. ... ok
test_move_track (test_GenomeDiagram.DiagramTest.test_move_track)
Move a track. ... ok
test_partial_diagram (test_GenomeDiagram.DiagramTest.test_partial_diagram)
Construct and draw SVG and PDF for just part of a SeqRecord. ... ok
test_renumber (test_GenomeDiagram.DiagramTest.test_renumber)
Test renumbering tracks. ... ok
test_str (test_GenomeDiagram.DiagramTest.test_str)
Test diagram's info as string. ... ok
test_write_arguments (test_GenomeDiagram.DiagramTest.test_write_arguments)
Check how the write methods respond to output format arguments. ... ok
test_limits (test_GenomeDiagram.GraphTest.test_limits)
Check line graphs. ... ok
test_slicing (test_GenomeDiagram.GraphTest.test_slicing)
Check GraphData slicing. ... ok
test_label_default (test_GenomeDiagram.LabelTest.test_label_default)
Feature labels - default. ... ok
test_all_sigils (test_GenomeDiagram.SigilsTest.test_all_sigils)
All sigils. ... ok
test_arrow_heads (test_GenomeDiagram.SigilsTest.test_arrow_heads)
Feature arrow sigils, varying heads. ... ok
test_arrow_shafts (test_GenomeDiagram.SigilsTest.test_arrow_shafts)
Feature arrow sigils, varying shafts. ... ok
test_big_arrow_shafts (test_GenomeDiagram.SigilsTest.test_big_arrow_shafts)
Feature big-arrow sigils, varying shafts. ... ok
test_labels (test_GenomeDiagram.SigilsTest.test_labels)
Feature labels. ... ok
test_long_arrow_heads (test_GenomeDiagram.SigilsTest.test_long_arrow_heads)
Feature ARROW sigil heads within bounding box. ... ok
test_long_bigarrow_heads (test_GenomeDiagram.SigilsTest.test_long_bigarrow_heads)
Feature BIGARROW sigil heads within bounding box. ... ok
test_long_jaggy (test_GenomeDiagram.SigilsTest.test_long_jaggy)
Feature JAGGY sigil heads within bounding box. ... ok
test_long_octo_heads (test_GenomeDiagram.SigilsTest.test_long_octo_heads)
Feature OCTO sigil heads within bounding box. ... ok
test_short_arrow (test_GenomeDiagram.SigilsTest.test_short_arrow)
Feature arrow sigil heads within bounding box. ... ok
test_short_bigarrow (test_GenomeDiagram.SigilsTest.test_short_bigarrow)
Feature big-arrow sigil heads within bounding box. ... ok
test_short_jaggy (test_GenomeDiagram.SigilsTest.test_short_jaggy)
Feature arrow sigil heads within bounding box. ... ok
test_short_octo (test_GenomeDiagram.SigilsTest.test_short_octo)
Feature big-arrow sigil heads within bounding box. ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 2.944 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsBitmaps.py
test_GraphicsBitmaps ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_simple_scatter_plot (test_GraphicsBitmaps.ComparativeTest.test_simple_scatter_plot)
Test creation of a simple PNG scatter plot. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.377 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsChromosome.py
test_GraphicsChromosome ... ok
test_add_count (test_GraphicsChromosome.ChromosomeCountTest.test_add_count)
Add counts to specific chromosome segments. ... ok
test_add_label (test_GraphicsChromosome.ChromosomeCountTest.test_add_label)
Add labels to chromosome segments. ... ok
test_color_from_count (test_GraphicsChromosome.ChromosomeCountTest.test_color_from_count)
Retrieve a color from a count number with the default color scheme. ... ok
test_fill_chromosome (test_GraphicsChromosome.ChromosomeCountTest.test_fill_chromosome)
Test filling out the information on a chromosome. ... ok
test_get_segment_info (test_GraphicsChromosome.ChromosomeCountTest.test_get_segment_info)
Test retrieval of segment information. ... ok
test_set_scale (test_GraphicsChromosome.ChromosomeCountTest.test_set_scale)
Set the scale for a chromosome segment. ... ok
test_random_organism (test_GraphicsChromosome.OrganismGraphicTest.test_random_organism)
Generate an organism with random chromosome info. ... ok
test_simple_organism (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism)
Test the basic functionality of drawing an organism. ... ok
test_simple_organism_pdf (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_pdf)
Output a simple organism to a PDF file. ... ok
test_simple_organism_ps (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_ps)
Output a simple organism to a postscript file. ... ok
test_simple_organism_svg (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_svg)
Output a simple organism to an SVG file. ... ok
test_widget (test_GraphicsChromosome.OrganismGraphicTest.test_widget)
Try widget derived functionality. ... ok
test_simple_tRNA_seqfeatures (test_GraphicsChromosome.OrganismSubAnnotationsTest.test_simple_tRNA_seqfeatures)
Test sub-annotations (as SeqFeatures) on a genome segment, tRNA for Arabidopsis. ... ok
test_simple_tRNA_tuples (test_GraphicsChromosome.OrganismSubAnnotationsTest.test_simple_tRNA_tuples)
Test sub-annotations (as tuples) on a genome segment, tRNA for Arabidopsis. ... ok
----------------------------------------------------------------------
Ran 1 test in 1.139 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsDistribution.py
test_GraphicsDistribution ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_multi_page (test_GraphicsDistribution.BarChartTest.test_multi_page)
Create a page with multiple distributions on it. ... ok
test_simple_page (test_GraphicsDistribution.BarChartTest.test_simple_page)
Test displaying a page with single distribution. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.202 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_simple_scatter_plot_1)
Test creation of a simple ScatterPlot with one list. ... ok
test_simple_scatter_plot_7 (test_GraphicsGeneral.ComparativeTest.test_simple_scatter_plot_7)
Test creation of a simple ScatterPlot with more lists. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.877 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_HMMCasino.py
test_HMMCasino ... ok
test_baum_welch_training_standard (test_HMMCasino.TestHMMCasino.test_baum_welch_training_standard)
Standard Training with known states. ... ok
test_baum_welch_training_without (test_HMMCasino.TestHMMCasino.test_baum_welch_training_without)
Baum-Welch training without known state sequences. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.533 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_HMMGeneral.py
test_HMMGeneral ... ok
test_log_likelihood (test_HMMGeneral.AbstractTrainerTest.test_log_likelihood)
Calculate log likelihood. ... ok
test_ml_estimator (test_HMMGeneral.AbstractTrainerTest.test_ml_estimator)
Test the maximum likelihood estimator for simple cases. ... ok
test_allow_transition (test_HMMGeneral.HiddenMarkovModelTest.test_allow_transition)
Testing allow_transition. ... ok
test_non_ergodic (test_HMMGeneral.HiddenMarkovModelTest.test_non_ergodic)
Non-ergodic model (meaning that some transitions are not allowed). ... ok
test_simple_hmm (test_HMMGeneral.HiddenMarkovModelTest.test_simple_hmm)
Test a simple model with 2 states and 2 symbols. ... ok
test_transitions_from (test_HMMGeneral.HiddenMarkovModelTest.test_transitions_from)
Testing the calculation of transitions_from. ... ok
test_transitions_to (test_HMMGeneral.HiddenMarkovModelTest.test_transitions_to)
Testing the calculation of transitions_to. ... ok
test_allow_all_transitions (test_HMMGeneral.MarkovModelBuilderTest.test_allow_all_transitions)
Testing allow_all_transitions. ... ok
test_set_equal_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_equal_probabilities) ... ok
test_set_initial_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_initial_probabilities) ... ok
test_set_random_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_random_probabilities) ... ok
test_test_initialize (test_HMMGeneral.MarkovModelBuilderTest.test_test_initialize)
Making sure MarkovModelBuilder is initialized correctly. ... ok
test_calculate_s_value (test_HMMGeneral.ScaledDPAlgorithmsTest.test_calculate_s_value)
Testing the calculation of s values. ... ok
test_empty_state_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_empty_state_training_sequence) ... ok
test_invalid_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_invalid_training_sequence) ... ok
test_valid_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_valid_training_sequence) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.062 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KEGG.py
test_KEGG ... ok
test_irregular (test_KEGG.CompoundTests.test_irregular)
compound.irregular tests. ... ok
test_mass (test_KEGG.CompoundTests.test_mass)
record.mass tests. ... ok
test_sample (test_KEGG.CompoundTests.test_sample)
compound.sample tests. ... ok
test_4letter (test_KEGG.EnzymeTests.test_4letter)
enzyme.4letter tests. ... ok
test_exceptions (test_KEGG.EnzymeTests.test_exceptions)
enzyme.exceptions tests. ... ok
test_irregular (test_KEGG.EnzymeTests.test_irregular)
enzyme.irregular tests. ... ok
test_new (test_KEGG.EnzymeTests.test_new)
enzyme.new tests. ... ok
test_sample (test_KEGG.EnzymeTests.test_sample)
enzyme.sample tests. ... ok
test_map00950 (test_KEGG.MapTests.test_map00950)
map00950.rea tests. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.132 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.079 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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.test_render_KGML_basic)
Basic rendering of KGML: write to PDF without modification. ... ok
test_render_KGML_modify (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_modify)
Rendering of KGML to PDF, with modification. ... ok
test_render_KGML_transparency (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_transparency)
Rendering of KGML to PDF, with color alpha channel. ... ok
----------------------------------------------------------------------
Ran 1 test in 5.381 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.047 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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.test_read_and_write_KGML_files)
Read KGML from, and write KGML to, local files. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.923 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KeyWList.py
test_KeyWList ... ok
test_parse (test_KeyWList.KeyWListTest.test_parse)
Test parsing keywlist.txt works. ... ok
test_parse2 (test_KeyWList.KeyWListTest.test_parse2)
Parsing keywlist2.txt (without header and footer). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.065 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_LogisticRegression.py
test_LogisticRegression ... ok
test_calculate_model (test_LogisticRegression.TestLogisticRegression.test_calculate_model) ... ok
test_calculate_model_with_update_callback (test_LogisticRegression.TestLogisticRegression.test_calculate_model_with_update_callback) ... ok
test_calculate_probability (test_LogisticRegression.TestLogisticRegression.test_calculate_probability) ... ok
test_classify (test_LogisticRegression.TestLogisticRegression.test_classify) ... ok
test_dimensionality_of_input_xs (test_LogisticRegression.TestLogisticRegression.test_dimensionality_of_input_xs) ... ok
test_leave_one_out (test_LogisticRegression.TestLogisticRegression.test_leave_one_out) ... ok
test_model_accuracy (test_LogisticRegression.TestLogisticRegression.test_model_accuracy) ... ok
test_xs_and_ys_input_parameter_lengths (test_LogisticRegression.TestLogisticRegression.test_xs_and_ys_input_parameter_lengths) ... ok
test_ys_input_class_assignments (test_LogisticRegression.TestLogisticRegression.test_ys_input_class_assignments) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.075 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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.
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.089 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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.test_bundle_without_target) ... ok
test_good_big (test_MafIO_index.NewIndexTest.test_good_big) ... ok
test_good_small (test_MafIO_index.NewIndexTest.test_good_small) ... ok
test_length_coords_mismatch (test_MafIO_index.NewIndexTest.test_length_coords_mismatch) ... ok
test_old (test_MafIO_index.PreBuiltIndexTest.test_old) ... ok
test_old_corrupt_index (test_MafIO_index.PreBuiltIndexTest.test_old_corrupt_index) ... ok
test_old_file_not_found (test_MafIO_index.PreBuiltIndexTest.test_old_file_not_found) ... ok
test_old_invalid_sqlite (test_MafIO_index.PreBuiltIndexTest.test_old_invalid_sqlite) ... ok
test_old_unfinished_index (test_MafIO_index.PreBuiltIndexTest.test_old_unfinished_index) ... ok
test_old_wrong_filename (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_filename) ... ok
test_old_wrong_target_seqname (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_target_seqname) ... ok
test_old_wrong_version (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_version) ... ok
test_region2bin (test_MafIO_index.StaticMethodTest.test_region2bin) ... ok
test_ucscbin (test_MafIO_index.StaticMethodTest.test_ucscbin) ... ok
test_records_begin (test_MafIO_index.TestGetRecord.test_records_begin) ... ok
test_records_end (test_MafIO_index.TestGetRecord.test_records_end) ... ok
test_incorrect_bundle_coords (test_MafIO_index.TestSearchBadMAF.test_incorrect_bundle_coords) ... ok
test_correct_block_boundary (test_MafIO_index.TestSearchGoodMAF.test_correct_block_boundary)
Following issues 504 and 1086. ... ok
test_correct_block_length (test_MafIO_index.TestSearchGoodMAF.test_correct_block_length)
Following issues 504 and 1086. ... ok
test_correct_retrieval_1 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_1)
Correct retrieval of Cnksr3 in mouse. ... ok
test_correct_retrieval_2 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_2) ... ok
test_correct_retrieval_3 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_3)
Following issue 1083. ... ok
test_correct_spliced_sequences_1 (test_MafIO_index.TestSearchGoodMAF.test_correct_spliced_sequences_1)
Checking that spliced sequences are correct. ... ok
test_correct_spliced_sequences_2 (test_MafIO_index.TestSearchGoodMAF.test_correct_spliced_sequences_2)
Checking that spliced sequences are correct. ... ok
test_invalid_exon_count (test_MafIO_index.TestSearchGoodMAF.test_invalid_exon_count) ... ok
test_invalid_exon_schema (test_MafIO_index.TestSearchGoodMAF.test_invalid_exon_schema) ... ok
test_invalid_type_1 (test_MafIO_index.TestSearchGoodMAF.test_invalid_type_1) ... ok
test_invalid_type_2 (test_MafIO_index.TestSearchGoodMAF.test_invalid_type_2) ... ok
test_bundle_without_target (test_MafIO_index.TestSpliceBadMAF.test_bundle_without_target) ... ok
test_inconsistent_strand (test_MafIO_index.TestSpliceBadMAF.test_inconsistent_strand) ... ok
test_correct_retrieval_1 (test_MafIO_index.TestSpliceGoodMAF.test_correct_retrieval_1)
Correct retrieval of Cnksr3 in mouse. ... ok
test_invalid_strand (test_MafIO_index.TestSpliceGoodMAF.test_invalid_strand) ... ok
test_no_alignment (test_MafIO_index.TestSpliceGoodMAF.test_no_alignment) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.372 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.064 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_MarkovModel.py
test_MarkovModel ... ok
test_argmaxes (test_MarkovModel.TestMarkovModel.test_argmaxes) ... ok
test_backward (test_MarkovModel.TestMarkovModel.test_backward) ... ok
test_baum_welch (test_MarkovModel.TestMarkovModel.test_baum_welch) ... ok
test_forward (test_MarkovModel.TestMarkovModel.test_forward) ... ok
test_logsum_and_exp_logsum (test_MarkovModel.TestMarkovModel.test_logsum_and_exp_logsum) ... ok
test_logvecadd (test_MarkovModel.TestMarkovModel.test_logvecadd) ... ok
test_mle (test_MarkovModel.TestMarkovModel.test_mle) ... ok
test_normalize_and_copy_and_check (test_MarkovModel.TestMarkovModel.test_normalize_and_copy_and_check) ... ok
test_random_norm (test_MarkovModel.TestMarkovModel.test_random_norm) ... ok
test_readline_and_check_start (test_MarkovModel.TestMarkovModel.test_readline_and_check_start) ... ok
test_save_and_load (test_MarkovModel.TestMarkovModel.test_save_and_load) ... ok
test_topcoder1 (test_MarkovModel.TestMarkovModel.test_topcoder1) ... ok
test_topcoder2 (test_MarkovModel.TestMarkovModel.test_topcoder2) ... ok
test_topcoder3 (test_MarkovModel.TestMarkovModel.test_topcoder3) ... ok
test_topcoder4 (test_MarkovModel.TestMarkovModel.test_topcoder4) ... ok
test_topcoder5 (test_MarkovModel.TestMarkovModel.test_topcoder5) ... ok
test_train_bw (test_MarkovModel.TestMarkovModel.test_train_bw) ... ok
test_train_visible (test_MarkovModel.TestMarkovModel.test_train_visible) ... ok
test_uniform_norm (test_MarkovModel.TestMarkovModel.test_uniform_norm) ... ok
test_viterbi (test_MarkovModel.TestMarkovModel.test_viterbi) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.260 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Medline.py
test_Medline ... ok
test_multiline_mesh (test_Medline.TestMedline.test_multiline_mesh) ... ok
test_parse (test_Medline.TestMedline.test_parse) ... ok
test_read (test_Medline.TestMedline.test_read) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.013 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.089 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBITextParser.py
test_NCBITextParser ... ok
test_conversion (test_NCBITextParser.TestBlastRecord.test_conversion)
Converting a Blast record multiple alignment. ... ok
test_text_2010L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_001)
Parsing BLASTN 2.0.10 output (text_2010L_blastn_001). ... ok
test_text_2010L_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_002)
Parsing BLASTN 2.0.10 output without alignments (text_2010L_blastn_002). ... ok
test_text_2010L_blastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_003)
Parsing BLASTN 2.0.10 output without descriptions (text_2010L_blastn_003). ... ok
test_text_2010L_blastn_004 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_004)
Parsing BLASTN 2.0.10 output (text_2010L_blastn_004). ... ok
test_text_2010L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_001)
Parsing BLASTP 2.0.10 output (text_2010L_blastp_001). ... ok
test_text_2010L_blastp_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_002)
Parsing BLASTP 2.0.10 output without hits (text_2010L_blastp_002). ... ok
test_text_2010L_blastp_003 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_003)
Parsing BLASTP 2.0.10 output (text_2010L_blastp_003). ... ok
test_text_2010L_blastp_004 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_004)
Parsing BLASTP 2.0.10 output without descriptions (text_2010L_blastp_004). ... ok
test_text_2010L_blastp_005 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_005)
Parsing BLASTP 2.0.10 output without alignments (text_2010L_blastp_005). ... ok
test_text_2010L_blastp_006 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_006)
Parsing BLASTP 2.0.10 output (text_2010L_blastp_006). ... ok
test_text_2010L_blastp_007 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_007)
Parsing BLASTP 2.0.10 output (text_2010L_blastp_007). ... ok
test_text_2010L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastx_001)
Parsing BLASTX 2.0.10 output (text_2010L_blastx_001). ... ok
test_text_2010L_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastx_002)
Parsing BLASTX 2.0.10 output without hits (text_2010L_blastx_002). ... ok
test_text_2010L_phiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_phiblast_001)
Parsing PHI-BLAST, BLASTP 2.0.10 output, one round (text_2010L_phiblast_001). ... ok
test_text_2010L_phiblast_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_phiblast_002)
Parsing PHI-BLAST, BLASTP 2.0.10 output, three rounds (text_2010L_phiblast_002). ... ok
test_text_2010L_phiblast_003 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_phiblast_003)
Parsing PHI-BLAST, BLASTP 2.0.10 output, two rounds (text_2010L_phiblast_003). ... ok
test_text_2010L_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_tblastn_001)
Parsing TBLASTN 2.0.10 output (text_2010L_tblastn_001). ... ok
test_text_2010L_tblastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_tblastn_002)
Parsing TBLASTN 2.0.10 output without hits (text_2010L_tblastn_002). ... ok
test_text_2010L_tblastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_tblastx_001)
Parsing TBLASTX 2.0.10 output (text_2010L_tblastx_001). ... ok
test_text_2011L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_001)
Parsing BLASTN 2.0.11 output (text_2011L_blastn_001). ... ok
test_text_2011L_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_002)
Parsing BLASTN 2.0.11 output without alignments (text_2011L_blastn_002). ... ok
test_text_2011L_blastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_003)
Parsing BLASTN 2.0.11 output without descriptions (text_2011L_blastn_003). ... ok
test_text_2011L_blastn_004 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_004)
Parsing BLASTN 2.0.11 output (text_2011L_blastn_004). ... ok
test_text_2011L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_001)
Parsing BLASTP 2.0.11 output (text_2011L_blastp_001). ... ok
test_text_2011L_blastp_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_002)
Parsing BLASTP 2.0.11 output without hits (text_2011L_blastp_002). ... ok
test_text_2011L_blastp_003 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_003)
Parsing BLASTP 2.0.11 output (text_2011L_blastp_003). ... ok
test_text_2011L_blastp_004 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_004)
Parsing BLASTP 2.0.11 output without descriptions (text_2011L_blastp_004). ... ok
test_text_2011L_blastp_005 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_005)
Parsing BLASTP 2.0.11 output without alignments (text_2011L_blastp_005). ... ok
test_text_2011L_blastp_006 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_006)
Parsing BLASTP 2.0.11 output (text_2011L_blastp_006). ... ok
test_text_2011L_blastp_007 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_007)
Parsing BLASTP 2.0.11 output (text_2011L_blastp_007). ... ok
test_text_2011L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastx_001)
Parsing BLASTX 2.0.11 output (text_2011L_blastx_001). ... ok
test_text_2011L_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastx_002)
Parsing BLASTX 2.0.11 output without hits (text_2011L_blastx_002). ... ok
test_text_2011L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_psiblast_001)
Parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_001). ... ok
test_text_2011L_psiblast_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_psiblast_002)
Parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_002). ... ok
test_text_2011L_psiblast_003 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_psiblast_003)
Parsing BLASTP 2.0.11 output (text_2011L_psiblast_003). ... ok
test_text_2011L_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_tblastn_001)
Parsing TBLASTN 2.0.11 output (text_2011L_tblastn_001). ... ok
test_text_2011L_tblastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_tblastn_002)
Parsing TBLASTN 2.0.11 output without hits (text_2011L_tblastn_002). ... ok
test_text_2011L_tblastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_tblastx_001)
Parsing TBLASTX 2.0.11 output (text_2011L_tblastx_001). ... ok
test_text_2012L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2012L_psiblast_001)
Parsing BLASTP 2.0.12 output (text_2012L_psiblast_001). ... ok
test_text_2014L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2014L_blastn_001)
Parsing BLASTN 2.0.14 output (text_2014L_blastn_001). ... ok
test_text_2014L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2014L_psiblast_001)
Parsing BLASTP 2.0.14 output (text_2014L_psiblast_001). ... ok
test_text_2201L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2201L_blastx_001)
Parsing BLASTX 2.2.1 output (text_2201L_blastx_001). ... ok
test_text_2202L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2202L_blastn_001)
Parsing BLASTN 2.2.2 output with error messages (text_2202L_blastn_001). ... ok
test_text_2202L_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2202L_blastn_002)
Parsing BLASTN 2.2.2 output with missing error messages (text_2202L_blastn_002). ... ok
test_text_2202L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2202L_blastp_001)
Parsing BLASTP 2.2.2 output with multiple records (text_2202L_blastp_001). ... ok
test_text_2208L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2208L_psiblast_001)
Parsing BLASTP 2.2.8 output (text_2208L_psiblast_001). ... ok
test_text_2215L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2215L_blastx_001)
Parsing BLASTX 2.2.15 output with no hits (text_2215L_blastx_001). ... ok
test_text_2216L_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2216L_tblastn_001)
Parsing TBLASTN 2.2.16 output (text_2216L_tblastn_001). ... ok
test_text_2220L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2220L_blastx_001)
Parsing BLASTX 2.2.20 output (text_2220L_blastx_001). ... ok
test_text_2220L_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2220L_blastx_002)
Parsing BLASTX 2.2.20 output with multiple queries (text_2220L_blastx_002). ... ok
test_text_2221L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2221L_blastp_001)
Parsing BLASTP 2.2.21 output with multiple queries (text_2221L_blastp_001). ... ok
test_text_2222L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2222L_blastx_001)
Parsing BLASTX 2.2.22 output with multiple queries (text_2222L_blastx_001). ... ok
test_text_2222_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2222_blastx_001)
Parsing BLASTX 2.2.22+ output with multiple queries (text_2222_blastx_001). ... ok
test_text_2226_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastn_001)
Parsing BLASTN 2.2.26+ output with no results. ... ok
test_text_2226_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastn_002)
Parsing BLASTN 2.2.26+ output with single hsp results. ... ok
test_text_2226_blastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastn_003)
Parsing BLASTN 2.2.26+ output with multiple hsp results present. ... ok
test_text_2226_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastp_001)
Parsing BLASTP 2.2.26+ with no results. ... ok
test_text_2226_blastp_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastp_002)
Parsing BLASTP 2.2.26+ with single hsp results. ... ok
test_text_2226_blastp_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastp_003)
Parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok
test_text_2226_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastx_001)
Parsing BLASTX 2.2.26+ with no results. ... ok
test_text_2226_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastx_002)
Parsing BLASTX 2.2.26+ with single hsp results. ... ok
test_text_2226_blastx_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastx_003)
Parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok
test_text_2226_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastn_001)
Parsing TBLASTN 2.2.26+ output with no results. ... ok
test_text_2226_tblastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastn_002)
Parsing TBLASTN 2.2.26+ output with single hsp results. ... ok
test_text_2226_tblastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastn_003)
Parsing TBLASTN 2.2.26+ output with multiple hsp results present. ... ok
test_text_2226_tblastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastx_001)
Parsing TBLASTX 2.2.26+ output with no results. ... ok
test_text_2226_tblastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastx_002)
Parsing TBLASTX 2.2.26+ output with single hsp results. ... ok
test_text_2226_tblastx_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastx_003)
Parsing TBLASTX 2.2.26+ output with multiple hsp results present. ... ok
test_text_2230_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2230_blastp_001)
Parsing BLASTP 2.2.30+ output with line of dashes. ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.511 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBIXML.py
test_NCBIXML ... ok
test_xml_2212L_blastn_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastn_001)
Parsing BLASTN 2.2.12, gi|1348916|gb|G26684.1|G26684 (xml_2212L_blastn_001). ... ok
test_xml_2212L_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastp_001)
Parsing BLASTP 2.2.12, gi|49176427|ref|NP_418280.3| (xml_2212L_blastp_001). ... ok
test_xml_2212L_blastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastx_001)
Parsing BLASTX 2.2.12, gi|1347369|gb|G25137.1|G25137 (xml_2212L_blastx_001). ... ok
test_xml_2212L_tblastn_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_tblastn_001)
Parsing TBLASTN 2.2.12, gi|729325|sp|P39483|DHG2_BACME (xml_2212L_tblastn_001). ... ok
test_xml_2212L_tblastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_tblastx_001)
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.test_xml_2218L_blastp_001)
Parsing BLASTP 2.2.18, Fake query (xml_2218L_blastp_001). ... ok
test_xml_2218L_rpsblast_001 (test_NCBIXML.TestNCBIXML.test_xml_2218L_rpsblast_001)
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.test_xml_2218_blastp_001)
Parsing BLASTP 2.2.18+, gi|160837788|ref|NP_075631.2| (xml_2218_blastp_001). ... ok
test_xml_2218_blastp_002 (test_NCBIXML.TestNCBIXML.test_xml_2218_blastp_002)
Parsing BLASTP 2.2.18+, SwissProt Q08386 and P07175, no hits (xml_2218_blastp_002). ... ok
test_xml_2222_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2222_blastp_001)
Parsing BLASTP 2.2.22+, multiple queries against NR (xml_2222_blastp_001). ... ok
test_xml_2222_blastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2222_blastx_001)
Parsing BLASTX 2.2.22+, multiple queries against NR (xml_2222_blastx_001). ... ok
test_xml_2900_blastn_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastn_001_v1) ... ok
test_xml_2900_blastn_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastn_001_v2) ... ok
test_xml_2900_blastp_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastp_001_v1) ... ok
test_xml_2900_blastp_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastp_001_v2) ... ok
test_xml_2900_blastx_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastx_001_v1) ... ok
test_xml_2900_blastx_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastx_001_v2) ... ok
test_xml_2900_tblastn_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastn_001_v1) ... ok
test_xml_2900_tblastn_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastn_001_v2) ... ok
test_xml_2900_tblastx_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastx_001_v1) ... ok
test_xml_2900_tblastx_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastx_001_v2) ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.774 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.015 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NMR.py
test_NMR ... ok
test_noetools (test_NMR.NmrTests.test_noetools)
Self test for NMR.NOEtools. ... ok
test_xpktools (test_NMR.NmrTests.test_xpktools)
Self test for NMR.xpktools. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.017 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NaiveBayes.py
test_NaiveBayes ... ok
test_car_data (test_NaiveBayes.CarTest.test_car_data)
Simple example using car data. ... ok
test_calculate_function_with_scale (test_NaiveBayes.NaiveBayesTest.test_calculate_function_with_scale) ... ok
test_calculate_function_wrong_dimensionality (test_NaiveBayes.NaiveBayesTest.test_calculate_function_wrong_dimensionality) ... ok
test_classify_function (test_NaiveBayes.NaiveBayesTest.test_classify_function) ... ok
test_train_function_input_lengths (test_NaiveBayes.NaiveBayesTest.test_train_function_input_lengths) ... ok
test_train_function_no_training_set (test_NaiveBayes.NaiveBayesTest.test_train_function_no_training_set) ... ok
test_train_function_uneven_dimension_of_training_set (test_NaiveBayes.NaiveBayesTest.test_train_function_uneven_dimension_of_training_set) ... ok
test_train_function_with_priors (test_NaiveBayes.NaiveBayesTest.test_train_function_with_priors) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.013 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_baseml.py
test_PAML_baseml ... ok
testAlignmentExists (test_PAML_baseml.ModTest.testAlignmentExists) ... ok
testAlignmentFileIsValid (test_PAML_baseml.ModTest.testAlignmentFileIsValid) ... ok
testAlignmentSpecified (test_PAML_baseml.ModTest.testAlignmentSpecified) ... ok
testCtlFileExistsOnRead (test_PAML_baseml.ModTest.testCtlFileExistsOnRead) ... ok
testCtlFileExistsOnRun (test_PAML_baseml.ModTest.testCtlFileExistsOnRun) ... ok
testCtlFileValidOnRead (test_PAML_baseml.ModTest.testCtlFileValidOnRead) ... ok
testCtlFileValidOnRun (test_PAML_baseml.ModTest.testCtlFileValidOnRun) ... ok
testOptionExists (test_PAML_baseml.ModTest.testOptionExists) ... ok
testOutputFileSpecified (test_PAML_baseml.ModTest.testOutputFileSpecified) ... ok
testPamlErrorsCaught (test_PAML_baseml.ModTest.testPamlErrorsCaught) ... ok
testParseAllVersions (test_PAML_baseml.ModTest.testParseAllVersions) ... ok
testParseAlpha1Rho1 (test_PAML_baseml.ModTest.testParseAlpha1Rho1) ... ok
testParseModel (test_PAML_baseml.ModTest.testParseModel) ... ok
testParseNhomo (test_PAML_baseml.ModTest.testParseNhomo) ... ok
testParseSEs (test_PAML_baseml.ModTest.testParseSEs) ... ok
testResultsExist (test_PAML_baseml.ModTest.testResultsExist) ... ok
testResultsParsable (test_PAML_baseml.ModTest.testResultsParsable) ... ok
testResultsValid (test_PAML_baseml.ModTest.testResultsValid) ... ok
testTreeExists (test_PAML_baseml.ModTest.testTreeExists) ... ok
testTreeFileValid (test_PAML_baseml.ModTest.testTreeFileValid) ... ok
testTreeSpecified (test_PAML_baseml.ModTest.testTreeSpecified) ... ok
testWorkingDirValid (test_PAML_baseml.ModTest.testWorkingDirValid) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.196 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_codeml.py
test_PAML_codeml ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
testAlignmentExists (test_PAML_codeml.ModTest.testAlignmentExists) ... ok
testAlignmentFileIsValid (test_PAML_codeml.ModTest.testAlignmentFileIsValid) ... ok
testAlignmentSpecified (test_PAML_codeml.ModTest.testAlignmentSpecified) ... ok
testCtlFileExistsOnRead (test_PAML_codeml.ModTest.testCtlFileExistsOnRead) ... ok
testCtlFileExistsOnRun (test_PAML_codeml.ModTest.testCtlFileExistsOnRun) ... ok
testCtlFileValidOnRead (test_PAML_codeml.ModTest.testCtlFileValidOnRead) ... ok
testCtlFileValidOnRun (test_PAML_codeml.ModTest.testCtlFileValidOnRun) ... ok
testOptionExists (test_PAML_codeml.ModTest.testOptionExists) ... ok
testOutputFileSpecified (test_PAML_codeml.ModTest.testOutputFileSpecified) ... ok
testPamlErrorsCaught (test_PAML_codeml.ModTest.testPamlErrorsCaught) ... ok
testParseAA (test_PAML_codeml.ModTest.testParseAA) ... ok
testParseAAPairwise (test_PAML_codeml.ModTest.testParseAAPairwise) ... ok
testParseAllNSsites (test_PAML_codeml.ModTest.testParseAllNSsites) ... ok
testParseBranchSiteA (test_PAML_codeml.ModTest.testParseBranchSiteA) ... ok
testParseCladeModelC (test_PAML_codeml.ModTest.testParseCladeModelC) ... ok
testParseFreeRatio (test_PAML_codeml.ModTest.testParseFreeRatio) ... ok
testParseM2arel (test_PAML_codeml.ModTest.testParseM2arel) ... ok
testParseNSsite3 (test_PAML_codeml.ModTest.testParseNSsite3) ... ok
testParseNgene2Mgene02 (test_PAML_codeml.ModTest.testParseNgene2Mgene02) ... ok
testParseNgene2Mgene1 (test_PAML_codeml.ModTest.testParseNgene2Mgene1) ... ok
testParseNgene2Mgene34 (test_PAML_codeml.ModTest.testParseNgene2Mgene34) ... ok
testParsePairwise (test_PAML_codeml.ModTest.testParsePairwise) ... ok
testParseSEs (test_PAML_codeml.ModTest.testParseSEs) ... ok
testParseSitesParamsForPairwise (test_PAML_codeml.ModTest.testParseSitesParamsForPairwise)
Verify that pairwise site estimates are indeed parsed. Fixes #483. ... ok
testResultsExist (test_PAML_codeml.ModTest.testResultsExist) ... ok
testResultsParsable (test_PAML_codeml.ModTest.testResultsParsable) ... ok
testResultsValid (test_PAML_codeml.ModTest.testResultsValid) ... ok
testTreeExists (test_PAML_codeml.ModTest.testTreeExists) ... ok
testTreeFileValid (test_PAML_codeml.ModTest.testTreeFileValid) ... ok
testTreeParseVersatility (test_PAML_codeml.ModTest.testTreeParseVersatility)
Test finding trees in the results. ... ok
testTreeSpecified (test_PAML_codeml.ModTest.testTreeSpecified) ... ok
testWorkingDirValid (test_PAML_codeml.ModTest.testWorkingDirValid) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.043 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.115 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_yn00.py
test_PAML_yn00 ... ok
testAlignmentExists (test_PAML_yn00.ModTest.testAlignmentExists) ... ok
testAlignmentFileIsValid (test_PAML_yn00.ModTest.testAlignmentFileIsValid) ... ok
testAlignmentSpecified (test_PAML_yn00.ModTest.testAlignmentSpecified) ... ok
testCtlFileExistsOnRead (test_PAML_yn00.ModTest.testCtlFileExistsOnRead) ... ok
testCtlFileExistsOnRun (test_PAML_yn00.ModTest.testCtlFileExistsOnRun) ... ok
testCtlFileValidOnRead (test_PAML_yn00.ModTest.testCtlFileValidOnRead) ... ok
testCtlFileValidOnRun (test_PAML_yn00.ModTest.testCtlFileValidOnRun) ... ok
testOptionExists (test_PAML_yn00.ModTest.testOptionExists) ... ok
testOutputFileSpecified (test_PAML_yn00.ModTest.testOutputFileSpecified) ... ok
testParseAllVersions (test_PAML_yn00.ModTest.testParseAllVersions) ... ok
testParseDottedNames (test_PAML_yn00.ModTest.testParseDottedNames) ... ok
testParseDottedNumNames (test_PAML_yn00.ModTest.testParseDottedNumNames) ... ok
testParseLongNames (test_PAML_yn00.ModTest.testParseLongNames) ... ok
testResultsExist (test_PAML_yn00.ModTest.testResultsExist) ... ok
testResultsParsable (test_PAML_yn00.ModTest.testResultsParsable) ... ok
testResultsValid (test_PAML_yn00.ModTest.testResultsValid) ... ok
testWorkingDirValid (test_PAML_yn00.ModTest.testWorkingDirValid) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.128 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDBList.py
test_PDBList ... skipping. internet not available
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.075 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_CEAligner.py
test_PDB_CEAligner ... ok
test_cealigner (test_PDB_CEAligner.CEAlignerTests.test_cealigner)
Test aligning 7CFN on 6WQA. ... ok
test_cealigner_no_transform (test_PDB_CEAligner.CEAlignerTests.test_cealigner_no_transform)
Test aligning 7CFN on 6WQA without transforming 7CFN. ... ok
test_cealigner_nucleic (test_PDB_CEAligner.CEAlignerTests.test_cealigner_nucleic)
Test aligning 1LCD on 1LCD. ... ok
----------------------------------------------------------------------
Ran 1 test in 3.227 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_DSSP.py
test_PDB_DSSP ... ok
test_DSSP_RSA (test_PDB_DSSP.DSSP_test.test_DSSP_RSA)
Tests the usage of different ASA tables. ... ok
test_DSSP_file (test_PDB_DSSP.DSSP_test.test_DSSP_file)
Test parsing of pregenerated DSSP. ... ok
test_DSSP_hbonds (test_PDB_DSSP.DSSP_test.test_DSSP_hbonds)
Test parsing of DSSP hydrogen bond information. ... ok
test_DSSP_in_model_obj (test_PDB_DSSP.DSSP_test.test_DSSP_in_model_obj)
All elements correctly added to xtra attribute of input model object. ... ok
test_DSSP_noheader_file (test_PDB_DSSP.DSSP_test.test_DSSP_noheader_file)
Test parsing of pregenerated DSSP missing header information. ... ok
setUpClass (test_PDB_DSSP.DSSP_tool_test) ... skipped 'Install dssp if you want to use it from Biopython.'
