Your message dated Wed, 6 Dec 2023 21:29:42 +0530
with message-id <[email protected]>
and subject line [FIXED] snippy: FTBFS: make[2]: *** [Makefile:32: S1/snps.tab]
Error 2
has caused the Debian Bug report #1031465,
regarding snippy: FTBFS: make[2]: *** [Makefile:32: S1/snps.tab] Error 2
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1031465: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1031465
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: snippy
Version: 4.6.0+dfsg-3
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: [email protected]
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;[email protected]
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230216&[email protected]&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.
--- End Message ---
--- Begin Message ---
This seems fixed and is not reproducible anymore. Closing.
Best,
Nilesh
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