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.