----------------------------------------------------------------------
Ran 1 test in 0.249 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Dice.py
test_PDB_Dice ... ok
test_dice (test_PDB_Dice.DiceTests.test_dice)
Self test for PDB.Dice module. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.105 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Disordered.py
test_PDB_Disordered ... ok
test_copy_and_write_disordered (test_PDB_Disordered.TestDisordered.test_copy_and_write_disordered)
Extract, save, and parse again disordered atoms. ... ok
test_copy_disordered_atom (test_PDB_Disordered.TestDisordered.test_copy_disordered_atom)
Copies disordered atoms and all their children. ... ok
test_copy_entire_chain (test_PDB_Disordered.TestDisordered.test_copy_entire_chain)
Copy propagates throughout SMCRA object. ... ok
test_disordered_cog (test_PDB_Disordered.TestDisordered.test_disordered_cog)
Calculate DisorderedAtom center of geometry. ... ok
test_empty_disordered (test_PDB_Disordered.TestDisordered.test_empty_disordered)
Raise ValueError on center of mass calculation of empty DisorderedAtom. ... ok
test_remove_disordered_atom (test_PDB_Disordered.TestDisordered.test_remove_disordered_atom)
Remove altlocs from DisorderedAtom entities. ... ok
test_remove_disordered_residue (test_PDB_Disordered.TestDisordered.test_remove_disordered_residue)
Remove residues from DisorderedResidue entities. ... ok
test_structure_w_disordered_com (test_PDB_Disordered.TestDisordered.test_structure_w_disordered_com)
Calculate center of mass of structure including DisorderedAtoms. ... ok
test_transform_disordered (test_PDB_Disordered.TestDisordered.test_transform_disordered)
Transform propagates through disordered atoms. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.115 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Exposure.py
test_PDB_Exposure ... ok
test_ExposureCN (test_PDB_Exposure.Exposure.test_ExposureCN)
HSExposureCN. ... ok
test_HSExposureCA (test_PDB_Exposure.Exposure.test_HSExposureCA)
HSExposureCA. ... ok
test_HSExposureCB (test_PDB_Exposure.Exposure.test_HSExposureCB)
HSExposureCB. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.538 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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.test_fragment_mapper)
Self test for FragmentMapper module. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.152 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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.test_KDTree_exceptions) ... ok
test_KDTree_neighbor_search_manual (test_PDB_KDTree.KDTreeTest.test_KDTree_neighbor_search_manual)
Test all fixed radius neighbor search. ... ok
test_KDTree_neighbor_search_simple (test_PDB_KDTree.KDTreeTest.test_KDTree_neighbor_search_simple)
Test all fixed radius neighbor search. ... ok
test_KDTree_point_search (test_PDB_KDTree.KDTreeTest.test_KDTree_point_search)
Test searching all points within a certain radius of center. ... ok
test_neighbor_search (test_PDB_KDTree.NeighborTest.test_neighbor_search)
NeighborSearch: Find nearby randomly generated coordinates. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.839 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIF2Dict.py
test_PDB_MMCIF2Dict ... ok
test_MMCIF2dict (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_MMCIF2dict) ... ok
test_inline_comments (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_inline_comments)
Comments may begin outside of column 1 if preceded by whitespace. ... ok
test_loop_keyword_case_insensitive (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_loop_keyword_case_insensitive)
Comments may begin outside of column 1. ... ok
test_quotefix (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_quotefix) ... ok
test_splitline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_splitline) ... ok
test_token_after_multiline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_token_after_multiline)
Multi-line string followed by token on the same line. ... ok
test_truncated_multiline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_truncated_multiline) ... ok
test_underscores (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_underscores) ... ok
test_verbatim_block (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_verbatim_block)
Verbatim blocks parsed correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.115 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIFIO.py
test_PDB_MMCIFIO ... ok
test_mmcifio_multimodel (test_PDB_MMCIFIO.WriteTest.test_mmcifio_multimodel)
Write a multi-model, multi-chain mmCIF file. ... ok
test_mmcifio_select (test_PDB_MMCIFIO.WriteTest.test_mmcifio_select)
Write a selection of the structure using a Select subclass. ... ok
test_mmcifio_write_custom_residue (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_custom_residue)
Write a chainless residue using PDBIO. ... ok
test_mmcifio_write_dict (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_dict)
Write an mmCIF dictionary out, read it in and compare them. ... ok
test_mmcifio_write_residue (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue)
Write a single residue using MMCIFIO. ... ok
test_mmcifio_write_residue_w_chain (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue_w_chain)
Write a single residue (chain id == X) using MMCIFIO. ... ok
test_mmcifio_write_residue_wout_chain (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue_wout_chain)
Write a single orphan residue using MMCIFIO. ... ok
test_mmcifio_write_structure (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_structure)
Write a full structure using MMCIFIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.330 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIFParser.py
test_PDB_MMCIFParser ... ok
test_conversion (test_PDB_MMCIFParser.CIFtoPDB.test_conversion)
Parse 1LCD.cif, write 1LCD.pdb, parse again and compare. ... ok
test_conversion_not_preserve_numbering (test_PDB_MMCIFParser.CIFtoPDB.test_conversion_not_preserve_numbering)
Convert mmCIF to PDB and renumber atom serials. ... ok
test_conversion_preserve_numbering (test_PDB_MMCIFParser.CIFtoPDB.test_conversion_preserve_numbering)
Convert mmCIF to PDB and preserve original serial numbering. ... ok
testModels (test_PDB_MMCIFParser.ParseReal.testModels)
Test file with multiple models. ... ok
test_filehandle (test_PDB_MMCIFParser.ParseReal.test_filehandle)
Test if the parser can handle file handle as well as filename. ... ok
test_header (test_PDB_MMCIFParser.ParseReal.test_header)
Test if the parser populates header data. ... ok
test_insertions (test_PDB_MMCIFParser.ParseReal.test_insertions)
Test file with residue insertion codes. ... ok
test_parsers (test_PDB_MMCIFParser.ParseReal.test_parsers)
Extract polypeptides from 1A80. ... ok
test_point_mutations_fast (test_PDB_MMCIFParser.ParseReal.test_point_mutations_fast)
Test if FastMMCIFParser can parse point mutations correctly. ... ok
test_point_mutations_main (test_PDB_MMCIFParser.ParseReal.test_point_mutations_main)
Test if MMCIFParser parse point mutations correctly. ... ok
test_with_anisotrop (test_PDB_MMCIFParser.ParseReal.test_with_anisotrop) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.555 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_NACCESS.py
test_PDB_NACCESS ... ok
test_NACCESS (test_PDB_NACCESS.NACCESS_test.test_NACCESS)
Test calling NACCESS from Bio.PDB. ... skipped 'Install naccess if you want to use it from Biopython.'
test_NACCESS_asa_file (test_PDB_NACCESS.NACCESS_test.test_NACCESS_asa_file)
Test parsing of pregenerated asa NACCESS file. ... ok
test_NACCESS_rsa_file (test_PDB_NACCESS.NACCESS_test.test_NACCESS_rsa_file)
Test parsing of pregenerated rsa NACCESS file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.077 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_PDBIO.py
test_PDB_PDBIO ... ok
test_model_numbering (test_PDB_PDBIO.WriteTest.test_model_numbering)
Preserve model serial numbers during I/O. ... ok
test_pdbio_missing_occupancy (test_PDB_PDBIO.WriteTest.test_pdbio_missing_occupancy)
Write PDB file with missing occupancy. ... ok
test_pdbio_pdb_format_limits (test_PDB_PDBIO.WriteTest.test_pdbio_pdb_format_limits)
Test raising error when structure cannot meet PDB format limits. ... ok
test_pdbio_select (test_PDB_PDBIO.WriteTest.test_pdbio_select)
Write a selection of the structure using a Select subclass. ... ok
test_pdbio_write_auto_numbering (test_PDB_PDBIO.WriteTest.test_pdbio_write_auto_numbering)
Test writing PDB and do not preserve atom numbering. ... ok
test_pdbio_write_custom_residue (test_PDB_PDBIO.WriteTest.test_pdbio_write_custom_residue)
Write a chainless residue using PDBIO. ... ok
test_pdbio_write_preserve_numbering (test_PDB_PDBIO.WriteTest.test_pdbio_write_preserve_numbering)
Test writing PDB and preserve atom numbering. ... ok
test_pdbio_write_residue (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue)
Write a single residue using PDBIO. ... ok
test_pdbio_write_residue_w_chain (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue_w_chain)
Write a single residue (chain id == X) using PDBIO. ... ok
test_pdbio_write_residue_wout_chain (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue_wout_chain)
Write a single orphan residue using PDBIO. ... ok
test_pdbio_write_structure (test_PDB_PDBIO.WriteTest.test_pdbio_write_structure)
Write a full structure using PDBIO. ... ok
test_pdbio_write_truncated (test_PDB_PDBIO.WriteTest.test_pdbio_write_truncated)
Test parsing of truncated lines. ... ok
test_pdbio_write_unk_element (test_PDB_PDBIO.WriteTest.test_pdbio_write_unk_element)
PDBIO raises PDBIOException when writing unrecognised atomic elements. ... ok
test_pdbio_write_x_element (test_PDB_PDBIO.WriteTest.test_pdbio_write_x_element)
Write a structure with atomic element X with PDBIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.297 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_PDBParser.py
test_PDB_PDBParser ... ok
test_1_flawedpdb_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_1_flawedpdb_permissive)
Parse a flawed PDB file in permissive mode: check warnings. ... ok
test_2_flawedpdb_strict (test_PDB_PDBParser.FlawedPDB_tests.test_2_flawedpdb_strict)
Parse a flawed PDB file in permissive mode: check errors. ... ok
test_3_bad_xyz_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_3_bad_xyz_permissive)
Parse an entry with bad x,y,z value with PERMISSIVE=True. ... ok
test_4_bad_xyz_strict (test_PDB_PDBParser.FlawedPDB_tests.test_4_bad_xyz_strict)
Parse an entry with bad x,y,z value with PERMISSIVE=False. ... ok
test_5_missing_occupancy_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_5_missing_occupancy_permissive)
Parse file with missing occupancy with PERMISSIVE=True. ... ok
test_6_missing_occupancy_strict (test_PDB_PDBParser.FlawedPDB_tests.test_6_missing_occupancy_strict)
Parse file with missing occupancy with PERMISSIVE=False. ... ok
test_structure_details (test_PDB_PDBParser.ParseDummyPDB_test.test_structure_details)
Verify details of the parsed example PDB file. ... ok
test_structure_integrity (test_PDB_PDBParser.ParseDummyPDB_test.test_structure_integrity)
Verify the structure of the parsed example PDB file. ... ok
test_1A8O_strict (test_PDB_PDBParser.ParseRealPDB_tests.test_1A8O_strict)
Parse 1A8O.pdb file in strict mode. ... ok
test_SMCRA (test_PDB_PDBParser.ParseRealPDB_tests.test_SMCRA)
Walk down the structure hierarchy and test parser reliability. ... ok
test_duplicated_residue_permissive (test_PDB_PDBParser.ParseRealPDB_tests.test_duplicated_residue_permissive)
Catch exception on duplicated residue. ... ok
test_duplicated_residue_strict (test_PDB_PDBParser.ParseRealPDB_tests.test_duplicated_residue_strict)
Throw exception on duplicated residue. ... ok
test_empty (test_PDB_PDBParser.ParseRealPDB_tests.test_empty)
Parse an empty file. ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_PSEA.py
test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path
----------------------------------------------------------------------
Ran 1 test in 0.076 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Polypeptide.py
test_PDB_Polypeptide ... ok
test_cappbuilder_real (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_real)
Test CaPPBuilder on real PDB file. ... ok
test_cappbuilder_real_nonstd (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_real_nonstd)
Test CaPPBuilder on real PDB file allowing non-standard amino acids. ... ok
test_cappbuilder_tau (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_tau)
Test tau angles calculated with CaPPBuilder. ... ok
test_ppbuilder_real (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_real)
Test PPBuilder on real PDB file. ... ok
test_ppbuilder_real_nonstd (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_real_nonstd)
Test PPBuilder on real PDB file allowing non-standard amino acids. ... ok
test_ppbuilder_torsion (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_torsion)
Test phi/psi angles calculated with PPBuilder. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.119 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_QCSuperimposer.py
test_PDB_QCSuperimposer ... ok
test_get_init_rms (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_get_init_rms)
Test initial RMS calculation. ... ok
test_get_transformed (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_get_transformed)
Test transformation of coordinates after QCP. ... ok
test_on_pdb (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_on_pdb)
Align a PDB to itself. ... ok
test_run (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_run)
Test QCP on dummy data. ... ok
test_set (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_set)
Test setting of initial parameters. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.115 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_ResidueDepth.py
test_PDB_ResidueDepth ... ok
setUpClass (test_PDB_ResidueDepth.MSMS_tests) ... skipped 'Install MSMS if you want to use it from Biopython.'
test_pdb_to_xyzr (test_PDB_ResidueDepth.ResidueDepth_tests.test_pdb_to_xyzr)
Test generation of xyzr (atomic radii) file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.090 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_SASA.py
test_PDB_SASA ... ok
test_custom_radii (test_PDB_SASA.TestShrakeRupley.test_custom_radii)
Run Shrake-Rupley with custom radii. ... ok
test_default_algorithm (test_PDB_SASA.TestShrakeRupley.test_default_algorithm)
Run Shrake-Rupley with default parameters. ... ok
test_fail_compute_entity_level (test_PDB_SASA.TestShrakeRupley.test_fail_compute_entity_level)
Raise exception on input Atom entity. ... ok
test_fail_compute_entity_type (test_PDB_SASA.TestShrakeRupley.test_fail_compute_entity_type)
Raise exception on unsupported entity type. ... ok
test_fail_compute_level_1 (test_PDB_SASA.TestShrakeRupley.test_fail_compute_level_1)
Raise exception on invalid level parameter: X. ... ok
test_fail_compute_level_2 (test_PDB_SASA.TestShrakeRupley.test_fail_compute_level_2)
Raise exception on invalid level parameter: S > C. ... ok
test_fail_empty_entity (test_PDB_SASA.TestShrakeRupley.test_fail_empty_entity)
Raise exception on invalid level parameter: S > C. ... ok
test_fail_n_points (test_PDB_SASA.TestShrakeRupley.test_fail_n_points)
Raise exception on bad n_points parameter. ... ok
test_fail_probe_radius (test_PDB_SASA.TestShrakeRupley.test_fail_probe_radius)
Raise exception on bad probe_radius parameter. ... ok
test_higher_resolution (test_PDB_SASA.TestShrakeRupley.test_higher_resolution)
Run Shrake-Rupley with 960 points per sphere. ... ok
test_level_C (test_PDB_SASA.TestShrakeRupley.test_level_C)
Run Shrake-Rupley with level C. ... ok
test_level_R (test_PDB_SASA.TestShrakeRupley.test_level_R)
Run Shrake-Rupley with level R. ... ok
----------------------------------------------------------------------
Ran 1 test in 4.356 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_SMCRA.py
test_PDB_SMCRA ... ok
test_assign_unknown_element (test_PDB_SMCRA.Atom_Element.test_assign_unknown_element)
Unknown element is assigned 'X'. ... ok
test_atom_element_assignment (test_PDB_SMCRA.Atom_Element.test_atom_element_assignment)
Atom Element. ... ok
test_hydrogens (test_PDB_SMCRA.Atom_Element.test_hydrogens) ... ok
test_ions (test_PDB_SMCRA.Atom_Element.test_ions)
Element for magnesium is assigned correctly. ... ok
test_chain_cog (test_PDB_SMCRA.CenterOfMassTests.test_chain_cog)
Calculate center of geometry of individual chains. ... ok
test_com_empty_structure (test_PDB_SMCRA.CenterOfMassTests.test_com_empty_structure)
Center of mass of empty structure raises ValueError. ... ok
test_structure_cog (test_PDB_SMCRA.CenterOfMassTests.test_structure_cog)
Calculate Structure center of geometry. ... ok
test_structure_com (test_PDB_SMCRA.CenterOfMassTests.test_structure_com)
Calculate Structure center of mass. ... ok
test_change_chain_id (test_PDB_SMCRA.ChangingIdTests.test_change_chain_id)
Change the id of a model. ... ok
test_change_id_to_self (test_PDB_SMCRA.ChangingIdTests.test_change_id_to_self)
Changing the id to itself does nothing (does not raise). ... ok
test_change_model_id (test_PDB_SMCRA.ChangingIdTests.test_change_model_id)
Change the id of a model. ... ok
test_change_model_id_raises (test_PDB_SMCRA.ChangingIdTests.test_change_model_id_raises)
Cannot change id to a value already in use by another child. ... ok
test_change_residue_id (test_PDB_SMCRA.ChangingIdTests.test_change_residue_id)
Change the id of a residue. ... ok
test_full_id_is_updated_chain (test_PDB_SMCRA.ChangingIdTests.test_full_id_is_updated_chain)
Invalidate cached full_ids if an id is changed. ... ok
test_full_id_is_updated_residue (test_PDB_SMCRA.ChangingIdTests.test_full_id_is_updated_residue)
Invalidate cached full_ids if an id is changed. ... ok
test_atom_copy (test_PDB_SMCRA.CopyTests.test_atom_copy) ... ok
test_entity_copy (test_PDB_SMCRA.CopyTests.test_entity_copy)
Make a copy of a residue. ... ok
test_get_atoms (test_PDB_SMCRA.IterationTests.test_get_atoms)
Yields all atoms from the structure, excluding duplicates and ALTLOCs which are not parsed. ... ok
test_get_chains (test_PDB_SMCRA.IterationTests.test_get_chains)
Yields chains from different models separately. ... ok
test_get_residues (test_PDB_SMCRA.IterationTests.test_get_residues)
Yields all residues from all models. ... ok
test_comparison_entities (test_PDB_SMCRA.SortingTests.test_comparison_entities)
Test comparing and sorting the several SMCRA objects. ... ok
test_residue_sort (test_PDB_SMCRA.SortingTests.test_residue_sort)
Test atoms are sorted correctly in residues. ... ok
test_transform (test_PDB_SMCRA.TransformTests.test_transform)
Transform entities (rotation and translation). ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.508 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Selection.py
test_PDB_Selection ... ok
test_entities_not_homogenous (test_PDB_Selection.UnfoldEntitiesTests.test_entities_not_homogenous) ... ok
test_from_atom_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_atom_level)
Unfold from lowest level to all levels. ... ok
test_from_chain_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_chain_level)
Unfold from chain level to all levels. ... ok
test_from_model_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_model_level)
Unfold from model to all levels. ... ok
test_from_residue_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_residue_level)
Unfold from chain level to all levels. ... ok
test_from_structure_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_structure_level)
Unfold from highest level to all levels. ... ok
test_invalid_level (test_PDB_Selection.UnfoldEntitiesTests.test_invalid_level) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.096 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_StructureAlignment.py
test_PDB_StructureAlignment ... ok
test_StructAlign (test_PDB_StructureAlignment.StructureAlignTests.test_StructAlign)
Tests on module to align two proteins according to a FASTA alignment file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.319 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_Superimposer)
Test on module that superimpose two protein structures. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.111 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_internal_coords.py
test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.097 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_parse_pdb_header.py
test_PDB_parse_pdb_header ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_1 (test_PDB_parse_pdb_header.ParseReal.test_1)
Parse the header of a known PDB file (1A8O). ... ok
test_2 (test_PDB_parse_pdb_header.ParseReal.test_2)
Parse the header of another PDB file (2BEG). ... ok
test_parse_header_line (test_PDB_parse_pdb_header.ParseReal.test_parse_header_line)
Unit test for parsing and converting fields in HEADER record. ... ok
test_parse_no_title (test_PDB_parse_pdb_header.ParseReal.test_parse_no_title)
Unit test for sensible result with no TITLE line. ... ok
test_parse_pdb_with_remark_465 (test_PDB_parse_pdb_header.ParseReal.test_parse_pdb_with_remark_465)
Tests that parse_pdb_header now can identify some REMARK 465 entries. ... ok
test_parse_pdb_with_remark_99 (test_PDB_parse_pdb_header.ParseReal.test_parse_pdb_with_remark_99)
Tests that parse_pdb_header can identify REMARK 99 ASTRAL entries. ... ok
test_parse_remark_465 (test_PDB_parse_pdb_header.ParseReal.test_parse_remark_465)
A UNIT-test for the private function _parse_remark_465. ... ok
test_parse_title_line (test_PDB_parse_pdb_header.ParseReal.test_parse_title_line)
Unit test for correct parsing of multiline title records. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.131 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_vectors.py
test_PDB_vectors ... ok
test_Vector (test_PDB_vectors.VectorTests.test_Vector)
Test Vector object. ... ok
test_Vector_angles (test_PDB_vectors.VectorTests.test_Vector_angles)
Test Vector angles. ... ok
test_coord_space (test_PDB_vectors.VectorTests.test_coord_space)
Confirm can generate coordinate space transform for 3 points. ... ok
test_division (test_PDB_vectors.VectorTests.test_division)
Confirm division works. ... ok
test_get_spherical_coordinates (test_PDB_vectors.VectorTests.test_get_spherical_coordinates)
Test spherical coordinates. ... ok
test_m2rotaxis_0 (test_PDB_vectors.VectorTests.test_m2rotaxis_0)
Test 0 deg rotation. Axis must be [1, 0, 0] as per Vector docs. ... ok
test_m2rotaxis_180 (test_PDB_vectors.VectorTests.test_m2rotaxis_180)
Test 180 deg rotation. ... ok
test_m2rotaxis_90 (test_PDB_vectors.VectorTests.test_m2rotaxis_90)
Test 90 deg rotation. ... ok
test_multi_coord_space (test_PDB_vectors.VectorTests.test_multi_coord_space)
Confirm multi_coord_space computes forward, reverse transforms. ... ok
test_normalization (test_PDB_vectors.VectorTests.test_normalization)
Test Vector normalization. ... ok
test_refmat (test_PDB_vectors.VectorTests.test_refmat)
Test refmat can mirror one matrix to another. ... ok
test_rotmat_0 (test_PDB_vectors.VectorTests.test_rotmat_0)
Test rotmat when the rotation is 0 deg (singularity). ... ok
test_rotmat_180 (test_PDB_vectors.VectorTests.test_rotmat_180)
Test rotmat when the rotation is 180 deg (singularity). ... ok
test_rotmat_90 (test_PDB_vectors.VectorTests.test_rotmat_90)
Test regular 90 deg rotation. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.081 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PQR.py
test_PQR ... ok
test_bad_charge (test_PQR.ParseSimplePQR.test_bad_charge)
Test if missing or malformed charge case is handled correctly. ... ok
test_bad_radius (test_PQR.ParseSimplePQR.test_bad_radius)
Test if missing, malformed or negative radius case is handled correctly. ... ok
test_bad_xyz (test_PQR.ParseSimplePQR.test_bad_xyz)
Test if bad coordinates exception is raised. ... ok
test_single_input (test_PQR.ParseSimplePQR.test_single_input)
Test if a single ATOM entry correctly parsed. ... ok
test_pdbio_write_pqr_structure (test_PQR.WriteTest.test_pdbio_write_pqr_structure)
Write a full structure using PDBIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.133 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Pathway.py
test_Pathway ... ok
testAdditionalFunctions (test_Pathway.GraphTestCase.testAdditionalFunctions) ... ok
test_Edges (test_Pathway.GraphTestCase.test_Edges) ... ok
test_Equals (test_Pathway.GraphTestCase.test_Equals) ... ok
test_Nodes (test_Pathway.GraphTestCase.test_Nodes) ... ok
test_RemoveNode (test_Pathway.GraphTestCase.test_RemoveNode) ... ok
testAdditionalFunctions (test_Pathway.MultiGraphTestCase.testAdditionalFunctions) ... ok
test_Edges (test_Pathway.MultiGraphTestCase.test_Edges) ... ok
test_Equals (test_Pathway.MultiGraphTestCase.test_Equals) ... ok
test_Nodes (test_Pathway.MultiGraphTestCase.test_Nodes) ... ok
test_RemoveNode (test_Pathway.MultiGraphTestCase.test_RemoveNode) ... ok
test_eq (test_Pathway.ReactionTestCase.test_eq) ... ok
test_rev (test_Pathway.ReactionTestCase.test_rev) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.013 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Phd.py
test_Phd ... ok
test_check_SeqIO (test_Phd.PhdTest454.test_check_SeqIO)
Test phd_454 using parser via SeqIO. ... ok
test_check_SeqIO (test_Phd.PhdTestOne.test_check_SeqIO)
Test phd1 using parser via SeqIO. ... ok
test_check_record_parser (test_Phd.PhdTestOne.test_check_record_parser)
Test phd1 file in detail. ... ok
test_check_SeqIO (test_Phd.PhdTestSolexa.test_check_SeqIO)
Test phd2 using parser via SeqIO. ... ok
test_check_SeqIO (test_Phd.PhdTestTwo.test_check_SeqIO)
Test phd2 using parser via SeqIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.095 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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.
