Your message dated Mon, 04 Jan 2021 15:51:07 +0000
with message-id <e1kws8r-000eyj...@fasolo.debian.org>
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 ow...@bugs.debian.org
immediately.)
--
978338: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=978338
Debian Bug Tracking System
Contact ow...@bugs.debian.org 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.
--- End Message ---
--- Begin Message ---
Source: nanosv
Source-Version: 1.2.4+git20190409.c1ae30c-3
Done: Andreas Tille <ti...@debian.org>
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 978...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (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 ftpmas...@ftp-master.debian.org)
-----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
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
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)
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nanosv_1.2.4+git20190409.c1ae30c-3.debian.tar.xz
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Files:
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nanosv_1.2.4+git20190409.c1ae30c-3.dsc
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nanosv_1.2.4+git20190409.c1ae30c-3.debian.tar.xz
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nanosv_1.2.4+git20190409.c1ae30c-3_amd64.buildinfo
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--- End Message ---
