Source: nanosv Version: 1.2.4+git20190409.c1ae30c-2 Severity: serious Justification: FTBFS on amd64 Tags: bullseye sid ftbfs Usertags: ftbfs-20201226 ftbfs-bullseye
Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[1]: Entering directory '/<<PKGBUILDDIR>>' > dh_auto_install > install -d /<<BUILDDIR>>/nanosv-1.2.4\+git20190409.c1ae30c/debian/nanosv > pybuild --install --test-nose -i python{version} -p 3.9 --dest-dir > /<<BUILDDIR>>/nanosv-1.2.4\+git20190409.c1ae30c/debian/nanosv > I: pybuild base:232: /usr/bin/python3 setup.py install --root > /<<PKGBUILDDIR>>/debian/nanosv > /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution > option: 'including_package_data' > warnings.warn(msg) > running install > running build > running build_py > running install_lib > creating /<<PKGBUILDDIR>>/debian/nanosv/usr > creating /<<PKGBUILDDIR>>/debian/nanosv/usr/lib > creating /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9 > creating /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages > creating /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv > copying > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_nanosv/build/nanosv/__init__.py -> > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv > creating > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils > copying > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils/parse_svs.py > -> /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils > copying > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils/__init__.py > -> /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils > copying > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils/phasing.py > -> /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils > copying > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils/coverage.py > -> /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils > copying > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils/create_vcf.py > -> > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils > copying > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils/parse_reads.py > -> > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils > copying > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils/parse_bam.py > -> /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils > copying > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils/parse_breakpoints.py > -> > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils > copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_nanosv/build/nanosv/config.ini > -> /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv > creating > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes > copying > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_nanosv/build/nanosv/classes/__init__.py > -> > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes > copying > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_nanosv/build/nanosv/classes/variant.py > -> > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes > copying > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_nanosv/build/nanosv/classes/read.py -> > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes > copying > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_nanosv/build/nanosv/classes/breakpoint.py > -> > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes > copying > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_nanosv/build/nanosv/classes/sv.py -> > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes > copying > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_nanosv/build/nanosv/classes/segment.py > -> > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes > copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_nanosv/build/nanosv/NanoSV.py > -> /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv > copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_nanosv/build/nanosv/version.py > -> /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv > creating > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/bedfiles > copying > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_nanosv/build/nanosv/bedfiles/human_hg19.bed > -> > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/bedfiles > byte-compiling > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/__init__.py > to __init__.cpython-39.pyc > byte-compiling > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils/parse_svs.py > to parse_svs.cpython-39.pyc > byte-compiling > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils/__init__.py > to __init__.cpython-39.pyc > byte-compiling > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils/phasing.py > to phasing.cpython-39.pyc > byte-compiling > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils/coverage.py > to coverage.cpython-39.pyc > byte-compiling > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils/create_vcf.py > to create_vcf.cpython-39.pyc > byte-compiling > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils/parse_reads.py > to parse_reads.cpython-39.pyc > byte-compiling > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils/parse_bam.py > to parse_bam.cpython-39.pyc > byte-compiling > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils/parse_breakpoints.py > to parse_breakpoints.cpython-39.pyc > byte-compiling > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes/__init__.py > to __init__.cpython-39.pyc > byte-compiling > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes/variant.py > to variant.cpython-39.pyc > byte-compiling > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes/read.py > to read.cpython-39.pyc > byte-compiling > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes/breakpoint.py > to breakpoint.cpython-39.pyc > byte-compiling > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes/sv.py > to sv.cpython-39.pyc > byte-compiling > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes/segment.py > to segment.cpython-39.pyc > byte-compiling > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/NanoSV.py > to NanoSV.cpython-39.pyc > byte-compiling > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/version.py > to version.cpython-39.pyc > running install_egg_info > running egg_info > creating NanoSV.egg-info > writing NanoSV.egg-info/PKG-INFO > writing dependency_links to NanoSV.egg-info/dependency_links.txt > writing entry points to NanoSV.egg-info/entry_points.txt > writing requirements to NanoSV.egg-info/requires.txt > writing top-level names to NanoSV.egg-info/top_level.txt > writing manifest file 'NanoSV.egg-info/SOURCES.txt' > reading manifest file 'NanoSV.egg-info/SOURCES.txt' > reading manifest template 'MANIFEST.in' > warning: no files found matching 'README.rst' > writing manifest file 'NanoSV.egg-info/SOURCES.txt' > Copying NanoSV.egg-info to > /<<PKGBUILDDIR>>/debian/nanosv/usr/lib/python3.9/dist-packages/NanoSV-1.2.4.egg-info > Skipping SOURCES.txt > running install_scripts > Installing NanoSV script to /<<PKGBUILDDIR>>/debian/nanosv/usr/bin > find /<<PKGBUILDDIR>>/debian -name "*.bed" -o -name "*.ini" | xargs -r chmod > -x > PYTHONPATH=./debian/nanosv/usr/lib/python3.8/dist-packages/ help2man > --include=debian/NanoSV.h2m ./debian/nanosv/usr/bin/NanoSV > > /<<PKGBUILDDIR>>/debian/NanoSV.1 > help2man: can't get `--help' info from ./debian/nanosv/usr/bin/NanoSV > Try `--no-discard-stderr' if option outputs to stderr > make[1]: *** [debian/rules:12: override_dh_auto_install] Error 1 The full build log is available from: http://qa-logs.debian.net/2020/12/26/nanosv_1.2.4+git20190409.c1ae30c-2_unstable.log A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! If you reassign this bug to another package, please marking it as 'affects'-ing this package. See https://www.debian.org/Bugs/server-control#affects If you fail to reproduce this, please provide a build log and diff it with me so that we can identify if something relevant changed in the meantime. About the archive rebuild: The rebuild was done on EC2 VM instances from Amazon Web Services, using a clean, minimal and up-to-date chroot. Every failed build was retried once to eliminate random failures.