On 10/15/21 11:06 AM, Andreas Tille wrote:
Cool. Did you used ratt or something else?
ruby-team/meta script: https://salsa.debian.org/ruby-team/meta -- I always vouch for this one.
Here is the rebuild output(please check the entire mail since there are a few questions at the end):
rebuild ariba ... PASS
rebuild atropos ... PASS
rebuild bcbio ... FAIL /tmp/python-pysam_0.17.0+ds-1_amd64.VAuvqfiqWS/buildlogs/bcbio.log
rebuild circlator ... PASS
rebuild cnvkit ... FAIL /tmp/python-pysam_0.17.0+ds-1_amd64.VAuvqfiqWS/buildlogs/cnvkit.log
rebuild fitgcp ... PASS
rebuild htseq ... PASS
rebuild iva ... PASS
rebuild lumpy-sv ... PASS
rebuild mapdamage ... PASS
rebuild mirtop ... PASS
rebuild paleomix ... PASS
rebuild python-deeptools ... PASS
rebuild python-nanoget ... PASS
rebuild python-pbcore ... PASS
rebuild python-pybedtools ... PASS
rebuild python-pyvcf ... FAIL /tmp/python-pysam_0.17.0+ds-1_amd64.VAuvqfiqWS/buildlogs/python-pyvcf.log
rebuild python-seqcluster ... FAIL /tmp/python-pysam_0.17.0+ds-1_amd64.VAuvqfiqWS/buildlogs/python-seqcluster.log
rebuild python-sqt ... PASS
rebuild sga ... PASS
rebuild svim ... PASS
rebuild yanosim ... PASS
There are 4 failures,
1. bcbio -- this was because it pulls seqcluster from contrib and I did not add contrib sources
in chroot -- will need to check this one manually
2. cnvkit -- This seems to have nothing to do with pysam. log below :-
changing mode of build/scripts-3.9/cnvkit-guess_baits from 644 to 755
changing mode of build/scripts-3.9/cnvkit-skg_convert from 644 to 755
changing mode of build/scripts-3.9/cnvkit-cnv_annotate from 644 to 755
cd scripts && for script in cnvkit-*; do \
mv ${script} ${script##cnvkit-}.py; \
done
mv cnvkit cnvkit.py
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd test && /usr/bin/make -j2
make[2]: Entering directory '/<<PKGBUILDDIR>>/test'
python3 ../cnvkit.py import-picard picard/p2-20_5.antitargetcoverage.csv picard/p2-20_5.targetcoverage.csv picard/p2-5_5.antitargetcoverage.csv picard/p2-5_5.targetcoverage.csv picard/p2-9_5.antitargetcoverage.csv picard/p2-9_5.targetcoverage.csv -d build/
python3 ../cnvkit.py import-picard picard/p2-5_5.targetcoverage.csv -d build/
Matplotlib created a temporary config/cache directory at /tmp/matplotlib-uert7fam because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
Matplotlib created a temporary config/cache directory at /tmp/matplotlib-c7jd93g7 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter'
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/test/../cnvkit.py", line 9, in <module>
Created directory build/
args.func(args)
File "/<<PKGBUILDDIR>>/cnvlib/commands.py", line 1456, in _cmd_import_picard
os.mkdir(args.output_dir)
FileExistsError: [Errno 17] File exists: 'build/'
Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions
make[2]: *** [Makefile:52: build/reference-picard.cnn] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[1]: *** [debian/rules:47: override_dh_auto_test] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:9: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
3. pyvcf: Again, unrelated to pysam. log below :-
dh clean --with python3 --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:232: python3.9 setup.py clean
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead
warnings.warn(
error in PyVCF setup command: use_2to3 is invalid.
E: pybuild pybuild:353: clean: plugin distutils failed with: exit code=1: python3.9 setup.py clean
dh_auto_clean: error: pybuild --clean --test-pytest -i python{version} -p 3.9 returned exit code 13
make: *** [debian/rules:14: clean] Error 25
dpkg-buildpackage: error: fakeroot debian/rules clean subprocess returned exit status 2
--------------------------------------------------------------------------------
4. seqcluster -- Depends on vienna-rna, which is non free and which chroot can not pull, will check manually.
===> So for now, I think pyvcf and cnvkit should be fixed, although they look unrelated to this update.
===> Meanwhile, everything looks good in pseudo-excuses page wrt pysam: https://release.debian.org/britney/pseudo-excuses-experimental.html
So I will stem ahead and upload pysam to unstable in a while, after doing a few more tests if you don't have any objections. Let me know.
Nilesh
Attachment:
OpenPGP_signature
Description: OpenPGP digital signature