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 '/<>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<>'
cd test && /usr/bin/make -j2
make[2]: Entering directory '/<>/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 "/<>/test/../cnvkit.py", line 9, in
Created directory build/
args.func(args)
File "/<>/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 '/<>/test'
make[1]: *** [debian/rules:47: override_dh_auto_test] Error 2
make[1]: Leaving directory '/<>'
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
