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