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.012 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop_EasyController.py
test_PopGen_GenePop_EasyController ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.012 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop_nodepend.py
test_PopGen_GenePop_nodepend ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_file_record_parser (test_PopGen_GenePop_nodepend.FileParserTest.test_file_record_parser)
Basic operation of the File Record Parser. ... ok
test_remove_features (test_PopGen_GenePop_nodepend.FileParserTest.test_remove_features)
Testing the ability to remove population/loci via class methods. ... ok
test_wrong_file_parser (test_PopGen_GenePop_nodepend.FileParserTest.test_wrong_file_parser)
Testing the ability to deal with wrongly formatted files. ... ok
test_record_parser (test_PopGen_GenePop_nodepend.ParserTest.test_record_parser)
Basic operation of the Record Parser. ... ok
test_wrong_file_parser (test_PopGen_GenePop_nodepend.ParserTest.test_wrong_file_parser)
Testing the ability to deal with wrongly formatted files. ... ok
test_record_basic (test_PopGen_GenePop_nodepend.RecordTest.test_record_basic)
Basic test on Record. ... ok
test_utils (test_PopGen_GenePop_nodepend.UtilsTest.test_utils)
Basic operation of GenePop Utils. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.024 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.093 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.090 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ProtParam.py
test_ProtParam ... ok
test_aromaticity (test_ProtParam.ProtParamTest.test_aromaticity)
Calculate protein aromaticity. ... ok
test_charge_at_pH (test_ProtParam.ProtParamTest.test_charge_at_pH)
Test charge_at_pH function. ... ok
test_count_amino_acids (test_ProtParam.ProtParamTest.test_count_amino_acids)
Calculate amino acid counts. ... ok
test_flexibility (test_ProtParam.ProtParamTest.test_flexibility)
Calculate protein flexibility. ... ok
test_get_amino_acids_percent (test_ProtParam.ProtParamTest.test_get_amino_acids_percent)
Calculate amino acid percentages. ... ok
test_get_molecular_weight (test_ProtParam.ProtParamTest.test_get_molecular_weight)
Calculate protein molecular weight. ... ok
test_get_molecular_weight_identical (test_ProtParam.ProtParamTest.test_get_molecular_weight_identical)
Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok
test_get_monoisotopic_molecular_weight (test_ProtParam.ProtParamTest.test_get_monoisotopic_molecular_weight)
Calculate monoisotopic molecular weight. ... ok
test_get_monoisotopic_molecular_weight_identical (test_ProtParam.ProtParamTest.test_get_monoisotopic_molecular_weight_identical)
Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok
test_gravy (test_ProtParam.ProtParamTest.test_gravy)
Calculate gravy. Tests all pre-defined scales. ... ok
test_instability_index (test_ProtParam.ProtParamTest.test_instability_index)
Calculate protein instability index. ... ok
test_isoelectric_point (test_ProtParam.ProtParamTest.test_isoelectric_point)
Calculate the isoelectric point. ... ok
test_molar_extinction_coefficient (test_ProtParam.ProtParamTest.test_molar_extinction_coefficient)
Molar extinction coefficient. ... ok
test_protein_scale (test_ProtParam.ProtParamTest.test_protein_scale)
Calculate the Kite Doolittle scale. ... ok
test_secondary_structure_fraction (test_ProtParam.ProtParamTest.test_secondary_structure_fraction)
Calculate secondary structure fractions. ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.080 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_RCSBFormats.py
test_RCSBFormats ... ok
test_compare_chains (test_RCSBFormats.CompareStructures.test_compare_chains)
Compare parsed chains. ... ok
test_compare_models (test_RCSBFormats.CompareStructures.test_compare_models)
Compared parsed models. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.645 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Restriction.py
test_Restriction ... ok
test_basic_isochizomers (test_Restriction.EnzymeComparison.test_basic_isochizomers)
Test to be sure isochizomer and neoschizomers are as expected. ... ok
test_comparisons (test_Restriction.EnzymeComparison.test_comparisons)
Test comparison operators between different enzymes. ... ok
test_change (test_Restriction.RestrictionBatchPrintTest.test_change)
Test that change() changes something. ... ok
test_make_format_map1 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map1)
Test that print_as('map'); print_that() correctly wraps round. ... ok
test_make_format_map2 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map2)
Test that print_as('map'); print_that() correctly wraps round. ... ok
test_make_format_map3 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map3)
Test that print_as('map'); print_that() correctly wraps round. ... ok
test_analysis_restrictions (test_Restriction.RestrictionBatches.test_analysis_restrictions)
Test Fancier restriction analysis. ... ok
test_batch_analysis (test_Restriction.RestrictionBatches.test_batch_analysis)
Sequence analysis with a restriction batch. ... ok
test_creating_batch (test_Restriction.RestrictionBatches.test_creating_batch)
Creating and modifying a restriction batch. ... ok
test_premade_batches (test_Restriction.RestrictionBatches.test_premade_batches)
Test content of premade batches CommOnly, NoComm, AllEnzymes. ... ok
test_search_premade_batches (test_Restriction.RestrictionBatches.test_search_premade_batches)
Test search with pre-made batches CommOnly, NoComm, AllEnzymes. ... ok
test_formatted_seq (test_Restriction.SequenceTesting.test_formatted_seq)
Test several methods of FormattedSeq. ... ok
test_non_iupac_letters (test_Restriction.SequenceTesting.test_non_iupac_letters)
Test if non-IUPAC letters raise a TypeError. ... ok
test_sequence_object (test_Restriction.SequenceTesting.test_sequence_object)
Test if sequence must be a Seq or MutableSeq object. ... ok
test_circular_sequences (test_Restriction.SimpleEnzyme.test_circular_sequences)
Deal with cutting circular sequences. ... ok
test_cutting_border_positions (test_Restriction.SimpleEnzyme.test_cutting_border_positions)
Check if cutting after first and penultimate position works. ... ok
test_ear_cutting (test_Restriction.SimpleEnzyme.test_ear_cutting)
Test basic cutting with EarI (ambiguous overhang). ... ok
test_eco_cutting (test_Restriction.SimpleEnzyme.test_eco_cutting)
Test basic cutting with EcoRI (5'overhang). ... ok
test_init (test_Restriction.SimpleEnzyme.test_init)
Check for error during __init__. ... ok
test_kpn_cutting (test_Restriction.SimpleEnzyme.test_kpn_cutting)
Test basic cutting with KpnI (3'overhang). ... ok
test_overlapping_cut_sites (test_Restriction.SimpleEnzyme.test_overlapping_cut_sites)
Check if overlapping recognition sites are properly handled. ... ok
test_recognition_site_on_both_strands (test_Restriction.SimpleEnzyme.test_recognition_site_on_both_strands)
Check if recognition sites on both strands are properly handled. ... ok
test_shortcuts (test_Restriction.SimpleEnzyme.test_shortcuts)
Check if '/' and '//' work as '.search' and '.catalyse'. ... ok
test_sma_cutting (test_Restriction.SimpleEnzyme.test_sma_cutting)
Test basic cutting with SmaI (blunt cutter). ... ok
test_sna_cutting (test_Restriction.SimpleEnzyme.test_sna_cutting)
Test basic cutting with SnaI (unknown). ... ok
test_print_that (test_Restriction.TestPrintOutputs.test_print_that)
Test print_that function. ... ok
test_str_method (test_Restriction.TestPrintOutputs.test_str_method)
Test __str__ and __repr__ outputs. ... ok
test_supplier (test_Restriction.TestPrintOutputs.test_supplier)
Test output of supplier list for different enzyme types. ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.229 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Astral.py
test_SCOP_Astral ... ok
testConstructWithCustomFile (test_SCOP_Astral.AstralTests.testConstructWithCustomFile) ... ok
testGetDomainsClustered (test_SCOP_Astral.AstralTests.testGetDomainsClustered) ... ok
testGetDomainsFromFile (test_SCOP_Astral.AstralTests.testGetDomainsFromFile) ... ok
testGetSeq (test_SCOP_Astral.AstralTests.testGetSeq) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.087 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Cla.py
test_SCOP_Cla ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
testError (test_SCOP_Cla.ClaTests.testError)
Test if a corrupt record raises the appropriate exception. ... ok
testIndex (test_SCOP_Cla.ClaTests.testIndex)
Test CLA file indexing. ... ok
testParse (test_SCOP_Cla.ClaTests.testParse)
Test if all records in a CLA file are being read. ... ok
testRecord (test_SCOP_Cla.ClaTests.testRecord)
Test one record in detail. ... ok
testStr (test_SCOP_Cla.ClaTests.testStr)
Test if we can convert each record to a string correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.081 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Des.py
test_SCOP_Des ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
testError (test_SCOP_Des.DesTests.testError)
Test if a corrupt record raises the appropriate exception. ... ok
testParse (test_SCOP_Des.DesTests.testParse)
Test if all records in a DES file are being read. ... ok
testRecord (test_SCOP_Des.DesTests.testRecord)
Test one record in detail. ... ok
testStr (test_SCOP_Des.DesTests.testStr)
Test if we can convert each record to a string correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.079 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Dom.py
test_SCOP_Dom ... ok
testError (test_SCOP_Dom.DomTests.testError)
Test if a corrupt record raises the appropriate exception. ... ok
testParse (test_SCOP_Dom.DomTests.testParse)
Test if all records in a DOM file are being read. ... ok
testRecord (test_SCOP_Dom.DomTests.testRecord)
Test one record in detail. ... ok
testStr (test_SCOP_Dom.DomTests.testStr)
Test if we can convert each record to a string correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.079 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Hie.py
test_SCOP_Hie ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
testError (test_SCOP_Hie.HieTests.testError)
Test if a corrupt record raises the appropriate exception. ... ok
testParse (test_SCOP_Hie.HieTests.testParse)
Test if all records in a HIE file are being read. ... ok
testStr (test_SCOP_Hie.HieTests.testStr)
Test if we can convert each record to a string correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.080 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Raf.py
test_SCOP_Raf ... ok
testParse (test_SCOP_Raf.RafTests.testParse)
Parse a RAF record. ... ok
testSeqMapAdd (test_SCOP_Raf.RafTests.testSeqMapAdd) ... ok
testSeqMapIndex (test_SCOP_Raf.RafTests.testSeqMapIndex) ... ok
testSeqMapSlice (test_SCOP_Raf.RafTests.testSeqMapSlice) ... ok
test_SeqMap_getAtoms_err (test_SCOP_Raf.RafTests.test_SeqMap_getAtoms_err) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.084 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Residues.py
test_SCOP_Residues ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
testAstralParse (test_SCOP_Residues.ResiduesTests.testAstralParse)
Test if we can parse residue subsets enclosed in brackets. ... ok
testJustPdbId (test_SCOP_Residues.ResiduesTests.testJustPdbId) ... ok
testParse (test_SCOP_Residues.ResiduesTests.testParse) ... ok
testParseError (test_SCOP_Residues.ResiduesTests.testParseError) ... ok
testPdbId (test_SCOP_Residues.ResiduesTests.testPdbId) ... ok
testStr (test_SCOP_Residues.ResiduesTests.testStr) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.091 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Scop.py
test_SCOP_Scop ... ok
testConstructFromDirectory (test_SCOP_Scop.ScopTests.testConstructFromDirectory) ... ok
testGetAscendent (test_SCOP_Scop.ScopTests.testGetAscendent) ... ok
testParse (test_SCOP_Scop.ScopTests.testParse) ... ok
testParseDomain (test_SCOP_Scop.ScopTests.testParseDomain) ... ok
testSccsOrder (test_SCOP_Scop.ScopTests.testSccsOrder) ... ok
test_get_descendents (test_SCOP_Scop.ScopTests.test_get_descendents)
Test getDescendents method. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.082 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.082 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SVDSuperimposer.py
test_SVDSuperimposer ... ok
test_get_init_rms (test_SVDSuperimposer.SVDSuperimposerTest.test_get_init_rms) ... ok
test_oldTest (test_SVDSuperimposer.SVDSuperimposerTest.test_oldTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.011 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_psl_34_001)
Test parsing blat output (psl_34_001.psl). ... ok
test_psl_34_002 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_002)
Test parsing blat output (psl_34_001.psl). ... ok
test_psl_34_003 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_003)
Test parsing blat output (psl_34_003.psl). ... ok
test_psl_34_004 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_004)
Test parsing blat output (psl_34_004.psl). ... ok
test_psl_34_005 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_005)
Test parsing blat output (psl_34_005.psl). ... ok
test_psl_35_001 (test_SearchIO_blat_psl.BlatPslCases.test_psl_35_001)
Test parsing blat output (psl_35_001.psl). ... ok
test_psl_35_002 (test_SearchIO_blat_psl.BlatPslCases.test_psl_35_002)
Test parsing blat output (psl_35_002.psl). ... ok
test_psl_34_001 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_001)
Test parsing blat output (psl_34_001.psl). ... ok
test_psl_34_002 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_002)
Test parsing blat output (psl_34_001.psl). ... ok
test_psl_34_003 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_003)
Test parsing blat output (psl_34_003.psl). ... ok
test_psl_34_004 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_004)
Test parsing blat output (psl_34_004.psl). ... ok
test_psl_34_005 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_005)
Test parsing blat output (psl_34_005.psl). ... ok
test_psl_35_001 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_35_001)
Test parsing blat output (psl_35_001.psl). ... ok
test_psl_35_002 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_35_002)
Test parsing blat output (psl_35_002.psl). ... ok
test_pslx_34_001 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_001)
Test parsing blat output (pslx_34_001.pslx). ... ok
test_pslx_34_002 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_002)
Test parsing blat output (pslx_34_002.pslx). ... ok
test_pslx_34_003 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_003)
Test parsing blat output (pslx_34_003.pslx). ... ok
test_pslx_34_004 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_004)
Test parsing blat output (pslx_34_004.pslx). ... ok
test_pslx_34_005 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_005)
Test parsing blat output (pslx_34_005.pslx). ... ok
test_pslx_35_002 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_35_002)
Test parsing blat output (pslx_35_002.pslx). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.114 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_psl_34_001)
Test blat-psl indexing, multiple queries. ... ok
test_psl_34_002 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_002)
Test blat-psl indexing, single query, no hits. ... ok
test_psl_34_003 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_003)
Test blat-psl indexing, single query, single hit. ... ok
test_psl_34_004 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_004)
Test blat-psl indexing, single query, multiple hits with multiple hsps. ... ok
test_psl_34_005 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_005)
Test blat-psl indexing, multiple queries, no header. ... ok
test_psl_34_006 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_006)
Test blat-pslx indexing, multiple queries. ... ok
test_psl_34_007 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_007)
Test blat-pslx indexing, single query, no hits. ... ok
test_psl_34_008 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_008)
Test blat-pslx indexing, single query, single hit. ... ok
test_psl_34_009 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_009)
Test blat-pslx indexing, single query, multiple hits with multiple hsps. ... ok
test_psl_34_010 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_010)
Test blat-pslx indexing, multiple queries, no header. ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.155 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_exn_22_o_vulgar_cigar)
Test parsing exonerate output (exn_22_o_vulgar_cigar.exn). ... ok
test_vulgar_text_similar_c2c (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_c2c)
Compares vulgar-text coordinate parsing for the coding2coding model. ... ok
test_vulgar_text_similar_g2g (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_g2g)
Compares vulgar-text coordinate parsing for the genome2genome model. ... ok
test_vulgar_text_similar_p2d (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_p2d)
Compares vulgar-text coordinate parsing for the protein2dna model. ... ok
test_exn_22_m_affine_local (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_affine_local)
Test parsing exonerate output (exn_22_m_affine_local.exn). ... ok
test_exn_22_m_cdna2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_cdna2genome)
Test parsing exonerate output (exn_22_m_cdna2genome.exn). ... ok
test_exn_22_m_coding2coding (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2coding)
Test parsing exonerate output (exn_22_m_coding2coding.exn). ... ok
test_exn_22_m_coding2coding_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2coding_fshifts)
Test parsing exonerate output (exn_22_m_coding2coding_fshifts.exn). ... ok
test_exn_22_m_coding2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2genome)
Test parsing exonerate output (exn_22_m_coding2genome.exn). ... ok
test_exn_22_m_dna2protein (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_dna2protein)
Test parsing exonerate output (exn_22_m_dna2protein.exn). ... ok
test_exn_22_m_est2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_est2genome)
Test parsing exonerate output (exn_22_m_est2genome.exn). ... ok
test_exn_22_m_genome2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_genome2genome)
Test parsing exonerate output (exn_22_m_genome2genome.exn). ... ok
test_exn_22_m_ner (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ner)
Test parsing exonerate output (exn_22_m_ner.exn). ... ok
test_exn_22_m_protein2dna_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_protein2dna_fshifts)
Test parsing exonerate output (exn_22_m_protein2dna_fshifts.exn). ... ok
test_exn_22_m_protein2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_protein2genome)
Test parsing exonerate output (exn_22_m_protein2genome.exn). ... ok
test_exn_22_m_ungapped (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ungapped)
Test parsing exonerate output (exn_22_m_ungapped.exn). ... ok
test_exn_22_m_ungapped_trans (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ungapped_trans)
Test parsing exonerate output (exn_22_m_ungapped_trans.exn). ... ok
test_exn_22_q_multiple (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_q_multiple)
Test parsing exonerate output (exn_22_q_multiple.exn). ... ok
test_exn_22_q_none (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_q_none)
Test parsing exonerate output (exn_22_q_none.exn). ... ok
test_exn_24_m_protein2genome_revcomp_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_24_m_protein2genome_revcomp_fshifts)
Test parsing exonerate output (exn_24_m_protein2genome_revcomp_fshifts.exn). ... ok
test_exn_24_protein2genome_met_intron (test_SearchIO_exonerate.ExonerateTextCases.test_exn_24_protein2genome_met_intron)
Test parsing exonerate output (exn_24_m_protein2genome_met_intron.exn). ... ok
test_exn_22_o_vulgar (test_SearchIO_exonerate.ExonerateVulgarCases.test_exn_22_o_vulgar)
Test parsing exonerate output (exn_22_o_vulgar.exn). ... ok
test_exn_22_o_vulgar_fshifts (test_SearchIO_exonerate.ExonerateVulgarCases.test_exn_22_o_vulgar_fshifts)
Test parsing exonerate output (exn_22_o_vulgar_fshifts.exn). ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.156 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_exn_22_m_est2genome)
Test exonerate-text indexing, single. ... ok
test_exn_22_q_multiple (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases.test_exn_22_q_multiple)
Test exonerate-text indexing, single. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.097 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_exn_22_m_est2genome)
Test exonerate-vulgar indexing, single. ... ok
test_exn_22_q_multiple (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases.test_exn_22_q_multiple)
Test exonerate-vulgar indexing, single. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.082 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_output002)
Test parsing fasta34 output (output002.m10). ... ok
test_output003 (test_SearchIO_fasta_m10.Fasta34Cases.test_output003)
Test parsing fasta34 output (output003.m10). ... ok
test_output001 (test_SearchIO_fasta_m10.Fasta35Cases.test_output001)
Test parsing fasta35 output (output001.m10). ... ok
test_output004 (test_SearchIO_fasta_m10.Fasta35Cases.test_output004)
Test parsing fasta35 output (output004.m10). ... ok
test_output005 (test_SearchIO_fasta_m10.Fasta35Cases.test_output005)
Test parsing ssearch35 output (output005.m10). ... ok
test_output006 (test_SearchIO_fasta_m10.Fasta35Cases.test_output006)
Test parsing fasta35 output (output006.m10). ... ok
test_output007 (test_SearchIO_fasta_m10.Fasta36Cases.test_output007)
Test parsing fasta36 output (output007.m10). ... ok
test_output008 (test_SearchIO_fasta_m10.Fasta36Cases.test_output008)
Test parsing tfastx36 output (output008.m10). ... ok
test_output009 (test_SearchIO_fasta_m10.Fasta36Cases.test_output009)
Test parsing fasta36 output (output009.m10). ... ok
test_output010 (test_SearchIO_fasta_m10.Fasta36Cases.test_output010)
Test parsing fasta36 output (output010.m10). ... ok
test_output011 (test_SearchIO_fasta_m10.Fasta36Cases.test_output011)
Test parsing fasta36 output (output011.m10). ... ok
test_output012 (test_SearchIO_fasta_m10.Fasta36Cases.test_output012)
Test parsing fasta36 output (output012.m10). ... ok
test_output013 (test_SearchIO_fasta_m10.Fasta36Cases.test_output013)
Test parsing fasta36 output (output013.m10). ... ok
test_output014 (test_SearchIO_fasta_m10.Fasta36Cases.test_output014)
Test parsing fasta36 output (output014.m10). ... ok
test_output015 (test_SearchIO_fasta_m10.Fasta36Cases.test_output015)
Test parsing fasta36 output (output015.m10). ... ok
test_output016 (test_SearchIO_fasta_m10.Fasta36Cases.test_output016)
Test parsing fasta36 output (output016.m10). ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.119 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_fasta_m10_index.py
test_SearchIO_fasta_m10_index ... ok
test_output_001 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_001)
Test fasta-m10 indexing, fasta35, multiple queries. ... ok
test_output_002 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_002)
Test fasta-m10 indexing, fasta34, multiple queries. ... ok
test_output_005 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_005)
Test fasta-m10 indexing, ssearch35, multiple queries. ... ok
test_output_008 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_008)
Test fasta-m10 indexing, tfastx36, multiple queries. ... ok
test_output_009 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_009)
Test fasta-m10 indexing, fasta36, multiple queries. ... ok
test_output_010 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_010)
Test fasta-m10 indexing, fasta36, single query, no hits. ... ok
test_output_011 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_011)
Test fasta-m10 indexing, fasta36, single query, hits with single hsp. ... ok
test_output_012 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_012)
Test fasta-m10 indexing, fasta36, single query with multiple hsps. ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.137 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hhsuite2_text.py
test_SearchIO_hhsuite2_text ... ok
test_2uvo (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo)
Parsing 2uvo. ... ok
test_2uvo_emptytable (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo_emptytable)
Parsing 4uvo with empty results table. ... ok
test_2uvo_onlyheader (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo_onlyheader)
Parsing 4uvo with only header present. ... ok
test_4p79 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_4p79)
Parsing 4p79_hhsearch_server_NOssm.hhr file. ... ok
test_4y9h_nossm (test_SearchIO_hhsuite2_text.HhsuiteCases.test_4y9h_nossm)
Parsing 4y9h_hhsearch_server_NOssm.hhr file. ... ok
test_9590198 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_9590198)
Parsing hhpred_9590198.hhr file. ... ok
test_allx (test_SearchIO_hhsuite2_text.HhsuiteCases.test_allx)
Parsing allx.hhr file. ... ok
test_q9bsu1 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_q9bsu1)
Parsing hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.hhr file. ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_hmmpfam_21)
Test parsing hmmpfam 2.1 file (text_21_hmmpfam_001.out). ... ok
test_hmmpfam_22 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_22)
Test parsing hmmpfam 2.2 file (text_22_hmmpfam_001.out). ... ok
test_hmmpfam_23 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23)
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_hmmpfam_23_break_in_end_of_seq)
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_hmmpfam_23_missing_consensus)
Test parsing hmmpfam 2.3 file (text_23_hmmpfam_003.out). ... ok
test_hmmpfam_23_no_match (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23_no_match)
Test parsing hmmpfam 2.3 file (text_23_hmmpfam_002.out). ... ok
test_hmmpfam_24 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_24)
Test parsing hmmpfam 2.4 file (text_24_hmmpfam_001.out). ... ok
test_hmmsearch_20 (test_SearchIO_hmmer2_text.HmmsearchTests.test_hmmsearch_20)
Test parsing hmmsearch 2.0 file (text_20_hmmsearch_001.out). ... ok
test_hmmsearch_22 (test_SearchIO_hmmer2_text.HmmsearchTests.test_hmmsearch_22)
Test parsing hmmsearch 2.2 file (text_22_hmmsearch_001.out). ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.193 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_hmmertext_text_21_hmmpfam_001)
Test hmmer2-text indexing, HMMER 2.1. ... ok
test_hmmertext_text_22_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_22_hmmpfam_001)
Test hmmer2-text indexing, HMMER 2.2. ... ok
test_hmmertext_text_22_hmmsearch_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_22_hmmsearch_001)
Test hmmer2-text indexing, HMMER 2.2. ... ok
test_hmmertext_text_23_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_23_hmmpfam_001)
Test hmmer2-text indexing, HMMER 2.3. ... ok
test_hmmertext_text_24_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_24_hmmpfam_001)
Test hmmer2-text indexing, HMMER 2.4. ... ok
test_hmmer2text_22_multiple_first_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_first_hmmpfam)
Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok
test_hmmer2text_22_multiple_last_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_last_hmmpfam)
Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok
test_hmmer2text_22_multiple_middle_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_middle_hmmpfam)
Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok
test_hmmer2text_22_single_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_single_hmmpfam)
Test hmmer2-text raw string retrieval, single query, hmmpfam. ... ok
test_hmmer2text_22_single_hmmsearch (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_single_hmmsearch)
Test hmmer2-text raw string retrieval, single query, hmmsearch. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.151 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_domtab_30_hmmsearch_001)
Parsing hmmsearch-domtab, hmmsearch 3.0, multiple queries (domtab_30_hmmsearch_001). ... ok
test_domtab_31b1_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases.test_domtab_31b1_hmmsearch_001)
Parsing hmmsearch-domtab, hmmsearch 3.1b1, single query (domtab_31b1_hmmsearch_001). ... ok
test_domtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_001)
Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_001). ... ok
test_domtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_002)
