[Debian-med-packaging] Bug#1031580: pigx-rnaseq: FTBFS in testing: E: Build killed with signal TERM after 150 minutes of inactivity

[Lucas Nussbaum]

Source: pigx-rnaseq
Version: 0.1.0-1.1
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20230217 ftbfs-bookworm

Hi,

During a rebuild of all packages in testing (bookworm), your package failed
to build on amd64.


Relevant part (hopefully):
>     input: /<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /<<PKGBUILDDIR>>/tests/output/colData.tsv
>     output: /<<PKGBUILDDIR>>/tests/output/report/hisat2/analysis1.deseq.report.html
>     log: /<<PKGBUILDDIR>>/tests/output/logs/hisat2/analysis1.report.log
>     jobid: 45
>     reason: Missing output files: /<<PKGBUILDDIR>>/tests/output/report/hisat2/analysis1.deseq.report.html; Input files updated by another job: /<<PKGBUILDDIR>>/tests/output/colData.tsv, /<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv
>     wildcards: analysis=analysis1
>     resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815
> 
> /usr/bin/Rscript --vanilla /<<PKGBUILDDIR>>/scripts/runDeseqReport.R --logo=/<<PKGBUILDDIR>>/images/Logo_PiGx.png --prefix='analysis1' --reportFile=/<<PKGBUILDDIR>>/scripts/deseqReport.Rmd --countDataFile=/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv --colDataFile=/<<PKGBUILDDIR>>/tests/output/colData.tsv --gtfFile=/<<PKGBUILDDIR>>/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates=''  --workdir=/<<PKGBUILDDIR>>/tests/output/report/hisat2 --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.' --selfContained='True' >> /<<PKGBUILDDIR>>/tests/output/logs/hisat2/analysis1.report.log 2>&1
> [Sat Feb 18 07:58:43 2023]
> Finished job 38.
> 35 of 48 steps (73%) done
> [Sat Feb 18 07:58:57 2023]
> Finished job 45.
> 36 of 48 steps (75%) done
> E: Build killed with signal TERM after 150 minutes of inactivity


The full build log is available from:
http://qa-logs.debian.net/2023/02/17/pigx-rnaseq_0.1.0-1.1_testing.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20230217;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230217&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.