[Debian-med-packaging] Bug#1105730: bedtools: FTBFS with make --shuffle=random: src/utils/version/version.cpp:2:10: fatal error: version_git.h: No such file or directory

[Lucas Nussbaum]

Source: bedtools
Version: 2.31.1+dfsg-2
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
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