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_domtab_30_hmmscan_003)
Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_003). ... ok
test_domtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_004)
Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_004). ... ok
test_domtab_31b1_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_31b1_hmmscan_001)
Parsing hmmscan-domtab, hmmscan 3.1b1, multiple queries (domtab_31b1_hmmscan_001). ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.077 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_hmmerdomtab_30_hmmscan_001)
Test hmmscan-domtab indexing, HMMER 3.0, multiple queries. ... ok
test_hmmerdomtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_002)
Test hmmscan-domtab indexing, HMMER 3.0, single query, no hits. ... ok
test_hmmerdomtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_003)
Test hmmscan-domtab indexing, HMMER 3.0, single query, multiple hits. ... ok
test_hmmerdomtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_004)
Test hmmscan-domtab indexing, HMMER 3.0, single query, no alignments. ... ok
test_hmmerdomtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmsearch_001)
Test hmmsearch-domtab indexing, HMMER 3.0, single query, no alignments. ... ok
test_hmmerdomtab_30_multiple_first (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_multiple_first)
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_hmmerdomtab_30_multiple_last)
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_hmmerdomtab_30_multiple_middle)
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_hmmerdomtab_30_single)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, single query (domtab_30_hmmscan_004.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.090 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_30_hmmscan_001)
Test parsing hmmer3-tab, hmmscan 3.0, multiple queries (tab_30_hmmscan_001). ... ok
test_30_hmmscan_002 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_002)
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_30_hmmscan_003)
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_30_hmmscan_004)
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_31b1_hmmscan_001)
Test parsing hmmer3-tab, hmmscan 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok
test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_tab.HmmsearchCases.test_31b1_hmmsearch_001)
Test parsing hmmer3-tab, hmmsearch 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.073 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_hmmer3tab_30_hmmscan_001)
Test hmmer3-tab indexing, HMMER 3.0, multiple queries. ... ok
test_hmmer3tab_30_hmmscan_002 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_002)
Test hmmer3-tab indexing, HMMER 3.0, single query, no hits. ... ok
test_hmmer3tab_30_hmmscan_003 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_003)
Test hmmer3-tab indexing, HMMER 3.0, single query, multiple hits. ... ok
test_hmmer3tab_30_hmmscan_004 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_004)
Test hmmer3-tab indexing, HMMER 3.0, single query, no alignments. ... ok
test_hmmer3tab_30_multiple_first (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_multiple_first)
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_hmmer3tab_30_multiple_last)
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_hmmer3tab_30_multiple_middle)
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_hmmer3tab_30_single)
Test hmmer3-tab raw string retrieval, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.080 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_30_hmmsearch_001)
Parsing hmmersearch 3.0 (text_30_hmmsearch_001). ... ok
test_30_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_002)
Parsing hmmersearch 3.0 (text_30_hmmsearch_002). ... ok
test_30_hmmsearch_003 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_003)
Parsing hmmersearch 3.0 (text_30_hmmsearch_003). ... ok
test_30_hmmsearch_004 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_004)
Parsing hmmersearch 3.0 (text_30_hmmsearch_004). ... ok
test_30_hmmsearch_005 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_005)
Parsing hmmersearch 3.0 (text_30_hmmsearch_005). ... ok
test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b1_hmmsearch_001)
Test parsing hmmsearch 3.1b1 (text_31b1_hmmsearch_001). ... ok
test_31b2_hmmscan_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmscan_001)
Test parsing hmmscan 3.1b2 (text_31b2_hmmscan_001). ... ok
test_31b2_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmsearch_001)
Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_001). ... ok
test_31b2_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmsearch_002)
Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_002). ... ok
test_30_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_001)
Parsing hmmscan 3.0 (text_30_hmmscan_001). ... ok
test_30_hmmscan_002 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_002)
Parsing hmmscan 3.0 (text_30_hmmscan_002). ... ok
test_30_hmmscan_003 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_003)
Parsing hmmscan 3.0 (text_30_hmmscan_003). ... ok
test_30_hmmscan_004 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_004)
Parsing hmmscan 3.0 (text_30_hmmscan_004). ... ok
test_30_hmmscan_005 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_005)
Parsing hmmscan 3.0 (text_30_hmmscan_005). ... ok
test_30_hmmscan_006 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_006)
Parsing hmmscan 3.0 (text_30_hmmscan_006). ... ok
test_30_hmmscan_007 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_007)
Parsing hmmscan 3.0 (text_30_hmmscan_007). ... ok
test_30_hmmscan_008 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_008)
Parsing hmmscan 3.0 (text_30_hmmscan_008). ... ok
test_30_hmmscan_009 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_009)
Parsing hmmscan 3.0 (text_30_hmmscan_009). ... ok
test_30_hmmscan_010 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_010)
Parsing hmmscan 3.0 (text_30_hmmscan_010). ... ok
test_31b1_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases.test_31b1_hmmscan_001)
Parsing hmmscan 3.1b1 (text_31b1_hmmscan_001). ... ok
test_31b2_phmmer_001 (test_SearchIO_hmmer3_text.PhmmerCases.test_31b2_phmmer_001)
Parsing phmmer 3.1b2 (text_31b2_phmmer_001). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.183 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_hmmertext_text_30_hmmscan_001)
Test hmmer3-text indexing, HMMER 3.0, multiple queries. ... ok
test_hmmertext_text_30_hmmscan_002 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_002)
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_hmmertext_text_30_hmmscan_006)
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_hmmertext_text_30_hmmscan_007)
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_hmmertext_text_30_hmmscan_008)
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_hmmertext_text_30_hmmsearch_005)
Test hmmer3-text indexing, HMMER 3.0, multiple queries. ... ok
test_hmmer3text_30_multiple_first (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_multiple_first)
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_hmmer3text_30_multiple_last)
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_hmmer3text_30_multiple_middle)
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_hmmer3text_30_single)
Test hmmer3-text raw string retrieval, HMMER 3.0, single query (text_30_hmmscan_003.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.122 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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.test_xml_001) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.067 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_legacy.py
test_SearchIO_legacy ... ok
test_TaggingConsumer (test_SearchIO_legacy.TestParserSupport.test_TaggingConsumer) ... ok
test_attempt_read_and_call (test_SearchIO_legacy.TestParserSupport.test_attempt_read_and_call) ... ok
test_is_blank_line (test_SearchIO_legacy.TestParserSupport.test_is_blank_line) ... ok
test_read_and_call (test_SearchIO_legacy.TestParserSupport.test_read_and_call) ... ok
test_safe_peekline (test_SearchIO_legacy.TestParserSupport.test_safe_peekline) ... ok
test_safe_readline (test_SearchIO_legacy.TestParserSupport.test_safe_readline) ... ok
test_one (test_SearchIO_legacy.UndoHandleTests.test_one)
First test. ... ok
test_read (test_SearchIO_legacy.UndoHandleTests.test_read)
Test read method. ... ok
test_undohandle_read_block (test_SearchIO_legacy.UndoHandleTests.test_undohandle_read_block)
Test reading in blocks. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.064 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_model.py
test_SearchIO_model ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_coords_setters_getters (test_SearchIO_model.HSPFragmentCases.test_coords_setters_getters)
Test HSPFragment query and hit coordinate-related setters and getters. ... ok
test_coords_setters_readonly (test_SearchIO_model.HSPFragmentCases.test_coords_setters_readonly)
Test HSPFragment query and hit coordinate-related read-only getters. ... ok
test_default_attrs (test_SearchIO_model.HSPFragmentCases.test_default_attrs)
Test HSPFragment attributes' default values. ... ok
test_frame_set_error (test_SearchIO_model.HSPFragmentCases.test_frame_set_error)
Test HSPFragment query and hit frame setters, invalid values. ... ok
test_frame_set_ok (test_SearchIO_model.HSPFragmentCases.test_frame_set_ok)
Test HSPFragment query and hit frame setters. ... ok
test_getitem (test_SearchIO_model.HSPFragmentCases.test_getitem)
Test HSPFragment.__getitem__. ... ok
test_getitem_alignment_annot (test_SearchIO_model.HSPFragmentCases.test_getitem_alignment_annot)
Test HSPFragment.__getitem__, with alignment annotation. ... ok
test_getitem_attrs (test_SearchIO_model.HSPFragmentCases.test_getitem_attrs)
Test HSPFragment.__getitem__, with attributes. ... ok
test_id_desc_set (test_SearchIO_model.HSPFragmentCases.test_id_desc_set)
Test HSPFragment query and hit id and description setters. ... ok
test_init_with_seqrecord (test_SearchIO_model.HSPFragmentCases.test_init_with_seqrecord)
Test HSPFragment.__init__, with SeqRecord. ... ok
test_init_wrong_seqtypes (test_SearchIO_model.HSPFragmentCases.test_init_wrong_seqtypes)
Test HSPFragment.__init__, wrong sequence argument types. ... ok
test_len (test_SearchIO_model.HSPFragmentCases.test_len)
Test HSPFragment.__len__. ... ok
test_molecule_type_no_seq (test_SearchIO_model.HSPFragmentCases.test_molecule_type_no_seq)
Test HSPFragment molecule_type property, query and hit sequences not present. ... ok
test_molecule_type_with_seq (test_SearchIO_model.HSPFragmentCases.test_molecule_type_with_seq)
Test HSPFragment molecule_type property, query or hit sequences present. ... ok
test_pickle (test_SearchIO_model.HSPFragmentCases.test_pickle)
Test pickling and unpickling of HSPFragment. ... ok
test_repr (test_SearchIO_model.HSPFragmentCases.test_repr)
Test HSPFragment.__repr__. ... ok
test_seq_unequal_hit_query_len (test_SearchIO_model.HSPFragmentCases.test_seq_unequal_hit_query_len)
Test HSPFragment sequence setter with unequal hit and query lengths. ... ok
test_seqmodel (test_SearchIO_model.HSPFragmentCases.test_seqmodel)
Test HSPFragment sequence attribute types and default values. ... ok
test_strand_set_error (test_SearchIO_model.HSPFragmentCases.test_strand_set_error)
Test HSPFragment query and hit strand setters, invalid values. ... ok
test_strand_set_from_minus_frame (test_SearchIO_model.HSPFragmentCases.test_strand_set_from_minus_frame)
Test HSPFragment query and hit strand getters, from minus frame. ... ok
test_strand_set_from_plus_frame (test_SearchIO_model.HSPFragmentCases.test_strand_set_from_plus_frame)
Test HSPFragment query and hit strand getters, from plus frame. ... ok
test_strand_set_from_zero_frame (test_SearchIO_model.HSPFragmentCases.test_strand_set_from_zero_frame)
Test HSPFragment query and hit strand getters, from zero frame. ... ok
test_strand_set_ok (test_SearchIO_model.HSPFragmentCases.test_strand_set_ok)
Test HSPFragment query and hit strand setters. ... ok
test_getitem (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_getitem)
Test HSPFragment.__getitem__, no alignments. ... ok
test_getitem_only_hit (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_getitem_only_hit)
Test HSPFragment.__getitem__, only hit. ... ok
test_getitem_only_query (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_getitem_only_query)
Test HSPFragment.__getitem__, only query. ... ok
test_init (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_init)
Test HSPFragment.__init__ attributes. ... ok
test_iter (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_iter)
Test HSP.__iter__, no alignments. ... ok
test_len (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_len)
Test HSPFragment.__len__, no alignments. ... ok
test_repr (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_repr)
Test HSPFragment.__repr__, no alignments. ... ok
test_seqmodel (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_seqmodel)
Test HSPFragment sequence attributes, no alignments. ... ok
test_contains (test_SearchIO_model.HSPMultipleFragmentCases.test_contains)
Test HSP.__contains__. ... ok
test_delitem (test_SearchIO_model.HSPMultipleFragmentCases.test_delitem)
Test HSP.__delitem__. ... ok
test_fragments (test_SearchIO_model.HSPMultipleFragmentCases.test_fragments)
Test HSP.fragments property. ... ok
test_getitem (test_SearchIO_model.HSPMultipleFragmentCases.test_getitem)
Test HSP.__getitem__. ... ok
test_id_desc_set (test_SearchIO_model.HSPMultipleFragmentCases.test_id_desc_set)
Test HSP query and hit id and description setters. ... ok
test_is_fragmented (test_SearchIO_model.HSPMultipleFragmentCases.test_is_fragmented)
Test HSP.is_fragmented property. ... ok
test_len (test_SearchIO_model.HSPMultipleFragmentCases.test_len)
Test HSP.__len__. ... ok
test_molecule_type (test_SearchIO_model.HSPMultipleFragmentCases.test_molecule_type)
Test HSP.molecule_type getter. ... ok
test_molecule_type_set (test_SearchIO_model.HSPMultipleFragmentCases.test_molecule_type_set)
Test HSP.molecule_type setter. ... ok
test_pickle (test_SearchIO_model.HSPMultipleFragmentCases.test_pickle)
Test pickling and unpickling of HSP. ... ok
test_range (test_SearchIO_model.HSPMultipleFragmentCases.test_range)
Test HSP range properties. ... ok
test_ranges (test_SearchIO_model.HSPMultipleFragmentCases.test_ranges)
Test HSP ranges properties. ... ok
test_seqs (test_SearchIO_model.HSPMultipleFragmentCases.test_seqs)
Test HSP sequence properties. ... ok
test_setitem_multiple (test_SearchIO_model.HSPMultipleFragmentCases.test_setitem_multiple)
Test HSP.__setitem__, multiple items. ... ok
test_setitem_single (test_SearchIO_model.HSPMultipleFragmentCases.test_setitem_single)
Test HSP.__setitem__, single item. ... ok
test_setters_readonly (test_SearchIO_model.HSPMultipleFragmentCases.test_setters_readonly)
Test HSP read-only properties. ... ok
test_span (test_SearchIO_model.HSPMultipleFragmentCases.test_span)
Test HSP span properties. ... ok
test_alignment (test_SearchIO_model.HSPSingleFragmentCases.test_alignment)
Test HSP.alignment property. ... ok
test_aln_span (test_SearchIO_model.HSPSingleFragmentCases.test_aln_span)
Test HSP.aln_span property. ... ok
test_fragment (test_SearchIO_model.HSPSingleFragmentCases.test_fragment)
Test HSP.fragment property. ... ok
test_init_no_fragment (test_SearchIO_model.HSPSingleFragmentCases.test_init_no_fragment)
Test HSP.__init__ without fragments. ... ok
test_is_fragmented (test_SearchIO_model.HSPSingleFragmentCases.test_is_fragmented)
Test HSP.is_fragmented property. ... ok
test_len (test_SearchIO_model.HSPSingleFragmentCases.test_len)
Test HSP.__len__. ... ok
test_range (test_SearchIO_model.HSPSingleFragmentCases.test_range)
Test HSP range properties. ... ok
test_seq (test_SearchIO_model.HSPSingleFragmentCases.test_seq)
Test HSP sequence properties. ... ok
test_setters_readonly (test_SearchIO_model.HSPSingleFragmentCases.test_setters_readonly)
Test HSP read-only properties. ... ok
test_span (test_SearchIO_model.HSPSingleFragmentCases.test_span)
Test HSP span properties. ... ok
test_append (test_SearchIO_model.HitCases.test_append)
Test Hit.append. ... ok
test_bool (test_SearchIO_model.HitCases.test_bool)
Test Hit.__bool__. ... ok
test_delitem (test_SearchIO_model.HitCases.test_delitem)
Test Hit.__delitem__. ... ok
test_desc_set (test_SearchIO_model.HitCases.test_desc_set)
Test Hit.description setter. ... ok
test_desc_set_no_seqrecord (test_SearchIO_model.HitCases.test_desc_set_no_seqrecord)
Test Hit.description setter, without HSP SeqRecords. ... ok
test_filter (test_SearchIO_model.HitCases.test_filter)
Test Hit.filter. ... ok
test_filter_no_filtered (test_SearchIO_model.HitCases.test_filter_no_filtered)
Test Hit.hit_filter, all hits filtered out. ... ok
test_filter_no_func (test_SearchIO_model.HitCases.test_filter_no_func)
Test Hit.filter, without arguments. ... ok
test_fragments (test_SearchIO_model.HitCases.test_fragments)
Test Hit.fragments. ... ok
test_getitem_multiple (test_SearchIO_model.HitCases.test_getitem_multiple)
Test Hit.__getitem__, multiple items. ... ok
test_getitem_single (test_SearchIO_model.HitCases.test_getitem_single)
Test Hit.__getitem__, single item. ... ok
test_hsp_map_no_func (test_SearchIO_model.HitCases.test_hsp_map_no_func)
Test Hit.map, without arguments. ... ok
test_hsps (test_SearchIO_model.HitCases.test_hsps)
Test Hit.hsps. ... ok
test_id_set (test_SearchIO_model.HitCases.test_id_set)
Test Hit.id setter. ... ok
test_index (test_SearchIO_model.HitCases.test_index)
Test Hit.index. ... ok
test_index_not_present (test_SearchIO_model.HitCases.test_index_not_present)
Test Hit.index, when index is not present. ... ok
test_init_hsps_only (test_SearchIO_model.HitCases.test_init_hsps_only)
Test Hit.__init__, with hsps only. ... ok
test_init_id_only (test_SearchIO_model.HitCases.test_init_id_only)
Test Hit.__init__, with ID only. ... ok
test_init_none (test_SearchIO_model.HitCases.test_init_none)
Test Hit.__init__, no arguments. ... ok
test_item_multiple (test_SearchIO_model.HitCases.test_item_multiple)
Test Hit.__setitem__, multiple items. ... ok
test_iter (test_SearchIO_model.HitCases.test_iter)
Test Hit.__iter__. ... ok
test_len (test_SearchIO_model.HitCases.test_len)
Test Hit.__len__. ... ok
test_map (test_SearchIO_model.HitCases.test_map)
Test Hit.hsp_map. ... ok
test_pickle (test_SearchIO_model.HitCases.test_pickle)
Test pickling and unpickling of Hit. ... ok
test_pop (test_SearchIO_model.HitCases.test_pop)
Test Hit.pop. ... ok
test_repr (test_SearchIO_model.HitCases.test_repr)
Test Hit.__repr__. ... ok
test_setitem_single (test_SearchIO_model.HitCases.test_setitem_single)
Test Hit.__setitem__, single item. ... ok
test_sort (test_SearchIO_model.HitCases.test_sort)
Test Hit.sort. ... ok
test_sort_not_in_place (test_SearchIO_model.HitCases.test_sort_not_in_place)
Test Hit.sort, not in place. ... ok
test_validate_hsp_ok (test_SearchIO_model.HitCases.test_validate_hsp_ok)
Test Hit._validate_hsp. ... ok
test_validate_hsp_wrong_hit_id (test_SearchIO_model.HitCases.test_validate_hsp_wrong_hit_id)
Test Hit._validate_hsp, wrong hit ID. ... ok
test_validate_hsp_wrong_query_id (test_SearchIO_model.HitCases.test_validate_hsp_wrong_query_id)
Test Hit._validate_hsp, wrong query ID. ... ok
test_validate_hsp_wrong_type (test_SearchIO_model.HitCases.test_validate_hsp_wrong_type)
Test Hit._validate_hsp, wrong type. ... ok
test_absorb_hit_does_not_exist (test_SearchIO_model.QueryResultCases.test_absorb_hit_does_not_exist)
Test QueryResult.absorb, hit does not exist. ... ok
test_absorb_hit_exists (test_SearchIO_model.QueryResultCases.test_absorb_hit_exists)
Test QueryResult.absorb, hit with the same ID exists. ... ok
test_append_alt_id_exists (test_SearchIO_model.QueryResultCases.test_append_alt_id_exists)
Test QueryResult.append, when alt ID exists. ... ok
test_append_alt_id_exists_alt (test_SearchIO_model.QueryResultCases.test_append_alt_id_exists_alt)
Test QueryResult.append, when alt ID exists as primary. ... ok
test_append_custom_hit_key_function_ok (test_SearchIO_model.QueryResultCases.test_append_custom_hit_key_function_ok)
Test QueryResult.append, with custom hit key function. ... ok
test_append_id_exists (test_SearchIO_model.QueryResultCases.test_append_id_exists)
Test QueryResult.append, when ID exists. ... ok
test_append_ok (test_SearchIO_model.QueryResultCases.test_append_ok)
Test QueryResult.append. ... ok
test_bool (test_SearchIO_model.QueryResultCases.test_bool)
Test QueryResult.__bool__. ... ok
test_contains (test_SearchIO_model.QueryResultCases.test_contains)
Test QueryResult.__contains__. ... ok
test_contains_alt (test_SearchIO_model.QueryResultCases.test_contains_alt)
Test QueryResult.__contains__, with alternative IDs. ... ok
test_delitem_alt_ok (test_SearchIO_model.QueryResultCases.test_delitem_alt_ok)
Test QueryResult.__delitem__, with alt ID. ... ok
test_delitem_int_ok (test_SearchIO_model.QueryResultCases.test_delitem_int_ok)
Test QueryResult.__delitem__. ... ok
test_delitem_slice_ok (test_SearchIO_model.QueryResultCases.test_delitem_slice_ok)
Test QueryResult.__delitem__, with slice. ... ok
test_delitem_string_ok (test_SearchIO_model.QueryResultCases.test_delitem_string_ok)
Test QueryResult.__getitem__, with string. ... ok
test_description_set (test_SearchIO_model.QueryResultCases.test_description_set)
Test QueryResult.description setter. ... ok
test_description_set_no_seqrecord (test_SearchIO_model.QueryResultCases.test_description_set_no_seqrecord)
Test QueryResult.description setter, without HSP SeqRecords. ... ok
test_fragments (test_SearchIO_model.QueryResultCases.test_fragments)
Test QueryResult.fragments. ... ok
test_getitem_alt_ok (test_SearchIO_model.QueryResultCases.test_getitem_alt_ok)
Test QueryResult.__getitem__, single item with alternative ID. ... ok
test_getitem_default_ok (test_SearchIO_model.QueryResultCases.test_getitem_default_ok)
Test QueryResult.__getitem__. ... ok
test_getitem_int_ok (test_SearchIO_model.QueryResultCases.test_getitem_int_ok)
Test QueryResult.__getitem__, with integer. ... ok
test_getitem_slice_ok (test_SearchIO_model.QueryResultCases.test_getitem_slice_ok)
Test QueryResult.__getitem__, with slice. ... ok
test_getitm_slice_alt_ok (test_SearchIO_model.QueryResultCases.test_getitm_slice_alt_ok)
Test QueryResult.__getitem__, with slice and alt IDs. ... ok
test_hit_filter (test_SearchIO_model.QueryResultCases.test_hit_filter)
Test QueryResult.hit_filter. ... ok
test_hit_filter_no_filtered (test_SearchIO_model.QueryResultCases.test_hit_filter_no_filtered)
Test QueryResult.hit_filter, all hits filtered out. ... ok
test_hit_filter_no_func (test_SearchIO_model.QueryResultCases.test_hit_filter_no_func)
Test QueryResult.hit_filter, without arguments. ... ok
test_hit_keys (test_SearchIO_model.QueryResultCases.test_hit_keys)
Test QueryResult.hit_keys. ... ok
test_hit_map (test_SearchIO_model.QueryResultCases.test_hit_map)
Test QueryResult.hit_map. ... ok
test_hit_map_no_func (test_SearchIO_model.QueryResultCases.test_hit_map_no_func)
Test QueryResult.hit_map, without arguments. ... ok
test_hits (test_SearchIO_model.QueryResultCases.test_hits)
Test QueryResult.hits. ... ok
test_hsp_filter (test_SearchIO_model.QueryResultCases.test_hsp_filter)
Test QueryResult.hsp_filter. ... ok
test_hsp_filter_no_filtered (test_SearchIO_model.QueryResultCases.test_hsp_filter_no_filtered)
Test QueryResult.hsp_filter, all hits filtered out. ... ok
test_hsp_filter_no_func (test_SearchIO_model.QueryResultCases.test_hsp_filter_no_func)
Test QueryResult.hsp_filter, no arguments. ... ok
test_hsp_map (test_SearchIO_model.QueryResultCases.test_hsp_map)
Test QueryResult.hsp_map. ... ok
test_hsp_map_no_func (test_SearchIO_model.QueryResultCases.test_hsp_map_no_func)
Test QueryResult.hsp_map, without arguments. ... ok
test_hsps (test_SearchIO_model.QueryResultCases.test_hsps)
Test QueryResult.hsps. ... ok
test_id_set (test_SearchIO_model.QueryResultCases.test_id_set)
Test QueryResult.id setter. ... ok
test_index (test_SearchIO_model.QueryResultCases.test_index)
Test QueryResult.index. ... ok
test_index_alt (test_SearchIO_model.QueryResultCases.test_index_alt)
Test QueryResult.index, with alt ID. ... ok
test_index_not_present (test_SearchIO_model.QueryResultCases.test_index_not_present)
Test QueryResult.index, when index is not present. ... ok
test_init_hits_only (test_SearchIO_model.QueryResultCases.test_init_hits_only)
Test QueryResult.__init__, with hits only. ... ok
test_init_id_only (test_SearchIO_model.QueryResultCases.test_init_id_only)
Test QueryResult.__init__, with ID only. ... ok
test_init_none (test_SearchIO_model.QueryResultCases.test_init_none)
Test QueryResult.__init__, no arguments. ... ok
test_items (test_SearchIO_model.QueryResultCases.test_items)
Test QueryResult.items. ... ok
test_iter (test_SearchIO_model.QueryResultCases.test_iter)
Test QueryResult.__iter__. ... ok
test_len (test_SearchIO_model.QueryResultCases.test_len)
Test QueryResult.__len__. ... ok
test_order (test_SearchIO_model.QueryResultCases.test_order) ... ok
test_pickle (test_SearchIO_model.QueryResultCases.test_pickle)
Test pickling and unpickling of QueryResult. ... ok
test_pop_int_index_ok (test_SearchIO_model.QueryResultCases.test_pop_int_index_ok)
Test QueryResult.pop, with integer index. ... ok
test_pop_nonexistent_key (test_SearchIO_model.QueryResultCases.test_pop_nonexistent_key)
Test QueryResult.pop with default for nonexistent key. ... ok
test_pop_nonexistent_with_default (test_SearchIO_model.QueryResultCases.test_pop_nonexistent_with_default)
Test QueryResult.pop with default for nonexistent key. ... ok
test_pop_ok (test_SearchIO_model.QueryResultCases.test_pop_ok)
Test QueryResult.pop. ... ok
test_pop_string_alt_ok (test_SearchIO_model.QueryResultCases.test_pop_string_alt_ok)
Test QueryResult.pop, with alternative ID. ... ok
test_pop_string_index_ok (test_SearchIO_model.QueryResultCases.test_pop_string_index_ok)
Test QueryResult.pop, with string index. ... ok
test_repr (test_SearchIO_model.QueryResultCases.test_repr)
Test QueryResult.__repr__. ... ok
test_setitem_from_empty (test_SearchIO_model.QueryResultCases.test_setitem_from_empty)
Test QueryResult.__setitem__, from empty container. ... ok
test_setitem_ok (test_SearchIO_model.QueryResultCases.test_setitem_ok)
Test QueryResult.__setitem__. ... ok
test_setitem_ok_alt (test_SearchIO_model.QueryResultCases.test_setitem_ok_alt)
Test QueryResult.__setitem__, checking alt hit IDs. ... ok
test_setitem_ok_alt_existing (test_SearchIO_model.QueryResultCases.test_setitem_ok_alt_existing)
Test QueryResult.__setitem__, existing key. ... ok
test_setitem_ok_alt_ok_promote (test_SearchIO_model.QueryResultCases.test_setitem_ok_alt_ok_promote)
Test QueryResult.__setitem__, previously alt ID. ... ok
test_setitem_wrong_key_type (test_SearchIO_model.QueryResultCases.test_setitem_wrong_key_type)
Test QueryResult.__setitem__, wrong key type. ... ok
test_setitem_wrong_query_id (test_SearchIO_model.QueryResultCases.test_setitem_wrong_query_id)
Test QueryResult.__setitem__, wrong query ID. ... ok
test_setitem_wrong_type (test_SearchIO_model.QueryResultCases.test_setitem_wrong_type)
Test QueryResult.__setitem__, wrong type. ... ok
test_sort_key_not_in_place_ok (test_SearchIO_model.QueryResultCases.test_sort_key_not_in_place_ok)
Test QueryResult.sort, with custom key, not in place. ... ok
test_sort_key_ok (test_SearchIO_model.QueryResultCases.test_sort_key_ok)
Test QueryResult.sort, with custom key. ... ok
test_sort_not_in_place_ok (test_SearchIO_model.QueryResultCases.test_sort_not_in_place_ok)
Test QueryResult.sort, not in place. ... ok
test_sort_ok (test_SearchIO_model.QueryResultCases.test_sort_ok)
Test QueryResult.sort. ... ok
test_sort_reverse_not_in_place_ok (test_SearchIO_model.QueryResultCases.test_sort_reverse_not_in_place_ok)
Test QueryResult.sort, reverse, not in place. ... ok
test_sort_reverse_ok (test_SearchIO_model.QueryResultCases.test_sort_reverse_ok)
Test QueryResult.sort, reverse. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.119 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_write.py
test_SearchIO_write ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy/__init__.py:12: BiopythonDeprecationWarning: The 'Bio.SearchIO._legacy' module for parsing BLAST plain text output is deprecated and will be removed in a future release of Biopython. Consider generating your BLAST output for parsing as XML or tabular format instead.
