[Debian-med-packaging] Bug#1031465: snippy: FTBFS: make[2]: *** [Makefile:32: S1/snps.tab] Error 2

[Lucas Nussbaum]

Source: snippy
Version: 4.6.0+dfsg-3
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at 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=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230216&fusertaguser=lucas@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.