Your message dated Wed, 24 Dec 2025 14:35:16 +0000
with message-id <[email protected]>
and subject line Bug#1105730: fixed in bedtools 2.31.1+dfsg-3
has caused the Debian Bug report #1105730,
regarding bedtools: FTBFS with make --shuffle=random:
src/utils/version/version.cpp:2:10: fatal error: version_git.h: No such file or
directory
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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--
1105730: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1105730
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: bedtools
Version: 2.31.1+dfsg-2
Severity: minor
Tags: trixie sid ftbfs
User: [email protected]
Usertags: ftbfs-shuffle
Hi,
GNU Make now has a --shuffle option that simulates non-deterministic ordering
of target prerequisites. See
https://trofi.github.io/posts/238-new-make-shuffle-mode.html and also previous
work in Debian by Santiago Vila:
https://people.debian.org/~sanvila/make-shuffle/
This package fails to build with make --shuffle=random.
This is likely to be caused by a missing dependency in
debian/rules or an upstream Makefile.
More information about this mass bug filing is available at
https://wiki.debian.org/qa.debian.org/FTBFS/Shuffle
Relevant part (hopefully):
> g++ -g -Wall -O2 -std=c++11 -g -O2
> -ffile-prefix-map=/build/reproducible-path/bedtools-2.31.1+dfsg=.
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -D_FILE_OFFSET_BITS=64
> -DWITH_HTS_CB_API -Isrc/annotateBed -Isrc/bamToBed -Isrc/bamToFastq
> -Isrc/bedToBam -Isrc/bedpeToBam -Isrc/bedToIgv -Isrc/bed12ToBed6
> -Isrc/closestFile -Isrc/clusterBed -Isrc/complementFile -Isrc/coverageFile
> -Isrc/expand -Isrc/fastaFromBed -Isrc/flankBed -Isrc/genomeCoverageBed
> -Isrc/getOverlap -Isrc/groupBy -Isrc/intersectFile -Isrc/fisher -Isrc/jaccard
> -Isrc/linksBed -Isrc/maskFastaFromBed -Isrc/mapFile -Isrc/mergeFile
> -Isrc/multiBamCov -Isrc/multiIntersectBed -Isrc/nucBed -Isrc/pairToBed
> -Isrc/pairToPair -Isrc/randomBed -Isrc/regressTest -Isrc/reldist
> -Isrc/sampleFile -Isrc/shiftBed -Isrc/shuffleBed -Isrc/slopBed -Isrc/sortBed
> -Isrc/spacingFile -Isrc/split -Isrc/subtractFile -Isrc/summaryFile
> -Isrc/tagBam -Isrc/unionBedGraphs -Isrc/windowBed -Isrc/windowMaker
> -Isrc/utils/FileRecordTools -Isrc/utils/FileRecordTools/FileReaders
> -Isrc/utils/FileRecordTools/Records -Isrc/utils/bedFile -Isrc/utils/BinTree
> -Isrc/utils/version -Isrc/utils/bedGraphFile -Isrc/utils/chromsweep
> -Isrc/utils/Contexts -Isrc/utils/general -Isrc/utils/gzstream
> -Isrc/utils/fileType -Isrc/utils/bedFilePE -Isrc/utils/KeyListOps
> -Isrc/utils/NewChromsweep -Isrc/utils/sequenceUtilities -Isrc/utils/tabFile
> -Isrc/utils/BamTools-Ancillary -Isrc/utils/BlockedIntervals -Isrc/utils/Fasta
> -Isrc/utils/VectorOps -Isrc/utils/GenomeFile -Isrc/utils/RecordOutputMgr
> -Isrc/utils/ToolBase -Isrc/utils/driver -Isrc/utils/BamTools
> -Isrc/utils/BamTools/include -Isrc/utils/htslib -Isrc/utils/lineFileUtilities
> -Isrc/utils/Point -Isrc/utils/stringUtilities -Wdate-time -D_FORTIFY_SOURCE=2
> -MT obj/version.o -MMD -MP -MF obj/version.Td -c -o obj/version.o
> src/utils/version/version.cpp
> src/utils/version/version.cpp:2:10: fatal error: version_git.h: No such file
> or directory
> 2 | #include "version_git.h"
> | ^~~~~~~~~~~~~~~
> compilation terminated.
> In file included from /usr/include/c++/14/ios:44,
> from /usr/include/c++/14/istream:40,
> from /usr/include/c++/14/sstream:40,
> from src/utils/lineFileUtilities/lineFileUtilities.h:8,
> from src/genomeCoverageBed/genomeCoverageBed.cpp:12:
> In member function ‘std::streamsize
> std::ios_base::precision(std::streamsize)’,
> inlined from ‘void BedGenomeCoverage::ReportChromCoverageBedGraph(const
> std::vector<DEPTH>&, const CHRPOS&, const std::string&)’ at
> src/genomeCoverageBed/genomeCoverageBed.cpp:541:23:
> /usr/include/c++/14/bits/ios_base.h:764:20: warning: ‘prec’ may be used
> uninitialized [-Wmaybe-uninitialized]
> 764 | _M_precision = __prec;
> | ~~~~~~~~~~~~~^~~~~~~~
> src/genomeCoverageBed/genomeCoverageBed.cpp: In member function ‘void
> BedGenomeCoverage::ReportChromCoverageBedGraph(const std::vector<DEPTH>&,
> const CHRPOS&, const std::string&)’:
> src/genomeCoverageBed/genomeCoverageBed.cpp:491:16: note: ‘prec’ was declared
> here
> 491 | streamsize prec;
> | ^~~~
> make[2]: *** [src/utils/version/Makefile.frag:4: obj/version.o] Error 1
> shuffle=3614032645
The full build log is available from:
http://qa-logs.debian.net/2025/05/05/shuffle/random/bedtools_2.31.1+dfsg-2_unstable_random.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
--- End Message ---
--- Begin Message ---
Source: bedtools
Source-Version: 2.31.1+dfsg-3
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
bedtools, 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 bedtools 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: SHA512
Format: 1.8
Date: Wed, 24 Dec 2025 15:10:11 +0100
Source: bedtools
Architecture: source
Version: 2.31.1+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1104751 1105730
Changes:
bedtools (2.31.1+dfsg-3) unstable; urgency=medium
.
[ Andreas Tille ]
* d/watch: version=5
* Standards-Version: 4.7.3 (routine-update)
* Remove Priority field to comply with Debian Policy 4.7.3 (routine-
update)
* d/copyright: review
.
[ Lucas Nussbaum ]
* Fix FTBFS with GNUMAKEFLAGS=--shuffle=random
Closes: #1104751, #1105730
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