Source: snippy Version: 4.6.0+dfsg-3 Severity: serious Justification: FTBFS Tags: bookworm sid ftbfs User: lu...@debian.org Usertags: ftbfs-20230216 ftbfs-bookworm
Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[2]: Entering directory '/<<PKGBUILDDIR>>/test' > mkdir -p S1 > wgsim -S 1 \ > -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ > example.fna S1/R2.fq S1/R1.fq > S1/dwgsim.tab > [wgsim] seed = 1 > [wgsim_core] calculating the total length of the reference sequence... > [wgsim_core] 3 sequences, total length: 317336 > mkdir -p S2 > wgsim -S 2 \ > -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ > example.fna S2/R2.fq S2/R1.fq > S2/dwgsim.tab > [wgsim] seed = 2 > [wgsim_core] calculating the total length of the reference sequence... > [wgsim_core] 3 sequences, total length: 317336 > mkdir -p S3 > wgsim -S 3 \ > -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ > example.fna S3/R2.fq S3/R1.fq > S3/dwgsim.tab > [wgsim] seed = 3 > [wgsim_core] calculating the total length of the reference sequence... > [wgsim_core] 3 sequences, total length: 317336 > mkdir -p S4 > wgsim -S 4 \ > -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ > example.fna S4/R2.fq S4/R1.fq > S4/dwgsim.tab > [wgsim] seed = 4 > [wgsim_core] calculating the total length of the reference sequence... > [wgsim_core] 3 sequences, total length: 317336 > ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S1 --R1 > S1/R1.fq --R2 S1/R2.fq > [01:21:32] This is snippy 4.6.0 > [01:21:32] Written by Torsten Seemann > [01:21:32] Obtained from https://github.com/tseemann/snippy > [01:21:32] Detected operating system: linux > [01:21:32] Enabling bundled linux tools. > [01:21:32] Found bwa - /usr/bin/bwa > [01:21:32] Found bcftools - /usr/bin/bcftools > [01:21:32] Found samtools - /usr/bin/samtools > [01:21:32] Found java - /usr/bin/java > [01:21:32] Found snpEff - /usr/bin/snpEff > [01:21:32] Found samclip - /usr/bin/samclip > [01:21:32] Found seqtk - /usr/bin/seqtk > [01:21:32] Found parallel - /usr/bin/parallel > [01:21:32] Found freebayes - /usr/bin/freebayes > [01:21:32] Found freebayes-parallel - > /usr/share/freebayes/scripts/freebayes-parallel > [01:21:32] Found fasta_generate_regions.py - > /usr/share/freebayes/scripts/fasta_generate_regions.py > [01:21:32] Found vcfstreamsort - /usr/bin/vcfstreamsort > [01:21:32] Found vcfuniq - /usr/bin/vcfuniq > [01:21:32] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader > [01:21:32] Found gzip - /bin/gzip > [01:21:32] Found vt - /usr/bin/vt > [01:21:32] Found snippy-vcf_to_tab - /<<PKGBUILDDIR>>/bin/snippy-vcf_to_tab > [01:21:32] Found snippy-vcf_report - /<<PKGBUILDDIR>>/bin/snippy-vcf_report > [01:21:32] Checking version: samtools --version is >= 1.7 - ok, have 1.16 > [01:21:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.16 > [01:21:32] Need freebayes --version >= 1.1 but you have 0 - please upgrade it. > make[2]: *** [Makefile:32: S1/snps.tab] Error 2 The full build log is available from: http://qa-logs.debian.net/2023/02/16/snippy_4.6.0+dfsg-3_unstable.log All bugs filed during this archive rebuild are listed at: https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20230216;users=lu...@debian.org or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230216&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results 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! 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.