warnings.warn(
ok
test_write_multiple_from_blasttab (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttab)
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_write_multiple_from_blasttabc)
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_write_multiple_from_blasttabc_allfields)
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_write_single_from_blasttab)
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_write_single_from_blasttabc)
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_write_multiple_from_blastxml)
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_write_single_from_blastxml)
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_write_multiple_from_blatpsl)
Test blat-psl writing from blat-psl, multiple queries (psl_34_001.psl). ... ok
test_write_multiple_from_blatpslx (test_SearchIO_write.BlatPslWriteCases.test_write_multiple_from_blatpslx)
Test blat-pslx writing from blat-pslx, multiple queries (pslx_34_001.pslx). ... ok
test_write_single_from_blatpsl (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpsl)
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_write_single_from_blatpsl_protein_query)
Test blat-psl writing from blat-psl, single query (psl_35_002.psl). ... ok
test_write_single_from_blatpslx (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpslx)
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_write_single_from_blatpslx_protein_query)
Test blat-pslx writing from blat-pslx, single query (pslx_35_002.pslx). ... ok
test_write_multiple_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_multiple_from_hmmscandomtab)
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_write_single_from_hmmscandomtab)
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_write_single_from_hmmsearchdomtab)
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_write_multiple_from_hmmertab)
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_write_single_from_hmmertab)
Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.338 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqFeature.py
test_SeqFeature ... ok
test_eq_identical (test_SeqFeature.TestCompoundLocation.test_eq_identical)
Test two identical locations are equal. ... ok
test_eq_not_identical (test_SeqFeature.TestCompoundLocation.test_eq_not_identical)
Test two different locations are not equal. ... ok
test_reference_in_compound_location_record (test_SeqFeature.TestExtract.test_reference_in_compound_location_record)
Test compound location with reference to another record. ... ok
test_reference_in_compound_location_sequence (test_SeqFeature.TestExtract.test_reference_in_compound_location_sequence)
Test compound location with reference to another sequence. ... ok
test_reference_in_location_record (test_SeqFeature.TestExtract.test_reference_in_location_record)
Test location with reference to another record. ... ok
test_reference_in_location_sequence (test_SeqFeature.TestExtract.test_reference_in_location_sequence)
Test location with reference to another sequence. ... ok
test_fuzzy (test_SeqFeature.TestLocations.test_fuzzy)
Test fuzzy representations. ... ok
test_pickle (test_SeqFeature.TestPositions.test_pickle)
Test pickle behaviour of position instances. ... ok
test_eq_identical (test_SeqFeature.TestReference.test_eq_identical)
Test two identical references eq() to True. ... ok
test_eq_identical (test_SeqFeature.TestSeqFeature.test_eq_identical) ... ok
test_translation_checks_cds (test_SeqFeature.TestSeqFeature.test_translation_checks_cds)
Test that a CDS feature is subject to respective checks. ... ok
test_eq_identical (test_SeqFeature.TestSimpleLocation.test_eq_identical)
Test two identical locations are equal. ... ok
test_eq_not_identical (test_SeqFeature.TestSimpleLocation.test_eq_not_identical)
Test two different locations are not equal. ... ok
test_offsets (test_SeqFeature.TestSimpleLocation.test_offsets)
Test adding and subtracting integer offsets. ... ok
test_start_before_end (test_SeqFeature.TestSimpleLocation.test_start_before_end) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.097 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO.py
test_SeqIO ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_abi1 (test_SeqIO.TestSeqIO.test_abi1) ... ok
test_abi2 (test_SeqIO.TestSeqIO.test_abi2) ... ok
test_abi3 (test_SeqIO.TestSeqIO.test_abi3) ... ok
test_ace1 (test_SeqIO.TestSeqIO.test_ace1) ... ok
test_ace2 (test_SeqIO.TestSeqIO.test_ace2) ... ok
test_ace3 (test_SeqIO.TestSeqIO.test_ace3) ... ok
test_cif_atom1 (test_SeqIO.TestSeqIO.test_cif_atom1) ... ok
test_cif_atom2 (test_SeqIO.TestSeqIO.test_cif_atom2) ... ok
test_cif_seqres1 (test_SeqIO.TestSeqIO.test_cif_seqres1) ... ok
test_cif_seqres2 (test_SeqIO.TestSeqIO.test_cif_seqres2) ... ok
test_clustal1 (test_SeqIO.TestSeqIO.test_clustal1) ... ok
test_clustal2 (test_SeqIO.TestSeqIO.test_clustal2) ... ok
test_clustal3 (test_SeqIO.TestSeqIO.test_clustal3) ... ok
test_clustal4 (test_SeqIO.TestSeqIO.test_clustal4) ... ok
test_clustal_to_nexus_with_mol_type (test_SeqIO.TestSeqIO.test_clustal_to_nexus_with_mol_type)
Convert Clustal to NEXUS with molecule type. ... ok
test_clustal_to_nexus_without_mol_type (test_SeqIO.TestSeqIO.test_clustal_to_nexus_without_mol_type)
Convert Clustal to NEXUS without molecule type. ... ok
test_embl1 (test_SeqIO.TestSeqIO.test_embl1) ... ok
test_embl10 (test_SeqIO.TestSeqIO.test_embl10) ... ok
test_embl11 (test_SeqIO.TestSeqIO.test_embl11) ... ok
test_embl12 (test_SeqIO.TestSeqIO.test_embl12) ... ok
test_embl13 (test_SeqIO.TestSeqIO.test_embl13)
Test parsing embl file with wrapped locations and unspecified type. ... ok
test_embl14 (test_SeqIO.TestSeqIO.test_embl14)
Test parsing file with features over-indented for EMBL. ... ok
test_embl2 (test_SeqIO.TestSeqIO.test_embl2) ... ok
test_embl3 (test_SeqIO.TestSeqIO.test_embl3) ... ok
test_embl4 (test_SeqIO.TestSeqIO.test_embl4) ... ok
test_embl5 (test_SeqIO.TestSeqIO.test_embl5) ... ok
test_embl6 (test_SeqIO.TestSeqIO.test_embl6) ... ok
test_embl7 (test_SeqIO.TestSeqIO.test_embl7) ... ok
test_embl8 (test_SeqIO.TestSeqIO.test_embl8) ... ok
test_embl9 (test_SeqIO.TestSeqIO.test_embl9) ... ok
test_emboss1 (test_SeqIO.TestSeqIO.test_emboss1) ... ok
test_emboss2 (test_SeqIO.TestSeqIO.test_emboss2) ... ok
test_emboss3 (test_SeqIO.TestSeqIO.test_emboss3) ... ok
test_empty_file (test_SeqIO.TestSeqIO.test_empty_file)
Check parsers can cope with an empty file. ... ok
test_fasta1 (test_SeqIO.TestSeqIO.test_fasta1) ... ok
test_fasta10 (test_SeqIO.TestSeqIO.test_fasta10) ... ok
test_fasta11 (test_SeqIO.TestSeqIO.test_fasta11) ... ok
test_fasta12 (test_SeqIO.TestSeqIO.test_fasta12) ... ok
test_fasta13 (test_SeqIO.TestSeqIO.test_fasta13) ... ok
test_fasta14 (test_SeqIO.TestSeqIO.test_fasta14) ... ok
test_fasta15 (test_SeqIO.TestSeqIO.test_fasta15) ... ok
test_fasta16 (test_SeqIO.TestSeqIO.test_fasta16) ... ok
test_fasta17 (test_SeqIO.TestSeqIO.test_fasta17) ... ok
test_fasta18 (test_SeqIO.TestSeqIO.test_fasta18) ... ok
test_fasta19 (test_SeqIO.TestSeqIO.test_fasta19) ... ok
test_fasta2 (test_SeqIO.TestSeqIO.test_fasta2) ... ok
test_fasta20 (test_SeqIO.TestSeqIO.test_fasta20) ... ok
test_fasta21 (test_SeqIO.TestSeqIO.test_fasta21) ... ok
test_fasta22 (test_SeqIO.TestSeqIO.test_fasta22) ... ok
test_fasta23 (test_SeqIO.TestSeqIO.test_fasta23) ... ok
test_fasta24 (test_SeqIO.TestSeqIO.test_fasta24) ... ok
test_fasta3 (test_SeqIO.TestSeqIO.test_fasta3) ... ok
test_fasta4 (test_SeqIO.TestSeqIO.test_fasta4) ... ok
test_fasta5 (test_SeqIO.TestSeqIO.test_fasta5) ... ok
test_fasta6 (test_SeqIO.TestSeqIO.test_fasta6) ... ok
test_fasta7 (test_SeqIO.TestSeqIO.test_fasta7) ... ok
test_fasta8 (test_SeqIO.TestSeqIO.test_fasta8) ... ok
test_fasta9 (test_SeqIO.TestSeqIO.test_fasta9) ... ok
test_fasta_2line1 (test_SeqIO.TestSeqIO.test_fasta_2line1) ... ok
test_fasta_to_seqxml_with_mol_type (test_SeqIO.TestSeqIO.test_fasta_to_seqxml_with_mol_type)
Convert FASTA to SeqXML with molecule type. ... ok
test_fasta_to_seqxml_without_mol_type (test_SeqIO.TestSeqIO.test_fasta_to_seqxml_without_mol_type)
Convert FASTA to SeqXML without molecule type. ... ok
test_fastq1 (test_SeqIO.TestSeqIO.test_fastq1) ... ok
test_fastq2 (test_SeqIO.TestSeqIO.test_fastq2) ... ok
test_fastq3 (test_SeqIO.TestSeqIO.test_fastq3) ... ok
test_fastq4 (test_SeqIO.TestSeqIO.test_fastq4) ... ok
test_fastq5 (test_SeqIO.TestSeqIO.test_fastq5) ... ok
test_fastq_illumina1 (test_SeqIO.TestSeqIO.test_fastq_illumina1) ... ok
test_fastq_solexa1 (test_SeqIO.TestSeqIO.test_fastq_solexa1) ... ok
test_fastq_solexa2 (test_SeqIO.TestSeqIO.test_fastq_solexa2) ... ok
test_genbank1 (test_SeqIO.TestSeqIO.test_genbank1) ... ok
test_genbank10 (test_SeqIO.TestSeqIO.test_genbank10) ... ok
test_genbank11 (test_SeqIO.TestSeqIO.test_genbank11) ... ok
test_genbank12 (test_SeqIO.TestSeqIO.test_genbank12) ... ok
test_genbank13 (test_SeqIO.TestSeqIO.test_genbank13) ... ok
test_genbank14 (test_SeqIO.TestSeqIO.test_genbank14) ... ok
test_genbank15 (test_SeqIO.TestSeqIO.test_genbank15) ... ok
test_genbank16 (test_SeqIO.TestSeqIO.test_genbank16)
Test parsing Genbank file from Vector NTI with an odd LOCUS line. ... ok
test_genbank17 (test_SeqIO.TestSeqIO.test_genbank17) ... ok
test_genbank18 (test_SeqIO.TestSeqIO.test_genbank18) ... ok
test_genbank19 (test_SeqIO.TestSeqIO.test_genbank19) ... ok
test_genbank2 (test_SeqIO.TestSeqIO.test_genbank2) ... ok
test_genbank20 (test_SeqIO.TestSeqIO.test_genbank20)
Test parsing GenPept file with nasty bond locations. ... ok
test_genbank21 (test_SeqIO.TestSeqIO.test_genbank21) ... ok
test_genbank22 (test_SeqIO.TestSeqIO.test_genbank22)
Test that genbank format write doesn't destroy db_source in annotations. ... ok
test_genbank23 (test_SeqIO.TestSeqIO.test_genbank23)
Test that peptide genbank files can be written with long names. ... ok
test_genbank3 (test_SeqIO.TestSeqIO.test_genbank3) ... ok
test_genbank4 (test_SeqIO.TestSeqIO.test_genbank4) ... ok
test_genbank5 (test_SeqIO.TestSeqIO.test_genbank5) ... ok
test_genbank6 (test_SeqIO.TestSeqIO.test_genbank6) ... ok
test_genbank7 (test_SeqIO.TestSeqIO.test_genbank7) ... ok
test_genbank8 (test_SeqIO.TestSeqIO.test_genbank8) ... ok
test_genbank9 (test_SeqIO.TestSeqIO.test_genbank9) ... ok
test_ig1 (test_SeqIO.TestSeqIO.test_ig1) ... ok
test_ig2 (test_SeqIO.TestSeqIO.test_ig2) ... ok
test_ig3 (test_SeqIO.TestSeqIO.test_ig3)
Test parsing a MASE alignment with sequence O_ANT70 being shorter. ... ok
test_imgt1 (test_SeqIO.TestSeqIO.test_imgt1)
Test parsing file with features over-indented for EMBL. ... ok
test_imgt2 (test_SeqIO.TestSeqIO.test_imgt2) ... ok
test_nexus1 (test_SeqIO.TestSeqIO.test_nexus1) ... ok
test_pdb_atom1 (test_SeqIO.TestSeqIO.test_pdb_atom1) ... ok
test_pdb_atom2 (test_SeqIO.TestSeqIO.test_pdb_atom2) ... ok
test_pdb_atom3 (test_SeqIO.TestSeqIO.test_pdb_atom3) ... ok
test_pdb_seqres1 (test_SeqIO.TestSeqIO.test_pdb_seqres1) ... ok
test_pdb_seqres2 (test_SeqIO.TestSeqIO.test_pdb_seqres2) ... ok
test_pdb_seqres3 (test_SeqIO.TestSeqIO.test_pdb_seqres3) ... ok
test_phd1 (test_SeqIO.TestSeqIO.test_phd1) ... ok
test_phd2 (test_SeqIO.TestSeqIO.test_phd2) ... ok
test_phd3 (test_SeqIO.TestSeqIO.test_phd3) ... ok
test_phd4 (test_SeqIO.TestSeqIO.test_phd4) ... ok
test_phylip1 (test_SeqIO.TestSeqIO.test_phylip1) ... ok
test_phylip2 (test_SeqIO.TestSeqIO.test_phylip2) ... ok
test_phylip3 (test_SeqIO.TestSeqIO.test_phylip3) ... ok
test_phylip4 (test_SeqIO.TestSeqIO.test_phylip4) ... ok
test_phylip5 (test_SeqIO.TestSeqIO.test_phylip5) ... ok
test_phylip6 (test_SeqIO.TestSeqIO.test_phylip6) ... ok
test_phylip7 (test_SeqIO.TestSeqIO.test_phylip7) ... ok
test_pir1 (test_SeqIO.TestSeqIO.test_pir1) ... ok
test_pir2 (test_SeqIO.TestSeqIO.test_pir2) ... ok
test_pir3 (test_SeqIO.TestSeqIO.test_pir3) ... ok
test_pir4 (test_SeqIO.TestSeqIO.test_pir4) ... ok
test_pir5 (test_SeqIO.TestSeqIO.test_pir5) ... ok
test_qual1 (test_SeqIO.TestSeqIO.test_qual1) ... ok
test_seqxml1 (test_SeqIO.TestSeqIO.test_seqxml1) ... ok
test_seqxml2 (test_SeqIO.TestSeqIO.test_seqxml2) ... ok
test_seqxml3 (test_SeqIO.TestSeqIO.test_seqxml3) ... ok
test_sff1 (test_SeqIO.TestSeqIO.test_sff1) ... ok
test_snapgene1 (test_SeqIO.TestSeqIO.test_snapgene1) ... ok
test_stockholm1 (test_SeqIO.TestSeqIO.test_stockholm1) ... ok
test_stockholm2 (test_SeqIO.TestSeqIO.test_stockholm2) ... ok
test_swiss1 (test_SeqIO.TestSeqIO.test_swiss1) ... ok
test_swiss11 (test_SeqIO.TestSeqIO.test_swiss11) ... ok
test_swiss12 (test_SeqIO.TestSeqIO.test_swiss12) ... ok
test_swiss13 (test_SeqIO.TestSeqIO.test_swiss13) ... ok
test_swiss14 (test_SeqIO.TestSeqIO.test_swiss14) ... ok
test_swiss15 (test_SeqIO.TestSeqIO.test_swiss15) ... ok
test_swiss16 (test_SeqIO.TestSeqIO.test_swiss16) ... ok
test_swiss17 (test_SeqIO.TestSeqIO.test_swiss17) ... ok
test_swiss18 (test_SeqIO.TestSeqIO.test_swiss18) ... ok
test_swiss19 (test_SeqIO.TestSeqIO.test_swiss19) ... ok
test_swiss2 (test_SeqIO.TestSeqIO.test_swiss2) ... ok
test_swiss20 (test_SeqIO.TestSeqIO.test_swiss20) ... ok
test_swiss3 (test_SeqIO.TestSeqIO.test_swiss3) ... ok
test_swiss4 (test_SeqIO.TestSeqIO.test_swiss4) ... ok
test_swiss5 (test_SeqIO.TestSeqIO.test_swiss5) ... ok
test_swiss6 (test_SeqIO.TestSeqIO.test_swiss6) ... ok
test_swiss7 (test_SeqIO.TestSeqIO.test_swiss7) ... ok
test_swiss8 (test_SeqIO.TestSeqIO.test_swiss8) ... ok
test_swiss9 (test_SeqIO.TestSeqIO.test_swiss9) ... ok
test_tab1 (test_SeqIO.TestSeqIO.test_tab1) ... ok
test_uniprot_xml1 (test_SeqIO.TestSeqIO.test_uniprot_xml1) ... ok
test_uniprot_xml2 (test_SeqIO.TestSeqIO.test_uniprot_xml2) ... ok
test_uniprot_xml3 (test_SeqIO.TestSeqIO.test_uniprot_xml3) ... ok
test_uniprot_xml4 (test_SeqIO.TestSeqIO.test_uniprot_xml4) ... ok
test_uniprot_xml5 (test_SeqIO.TestSeqIO.test_uniprot_xml5) ... ok
test_xdna1 (test_SeqIO.TestSeqIO.test_xdna1) ... ok
test_gzip_fasta (test_SeqIO.TestZipped.test_gzip_fasta)
Testing FASTA with gzip. ... ok
test_gzip_fastq (test_SeqIO.TestZipped.test_gzip_fastq)
Testing FASTQ with gzip. ... ok
test_gzip_genbank (test_SeqIO.TestZipped.test_gzip_genbank)
Testing GenBank with gzip. ... ok
----------------------------------------------------------------------
Ran 1 test in 22.521 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_file_type)
Test if filetype is ABIF. ... ok
test_no_smpl1 (test_SeqIO_AbiIO.TestAbi.test_no_smpl1)
Test parsing of ABIF file without the normally expected SMPL1 tag. ... ok
test_raw (test_SeqIO_AbiIO.TestAbi.test_raw)
Test access to raw ABIF tags. ... ok
test_seqrecord (test_SeqIO_AbiIO.TestAbi.test_seqrecord)
Test if the extracted seqrecords data are equal to expected values. ... ok
test_trim (test_SeqIO_AbiIO.TestAbi.test_trim)
Test if trim works. ... ok
test_file_type (test_SeqIO_AbiIO.TestAbiFake.test_file_type)
Test if error is raised if filetype is not ABIF. ... ok
test_nonascii_tag (test_SeqIO_AbiIO.TestAbiNonAscii.test_nonascii_tag)
Test that we can handle non-ascii tags. ... ok
test_file_mode (test_SeqIO_AbiIO.TestAbiWrongMode.test_file_mode)
Test if exception is raised if file is not opened in 'rb' mode. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.338 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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_edgecases_FastaTwoLineParser)
Test FastaTwoLineParser edge-cases. ... ok
test_edgecases_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_edgecases_SimpleFastaParser)
Test SimpleFastaParser edge-cases. ... ok
test_exceptions_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_exceptions_FastaTwoLineParser)
Test FastaTwoLineParser exceptions. ... ok
test_regular_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_regular_FastaTwoLineParser)
Test regular FastaTwoLineParser cases. ... ok
test_regular_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_regular_SimpleFastaParser)
Test regular SimpleFastaParser cases. ... ok
test_multi_dna_files (test_SeqIO_FastaIO.TitleFunctions.test_multi_dna_files)
Test Fasta files containing multiple nucleotide sequences. ... ok
test_multi_protein_files (test_SeqIO_FastaIO.TitleFunctions.test_multi_protein_files)
Test Fasta files containing multiple protein sequences. ... ok
test_no_name (test_SeqIO_FastaIO.TitleFunctions.test_no_name)
Test FASTA record with no identifier. ... ok
test_single_nucleic_files (test_SeqIO_FastaIO.TitleFunctions.test_single_nucleic_files)
Test Fasta files containing a single nucleotide sequence. ... ok
test_single_proteino_files (test_SeqIO_FastaIO.TitleFunctions.test_single_proteino_files)
Test Fasta files containing a single protein sequence. ... ok
test_fails (test_SeqIO_FastaIO.Wrapping.test_fails)
Test case which should fail. ... ok
test_passes (test_SeqIO_FastaIO.Wrapping.test_passes)
Test case which should pass. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.095 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Gck.py
test_SeqIO_Gck ... ok
test_conflicting_lengths (test_SeqIO_Gck.TestGckWithArtificialData.test_conflicting_lengths)
Read a file with incorrect length. ... ok
test_read (test_SeqIO_Gck.TestGckWithArtificialData.test_read)
Read an artificial sample file. ... ok
test_read (test_SeqIO_Gck.TestGckWithImproperHeader.test_read)
Read a file with an incomplete header. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.083 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Insdc.py
test_SeqIO_Insdc ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/GenBank/Scanner.py:303: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)?
warnings.warn(
/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: mRNA
warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: unassigned DNA
warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA
warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
ok
test_conversion (test_SeqIO_Insdc.ConvertTestsInsdc.test_conversion)
Test format conversion by SeqIO.write/SeqIO.parse and SeqIO.convert. ... ok
test_annotation1 (test_SeqIO_Insdc.TestEmbl.test_annotation1)
Check parsing of annotation from EMBL files (1). ... ok
test_annotation2 (test_SeqIO_Insdc.TestEmbl.test_annotation2)
Check parsing of annotation from EMBL files (2). ... ok
test_annotation3 (test_SeqIO_Insdc.TestEmbl.test_annotation3)
Check parsing of annotation from EMBL files (3). ... ok
test_annotation4 (test_SeqIO_Insdc.TestEmbl.test_annotation4)
Check parsing of annotation from EMBL files (4). ... ok
test_writing_empty_qualifiers (test_SeqIO_Insdc.TestEmbl.test_writing_empty_qualifiers) ... ok
test_annotation1 (test_SeqIO_Insdc.TestEmblRewrite.test_annotation1)
Check writing-and-parsing EMBL file (1). ... ok
test_annotation2 (test_SeqIO_Insdc.TestEmblRewrite.test_annotation2)
Check writing-and-parsing EMBL file (2). ... ok
test_annotation3 (test_SeqIO_Insdc.TestEmblRewrite.test_annotation3)
Check writing-and-parsing EMBL file (3). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.131 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_NibIO.py
test_SeqIO_NibIO ... ok
test_read_even (test_SeqIO_NibIO.TestNibReaderWriter.test_read_even) ... ok
test_read_odd (test_SeqIO_NibIO.TestNibReaderWriter.test_read_odd) ... ok
test_write_even (test_SeqIO_NibIO.TestNibReaderWriter.test_write_even) ... ok
test_write_odd (test_SeqIO_NibIO.TestNibReaderWriter.test_write_odd) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.084 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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.test_atom_parse)
Parse a multi-chain structure by ATOM entries. ... ok
test_atom_read (test_SeqIO_PdbIO.TestCifAtom.test_atom_read)
Read a single-chain structure by ATOM entries. ... ok
test_atom_read_noheader (test_SeqIO_PdbIO.TestCifAtom.test_atom_read_noheader)
Read a single-chain CIF without a header by ATOM entries. ... ok
test_seqres_missing (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_missing)
Parse a PDB with no SEQRES entries. ... ok
test_seqres_parse (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_parse)
Parse a multi-chain PDB by SEQRES entries. ... ok
test_seqres_read (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_read)
Read a single-chain structure by sequence entries. ... ok
test_atom_noheader (test_SeqIO_PdbIO.TestPdbAtom.test_atom_noheader)
Parse a PDB with no HEADER line. ... ok
test_atom_parse (test_SeqIO_PdbIO.TestPdbAtom.test_atom_parse)
Parse a multi-chain structure by ATOM entries. ... ok
test_atom_read (test_SeqIO_PdbIO.TestPdbAtom.test_atom_read)
Read a single-chain structure by ATOM entries. ... ok
test_atom_read_noheader (test_SeqIO_PdbIO.TestPdbAtom.test_atom_read_noheader)
Read a single-chain PDB without a header by ATOM entries. ... ok
test_atom_with_insertion (test_SeqIO_PdbIO.TestPdbAtom.test_atom_with_insertion)
Read a PDB with residue insertion code. ... ok
test_seqres_missing (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_missing)
Parse a PDB with no SEQRES entries. ... ok
test_seqres_parse (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_parse)
Parse a multi-chain PDB by SEQRES entries. ... ok
test_seqres_read (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_read)
Read a single-chain structure by sequence entries. ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 3.048 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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.test_illumina_to_sanger)
Mapping check for FASTQ Illumina (0 to 62) to Sanger (0 to 62). ... ok
test_phred_quality_from_solexa (test_SeqIO_QualityIO.MappingTests.test_phred_quality_from_solexa)
Mapping check for function phred_quality_from_solexa. ... ok
test_sanger_to_illumina (test_SeqIO_QualityIO.MappingTests.test_sanger_to_illumina)
Mapping check for FASTQ Sanger (0 to 93) to Illumina (0 to 62). ... ok
test_sanger_to_solexa (test_SeqIO_QualityIO.MappingTests.test_sanger_to_solexa)
Mapping check for FASTQ Sanger (0 to 93) to Solexa (-5 to 62). ... ok
test_solexa_quality_from_phred (test_SeqIO_QualityIO.MappingTests.test_solexa_quality_from_phred)
Mapping check for function solexa_quality_from_phred. ... ok
test_solexa_to_sanger (test_SeqIO_QualityIO.MappingTests.test_solexa_to_sanger)
Mapping check for FASTQ Solexa (-5 to 62) to Sanger (0 to 62). ... ok
test_fasta_as_fastq (test_SeqIO_QualityIO.NonFastqTests.test_fasta_as_fastq) ... ok
test_sff_as_fastq (test_SeqIO_QualityIO.NonFastqTests.test_sff_as_fastq) ... ok
test_reject_high_and_low (test_SeqIO_QualityIO.TestFastqErrors.test_reject_high_and_low) ... ok
test_reject_high_but_not_low (test_SeqIO_QualityIO.TestFastqErrors.test_reject_high_but_not_low) ... ok
test_fasta (test_SeqIO_QualityIO.TestQual.test_fasta)
Check FASTQ parsing matches FASTA parsing. ... ok
test_fasta_out (test_SeqIO_QualityIO.TestQual.test_fasta_out)
Check FASTQ to FASTA output. ... ok
test_paired (test_SeqIO_QualityIO.TestQual.test_paired)
Check FASTQ parsing matches FASTA+QUAL parsing. ... ok
test_qual (test_SeqIO_QualityIO.TestQual.test_qual)
Check FASTQ parsing matches QUAL parsing. ... ok
test_qual_negative (test_SeqIO_QualityIO.TestQual.test_qual_negative)
Check QUAL negative scores mapped to PHRED zero. ... ok
test_qual_out (test_SeqIO_QualityIO.TestQual.test_qual_out)
Check FASTQ to QUAL output. ... ok
test_fastq_1000 (test_SeqIO_QualityIO.TestReadWrite.test_fastq_1000)
Read and write back simple example with mixed case 1000bp read. ... ok
test_fastq_2000 (test_SeqIO_QualityIO.TestReadWrite.test_fastq_2000)
Read and write back simple example with upper case 2000bp read. ... ok
test_fastq_dna (test_SeqIO_QualityIO.TestReadWrite.test_fastq_dna)
Read and write back simple example with ambiguous DNA. ... ok
test_fastq_rna (test_SeqIO_QualityIO.TestReadWrite.test_fastq_rna)
Read and write back simple example with ambiguous RNA. ... ok
test_reference_conversion (test_SeqIO_QualityIO.TestReferenceFastqConversions.test_reference_conversion) ... ok
test_alt_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_at_end)
Test converting E3MFGYR02_alt_index_at_end into FASTA+QUAL. ... ok
test_alt_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_at_start)
Test converting E3MFGYR02_alt_index_at_start into FASTA+QUAL. ... ok
test_alt_index_in_middle (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_in_middle)
Test converting E3MFGYR02_alt_index_in_middle into FASTA+QUAL. ... ok
test_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions.test_index_at_end)
Test converting E3MFGYR02_index_in_middle into FASTA+QUAL. ... ok
test_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions.test_index_at_start)
Test converting E3MFGYR02_index_at_start into FASTA+QUAL. ... ok
test_no_manifest (test_SeqIO_QualityIO.TestReferenceSffConversions.test_no_manifest)
Test converting E3MFGYR02_no_manifest.sff into FASTA+QUAL. ... ok
test_original (test_SeqIO_QualityIO.TestReferenceSffConversions.test_original)
Test converting E3MFGYR02_random_10_reads.sff into FASTA+QUAL. ... ok
test_negative_clip (test_SeqIO_QualityIO.TestSFF.test_negative_clip) ... ok
test_overlapping_clip (test_SeqIO_QualityIO.TestSFF.test_overlapping_clip) ... ok
test_E3MFGYR02 (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02)
Write and read back E3MFGYR02_random_10_reads.sff. ... ok
test_E3MFGYR02_alt_index_at_end (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_at_end)
Write and read back E3MFGYR02_alt_index_at_end.sff. ... ok
test_E3MFGYR02_alt_index_at_start (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_at_start)
Write and read back E3MFGYR02_alt_index_at_start.sff. ... ok
test_E3MFGYR02_alt_index_in_middle (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_in_middle)
Write and read back E3MFGYR02_alt_index_in_middle.sff. ... ok
test_E3MFGYR02_index_at_start (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_index_at_start)
Write and read back E3MFGYR02_index_at_start.sff. ... ok
test_E3MFGYR02_index_in_middle (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_index_in_middle)
Write and read back E3MFGYR02_index_in_middle.sff. ... ok
test_E3MFGYR02_no_manifest (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_no_manifest)
Write and read back E3MFGYR02_no_manifest.sff. ... ok
test_E3MFGYR02_trimmed (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_trimmed)
Write and read back E3MFGYR02_random_10_reads.sff (trimmed). ... ok
test_example_fasta (test_SeqIO_QualityIO.TestWriteRead.test_example_fasta)
Write and read back example.fasta. ... ok
test_example_fastq (test_SeqIO_QualityIO.TestWriteRead.test_example_fastq)
Write and read back example.fastq. ... ok
test_example_qual (test_SeqIO_QualityIO.TestWriteRead.test_example_qual)
Write and read back example.qual. ... ok
test_generated (test_SeqIO_QualityIO.TestWriteRead.test_generated)
Write and read back odd SeqRecord objects. ... ok
test_greek_sff (test_SeqIO_QualityIO.TestWriteRead.test_greek_sff)
Write and read back greek.sff. ... ok
test_illumina_faked (test_SeqIO_QualityIO.TestWriteRead.test_illumina_faked)
Write and read back illumina_faked.fastq. ... ok
test_paired_sff (test_SeqIO_QualityIO.TestWriteRead.test_paired_sff)
Write and read back paired.sff. ... ok
test_sanger_93 (test_SeqIO_QualityIO.TestWriteRead.test_sanger_93)
Write and read back sanger_93.fastq. ... ok
test_sanger_faked (test_SeqIO_QualityIO.TestWriteRead.test_sanger_faked)
Write and read back sanger_faked.fastq. ... ok
test_solexa_example (test_SeqIO_QualityIO.TestWriteRead.test_solexa_example)
Write and read back solexa_example.fastq. ... ok
test_solexa_faked (test_SeqIO_QualityIO.TestWriteRead.test_solexa_faked)
Write and read back solexa_faked.fastq. ... ok
test_tricky (test_SeqIO_QualityIO.TestWriteRead.test_tricky)
Write and read back tricky.fastq. ... ok
test_conversion (test_SeqIO_QualityIO.TestsConverter.test_conversion) ... ok
test_failure_detection (test_SeqIO_QualityIO.TestsConverter.test_failure_detection) ... ok
----------------------------------------------------------------------
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
Ran 1 test in 0.539 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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.test_duplicated_dbxref)
Read multiple cross references to a single source. ... ok
test_duplicated_property (test_SeqIO_SeqXML.TestDetailedRead.test_duplicated_property)
Read property with multiple values. ... ok
test_empty_description (test_SeqIO_SeqXML.TestDetailedRead.test_empty_description)
Check empty description. ... ok
test_full_characters_set_read (test_SeqIO_SeqXML.TestDetailedRead.test_full_characters_set_read)
Read full characters set for each type. ... ok
test_global_species (test_SeqIO_SeqXML.TestDetailedRead.test_global_species)
Check global species. ... ok
test_local_source_definition (test_SeqIO_SeqXML.TestDetailedRead.test_local_source_definition)
Check local source. ... ok
test_local_species (test_SeqIO_SeqXML.TestDetailedRead.test_local_species)
Check local species. ... ok
test_read_minimal_required (test_SeqIO_SeqXML.TestDetailedRead.test_read_minimal_required)
Check minimal record. ... ok
test_special_characters_desc (test_SeqIO_SeqXML.TestDetailedRead.test_special_characters_desc)
Read special XML characters in description. ... ok
test_unicode_characters_desc (test_SeqIO_SeqXML.TestDetailedRead.test_unicode_characters_desc)
Test special unicode characters in the description. ... ok
test_read_write_dna (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_dna)
Read and write DNA. ... ok
test_read_write_globalSpecies (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_globalSpecies)
Read and write global species. ... ok
test_read_write_protein (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_protein)
Read and write protein. ... ok
test_read_write_rna (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_rna)
Read and write RNA. ... ok
test_write_species (test_SeqIO_SeqXML.TestReadAndWrite.test_write_species)
Test writing species from annotation tags. ... ok
test_for_errors (test_SeqIO_SeqXML.TestReadCorruptFiles.test_for_errors)
Handling of corrupt files. ... ok
test_check_dna_header (test_SeqIO_SeqXML.TestReadHeader.test_check_dna_header)
Check if the header information is parsed. ... ok
test_check_global_species_example_header (test_SeqIO_SeqXML.TestReadHeader.test_check_global_species_example_header)
Check if the header information is parsed. ... ok
test_check_protein_header (test_SeqIO_SeqXML.TestReadHeader.test_check_protein_header)
Check if the header information is parsed. ... ok
test_check_rna_header (test_SeqIO_SeqXML.TestReadHeader.test_check_rna_header)
Check if the header information is parsed. ... ok
test_check_SeqIO (test_SeqIO_SeqXML.TestSimpleRead.test_check_SeqIO)
Files readable using parser via SeqIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.106 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_SnapGene.py
test_SeqIO_SnapGene ... ok
test_extra_dna (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_extra_dna)
Read a file with supernumerary DNA packet. ... ok
test_invalid_cookie (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_invalid_cookie)
Read a file with missing or invalid cookie packet. ... ok
