Source: gmap Version: 2020-06-30+ds-1 Severity: serious Justification: FTBFS on amd64 Tags: bullseye sid ftbfs Usertags: ftbfs-20200802 ftbfs-bullseye
Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" > -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. > -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro > -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o > gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o > gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o > gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o > gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o > gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o > gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o > gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o > gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o > gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o > gmapl_nosimd-popcount.o gmapl_nosimd-genome_sites.o > gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o > gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o > gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o > gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-gregion.o > gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o > gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o > gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o > gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-transcript.o gmapl_nosimd-intron.o > gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o > gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o > gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o > gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o > gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o > gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o > gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o > gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o > gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o > gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o > gmapl_nosimd-samheader.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o > gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o > gmapl_nosimd-gmap.o -lz -lbz2 -lm > /usr/bin/ld: gmap_nosimd-dynprog_end.o:./src/dynprog_end.c:112: multiple > definition of `homopolymerp'; > gmap_nosimd-dynprog_single.o:./src/dynprog_single.c:94: first defined here > /usr/bin/ld: gmapl_nosimd-dynprog_end.o:./src/dynprog_end.c:112: multiple > definition of `homopolymerp'; > gmapl_nosimd-dynprog_single.o:./src/dynprog_single.c:94: first defined here > gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" > -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 > -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd > gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o > gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o > gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o > gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o > gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o > gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o > gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o > gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o > gsnap_nosimd-genome128_hr.o gsnap_nosimd-genome128_consec.o > gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o > gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-merge-uint4.o > gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o > gsnap_nosimd-regiondb.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o > gsnap_nosimd-maxent_hr.o gsnap_nosimd-mdprint.o gsnap_nosimd-cigar.o > gsnap_nosimd-samprint.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o > gsnap_nosimd-shortread.o gsnap_nosimd-substring.o gsnap_nosimd-junction.o > gsnap_nosimd-transcript.o gsnap_nosimd-method.o gsnap_nosimd-stage3hr.o > gsnap_nosimd-ladder.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o > gsnap_nosimd-maxent.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o > gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o > gsnap_nosimd-hitlistpool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o > gsnap_nosimd-knownsplicing.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o > gsnap_nosimd-bitpack64-access.o gsnap_nosimd-univdiag.o > gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-intersect.o > gsnap_nosimd-kmer-search.o gsnap_nosimd-path-solve.o > gsnap_nosimd-extension-search.o gsnap_nosimd-segment-search.o > gsnap_nosimd-terminal.o gsnap_nosimd-distant-rna.o gsnap_nosimd-distant-dna.o > gsnap_nosimd-uint8table_rh.o gsnap_nosimd-uinttable_rh.o > gsnap_nosimd-stage1hr.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o > gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o > gsnap_nosimd-outbuffer.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o > gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm > collect2: error: ld returned 1 exit status The full build log is available from: http://qa-logs.debian.net/2020/08/02/gmap_2020-06-30+ds-1_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! 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.
