Your message dated Mon, 04 Jan 2021 15:51:07 +0000 with message-id <[email protected]> and subject line Bug#978338: fixed in nanosv 1.2.4+git20190409.c1ae30c-3 has caused the Debian Bug report #978338, regarding nanosv: FTBFS: help2man: can't get `--help' info from ./debian/nanosv/usr/bin/NanoSV to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 978338: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=978338 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---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.
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--- Begin Message ---Source: nanosv Source-Version: 1.2.4+git20190409.c1ae30c-3 Done: Andreas Tille <[email protected]> We believe that the bug you reported is fixed in the latest version of nanosv, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <[email protected]> (supplier of updated nanosv package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Mon, 04 Jan 2021 13:26:30 +0100 Source: nanosv Architecture: source Version: 1.2.4+git20190409.c1ae30c-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Andreas Tille <[email protected]> Closes: 978338 Changes: nanosv (1.2.4+git20190409.c1ae30c-3) unstable; urgency=medium . * Team upload. * Enable building with Python3.9 Closes: #978338 * Standards-Version: 4.5.1 (routine-update) Checksums-Sha1: ea1b70c6434791b3de49a01efa3acc6aaeff50bb 2144 nanosv_1.2.4+git20190409.c1ae30c-3.dsc 0d5e02d8d56ea60c823f118fe1a7d2daae4b62ff 3748 nanosv_1.2.4+git20190409.c1ae30c-3.debian.tar.xz 71052f745d643af7092ac46911f9a2f827aff4a7 7057 nanosv_1.2.4+git20190409.c1ae30c-3_amd64.buildinfo Checksums-Sha256: ebbd4f9ce919c13b4726a4a17e959328e08ff2e9a503dbe6b5e01b07baea59fe 2144 nanosv_1.2.4+git20190409.c1ae30c-3.dsc dffa31f923520b715918c6c5cd9cbeb199980be40fa1162222636200fa82a92d 3748 nanosv_1.2.4+git20190409.c1ae30c-3.debian.tar.xz 90c3f1be6af4f17dd2b2d06ad9cb3b6ad5032eb48c1f7427e5998a2b077f7729 7057 nanosv_1.2.4+git20190409.c1ae30c-3_amd64.buildinfo Files: 04106294c737eded8a3f5c37e3de360f 2144 science optional nanosv_1.2.4+git20190409.c1ae30c-3.dsc a9a58f10bdbeab3d7ce561905faf293f 3748 science optional nanosv_1.2.4+git20190409.c1ae30c-3.debian.tar.xz 9db942448277077dc015bd8bdebd5021 7057 science optional nanosv_1.2.4+git20190409.c1ae30c-3_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl/zDDgRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGK4g//VWBlVVNM4Nt5LJ8Q0CqTmaUx/ZJkB7yB 0yHI7ShBA/YIRndVQH4mFi5ExDU5hBv6U3yPz8Qv3iZ5NH3Uwd1YDNJJPThE4PYT 5nLWxma8LNMi1kbulHx3jAojwDQylMLL2QkyeLXsj+5/UCfHvMIKF1UF2gr6jde/ vAZNd7nSCfJuCQvXxepsMXfoZ6Nge8nNMJ+QGsuetcoS4BlKm02Gyb3P59mqYg+o 4V3uPUJHW9t1fkZK/cbOhOnlUkGT2UV2wdmav/tzloGf4f3eToIaLqPZfKc36qEr eyZFuv97hbR1aqE1RbjJRg0tzY4+3mBovr+eapKLmKQ7GsMZZQvLgVKkzgcIaBtJ 6fhkwNKmTfUilnfcBon2TlUSbvjzpk5Qu/Sy+3cVbY7kMBt31kkpYmC5q4kLJPSX Tp1M7D6Vw0TvC0Tb+/3kkGUpDVQv1D3PiAsUZ/0LygbmAC4ONwcQS9h92f35zQr+ NcFfkeLND4RfZJ9JhtztPtSkCNE+C/V/ROn1nISjhQRXC38rwJpa4twIc3z8vK8V x7oVMUmAFEHRQyayCTH4MAxqTtHKRD2HhzkmrvTO5Fsnp0vN/FQSHn5sIJlQHEKv 9kEpsDNGOQXzhZIA5ubb+ZYBnK//x2oJlPzfqCxGN6QbQ+GRNbzOwaaiQCGqAyPE B5Sd9J1wjVo= =A2NS -----END PGP SIGNATURE-----
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