test_missing_dna (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_missing_dna)
Read a file without a DNA packet. ... ok
test_truncated_packet (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_truncated_packet)
Read a file with incomplete packet. ... ok
test_read (test_SeqIO_SnapGene.TestSnapGene.test_read)
Read sample files. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.093 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_TwoBitIO.py
test_SeqIO_TwoBitIO ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_bigendian (test_SeqIO_TwoBitIO.Parsing.test_bigendian) ... ok
test_littleendian (test_SeqIO_TwoBitIO.Parsing.test_littleendian) ... ok
test_sequence_long (test_SeqIO_TwoBitIO.Parsing.test_sequence_long) ... ok
test_add (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_add) ... ok
test_bytes (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_bytes) ... ok
test_contains (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_contains) ... ok
test_count (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_count) ... ok
test_defined (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_defined) ... ok
test_endswith (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_endswith) ... ok
test_find (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_find) ... ok
test_getitem (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_getitem) ... ok
test_hash (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_hash) ... ok
test_index (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_index) ... ok
test_islower (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_islower) ... ok
test_isupper (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_isupper) ... ok
test_lower (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_lower) ... ok
test_lstrip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_lstrip) ... ok
test_mul (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_mul) ... ok
test_radd (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_radd) ... ok
test_replace (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_replace) ... ok
test_repr (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_repr) ... ok
test_rfind (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rfind) ... ok
test_rindex (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rindex) ... ok
test_rsplit (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rsplit) ... ok
test_rstrip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rstrip) ... ok
test_split (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_split) ... ok
test_startswith (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_startswith) ... ok
test_str (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_str) ... ok
test_strip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_strip) ... ok
test_translate (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_translate) ... ok
test_upper (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_upper) ... ok
test_eq (test_SeqIO_TwoBitIO.TestComparisons.test_eq) ... ok
test_ge (test_SeqIO_TwoBitIO.TestComparisons.test_ge) ... ok
test_gt (test_SeqIO_TwoBitIO.TestComparisons.test_gt) ... ok
test_le (test_SeqIO_TwoBitIO.TestComparisons.test_le) ... ok
test_lt (test_SeqIO_TwoBitIO.TestComparisons.test_lt) ... ok
test_ne (test_SeqIO_TwoBitIO.TestComparisons.test_ne) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.600 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Xdna.py
test_SeqIO_Xdna ... ok
test_corrupted_length (test_SeqIO_Xdna.TestInvalidXdna.test_corrupted_length)
Read a file with incorrect length. ... ok
test_invalid_sequence_type (test_SeqIO_Xdna.TestInvalidXdna.test_invalid_sequence_type)
Read a file with an unknown sequence type. ... ok
test_missing_features (test_SeqIO_Xdna.TestInvalidXdna.test_missing_features)
Read a file with an incorrect number of features. ... ok
test_unsupported_version (test_SeqIO_Xdna.TestInvalidXdna.test_unsupported_version)
Read a file with unexpected version number. ... ok
test_read (test_SeqIO_Xdna.TestXdna.test_read)
Read sample files. ... ok
test_warnings_on_data_loss (test_SeqIO_Xdna.TestXdnaWriter.test_warnings_on_data_loss)
Emit warnings when dropping data on write. ... ok
test_write_sequence_type (test_SeqIO_Xdna.TestXdnaWriter.test_write_sequence_type)
Write correct sequence type. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.091 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_features.py
test_SeqIO_features ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: unassigned DNA
warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA
warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: mRNA
warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:550: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line
warnings.warn(
ok
test_after (test_SeqIO_features.FeatureWriting.test_after)
Features: write/read simple after locations. ... ok
test_before (test_SeqIO_features.FeatureWriting.test_before)
Features: write/read simple before locations. ... ok
test_between (test_SeqIO_features.FeatureWriting.test_between)
GenBank/EMBL write/read simple between locations. ... ok
test_exact (test_SeqIO_features.FeatureWriting.test_exact)
GenBank/EMBL write/read simple exact locations. ... ok
test_fuzzy_join (test_SeqIO_features.FeatureWriting.test_fuzzy_join)
Features: write/read fuzzy join locations. ... ok
test_join (test_SeqIO_features.FeatureWriting.test_join)
GenBank/EMBL write/read simple join locations. ... ok
test_oneof (test_SeqIO_features.FeatureWriting.test_oneof)
Features: write/read simple one-of locations. ... ok
test_unknown (test_SeqIO_features.FeatureWriting.test_unknown)
GenBank/EMBL write/read with unknown end points. ... ok
test_within (test_SeqIO_features.FeatureWriting.test_within)
Features: write/read simple within locations. ... ok
test_mixed_strand (test_SeqIO_features.GenBankLocations.test_mixed_strand) ... ok
test_rev_comp_styles (test_SeqIO_features.GenBankLocations.test_rev_comp_styles) ... ok
test_CDS (test_SeqIO_features.NC_000932.test_CDS)
Checking GenBank CDS translations vs FASTA faa file. ... ok
test_CDS (test_SeqIO_features.NC_005816.test_CDS)
Checking GenBank CDS translations vs FASTA faa file. ... ok
test_Features (test_SeqIO_features.NC_005816.test_Features)
Checking GenBank features sequences vs FASTA ffn file. ... ok
test_GenBank_vs_EMBL (test_SeqIO_features.NC_005816.test_GenBank_vs_EMBL) ... ok
test_Genome (test_SeqIO_features.NC_005816.test_Genome)
Checking GenBank sequence vs FASTA fna file. ... ok
test_Translations (test_SeqIO_features.NC_005816.test_Translations)
Checking translation of FASTA features (faa vs ffn). ... ok
test_qualifiers (test_SeqIO_features.SeqFeatureCreation.test_qualifiers)
Pass in qualifiers to SeqFeatures. ... ok
test_mixed_strand_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_mixed_strand_dna_join)
Feature on DNA (join, mixed strand). ... ok
test_mixed_strand_dna_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_mixed_strand_dna_multi_join)
Feature on DNA (multi-join, mixed strand). ... ok
test_protein_between (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_between)
Feature on protein (between location, zero length). ... ok
test_protein_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_join)
Feature on protein (join). ... ok
test_protein_join_fuzzy (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_join_fuzzy)
Feature on protein (fuzzy join). ... ok
test_protein_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_multi_join)
Feature on protein (multi-join). ... ok
test_protein_oneof (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_oneof)
Feature on protein (one-of positions). ... ok
test_protein_simple (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_simple)
Feature on protein (simple). ... ok
test_simple_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna)
Feature on DNA (simple, default strand). ... ok
test_simple_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join)
Feature on DNA (join, strand +1). ... ok
test_simple_dna_join_after (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_after)
Feature on DNA (join, strand -1, after position). ... ok
test_simple_dna_join_before (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_before)
Feature on DNA (join, strand -1, before position). ... ok
test_simple_dna_join_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_strand_minus)
Feature on DNA (join, strand -1). ... ok
test_simple_dna_strand0 (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand0)
Feature on DNA (simple, strand 0). ... ok
test_simple_dna_strand1 (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand1)
Feature on DNA (simple, strand +1). ... ok
test_simple_dna_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand_minus)
Feature on DNA (simple, strand -1). ... ok
test_simple_dna_strand_none (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand_none)
Feature on DNA (simple, strand None). ... ok
test_simple_rna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_rna)
Feature on RNA (simple, default strand). ... ok
test_single_letter_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_single_letter_dna)
Feature on DNA (single letter, default strand). ... ok
test_zero_len_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_zero_len_dna)
Feature on DNA (between location, zero length, default strand). ... ok
test_zero_len_dna_end (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_zero_len_dna_end)
Feature on DNA (between location at end, zero length, default strand). ... ok
test_AAA03323 (test_SeqIO_features.TestWriteRead.test_AAA03323)
Write and read back AAA03323.embl. ... ok
test_AE017046 (test_SeqIO_features.TestWriteRead.test_AE017046)
Write and read back AE017046.embl. ... ok
test_DD231055_edited (test_SeqIO_features.TestWriteRead.test_DD231055_edited)
Write and read back DD231055_edited.embl. ... ok
test_Human_contigs (test_SeqIO_features.TestWriteRead.test_Human_contigs)
Write and read back Human_contigs.embl. ... ok
test_NC_000932 (test_SeqIO_features.TestWriteRead.test_NC_000932)
Write and read back NC_000932.gb. ... ok
test_NC_005816 (test_SeqIO_features.TestWriteRead.test_NC_005816)
Write and read back NC_005816.gb. ... ok
test_NT_019265 (test_SeqIO_features.TestWriteRead.test_NT_019265)
Write and read back NT_019265.gb. ... ok
test_SC10H5 (test_SeqIO_features.TestWriteRead.test_SC10H5)
Write and read back SC10H5.embl. ... ok
test_TRBG361 (test_SeqIO_features.TestWriteRead.test_TRBG361)
Write and read back TRBG361.embl. ... ok
test_U87107 (test_SeqIO_features.TestWriteRead.test_U87107)
Write and read back U87107.embl. ... ok
test_arab1 (test_SeqIO_features.TestWriteRead.test_arab1)
Write and read back arab1.gb. ... ok
test_blank_seq (test_SeqIO_features.TestWriteRead.test_blank_seq)
Write and read back blank_seq.gb. ... ok
test_cor6 (test_SeqIO_features.TestWriteRead.test_cor6)
Write and read back cor6_6.gb. ... ok
test_dbsource_wrap (test_SeqIO_features.TestWriteRead.test_dbsource_wrap)
Write and read back dbsource_wrap.gb. ... ok
test_extra_keywords (test_SeqIO_features.TestWriteRead.test_extra_keywords)
Write and read back extra_keywords.gb. ... ok
test_gbvrl1_start (test_SeqIO_features.TestWriteRead.test_gbvrl1_start)
Write and read back gbvrl1_start.seq. ... ok
test_noref (test_SeqIO_features.TestWriteRead.test_noref)
Write and read back noref.gb. ... ok
test_one_of (test_SeqIO_features.TestWriteRead.test_one_of)
Write and read back of_one.gb. ... ok
test_origin_line (test_SeqIO_features.TestWriteRead.test_origin_line)
Write and read back origin_line.gb. ... ok
test_pri1 (test_SeqIO_features.TestWriteRead.test_pri1)
Write and read back pri1.gb. ... ok
test_protein_refseq (test_SeqIO_features.TestWriteRead.test_protein_refseq)
Write and read back protein_refseq.gb. ... ok
test_protein_refseq2 (test_SeqIO_features.TestWriteRead.test_protein_refseq2)
Write and read back protein_refseq2.gb. ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.683 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_index.py
test_SeqIO_index ... ok
test_alpha_fails (test_SeqIO_index.IndexDictTests.test_alpha_fails)
Reject alphabet argument in Bio.SeqIO.index(). ... ok
test_alpha_fails_db (test_SeqIO_index.IndexDictTests.test_alpha_fails_db)
Reject alphabet argument in Bio.SeqIO.index_db(). ... ok
test_duplicates_index (test_SeqIO_index.IndexDictTests.test_duplicates_index)
Index file with duplicate identifiers with Bio.SeqIO.index(). ... ok
test_duplicates_index_db (test_SeqIO_index.IndexDictTests.test_duplicates_index_db)
Index file with duplicate identifiers with Bio.SeqIO.index_db(). ... ok
test_duplicates_to_dict (test_SeqIO_index.IndexDictTests.test_duplicates_to_dict)
Index file with duplicate identifiers with Bio.SeqIO.to_dict(). ... ok
test_key_checks (test_SeqIO_index.IndexDictTests.test_key_checks) ... ok
test_raw_checks (test_SeqIO_index.IndexDictTests.test_raw_checks) ... ok
test_simple_checks (test_SeqIO_index.IndexDictTests.test_simple_checks) ... ok
test_order_index_db (test_SeqIO_index.IndexOrderingManyFiles.test_order_index_db)
Check index_db preserves order in multiple indexed files. ... ok
test_order_index (test_SeqIO_index.IndexOrderingSingleFile.test_order_index)
Check index preserves order in indexed file. ... ok
test_order_index_db (test_SeqIO_index.IndexOrderingSingleFile.test_order_index_db)
Check index_db preserves ordering indexed file. ... ok
test_order_to_dict (test_SeqIO_index.IndexOrderingSingleFile.test_order_to_dict)
Check to_dict preserves order in indexed file. ... ok
test_child_folder_rel (test_SeqIO_index.NewIndexTest.test_child_folder_rel)
Check relative links to child folder. ... ok
test_same_folder (test_SeqIO_index.NewIndexTest.test_same_folder)
Check relative links in same folder. ... ok
test_some_abs (test_SeqIO_index.NewIndexTest.test_some_abs)
Check absolute filenames in index. ... ok
test_old (test_SeqIO_index.OldIndexTest.test_old)
Load existing index with no options (from parent directory). ... ok
test_old_check_same_thread (test_SeqIO_index.OldIndexTest.test_old_check_same_thread)
Setting check_same_thread to False doesn't raise an exception. ... ok
test_old_contents (test_SeqIO_index.OldIndexTest.test_old_contents)
Check actual filenames in existing indexes. ... ok
test_old_files (test_SeqIO_index.OldIndexTest.test_old_files)
Load existing index with correct files (from parent directory). ... ok
test_old_files_same_dir (test_SeqIO_index.OldIndexTest.test_old_files_same_dir)
Load existing index with correct files (from same directory). ... ok
test_old_files_wrong (test_SeqIO_index.OldIndexTest.test_old_files_wrong)
Load existing index with wrong files. ... ok
test_old_files_wrong2 (test_SeqIO_index.OldIndexTest.test_old_files_wrong2)
Load existing index with wrong number of files. ... ok
test_old_format (test_SeqIO_index.OldIndexTest.test_old_format)
Load existing index with correct format. ... ok
test_old_format_wrong (test_SeqIO_index.OldIndexTest.test_old_format_wrong)
Load existing index with wrong format. ... ok
test_old_rel (test_SeqIO_index.OldIndexTest.test_old_rel)
Load existing index (with relative paths) with no options (from parent directory). ... ok
test_old_same_dir (test_SeqIO_index.OldIndexTest.test_old_same_dir)
Load existing index with no options (from same directory). ... ok
test_old_same_dir_rel (test_SeqIO_index.OldIndexTest.test_old_same_dir_rel)
Load existing index (with relative paths) with no options (from same directory). ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 11.519 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_online.py
test_SeqIO_online ... skipping. internet not available
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.081 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_write.py
test_SeqIO_write ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_alignment_formats (test_SeqIO_write.WriterTests.test_alignment_formats) ... ok
test_bad_handle (test_SeqIO_write.WriterTests.test_bad_handle) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.124 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqRecord.py
test_SeqRecord ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_annotations (test_SeqRecord.SeqRecordCreation.test_annotations)
Pass in annotations to SeqRecords. ... ok
test_letter_annotations (test_SeqRecord.SeqRecordCreation.test_letter_annotations)
Pass in letter annotations to SeqRecords. ... ok
test_replacing_seq (test_SeqRecord.SeqRecordCreation.test_replacing_seq)
Replacing .seq if .letter_annotation present. ... ok
test_valid_annotations (test_SeqRecord.SeqRecordCreation.test_valid_annotations) ... ok
test_valid_dbxrefs (test_SeqRecord.SeqRecordCreation.test_valid_dbxrefs) ... ok
test_valid_description (test_SeqRecord.SeqRecordCreation.test_valid_description) ... ok
test_valid_features (test_SeqRecord.SeqRecordCreation.test_valid_features) ... ok
test_valid_id (test_SeqRecord.SeqRecordCreation.test_valid_id) ... ok
test_valid_name (test_SeqRecord.SeqRecordCreation.test_valid_name) ... ok
test_add_seq (test_SeqRecord.SeqRecordMethods.test_add_seq)
Simple addition of Seq or string. ... ok
test_add_seq_left (test_SeqRecord.SeqRecordMethods.test_add_seq_left)
Simple left addition of Seq or string. ... ok
test_add_seqrecord (test_SeqRecord.SeqRecordMethods.test_add_seqrecord)
Simple left addition of SeqRecord from genbank file. ... ok
test_add_simple (test_SeqRecord.SeqRecordMethods.test_add_simple)
Simple addition. ... ok
test_contains (test_SeqRecord.SeqRecordMethods.test_contains) ... ok
test_count (test_SeqRecord.SeqRecordMethods.test_count) ... ok
test_format (test_SeqRecord.SeqRecordMethods.test_format) ... ok
test_format_spaces (test_SeqRecord.SeqRecordMethods.test_format_spaces) ... ok
test_format_str (test_SeqRecord.SeqRecordMethods.test_format_str) ... ok
test_format_str_binary (test_SeqRecord.SeqRecordMethods.test_format_str_binary) ... ok
test_islower (test_SeqRecord.SeqRecordMethods.test_islower) ... ok
test_isupper (test_SeqRecord.SeqRecordMethods.test_isupper) ... ok
test_iter (test_SeqRecord.SeqRecordMethods.test_iter) ... ok
test_lower (test_SeqRecord.SeqRecordMethods.test_lower) ... ok
test_repr (test_SeqRecord.SeqRecordMethods.test_repr) ... ok
test_slice_add_shift (test_SeqRecord.SeqRecordMethods.test_slice_add_shift)
Simple slice and add to shift. ... ok
test_slice_add_simple (test_SeqRecord.SeqRecordMethods.test_slice_add_simple)
Simple slice and add. ... ok
test_slice_simple (test_SeqRecord.SeqRecordMethods.test_slice_simple)
Simple slice. ... ok
test_slice_variants (test_SeqRecord.SeqRecordMethods.test_slice_variants)
Simple slices using different start/end values. ... ok
test_slice_zero (test_SeqRecord.SeqRecordMethods.test_slice_zero)
Zero slice. ... ok
test_slicing (test_SeqRecord.SeqRecordMethods.test_slicing) ... ok
test_str (test_SeqRecord.SeqRecordMethods.test_str) ... ok
test_upper (test_SeqRecord.SeqRecordMethods.test_upper) ... ok
test_eq_exception (test_SeqRecord.SeqRecordMethodsMore.test_eq_exception) ... ok
test_ge_exception (test_SeqRecord.SeqRecordMethodsMore.test_ge_exception) ... ok
test_gt_exception (test_SeqRecord.SeqRecordMethodsMore.test_gt_exception) ... ok
test_hash_exception (test_SeqRecord.SeqRecordMethodsMore.test_hash_exception) ... ok
test_le_exception (test_SeqRecord.SeqRecordMethodsMore.test_le_exception) ... ok
test_lt_exception (test_SeqRecord.SeqRecordMethodsMore.test_lt_exception) ... ok
test_ne_exception (test_SeqRecord.SeqRecordMethodsMore.test_ne_exception) ... ok
test_reverse_complement_mutable_seq (test_SeqRecord.SeqRecordMethodsMore.test_reverse_complement_mutable_seq) ... ok
test_reverse_complement_seq (test_SeqRecord.SeqRecordMethodsMore.test_reverse_complement_seq) ... ok
test_translate (test_SeqRecord.SeqRecordMethodsMore.test_translate) ... ok
test_defaults (test_SeqRecord.TestTranslation.test_defaults) ... ok
test_new_annot (test_SeqRecord.TestTranslation.test_new_annot) ... ok
test_preserve (test_SeqRecord.TestTranslation.test_preserve) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.177 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqUtils.py
test_SeqUtils ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_GC_skew (test_SeqUtils.SeqUtilsTests.test_GC_skew) ... ok
test_checksum1 (test_SeqUtils.SeqUtilsTests.test_checksum1) ... ok
test_checksum2 (test_SeqUtils.SeqUtilsTests.test_checksum2) ... ok
test_checksum3 (test_SeqUtils.SeqUtilsTests.test_checksum3) ... ok
test_codon_adaptation_index (test_SeqUtils.SeqUtilsTests.test_codon_adaptation_index) ... ok
test_codon_adaptation_index_calculation (test_SeqUtils.SeqUtilsTests.test_codon_adaptation_index_calculation)
Test Codon Adaptation Index (CAI) calculation for an mRNA. ... ok
test_codon_adaptation_index_initialization (test_SeqUtils.SeqUtilsTests.test_codon_adaptation_index_initialization)
Test Codon Adaptation Index (CAI) initialization from sequences. ... ok
test_codon_usage_custom_old (test_SeqUtils.SeqUtilsTests.test_codon_usage_custom_old)
Test Codon Adaptation Index (CAI) using FASTA file for background. ... ok
test_codon_usage_ecoli (test_SeqUtils.SeqUtilsTests.test_codon_usage_ecoli)
Test Codon Adaptation Index (CAI) using default E. coli data. ... ok
test_crc_checksum_collision (test_SeqUtils.SeqUtilsTests.test_crc_checksum_collision) ... ok
test_gc_fraction (test_SeqUtils.SeqUtilsTests.test_gc_fraction)
Tests gc_fraction function. ... ok
test_lcc_mult (test_SeqUtils.SeqUtilsTests.test_lcc_mult) ... ok
test_lcc_simp (test_SeqUtils.SeqUtilsTests.test_lcc_simp) ... ok
test_seq1_seq3 (test_SeqUtils.SeqUtilsTests.test_seq1_seq3) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.245 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Seq_objs.py
test_Seq_objs ... ok
test_eq (test_Seq_objs.ComparisonTests.test_eq) ... ok
test_ge (test_Seq_objs.ComparisonTests.test_ge) ... ok
test_gt (test_Seq_objs.ComparisonTests.test_gt) ... ok
test_le (test_Seq_objs.ComparisonTests.test_le) ... ok
test_lt (test_Seq_objs.ComparisonTests.test_lt) ... ok
test_ne (test_Seq_objs.ComparisonTests.test_ne) ... ok
test_unknown_seq (test_Seq_objs.FileBasedTests.test_unknown_seq)
Test if feature extraction works properly for unknown sequences. ... ok
test_addition (test_Seq_objs.PartialSequenceTests.test_addition) ... ok
test_complement (test_Seq_objs.PartialSequenceTests.test_complement) ... ok
test_getitem (test_Seq_objs.PartialSequenceTests.test_getitem) ... ok
test_init (test_Seq_objs.PartialSequenceTests.test_init) ... ok
test_lower_upper (test_Seq_objs.PartialSequenceTests.test_lower_upper) ... ok
test_multiplication (test_Seq_objs.PartialSequenceTests.test_multiplication) ... ok
test_replace (test_Seq_objs.PartialSequenceTests.test_replace) ... ok
test_repr (test_Seq_objs.PartialSequenceTests.test_repr) ... ok
test_transcribe (test_Seq_objs.PartialSequenceTests.test_transcribe) ... ok
test_MutableSeq_extend (test_Seq_objs.StringMethodTests.test_MutableSeq_extend)
Check extending a MutableSeq object. ... ok
test_MutableSeq_init_error (test_Seq_objs.StringMethodTests.test_MutableSeq_init_error)
Check MutableSeq __init__ raises the appropriate exceptions. ... ok
test_MutableSeq_setitem (test_Seq_objs.StringMethodTests.test_MutableSeq_setitem)
Check setting sequence contents of a MutableSeq object. ... ok
test_Seq_init_error (test_Seq_objs.StringMethodTests.test_Seq_init_error)
Check Seq __init__ raises the appropriate exceptions. ... ok
test_count_overlap (test_Seq_objs.StringMethodTests.test_count_overlap)
Check count_overlap exception matches python string count method. ... ok
test_count_overlap_start_end_GG (test_Seq_objs.StringMethodTests.test_count_overlap_start_end_GG)
Check our count_overlap method using GG with variable ends and starts. ... ok
test_count_overlap_start_end_NN (test_Seq_objs.StringMethodTests.test_count_overlap_start_end_NN)
Check our count_overlap method using NN with variable ends and starts. ... ok
test_equality (test_Seq_objs.StringMethodTests.test_equality)
Test equality when mixing types. ... ok
test_join_MutableSeq (test_Seq_objs.StringMethodTests.test_join_MutableSeq)
Checks if MutableSeq join correctly concatenates sequence with the spacer. ... ok
test_join_MutableSeq_TypeError_iter (test_Seq_objs.StringMethodTests.test_join_MutableSeq_TypeError_iter)
Checks that a TypeError is thrown for all non-iterable types. ... ok
test_join_MutableSeq_mixed (test_Seq_objs.StringMethodTests.test_join_MutableSeq_mixed)
Check MutableSeq objects can be joined. ... ok
test_join_MutableSeq_with_file (test_Seq_objs.StringMethodTests.test_join_MutableSeq_with_file)
Checks if MutableSeq join correctly concatenates sequence from a file with the spacer. ... ok
test_join_Seq (test_Seq_objs.StringMethodTests.test_join_Seq)
Checks if Seq join correctly concatenates sequence with the spacer. ... ok
test_join_Seq_TypeError (test_Seq_objs.StringMethodTests.test_join_Seq_TypeError)
Checks that a TypeError is thrown for all non-iterable types. ... ok
test_join_Seq_with_file (test_Seq_objs.StringMethodTests.test_join_Seq_with_file)
Checks if Seq join correctly concatenates sequence from a file with the spacer. ... ok
test_join_UnknownSeq (test_Seq_objs.StringMethodTests.test_join_UnknownSeq)
Checks if UnknownSeq join correctly concatenates sequence with the spacer. ... ok
test_join_UnknownSeq_TypeError_iter (test_Seq_objs.StringMethodTests.test_join_UnknownSeq_TypeError_iter)
Checks that a TypeError is thrown for all non-iterable types. ... ok
test_join_UnknownSeq_with_file (test_Seq_objs.StringMethodTests.test_join_UnknownSeq_with_file)
Checks if UnknownSeq join correctly concatenates sequence from a file with the spacer. ... ok
test_str_comparison (test_Seq_objs.StringMethodTests.test_str_comparison) ... ok
test_str_count (test_Seq_objs.StringMethodTests.test_str_count)
Check matches the python string count method. ... ok
test_str_count_overlap_GG (test_Seq_objs.StringMethodTests.test_str_count_overlap_GG)
Check our count_overlap method using GG. ... ok
test_str_count_overlap_NN (test_Seq_objs.StringMethodTests.test_str_count_overlap_NN)
Check our count_overlap method using NN. ... ok
test_str_encode (test_Seq_objs.StringMethodTests.test_str_encode)
Check matches the python string encode method. ... ok
test_str_endswith (test_Seq_objs.StringMethodTests.test_str_endswith)
Check matches the python string endswith method. ... ok
test_str_find (test_Seq_objs.StringMethodTests.test_str_find)
Check matches the python string find method. ... ok
test_str_getitem (test_Seq_objs.StringMethodTests.test_str_getitem)
Check slicing and indexing works like a string. ... ok
test_str_hash (test_Seq_objs.StringMethodTests.test_str_hash) ... ok
test_str_index (test_Seq_objs.StringMethodTests.test_str_index)
Check matches the python string index method. ... ok
test_str_islower (test_Seq_objs.StringMethodTests.test_str_islower)
Check matches the python string islower method. ... ok
test_str_isupper (test_Seq_objs.StringMethodTests.test_str_isupper)
Check matches the python string isupper method. ... ok
test_str_length (test_Seq_objs.StringMethodTests.test_str_length)
Check matches the python string __len__ method. ... ok
test_str_lower (test_Seq_objs.StringMethodTests.test_str_lower)
Check matches the python string lower method. ... ok
test_str_lstrip (test_Seq_objs.StringMethodTests.test_str_lstrip)
Check matches the python string lstrip method. ... ok
test_str_replace (test_Seq_objs.StringMethodTests.test_str_replace)
Check matches the python string replace method. ... ok
test_str_rfind (test_Seq_objs.StringMethodTests.test_str_rfind)
Check matches the python string rfind method. ... ok
test_str_rindex (test_Seq_objs.StringMethodTests.test_str_rindex)
Check matches the python string rindex method. ... ok
test_str_rsplit (test_Seq_objs.StringMethodTests.test_str_rsplit)
Check matches the python string rsplit method. ... ok
test_str_rstrip (test_Seq_objs.StringMethodTests.test_str_rstrip)
Check matches the python string rstrip method. ... ok
test_str_split (test_Seq_objs.StringMethodTests.test_str_split)
Check matches the python string split method. ... ok
test_str_startswith (test_Seq_objs.StringMethodTests.test_str_startswith)
Check matches the python string startswith method. ... ok
test_str_strip (test_Seq_objs.StringMethodTests.test_str_strip)
Check matches the python string strip method. ... ok
test_str_upper (test_Seq_objs.StringMethodTests.test_str_upper)
Check matches the python string upper method. ... ok
test_the_back_transcription (test_Seq_objs.StringMethodTests.test_the_back_transcription)
Check obj.back_transcribe() method. ... ok
test_the_complement (test_Seq_objs.StringMethodTests.test_the_complement)
Check obj.complement() method. ... ok
test_the_reverse_complement (test_Seq_objs.StringMethodTests.test_the_reverse_complement)
Check obj.reverse_complement() method. ... ok
test_the_transcription (test_Seq_objs.StringMethodTests.test_the_transcription)
Check obj.transcribe() method. ... ok
test_the_translate (test_Seq_objs.StringMethodTests.test_the_translate)
Check obj.translate() method. ... ok
test_the_translation_of_ambig_codons (test_Seq_objs.StringMethodTests.test_the_translation_of_ambig_codons)
Check obj.translate() method with ambiguous codons. ... ok
test_the_translation_of_invalid_codons (test_Seq_objs.StringMethodTests.test_the_translation_of_invalid_codons)
Check obj.translate() method with invalid codons. ... ok
test_the_translation_of_stops (test_Seq_objs.StringMethodTests.test_the_translation_of_stops)
Check obj.translate() method with stop codons. ... ok
test_tomutable (test_Seq_objs.StringMethodTests.test_tomutable)
Check creating a MutableSeq object. ... ok
test_toseq (test_Seq_objs.StringMethodTests.test_toseq)
Check creating a Seq object. ... ok
----------------------------------------------------------------------
Ran 1 test in 3.121 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SffIO.py
test_SffIO ... ok
test_alt_index_at_end (test_SffIO.TestAlternativeIndexes.test_alt_index_at_end) ... ok
test_alt_index_at_start (test_SffIO.TestAlternativeIndexes.test_alt_index_at_start) ... ok
test_alt_index_in_middle (test_SffIO.TestAlternativeIndexes.test_alt_index_in_middle) ... ok
test_index_at_start (test_SffIO.TestAlternativeIndexes.test_index_at_start) ... ok
test_index_in_middle (test_SffIO.TestAlternativeIndexes.test_index_in_middle) ... ok
test_trim (test_SffIO.TestAlternativeIndexes.test_trim) ... ok
test_index1 (test_SffIO.TestConcatenated.test_index1) ... ok
test_index2 (test_SffIO.TestConcatenated.test_index2) ... ok
test_parse1 (test_SffIO.TestConcatenated.test_parse1) ... ok
test_parse2 (test_SffIO.TestConcatenated.test_parse2) ... ok
test_parses_gzipped_stream (test_SffIO.TestConcatenated.test_parses_gzipped_stream) ... ok
test_30bytes (test_SffIO.TestErrors.test_30bytes) ... ok
test_31bytes (test_SffIO.TestErrors.test_31bytes) ... ok
test_31bytes_bad_flowgram (test_SffIO.TestErrors.test_31bytes_bad_flowgram) ... ok
