[Debian-med-packaging] Bug#985144: pigx-rnaseq -- Fails to build reproducibly: different binaries on usrmerge system

[Nilesh Patra]

Package: pigx-rnaseq
Version: 0.0.10+ds-2
Severity: normal
Tags: patch
User: reproducible-builds at lists.alioth.debian.org
Usertags: usrmerge
X-Debbugs-Cc: nilesh at debian.org, reproducible-bugs at lists.alioth.debian.org

Dear Maintainer,

When built on usrmerge system, the binaries gunzip and sed end up having
different paths i.e. /bin/foo and /usr/bin/foo

In order to mitigate this, it can be passed directly to configure so
that the location is ascertained.

The patch for the same is commited into salsa here[1]

This should be ready for upload after bullseye release. I am reporting bug so that
this change is not lost somehow.

[1]: https://salsa.debian.org/med-team/pigx-rnaseq/-/commit/70b31a920f5985c70214f77e47a5e3b26ee42f07

Nilesh

-- System Information:
Debian Release: bullseye/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)

Kernel: Linux 5.7.0-2-amd64 (SMP w/8 CPU threads)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: unable to detect

Versions of packages pigx-rnaseq depends on:
pn  fastqc                       <none>
ii  libjs-jquery-datatables      1.10.21+dfsg-1
ii  libjs-jquery-tablesorter     1:2.31.3+dfsg1-1
pn  multiqc                      <none>
pn  pandoc-citeproc              <none>
ii  python3                      3.9.1-1
pn  python3-deeptools            <none>
pn  python3-htseq                <none>
pn  r-bioc-deseq2                <none>
pn  r-bioc-rtracklayer           <none>
pn  r-bioc-summarizedexperiment  <none>
pn  r-bioc-tximport              <none>
pn  r-cran-corrplot              <none>
ii  r-cran-crosstalk             1.1.0.1+dfsg-3
ii  r-cran-data.table            1.13.0+dfsg-1
ii  r-cran-dt                    0.15+dfsg-2
ii  r-cran-ggplot2               3.3.2+dfsg-2
pn  r-cran-ggrepel               <none>
pn  r-cran-gprofiler             <none>
pn  r-cran-pheatmap              <none>
pn  r-cran-plotly                <none>
pn  r-cran-reshape2              <none>
pn  r-cran-rjson                 <none>
ii  r-cran-rlang                 0.4.7-1
ii  r-cran-rmarkdown             2.3+dfsg-2
ii  r-cran-scales                1.1.1-1
pn  rna-star                     <none>
pn  salmon                       <none>
ii  samtools                     1.10-4
ii  snakemake                    5.24.1-1
pn  trim-galore                  <none>

pigx-rnaseq recommends no packages.

pigx-rnaseq suggests no packages.