Your message dated Sun, 01 Dec 2024 16:49:20 +0000
with message-id <[email protected]>
and subject line Bug#1049588: fixed in nim-hts 0.3.25+ds-1
has caused the Debian Bug report #1049588,
regarding nim-hts: Fails to build binary packages again after successful build
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.
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--
1049588: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1049588
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: nim-hts
Version: 0.3.19+ds-1
Severity: minor
Tags: trixie sid ftbfs
User: [email protected]
Usertags: ftbfs-binary-20230816 ftbfs-binary-after-build
User: [email protected]
Usertags: qa-doublebuild
Hi,
This package fails to do build a binary-only build (not source) after a
successful build (dpkg-buildpackage ; dpkg-buildpackage -b).
This is probably a clear violation of Debian Policy section 4.9 (clean target),
but this is filed as severity:minor for now, because a discussion on
debian-devel showed that we might want to revisit the requirement of a working
'clean' target.
More information about this class of issues, included common problems and
solutions, is available at
https://wiki.debian.org/qa.debian.org/FTBFS/DoubleBuild
Relevant part of the build log:
> cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env
> -us -uc -rfakeroot -b
> -------------------------------------------------------------------------------------------------------------------------
>
> dpkg-buildpackage: info: source package nim-hts
> dpkg-buildpackage: info: source version 0.3.19+ds-1
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Nilesh Patra <[email protected]>
> dpkg-source --before-build .
> dpkg-buildpackage: info: host architecture amd64
> debian/rules clean
> dh clean
> debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean
> # remnants from testing
> rm -f ____t.vcf t.gz ti.txt.gz ti.txt.gz.csi
> rm -f tests/run tests/HG02002.bam.csi tests/auxtest tests/newsample.vcf
> tests/outmissing.vcf tests/outv.vcf tests/outz.vcf tests/sample.fa.fai
> tests/all tests/htstest tests/bgzftest tests/bamtest
> rm -rf tests/nimcache
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_clean
> rm -f debian/debhelper-build-stamp
> rm -rf debian/.debhelper/
> rm -f -- debian/nim-hts-dev.substvars debian/nim-hts-examples.substvars
> debian/files
> rm -fr -- debian/nim-hts-dev/ debian/tmp/ debian/nim-hts-examples/
> find . \( \( \
> \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path
> .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o
> -type f -a \
> \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
> -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
> -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
> -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
> \) -exec rm -f {} + \) -o \
> \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \)
> \)
> debian/rules binary
> dh binary
> dh_update_autotools_config
> dh_autoreconf
> debian/rules override_dh_auto_build
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_build
> # Regenerate repacked files
> cat tests/sa.sam | samtools view -Sb - > tests/sa.bam
> samtools index tests/sa.bam tests/sa.bam.bai
> cat debian/missing-sources/HG02002.sam | samtools view -Sb - >
> tests/HG02002.bam
> samtools index tests/HG02002.bam tests/HG02002.bam.bai
> tabix tests/test.vcf.gz
> [tabix] the index file exists. Please use '-f' to overwrite.
> make[1]: *** [debian/rules:15: override_dh_auto_build] Error 1
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> make: *** [debian/rules:6: binary] Error 2
> dpkg-buildpackage: error: debian/rules binary subprocess returned exit status
> 2
>
> E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage
> --sanitize-env -us -uc -rfakeroot -b' failed to run.
The full build log is available from:
http://qa-logs.debian.net/2023/08/16/nim-hts_0.3.19+ds-1_unstable.log
If you reassign this bug to another package, please mark 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 mine
so that we can identify if something relevant changed in the meantime.
--- End Message ---
--- Begin Message ---
Source: nim-hts
Source-Version: 0.3.25+ds-1
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
nim-hts, 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 nim-hts 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: Sun, 01 Dec 2024 17:31:32 +0100
Source: nim-hts
Architecture: source
Version: 0.3.25+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1046095 1049588 1081123
Changes:
nim-hts (0.3.25+ds-1) unstable; urgency=medium
.
* Team upload.
* Fix watch file
* New upstream version
* Standards-Version: 4.7.0 (routine-update)
* Tolerate incompatible pointer types to build smoothly
Closes: #1081123
* Also tolerate incompatible pointer types in autopkgtest
* Fix clean target
Closes: #1049588, #1046095
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