test_31bytes_bad_ver (test_SffIO.TestErrors.test_31bytes_bad_ver) ... ok
test_31bytes_index_header (test_SffIO.TestErrors.test_31bytes_index_header) ... ok
test_bad_index_eof (test_SffIO.TestErrors.test_bad_index_eof) ... ok
test_bad_index_length (test_SffIO.TestErrors.test_bad_index_length) ... ok
test_bad_index_offset (test_SffIO.TestErrors.test_bad_index_offset) ... ok
test_empty (test_SffIO.TestErrors.test_empty) ... ok
test_index_lengths (test_SffIO.TestErrors.test_index_lengths) ... ok
test_index_mft_data_size (test_SffIO.TestErrors.test_index_mft_data_size) ... ok
test_index_mft_version (test_SffIO.TestErrors.test_index_mft_version) ... ok
test_index_name_no_null (test_SffIO.TestErrors.test_index_name_no_null) ... ok
test_no_index (test_SffIO.TestErrors.test_no_index) ... ok
test_no_manifest_xml (test_SffIO.TestErrors.test_no_manifest_xml) ... ok
test_premature_end_of_index (test_SffIO.TestErrors.test_premature_end_of_index) ... ok
test_unknown_index (test_SffIO.TestErrors.test_unknown_index) ... ok
test_both_ways (test_SffIO.TestIndex.test_both_ways) ... ok
test_manifest (test_SffIO.TestIndex.test_manifest) ... ok
test_index (test_SffIO.TestSelf.test_index) ... ok
test_read (test_SffIO.TestSelf.test_read) ... ok
test_read_wrong (test_SffIO.TestSelf.test_read_wrong) ... ok
test_write (test_SffIO.TestSelf.test_write) ... ok
test_coords (test_SffIO.TestUAN.test_coords) ... ok
test_region (test_SffIO.TestUAN.test_region) ... ok
test_time (test_SffIO.TestUAN.test_time) ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.113 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SwissProt.py
test_SwissProt ... ok
test_O23729 (test_SwissProt.TestSwissProt.test_O23729)
Parsing SwissProt file O23729.txt. ... ok
test_O95832 (test_SwissProt.TestSwissProt.test_O95832)
Parsing SwissProt file O95832.txt. ... ok
test_P04439 (test_SwissProt.TestSwissProt.test_P04439)
Parsing SwissProt file P04439.txt. ... ok
test_P0A186 (test_SwissProt.TestSwissProt.test_P0A186)
Parsing SwissProt file P0A186.txt. ... ok
test_P0CK95 (test_SwissProt.TestSwissProt.test_P0CK95)
Parsing SwissProt file P0CK95.txt. ... ok
test_P16235 (test_SwissProt.TestSwissProt.test_P16235)
Parsing SwissProt file P16235.txt. ... ok
test_P39896 (test_SwissProt.TestSwissProt.test_P39896)
Parsing SwissProt file P39896.txt. ... ok
test_P60137 (test_SwissProt.TestSwissProt.test_P60137)
Parsing SwissProt file P60137.txt. ... ok
test_P60904 (test_SwissProt.TestSwissProt.test_P60904)
Parsing SwissProt file P60904.txt. ... ok
test_P62258 (test_SwissProt.TestSwissProt.test_P62258)
Parsing SwissProt file P62258. ... ok
test_P68308 (test_SwissProt.TestSwissProt.test_P68308)
Parsing SwissProt file P68308.txt. ... ok
test_Q13454 (test_SwissProt.TestSwissProt.test_Q13454)
Parsing SwissProt file Q13454.txt. ... ok
test_Q13639 (test_SwissProt.TestSwissProt.test_Q13639)
Parsing SwissProt file Q13639. ... ok
test_Q7Z739 (test_SwissProt.TestSwissProt.test_Q7Z739)
Parsing SwissProt file Q7Z739.txt, which has new qualifiers for ligands from Uniprot version 2022_03. ... ok
test_ft_line (test_SwissProt.TestSwissProt.test_ft_line)
Parsing SwissProt file O23729, which has a new-style FT line. ... ok
test_sp012 (test_SwissProt.TestSwissProt.test_sp012)
Parsing SwissProt file sp012. ... ok
test_sp013 (test_SwissProt.TestSwissProt.test_sp013)
Parsing SwissProt file sp013. ... ok
test_sp015 (test_SwissProt.TestSwissProt.test_sp015)
Parsing SwissProt file sp015. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.236 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.091 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_TogoWS.py
test_TogoWS ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.085 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_TreeConstruction.py
test_TreeConstruction ... ok
test_known_matrices (test_TreeConstruction.DistanceCalculatorTest.test_known_matrices) ... ok
test_nonmatching_seqs (test_TreeConstruction.DistanceCalculatorTest.test_nonmatching_seqs) ... ok
test_bad_construction (test_TreeConstruction.DistanceMatrixTest.test_bad_construction) ... ok
test_bad_manipulation (test_TreeConstruction.DistanceMatrixTest.test_bad_manipulation) ... ok
test_format_phylip (test_TreeConstruction.DistanceMatrixTest.test_format_phylip) ... ok
test_good_construction (test_TreeConstruction.DistanceMatrixTest.test_good_construction) ... ok
test_good_manipulation (test_TreeConstruction.DistanceMatrixTest.test_good_manipulation) ... ok
test_built_tree (test_TreeConstruction.DistanceTreeConstructorTest.test_built_tree) ... ok
test_nj (test_TreeConstruction.DistanceTreeConstructorTest.test_nj) ... ok
test_upgma (test_TreeConstruction.DistanceTreeConstructorTest.test_upgma) ... ok
test_get_neighbors (test_TreeConstruction.NNITreeSearcherTest.test_get_neighbors) ... ok
test_get_score (test_TreeConstruction.ParsimonyScorerTest.test_get_score) ... ok
test_build_tree (test_TreeConstruction.ParsimonyTreeConstructorTest.test_build_tree) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.443 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_UniGene.py
test_UniGene ... ok
test_parse (test_UniGene.TestUniGene.test_parse) ... ok
test_read (test_UniGene.TestUniGene.test_read) ... ok
test_read_value_error (test_UniGene.TestUniGene.test_read_value_error) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.029 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_UniProt_GOA.py
test_UniProt_GOA ... ok
test_gaf_iterator (test_UniProt_GOA.GoaTests.test_gaf_iterator)
Test GOA GAF file iterator. ... ok
test_gpa_iterator (test_UniProt_GOA.GoaTests.test_gpa_iterator)
Test GOA GPA file iterator. ... ok
test_gpi_iterator (test_UniProt_GOA.GoaTests.test_gpi_iterator)
Test GOA GPI file iterator, gpi-version: 1.1. ... ok
test_gpi_iterator_one_two (test_UniProt_GOA.GoaTests.test_gpi_iterator_one_two)
Test GOA GPI file iterator, gpi-version: 1.2. ... ok
test_selection_writing (test_UniProt_GOA.GoaTests.test_selection_writing)
Test record_has, and writerec. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.031 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Uniprot.py
test_Uniprot ... ok
test_F2CXE6 (test_Uniprot.TestUniprot.test_F2CXE6)
Compare SwissProt text and uniprot XML versions of F2CXE6. ... ok
test_H2CNN8 (test_Uniprot.TestUniprot.test_H2CNN8)
Compare SwissProt text and uniprot XML versions of H2CNN8. ... ok
test_P60904 (test_Uniprot.TestUniprot.test_P60904)
Parsing SwissProt file P60904.txt. ... ok
test_P84001 (test_Uniprot.TestUniprot.test_P84001)
Parse mass spec structured comment with unknown loc. ... ok
test_Q13639 (test_Uniprot.TestUniprot.test_Q13639)
Compare SwissProt text and uniprot XML versions of Q13639. ... ok
test_multi_ex (test_Uniprot.TestUniprot.test_multi_ex)
Compare SwissProt text and uniprot XML versions of several examples. ... ok
test_multi_ex_index (test_Uniprot.TestUniprot.test_multi_ex_index)
Index SwissProt text and uniprot XML versions of several examples. ... ok
test_sp016 (test_Uniprot.TestUniprot.test_sp016)
Parsing SwissProt file sp016. ... ok
test_submittedName_allowed (test_Uniprot.TestUniprot.test_submittedName_allowed)
Checks if parser supports new XML Element (submittedName). ... ok
test_uni001 (test_Uniprot.TestUniprot.test_uni001)
Parsing Uniprot file uni001. ... ok
test_uni003 (test_Uniprot.TestUniprot.test_uni003)
Parsing Uniprot file uni003. ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.238 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.016 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.085 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_align.py
test_align ... ok
test_basic_alignment (test_align.TestBasics.test_basic_alignment)
Basic tests on a simple alignment of three sequences. ... ok
test_empty_alignment (test_align.TestBasics.test_empty_alignment)
Very simple tests on an empty alignment. ... ok
test_format_conversion (test_align.TestReading.test_format_conversion)
Parse the alignment file and get an alignment object. ... ok
test_read_clustal1 (test_align.TestReading.test_read_clustal1)
Parse an alignment file and get an alignment object. ... ok
test_read_clustal2 (test_align.TestReading.test_read_clustal2)
Parse an alignment file and get an alignment object. ... ok
test_read_fasta (test_align.TestReading.test_read_fasta) ... ok
test_read_write_clustal (test_align.TestReading.test_read_write_clustal)
Test the base alignment stuff. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.118 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_align_substitution_matrices.py
test_align_substitution_matrices ... ok
test_basics_matrix (test_align_substitution_matrices.TestBasics.test_basics_matrix)
Test basic matrix operations. ... ok
test_basics_vector (test_align_substitution_matrices.TestBasics.test_basics_vector)
Test basic vector operations. ... ok
test_nucleotide_freq (test_align_substitution_matrices.TestBasics.test_nucleotide_freq)
Test nucleotide frequency calculations. ... ok
test_pickling (test_align_substitution_matrices.TestBasics.test_pickling)
Test pickling a substitution matrix. ... ok
test_protein_freq (test_align_substitution_matrices.TestBasics.test_protein_freq)
Test amino acid frequency calculations. ... ok
test_read_write (test_align_substitution_matrices.TestBasics.test_read_write)
Test reading and writing substitution matrices. ... ok
test_loading (test_align_substitution_matrices.TestLoading.test_loading)
Confirm that all provided substitution matrices can be loaded. ... ok
test1_observed_frequencies (test_align_substitution_matrices.TestScoringMatrices.test1_observed_frequencies)
Test calculating substitution frequencies. ... ok
test2_observed_probabilities (test_align_substitution_matrices.TestScoringMatrices.test2_observed_probabilities)
Test calculating substitution probabilities. ... ok
test3_observed_symmetric_probabilities (test_align_substitution_matrices.TestScoringMatrices.test3_observed_symmetric_probabilities)
Test symmetrizing substitution probabilities. ... ok
test4_aminoacid_probabilities (test_align_substitution_matrices.TestScoringMatrices.test4_aminoacid_probabilities)
Test calculating expected amino acid probabilities. ... ok
test5_expected_probabilities (test_align_substitution_matrices.TestScoringMatrices.test5_expected_probabilities)
Test calculating expected amino acid substitution probabilities. ... ok
test6_scores (test_align_substitution_matrices.TestScoringMatrices.test6_scores)
Test calculating amino acid substitution log-ratios. ... ok
test_ident (test_align_substitution_matrices.TestScoringMatrices.test_ident)
Test calculating the +6/-1 matrix as an approximation of BLOSUM62. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.477 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_cellosaurus.py
test_cellosaurus ... ok
test__str__ (test_cellosaurus.TestCellosaurus.test__str__)
Test string function. ... ok
test_parse (test_cellosaurus.TestCellosaurus.test_parse)
Test parsing function. ... ok
test_read (test_cellosaurus.TestCellosaurus.test_read)
Test read function. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.012 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_codonalign.py
test_codonalign ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/codonalign/codonalignment.py:113: BiopythonWarning: Please make sure the two CodonAlignment objects are sharing the same codon table. This is not checked by Biopython.
warnings.warn(
/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/Seq.py:3457: 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.
warnings.warn(
/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/codonalign/__init__.py:612: BiopythonWarning: start codon of pro1 (S 0) does not correspond to pro1 (TCA)
warnings.warn(
/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/codonalign/__init__.py:678: BiopythonWarning: start codon of pro2(S 0) does not correspond to pro2(TCA)
warnings.warn(
ok
test_TypeError (test_codonalign.TestAddition.test_TypeError)
Check that TypeError is thrown for non CodonAlignment/MultipleSequenceAlignment objects. ... ok
test_ValueError (test_codonalign.TestAddition.test_ValueError)
Check that ValueError is thrown for Alignments of different lengths. ... ok
test_addition_CodonAlignment (test_codonalign.TestAddition.test_addition_CodonAlignment)
Check addition of CodonAlignment and CodonAlignment. ... ok
test_addition_MultipleSeqAlignment (test_codonalign.TestAddition.test_addition_MultipleSeqAlignment)
Check addition of CodonAlignment and MultipleSeqAlignment. ... ok
test_IO (test_codonalign.TestBuildAndIO.test_IO) ... ok
test_align (test_codonalign.TestCodonAlignment.test_align) ... ok
test_seq (test_codonalign.TestCodonSeq.test_seq) ... ok
test_mk (test_codonalign.Test_MK.test_mk) ... ok
test_build (test_codonalign.Test_build.test_build) ... ok
test_dn_ds (test_codonalign.Test_dn_ds.test_dn_ds) ... ok
test_dn_ds_matrix (test_codonalign.Test_dn_ds.test_dn_ds_matrix) ... ok
----------------------------------------------------------------------
Ran 1 test in 6.935 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_geo.py
test_geo ... ok
test_GSE16 (test_geo.TestGeo.test_GSE16) ... ok
test_GSM645 (test_geo.TestGeo.test_GSM645) ... ok
test_GSM691 (test_geo.TestGeo.test_GSM691) ... ok
test_GSM700 (test_geo.TestGeo.test_GSM700) ... ok
test_GSM804 (test_geo.TestGeo.test_GSM804) ... ok
test_record_str (test_geo.TestGeo.test_record_str) ... ok
test_soft_ex_affy (test_geo.TestGeo.test_soft_ex_affy) ... ok
test_soft_ex_affy_chp (test_geo.TestGeo.test_soft_ex_affy_chp) ... ok
test_soft_ex_dual (test_geo.TestGeo.test_soft_ex_dual) ... ok
test_soft_ex_family (test_geo.TestGeo.test_soft_ex_family) ... ok
test_soft_ex_platform (test_geo.TestGeo.test_soft_ex_platform) ... ok
test_soft_ex_series (test_geo.TestGeo.test_soft_ex_series) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.066 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_kNN.py
test_kNN ... ok
test_calculate_model (test_kNN.TestKNN.test_calculate_model) ... ok
test_calculate_probability (test_kNN.TestKNN.test_calculate_probability) ... ok
test_classify (test_kNN.TestKNN.test_classify) ... ok
test_leave_one_out (test_kNN.TestKNN.test_leave_one_out) ... ok
test_model_accuracy (test_kNN.TestKNN.test_model_accuracy) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.016 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.077 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.076 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_motifs.py
test_motifs ... ok
test_calculate_pseudocounts (test_motifs.MotifTestPWM.test_calculate_pseudocounts) ... ok
test_getitem (test_motifs.MotifTestPWM.test_getitem) ... ok
test_simple (test_motifs.MotifTestPWM.test_simple)
Test if Bio.motifs PWM scoring works. ... ok
test_with_bad_char (test_motifs.MotifTestPWM.test_with_bad_char)
Test if Bio.motifs PWM scoring works with unexpected letters like N. ... ok
test_with_mixed_case (test_motifs.MotifTestPWM.test_with_mixed_case)
Test if Bio.motifs PWM scoring works with mixed case. ... ok
test_TFoutput (test_motifs.MotifTestsBasic.test_TFoutput)
Ensure that we can write proper TransFac output files. ... ok
test_alignace_parsing (test_motifs.MotifTestsBasic.test_alignace_parsing)
Test if Bio.motifs can parse AlignAce output files. ... ok
test_clusterbuster_parsing_and_output (test_motifs.MotifTestsBasic.test_clusterbuster_parsing_and_output)
Test if Bio.motifs can parse and output Cluster Buster PFM files. ... ok
test_format (test_motifs.MotifTestsBasic.test_format) ... ok
test_pfm_four_columns_parsing (test_motifs.MotifTestsBasic.test_pfm_four_columns_parsing)
Test if Bio.motifs.pfm can parse motifs in position frequency matrix format (4 columns). ... ok
test_pfm_four_rows_parsing (test_motifs.MotifTestsBasic.test_pfm_four_rows_parsing)
Test if Bio.motifs.pfm can parse motifs in position frequency matrix format (4 rows). ... ok
test_pfm_parsing (test_motifs.MotifTestsBasic.test_pfm_parsing)
Test if Bio.motifs can parse JASPAR-style pfm files. ... ok
test_reverse_complement (test_motifs.MotifTestsBasic.test_reverse_complement)
Test if motifs can be reverse-complemented. ... ok
test_sites_parsing (test_motifs.MotifTestsBasic.test_sites_parsing)
Test if Bio.motifs can parse JASPAR-style sites files. ... ok
test_xms_parsing (test_motifs.MotifTestsBasic.test_xms_parsing)
Test if Bio.motifs can parse and output xms PFM files. ... ok
test_mast_parser_1 (test_motifs.TestMAST.test_mast_parser_1)
Parse motifs/mast.crp0.de.oops.txt.xml file. ... ok
test_mast_parser_2 (test_motifs.TestMAST.test_mast_parser_2)
Parse motifs/mast.adh.de.oops.html.xml file. ... ok
test_mast_parser_3 (test_motifs.TestMAST.test_mast_parser_3)
Parse motifs/mast.Klf1-200.cd.oops.xml.xml file. ... ok
test_meme_parser_1 (test_motifs.TestMEME.test_meme_parser_1)
Parse motifs/meme.INO_up800.classic.oops.xml file. ... ok
test_meme_parser_2 (test_motifs.TestMEME.test_meme_parser_2)
Parsing motifs/meme.adh.classic.oops.xml file. ... ok
test_meme_parser_3 (test_motifs.TestMEME.test_meme_parser_3)
Parse motifs/meme.farntrans5.classic.anr.xml file. ... ok
test_meme_parser_rna (test_motifs.TestMEME.test_meme_parser_rna)
Test if Bio.motifs can parse MEME output files using RNA. ... ok
test_minimal_meme_parser (test_motifs.TestMEME.test_minimal_meme_parser)
Parse motifs/minimal_test.meme file. ... ok
test_permissive_transfac_parser (test_motifs.TestTransfac.test_permissive_transfac_parser)
Parse the TRANSFAC-like file motifs/MA0056.1.transfac. ... ok
test_transfac_parser (test_motifs.TestTransfac.test_transfac_parser)
Parse motifs/transfac.dat file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.144 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.059 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_pairwise2.py
test_pairwise2 ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
warnings.warn(
ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_alignments_can_be_pickled (pairwise2_testCases.TestOtherFunctions.test_alignments_can_be_pickled) ... ok
test_clean_alignments (pairwise2_testCases.TestOtherFunctions.test_clean_alignments)
``_clean_alignments`` removes redundant and wrong alignments. ... ok
test_print_matrix (pairwise2_testCases.TestOtherFunctions.test_print_matrix)
``print_matrix`` prints nested lists as nice matrices. ... ok
test_recover_alignments (pairwise2_testCases.TestOtherFunctions.test_recover_alignments)
One possible start position in local alignment is not a match. ... ok
test_function_name (pairwise2_testCases.TestPairwiseErrorConditions.test_function_name)
Test for wrong function names. ... ok
test_function_parameters (pairwise2_testCases.TestPairwiseErrorConditions.test_function_parameters)
Test for number of parameters. ... ok
test_param_names (pairwise2_testCases.TestPairwiseErrorConditions.test_param_names)
Test for unknown parameter in parameter names. ... ok
test_warnings (pairwise2_testCases.TestPairwiseErrorConditions.test_warnings)
Test for warnings. ... ok
test_extend_penalty1 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty1)
Test 1. ... ok
test_extend_penalty2 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty2)
Test 2. ... ok
test_globalxx_simple (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple)
Test globalxx. ... ok
test_globalxx_simple2 (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple2)
Do the same test with sequence order reversed. ... ok
test_list_input (pairwise2_testCases.TestPairwiseGlobal.test_list_input)
Do a global alignment with sequences supplied as lists. ... ok
test_one_alignment_only (pairwise2_testCases.TestPairwiseGlobal.test_one_alignment_only)
Test one_alignment_only parameter. ... ok
test_keywords (pairwise2_testCases.TestPairwiseKeywordUsage.test_keywords)
Test equality of calls with and without keywords. ... ok
test_blosum62 (pairwise2_testCases.TestPairwiseLocal.test_blosum62)
Test localds with blosum62. ... ok
test_empty_result (pairwise2_testCases.TestPairwiseLocal.test_empty_result)
Return no alignment. ... ok
test_localds_zero_score_segments_symmetric (pairwise2_testCases.TestPairwiseLocal.test_localds_zero_score_segments_symmetric)
Test if alignment is independent on direction of sequence. ... ok
test_localms (pairwise2_testCases.TestPairwiseLocal.test_localms)
Two different local alignments. ... ok
test_localxs_1 (pairwise2_testCases.TestPairwiseLocal.test_localxs_1)
Test localxx. ... ok
test_localxs_2 (pairwise2_testCases.TestPairwiseLocal.test_localxs_2)
Test localxx with ``full_sequences=True``. ... ok
test_localxs_generic (pairwise2_testCases.TestPairwiseLocal.test_localxs_generic)
Test the generic method with local alignments. ... ok
test_match_dictionary1 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary1)
Test 1. ... ok
test_match_dictionary2 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary2)
Test 2. ... ok
test_match_dictionary3 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary3)
Test 3. ... ok
test_align_one_char1 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char1)
Test sequence with only one match. ... ok
test_align_one_char2 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char2)
Test sequences with two possible match positions. ... ok
test_align_one_char3 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char3)
Like test 1, but global alignment. ... ok
test_match_score_open_penalty1 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty1)
Test 1. ... ok
test_match_score_open_penalty2 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty2)
Test 2. ... ok
test_match_score_open_penalty3 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty3)
Test 3. ... ok
test_match_score_open_penalty4 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty4)
Test 4. ... ok
test_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps)
Turn off end-gap penalties. ... ok
test_penalize_end_gaps2 (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps2)
Do the same, but use the generic method (with the same result). ... ok
test_separate_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_separate_penalize_end_gaps)
Test alignment where end-gaps are differently penalized. ... ok
test_penalize_extend_when_opening (pairwise2_testCases.TestPairwisePenalizeExtendWhenOpening.test_penalize_extend_when_opening)
Add gap-extend penalty to gap-opening penalty. ... ok
test_separate_gap_penalties1 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties1)
Test 1. ... ok
test_separate_gap_penalties2 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties2)
Test 2. ... ok
test_separate_gap_penalties_with_extension (pairwise2_testCases.TestPairwiseSeparateGapPenaltiesWithExtension.test_separate_gap_penalties_with_extension)
Test separate gap-extension penalties and list input. ... ok
test_gap_here_only_1 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_1)
Open a gap in second sequence only. ... ok
test_gap_here_only_2 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_2)
Force a bad alignment. ... ok
test_score_only_global (pairwise2_testCases.TestScoreOnly.test_score_only_global)
Test ``score_only`` in a global alignment. ... ok
test_score_only_local (pairwise2_testCases.TestScoreOnly.test_score_only_local)
Test ``score_only`` in a local alignment. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.118 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_pairwise2_no_C.py
test_pairwise2_no_C ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
warnings.warn(
ok
test_alignments_can_be_pickled (pairwise2_testCases.TestOtherFunctions.test_alignments_can_be_pickled) ... ok
test_clean_alignments (pairwise2_testCases.TestOtherFunctions.test_clean_alignments)
``_clean_alignments`` removes redundant and wrong alignments. ... ok
test_print_matrix (pairwise2_testCases.TestOtherFunctions.test_print_matrix)
``print_matrix`` prints nested lists as nice matrices. ... ok
test_recover_alignments (pairwise2_testCases.TestOtherFunctions.test_recover_alignments)
One possible start position in local alignment is not a match. ... ok
test_function_name (pairwise2_testCases.TestPairwiseErrorConditions.test_function_name)
Test for wrong function names. ... ok
test_function_parameters (pairwise2_testCases.TestPairwiseErrorConditions.test_function_parameters)
Test for number of parameters. ... ok
test_param_names (pairwise2_testCases.TestPairwiseErrorConditions.test_param_names)
Test for unknown parameter in parameter names. ... ok
test_warnings (pairwise2_testCases.TestPairwiseErrorConditions.test_warnings)
Test for warnings. ... ok
test_extend_penalty1 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty1)
Test 1. ... ok
test_extend_penalty2 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty2)
Test 2. ... ok
test_globalxx_simple (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple)
Test globalxx. ... ok
test_globalxx_simple2 (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple2)
Do the same test with sequence order reversed. ... ok
test_list_input (pairwise2_testCases.TestPairwiseGlobal.test_list_input)
Do a global alignment with sequences supplied as lists. ... ok
test_one_alignment_only (pairwise2_testCases.TestPairwiseGlobal.test_one_alignment_only)
Test one_alignment_only parameter. ... ok
test_keywords (pairwise2_testCases.TestPairwiseKeywordUsage.test_keywords)
Test equality of calls with and without keywords. ... ok
test_blosum62 (pairwise2_testCases.TestPairwiseLocal.test_blosum62)
Test localds with blosum62. ... ok
test_empty_result (pairwise2_testCases.TestPairwiseLocal.test_empty_result)
Return no alignment. ... ok
test_localds_zero_score_segments_symmetric (pairwise2_testCases.TestPairwiseLocal.test_localds_zero_score_segments_symmetric)
Test if alignment is independent on direction of sequence. ... ok
test_localms (pairwise2_testCases.TestPairwiseLocal.test_localms)
Two different local alignments. ... ok
test_localxs_1 (pairwise2_testCases.TestPairwiseLocal.test_localxs_1)
Test localxx. ... ok
test_localxs_2 (pairwise2_testCases.TestPairwiseLocal.test_localxs_2)
Test localxx with ``full_sequences=True``. ... ok
test_localxs_generic (pairwise2_testCases.TestPairwiseLocal.test_localxs_generic)
Test the generic method with local alignments. ... ok
test_match_dictionary1 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary1)
Test 1. ... ok
test_match_dictionary2 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary2)
Test 2. ... ok
test_match_dictionary3 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary3)
Test 3. ... ok
test_align_one_char1 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char1)
Test sequence with only one match. ... ok
test_align_one_char2 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char2)
Test sequences with two possible match positions. ... ok
test_align_one_char3 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char3)
Like test 1, but global alignment. ... ok
test_match_score_open_penalty1 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty1)
Test 1. ... ok
test_match_score_open_penalty2 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty2)
Test 2. ... ok
test_match_score_open_penalty3 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty3)
Test 3. ... ok
test_match_score_open_penalty4 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty4)
Test 4. ... ok
test_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps)
Turn off end-gap penalties. ... ok
test_penalize_end_gaps2 (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps2)
Do the same, but use the generic method (with the same result). ... ok
test_separate_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_separate_penalize_end_gaps)
Test alignment where end-gaps are differently penalized. ... ok
test_penalize_extend_when_opening (pairwise2_testCases.TestPairwisePenalizeExtendWhenOpening.test_penalize_extend_when_opening)
Add gap-extend penalty to gap-opening penalty. ... ok
test_separate_gap_penalties1 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties1)
Test 1. ... ok
test_separate_gap_penalties2 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties2)
Test 2. ... ok
test_separate_gap_penalties_with_extension (pairwise2_testCases.TestPairwiseSeparateGapPenaltiesWithExtension.test_separate_gap_penalties_with_extension)
Test separate gap-extension penalties and list input. ... ok
test_gap_here_only_1 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_1)
Open a gap in second sequence only. ... ok
test_gap_here_only_2 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_2)
Force a bad alignment. ... ok
test_score_only_global (pairwise2_testCases.TestScoreOnly.test_score_only_global)
Test ``score_only`` in a global alignment. ... ok
test_score_only_local (pairwise2_testCases.TestScoreOnly.test_score_only_local)
Test ``score_only`` in a local alignment. ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.112 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_pairwise_alignment_map.py
test_pairwise_alignment_map ... ok
test1 (test_pairwise_alignment_map.TestComplex.test1) ... ok
test2 (test_pairwise_alignment_map.TestComplex.test2) ... ok
test_internal (test_pairwise_alignment_map.TestSimple.test_internal) ... ok
test_left_overhang (test_pairwise_alignment_map.TestSimple.test_left_overhang) ... ok
test_reverse_sequence (test_pairwise_alignment_map.TestSimple.test_reverse_sequence) ... ok
test_reverse_transcript (test_pairwise_alignment_map.TestSimple.test_reverse_transcript) ... ok
test_reverse_transcript_sequence (test_pairwise_alignment_map.TestSimple.test_reverse_transcript_sequence) ... ok
test_right_overhang (test_pairwise_alignment_map.TestSimple.test_right_overhang) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.096 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_phenotype.py
test_phenotype ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_CsvIterator (test_phenotype.TestPhenoMicro.test_CsvIterator)
Test basic functionalities of CsvIterator file parser. ... ok
test_JsonIterator (test_phenotype.TestPhenoMicro.test_JsonIterator)
Test basic functionalities of JsonIterator file parser. ... ok
test_PlateRecord (test_phenotype.TestPhenoMicro.test_PlateRecord)
Test basic functionalities of PlateRecord objects. ... ok
test_PlateRecord_errors (test_phenotype.TestPhenoMicro.test_PlateRecord_errors)
Test bad arguments with PlateRecord objects. ... ok
test_WellRecord (test_phenotype.TestPhenoMicro.test_WellRecord)
Test basic functionalities of WellRecord objects. ... ok
test_bad_fit_args (test_phenotype.TestPhenoMicro.test_bad_fit_args)
Test error handling of the fit method. ... ok
test_phenotype_IO (test_phenotype.TestPhenoMicro.test_phenotype_IO)
Test basic functionalities of phenotype IO methods. ... ok
test_phenotype_IO_errors (test_phenotype.TestPhenoMicro.test_phenotype_IO_errors)
Test bad arguments to phenotype IO methods. ... ok
----------------------------------------------------------------------
Ran 1 test in 9.871 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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.
