[Debian-med-packaging] Bug#978338: nanosv: FTBFS: help2man: can't get `--help' info from ./debian/nanosv/usr/bin/NanoSV

[Lucas Nussbaum]

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.