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.010 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_phyml_tool.py
test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper.
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.124 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_prodoc.py
test_prodoc ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_parse_pdoc (test_prodoc.TestProdocParse.test_parse_pdoc)
Parsing an excerpt of prosite.doc. ... ok
test_read_pdoc00100 (test_prodoc.TestProdocRead.test_read_pdoc00100)
Reading Prodoc record PDOC00100. ... ok
test_read_pdoc00113 (test_prodoc.TestProdocRead.test_read_pdoc00113)
Reading Prodoc record PDOC00113. ... ok
test_read_pdoc00144 (test_prodoc.TestProdocRead.test_read_pdoc00144)
Reading Prodoc record PDOC00144. ... ok
test_read_pdoc00149 (test_prodoc.TestProdocRead.test_read_pdoc00149)
Reading Prodoc record PDOC00149. ... ok
test_read_pdoc00340 (test_prodoc.TestProdocRead.test_read_pdoc00340)
Reading Prodoc record PDOC00340. ... ok
test_read_pdoc00424 (test_prodoc.TestProdocRead.test_read_pdoc00424)
Reading Prodoc record PDOC00424. ... ok
test_read_pdoc00472 (test_prodoc.TestProdocRead.test_read_pdoc00472)
Reading Prodoc record PDOC00472. ... ok
test_read_pdoc00640 (test_prodoc.TestProdocRead.test_read_pdoc00640)
Reading Prodoc record PDOC00640. ... ok
test_read_pdoc00787 (test_prodoc.TestProdocRead.test_read_pdoc00787)
Reading Prodoc record PDOC00787. ... ok
test_read_pdoc0933 (test_prodoc.TestProdocRead.test_read_pdoc0933)
Reading Prodoc record PDOC00933. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.017 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_prosite.py
test_prosite ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_read1 (test_prosite.TestPrositeRead.test_read1)
Parsing Prosite record ps00107.txt. ... ok
test_read2 (test_prosite.TestPrositeRead.test_read2)
Parsing Prosite record ps00159.txt. ... ok
test_read3 (test_prosite.TestPrositeRead.test_read3)
Parsing Prosite record ps00165.txt. ... ok
test_read4 (test_prosite.TestPrositeRead.test_read4)
Parsing Prosite record ps00432.txt. ... ok
test_read5 (test_prosite.TestPrositeRead.test_read5)
Parsing Prosite record ps00488.txt. ... ok
test_read6 (test_prosite.TestPrositeRead.test_read6)
Parsing Prosite record ps00546.txt. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.089 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.117 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/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 0.015 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_seq.py
test_seq ... ok
test_ambiguous_values (test_seq.TestAmbiguousComplements.test_ambiguous_values)
Test that other tests do not introduce characters to our values. ... ok
test_mutable_seq (test_seq.TestAttributes.test_mutable_seq) ... ok
test_seq (test_seq.TestAttributes.test_seq) ... ok
test_complement_ambiguous_dna_values (test_seq.TestComplement.test_complement_ambiguous_dna_values) ... ok
test_complement_ambiguous_rna_values (test_seq.TestComplement.test_complement_ambiguous_rna_values) ... ok
test_complement_incompatible_letters (test_seq.TestComplement.test_complement_incompatible_letters) ... ok
test_complement_of_dna (test_seq.TestComplement.test_complement_of_dna) ... ok
test_complement_of_mixed_dna_rna (test_seq.TestComplement.test_complement_of_mixed_dna_rna) ... ok
test_complement_of_rna (test_seq.TestComplement.test_complement_of_rna) ... ok
test_immutable (test_seq.TestComplement.test_immutable) ... ok
test_reverse_complements (test_seq.TestDoubleReverseComplement.test_reverse_complements)
Test double reverse complement preserves the sequence. ... ok
test_add_method (test_seq.TestMutableSeq.test_add_method)
Test adding wrong type to MutableSeq. ... ok
test_appending (test_seq.TestMutableSeq.test_appending) ... ok
test_as_string (test_seq.TestMutableSeq.test_as_string) ... ok
test_complement (test_seq.TestMutableSeq.test_complement) ... ok
test_complement_dna_string (test_seq.TestMutableSeq.test_complement_dna_string) ... ok
test_complement_mixed_aphabets (test_seq.TestMutableSeq.test_complement_mixed_aphabets) ... ok
test_complement_old (test_seq.TestMutableSeq.test_complement_old) ... ok
test_complement_rna (test_seq.TestMutableSeq.test_complement_rna) ... ok
test_complement_rna_string (test_seq.TestMutableSeq.test_complement_rna_string) ... ok
test_contains_method (test_seq.TestMutableSeq.test_contains_method) ... ok
test_converting_to_immutable (test_seq.TestMutableSeq.test_converting_to_immutable) ... ok
test_count (test_seq.TestMutableSeq.test_count) ... ok
test_delete_stride_slice (test_seq.TestMutableSeq.test_delete_stride_slice) ... ok
test_deleting_item (test_seq.TestMutableSeq.test_deleting_item) ... ok
test_deleting_slice (test_seq.TestMutableSeq.test_deleting_slice) ... ok
test_endswith (test_seq.TestMutableSeq.test_endswith) ... ok
test_equal_comparison (test_seq.TestMutableSeq.test_equal_comparison)
Test __eq__ comparison method. ... ok
test_extend_method (test_seq.TestMutableSeq.test_extend_method) ... ok
test_extend_with_mutable_seq (test_seq.TestMutableSeq.test_extend_with_mutable_seq) ... ok
test_extract_third_nucleotide (test_seq.TestMutableSeq.test_extract_third_nucleotide)
Test extracting every third nucleotide (slicing with stride 3). ... ok
test_first_nucleotide (test_seq.TestMutableSeq.test_first_nucleotide) ... ok
test_greater_than_comparison (test_seq.TestMutableSeq.test_greater_than_comparison)
Test __gt__ comparison method. ... ok
test_greater_than_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_greater_than_comparison_of_incompatible_types) ... ok
test_greater_than_comparison_with_str (test_seq.TestMutableSeq.test_greater_than_comparison_with_str) ... ok
test_greater_than_or_equal_comparison (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison)
Test __ge__ comparison method. ... ok
test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison_of_incompatible_types) ... ok
test_greater_than_or_equal_comparison_with_str (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison_with_str) ... ok
test_index (test_seq.TestMutableSeq.test_index) ... ok
test_inserting (test_seq.TestMutableSeq.test_inserting) ... ok
test_length (test_seq.TestMutableSeq.test_length) ... ok
test_less_than_comparison (test_seq.TestMutableSeq.test_less_than_comparison)
Test __lt__ comparison method. ... ok
test_less_than_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_less_than_comparison_of_incompatible_types) ... ok
test_less_than_comparison_with_str (test_seq.TestMutableSeq.test_less_than_comparison_with_str) ... ok
test_less_than_or_equal_comparison (test_seq.TestMutableSeq.test_less_than_or_equal_comparison)
Test __le__ comparison method. ... ok
test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_less_than_or_equal_comparison_of_incompatible_types) ... ok
test_less_than_or_equal_comparison_with_str (test_seq.TestMutableSeq.test_less_than_or_equal_comparison_with_str) ... ok
test_mutableseq_construction (test_seq.TestMutableSeq.test_mutableseq_construction)
Test MutableSeq object initialization. ... ok
test_not_equal_comparison (test_seq.TestMutableSeq.test_not_equal_comparison)
Test __ne__ comparison method. ... ok
test_popping_last_item (test_seq.TestMutableSeq.test_popping_last_item) ... ok
test_radd_method_wrong_type (test_seq.TestMutableSeq.test_radd_method_wrong_type) ... ok
test_remove_items (test_seq.TestMutableSeq.test_remove_items) ... ok
test_repr (test_seq.TestMutableSeq.test_repr) ... ok
test_reverse (test_seq.TestMutableSeq.test_reverse)
Test using reverse method. ... ok
test_reverse_complement (test_seq.TestMutableSeq.test_reverse_complement) ... ok
test_reverse_complement_old (test_seq.TestMutableSeq.test_reverse_complement_old) ... ok
test_reverse_complement_rna (test_seq.TestMutableSeq.test_reverse_complement_rna) ... ok
test_reverse_with_stride (test_seq.TestMutableSeq.test_reverse_with_stride)
Test reverse using -1 stride. ... ok
test_set_wobble_codon_to_n (test_seq.TestMutableSeq.test_set_wobble_codon_to_n)
Test setting wobble codon to N (set slice with stride 3). ... ok
test_setting_item (test_seq.TestMutableSeq.test_setting_item) ... ok
test_setting_slices (test_seq.TestMutableSeq.test_setting_slices) ... ok
test_startswith (test_seq.TestMutableSeq.test_startswith) ... ok
test_transcribe (test_seq.TestMutableSeq.test_transcribe) ... ok
test_truncated_repr (test_seq.TestMutableSeq.test_truncated_repr) ... ok
test_immutable (test_seq.TestReverseComplement.test_immutable) ... ok
test_reverse_complement (test_seq.TestReverseComplement.test_reverse_complement) ... ok
test_reverse_complement_of_dna (test_seq.TestReverseComplement.test_reverse_complement_of_dna) ... ok
test_reverse_complement_of_mixed_dna_rna (test_seq.TestReverseComplement.test_reverse_complement_of_mixed_dna_rna) ... ok
test_reverse_complement_of_rna (test_seq.TestReverseComplement.test_reverse_complement_of_rna) ... ok
test_as_string (test_seq.TestSeq.test_as_string)
Test converting Seq to string. ... ok
test_cast_to_list (test_seq.TestSeq.test_cast_to_list) ... ok
test_concatenation_of_seq (test_seq.TestSeq.test_concatenation_of_seq) ... ok
test_extract_third_nucleotide (test_seq.TestSeq.test_extract_third_nucleotide)
Test extracting every third nucleotide (slicing with stride 3). ... ok
test_first_nucleotide (test_seq.TestSeq.test_first_nucleotide)
Test getting first nucleotide of Seq. ... ok
test_last_nucleotide (test_seq.TestSeq.test_last_nucleotide)
Test getting last nucleotide of Seq. ... ok
test_length (test_seq.TestSeq.test_length)
Test len method on Seq object. ... ok
test_replace (test_seq.TestSeq.test_replace) ... ok
test_repr (test_seq.TestSeq.test_repr)
Test representation of Seq object. ... ok
test_reverse (test_seq.TestSeq.test_reverse)
Test reverse using -1 stride. ... ok
test_seq_construction (test_seq.TestSeq.test_seq_construction)
Test Seq object initialization. ... ok
test_slicing (test_seq.TestSeq.test_slicing)
Test slicing of Seq. ... ok
test_truncated_repr (test_seq.TestSeq.test_truncated_repr) ... ok
test_adding_generic_nucleotide_with_other_nucleotides (test_seq.TestSeqAddition.test_adding_generic_nucleotide_with_other_nucleotides) ... ok
test_adding_generic_nucleotide_with_other_nucleotides_inplace (test_seq.TestSeqAddition.test_adding_generic_nucleotide_with_other_nucleotides_inplace) ... ok
test_adding_protein_with_nucleotides (test_seq.TestSeqAddition.test_adding_protein_with_nucleotides) ... ok
test_addition_dna_rna_with_generic_nucleotides (test_seq.TestSeqAddition.test_addition_dna_rna_with_generic_nucleotides) ... ok
test_addition_dna_rna_with_generic_nucleotides_inplace (test_seq.TestSeqAddition.test_addition_dna_rna_with_generic_nucleotides_inplace) ... ok
test_addition_dna_with_dna (test_seq.TestSeqAddition.test_addition_dna_with_dna) ... ok
test_addition_dna_with_dna_inplace (test_seq.TestSeqAddition.test_addition_dna_with_dna_inplace) ... ok
test_addition_dna_with_rna (test_seq.TestSeqAddition.test_addition_dna_with_rna) ... ok
test_addition_proteins (test_seq.TestSeqAddition.test_addition_proteins) ... ok
test_addition_proteins_inplace (test_seq.TestSeqAddition.test_addition_proteins_inplace) ... ok
test_addition_rna_with_rna (test_seq.TestSeqAddition.test_addition_rna_with_rna) ... ok
test_addition_rna_with_rna_inplace (test_seq.TestSeqAddition.test_addition_rna_with_rna_inplace) ... ok
test_defined (test_seq.TestSeqDefined.test_defined) ... ok
test_undefined (test_seq.TestSeqDefined.test_undefined) ... ok
test_zero_length (test_seq.TestSeqDefined.test_zero_length) ... ok
test_imul_method (test_seq.TestSeqMultiplication.test_imul_method)
Test imul method; relies on addition and mull methods. ... ok
test_imul_method_exceptions (test_seq.TestSeqMultiplication.test_imul_method_exceptions)
Test imul method exceptions. ... ok
test_mul_method (test_seq.TestSeqMultiplication.test_mul_method)
Test mul method; relies on addition method. ... ok
test_mul_method_exceptions (test_seq.TestSeqMultiplication.test_mul_method_exceptions)
Test mul method exceptions. ... ok
test_rmul_method (test_seq.TestSeqMultiplication.test_rmul_method)
Test rmul method; relies on addition method. ... ok
test_rmul_method_exceptions (test_seq.TestSeqMultiplication.test_rmul_method_exceptions)
Test rmul method exceptions. ... ok
test_add_method_using_wrong_object (test_seq.TestSeqStringMethods.test_add_method_using_wrong_object) ... ok
test_append_nucleotides (test_seq.TestSeqStringMethods.test_append_nucleotides) ... ok
test_append_proteins (test_seq.TestSeqStringMethods.test_append_proteins) ... ok
test_contains_method (test_seq.TestSeqStringMethods.test_contains_method) ... ok
test_counting_characters (test_seq.TestSeqStringMethods.test_counting_characters) ... ok
test_endswith (test_seq.TestSeqStringMethods.test_endswith) ... ok
test_finding_characters (test_seq.TestSeqStringMethods.test_finding_characters) ... ok
test_greater_than_comparison (test_seq.TestSeqStringMethods.test_greater_than_comparison)
Test __gt__ comparison method. ... ok
test_greater_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_greater_than_comparison_of_incompatible_types)
Test incompatible types __gt__ comparison method. ... ok
test_greater_than_or_equal_comparison (test_seq.TestSeqStringMethods.test_greater_than_or_equal_comparison)
Test __ge__ comparison method. ... ok
test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_greater_than_or_equal_comparison_of_incompatible_types)
Test incompatible types __ge__ comparison method. ... ok
test_hash (test_seq.TestSeqStringMethods.test_hash) ... ok
test_less_than_comparison (test_seq.TestSeqStringMethods.test_less_than_comparison)
Test __lt__ comparison method. ... ok
test_less_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_less_than_comparison_of_incompatible_types)
Test incompatible types __lt__ comparison method. ... ok
test_less_than_or_equal_comparison (test_seq.TestSeqStringMethods.test_less_than_or_equal_comparison)
Test __le__ comparison method. ... ok
test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_less_than_or_equal_comparison_of_incompatible_types)
Test incompatible types __le__ comparison method. ... ok
test_mutableseq_upper_lower (test_seq.TestSeqStringMethods.test_mutableseq_upper_lower) ... ok
test_not_equal_comparsion (test_seq.TestSeqStringMethods.test_not_equal_comparsion)
Test __ne__ comparison method. ... ok
test_radd_method_using_wrong_object (test_seq.TestSeqStringMethods.test_radd_method_using_wrong_object) ... ok
test_splits (test_seq.TestSeqStringMethods.test_splits) ... ok
test_startswith (test_seq.TestSeqStringMethods.test_startswith) ... ok
test_string_methods (test_seq.TestSeqStringMethods.test_string_methods) ... ok
test_stripping_characters (test_seq.TestSeqStringMethods.test_stripping_characters) ... ok
test_stops (test_seq.TestStopCodons.test_stops) ... ok
test_translation_of_stops (test_seq.TestStopCodons.test_translation_of_stops) ... ok
test_back_transcribe_rna_into_dna (test_seq.TestTranscription.test_back_transcribe_rna_into_dna) ... ok
test_back_transcribe_rna_string_into_dna (test_seq.TestTranscription.test_back_transcribe_rna_string_into_dna) ... ok
test_seq_object_back_transcription_method (test_seq.TestTranscription.test_seq_object_back_transcription_method) ... ok
test_seq_object_transcription_method (test_seq.TestTranscription.test_seq_object_transcription_method) ... ok
test_transcription_dna_into_rna (test_seq.TestTranscription.test_transcription_dna_into_rna) ... ok
test_transcription_dna_string_into_rna (test_seq.TestTranscription.test_transcription_dna_string_into_rna) ... ok
test_gapped_seq_no_gap_char_given (test_seq.TestTranslating.test_gapped_seq_no_gap_char_given) ... ok
test_gapped_seq_with_gap_char_given (test_seq.TestTranslating.test_gapped_seq_with_gap_char_given) ... ok
test_translation (test_seq.TestTranslating.test_translation) ... ok
test_translation_extra_stop_codon (test_seq.TestTranslating.test_translation_extra_stop_codon) ... ok
test_translation_incomplete_codon (test_seq.TestTranslating.test_translation_incomplete_codon) ... ok
test_translation_of_asparagine (test_seq.TestTranslating.test_translation_of_asparagine) ... ok
test_translation_of_gapped_string_no_gap_char_given (test_seq.TestTranslating.test_translation_of_gapped_string_no_gap_char_given) ... ok
test_translation_of_gapped_string_with_gap_char_given (test_seq.TestTranslating.test_translation_of_gapped_string_with_gap_char_given) ... ok
test_translation_of_glutamine (test_seq.TestTranslating.test_translation_of_glutamine) ... ok
test_translation_of_invalid_codon (test_seq.TestTranslating.test_translation_of_invalid_codon) ... ok
test_translation_of_leucine (test_seq.TestTranslating.test_translation_of_leucine) ... ok
test_translation_of_string (test_seq.TestTranslating.test_translation_of_string) ... ok
test_translation_on_proteins (test_seq.TestTranslating.test_translation_on_proteins)
Check translation fails on a protein. ... ok
test_translation_to_stop (test_seq.TestTranslating.test_translation_to_stop) ... ok
test_translation_using_cds (test_seq.TestTranslating.test_translation_using_cds) ... ok
test_translation_using_tables_with_ambiguous_stop_codons (test_seq.TestTranslating.test_translation_using_tables_with_ambiguous_stop_codons)
Check for error and warning messages. ... ok
test_translation_with_bad_table_argument (test_seq.TestTranslating.test_translation_with_bad_table_argument) ... ok
test_translation_with_codon_table_as_table_argument (test_seq.TestTranslating.test_translation_with_codon_table_as_table_argument) ... ok
test_translation_wrong_type (test_seq.TestTranslating.test_translation_wrong_type)
Test translation table cannot be CodonTable. ... ok
test_add_method (test_seq.TestUnknownSeq.test_add_method) ... ok
test_back_transcribe (test_seq.TestUnknownSeq.test_back_transcribe) ... ok
test_complement (test_seq.TestUnknownSeq.test_complement) ... ok
test_count (test_seq.TestUnknownSeq.test_count) ... ok
test_getitem_method (test_seq.TestUnknownSeq.test_getitem_method) ... ok
test_length (test_seq.TestUnknownSeq.test_length) ... ok
test_lower (test_seq.TestUnknownSeq.test_lower) ... ok
test_repr (test_seq.TestUnknownSeq.test_repr) ... ok
test_reverse_complement (test_seq.TestUnknownSeq.test_reverse_complement) ... ok
test_transcribe (test_seq.TestUnknownSeq.test_transcribe) ... ok
test_translation (test_seq.TestUnknownSeq.test_translation) ... ok
test_ungap (test_seq.TestUnknownSeq.test_ungap) ... ok
test_unknownseq_construction (test_seq.TestUnknownSeq.test_unknownseq_construction) ... ok
test_upper (test_seq.TestUnknownSeq.test_upper) ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.112 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/lib64/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_translate.py
test_translate ... ok
test_ambiguous (test_translate.TestTranscriptionTranslation.test_ambiguous) ... ok
test_dna_rna_translation (test_translate.TestTranscriptionTranslation.test_dna_rna_translation) ... ok
test_transcription (test_translate.TestTranscriptionTranslation.test_transcription) ... ok
test_translation (test_translate.TestTranscriptionTranslation.test_translation) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.059 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
~/build/BUILD/python-biopython-1.80
+ popd
+ RPM_EC=0
++ jobs -p
Processing files: python3-biopython-1.80-1.fc38.ppc64le
+ exit 0
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.bql74n
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.80
+ DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/share/doc/python3-biopython
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/share/doc/python3-biopython
+ cp -pr python3/Scripts /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/share/doc/python3-biopython
+ cp -pr python3/CONTRIB.rst /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/share/doc/python3-biopython
+ cp -pr python3/DEPRECATED.rst /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/share/doc/python3-biopython
+ cp -pr python3/NEWS.rst /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/share/doc/python3-biopython
+ cp -pr python3/README.rst /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/share/doc/python3-biopython
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.FztUSU
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.80
+ LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/share/licenses/python3-biopython
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/share/licenses/python3-biopython
+ cp -pr python3/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/share/licenses/python3-biopython
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: python-biopython = 1.80-1.fc38 python3-biopython = 1.80-1.fc38 python3-biopython(ppc-64) = 1.80-1.fc38 python3.11-biopython = 1.80-1.fc38 python3.11dist(biopython) = 1.80 python3dist(biopython) = 1.80
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()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.32)(64bit) python(abi) = 3.11 python3.11dist(numpy) rtld(GNU_HASH)
Obsoletes: python-biopython < 1.80-1.fc38
Processing files: python-biopython-doc-1.80-1.fc38.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.2RYWSv
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.80
+ DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/share/doc/python-biopython-doc
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/share/doc/python-biopython-doc
+ cp -pr biopython-1.80/Doc /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/share/doc/python-biopython-doc
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.NkdISg
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.80
+ LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/share/licenses/python-biopython-doc
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/share/licenses/python-biopython-doc
+ cp -pr biopython-1.80/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le/usr/share/licenses/python-biopython-doc
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: python-biopython-doc = 1.80-1.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python-biopython-debugsource-1.80-1.fc38.ppc64le
Provides: python-biopython-debugsource = 1.80-1.fc38 python-biopython-debugsource(ppc-64) = 1.80-1.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python3-biopython-debuginfo-1.80-1.fc38.ppc64le
Provides: debuginfo(build-id) = 14cab99f116779e4620505042296654b7cf5d128 debuginfo(build-id) = 176fe5258eeb615e0bd59be07ed54903231c457f debuginfo(build-id) = 538a4697fd303db8fd6562786c1dd2e2294d49e5 debuginfo(build-id) = 7ac5dc460117632f24891364378287d14e074fe1 debuginfo(build-id) = 8ec6772848667645ecd08482112f1c13904cc4cd debuginfo(build-id) = 9956a72786b727581e2a5ddf5ae2d64d3178d571 debuginfo(build-id) = bd92cca5c2e548661171c3c10bf7c14b71e1ce4c debuginfo(build-id) = bf9ac8e1daec80d18bfaadccd3fb88ae3f117d4c debuginfo(build-id) = d1e3f19cf75998dd742d8fd9c340cbfb0a6e9f51 python-biopython-debuginfo = 1.80-1.fc38 python3-biopython-debuginfo = 1.80-1.fc38 python3-biopython-debuginfo(ppc-64) = 1.80-1.fc38 python3.11-biopython-debuginfo = 1.80-1.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: python-biopython-debugsource(ppc-64) = 1.80-1.fc38
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le
Wrote: /builddir/build/RPMS/python-biopython-debugsource-1.80-1.fc38.ppc64le.rpm
Wrote: /builddir/build/RPMS/python3-biopython-debuginfo-1.80-1.fc38.ppc64le.rpm
Wrote: /builddir/build/RPMS/python-biopython-doc-1.80-1.fc38.noarch.rpm
Wrote: /builddir/build/RPMS/python3-biopython-1.80-1.fc38.ppc64le.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.9Xrrb0
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.80
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.ppc64le
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.GrTiPx
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf python-biopython-1.80 python-biopython-1.80.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild python-biopython-1.80-1.fc38.src.rpm
Finish: build phase for python-biopython-1.80-1.fc38.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-ppc64le-1672075344.750807/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-ppc64le-1672075344.750807/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-ppc64le-1672075344.750807/root/var/log/dnf.log
INFO: Done(/var/lib/copr-rpmbuild/results/python-biopython-1.80-1.fc38.src.rpm) Config(child) 4 minutes 43 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running RPMResults tool