Debian Bug report logs - #985144
pigx-rnaseq -- Fails to build reproducibly: different binaries on usrmerge system

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Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Nilesh Patra <nilesh@debian.org>

To: Debian Bug Tracking System <submit@bugs.debian.org>

Subject: pigx-rnaseq -- Fails to build reproducibly: different binaries on usrmerge system

Date: Sat, 13 Mar 2021 16:09:53 +0000

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

Message #10 received at 985144-close@bugs.debian.org (full text, mbox, reply):

From: Debian FTP Masters <ftpmaster@ftp-master.debian.org>

To: 985144-close@bugs.debian.org

Subject: Bug#985144: fixed in pigx-rnaseq 0.0.19-1

Date: Wed, 15 Sep 2021 21:18:54 +0000

Source: pigx-rnaseq
Source-Version: 0.0.19-1
Done: Nilesh Patra <nilesh@debian.org>

We believe that the bug you reported is fixed in the latest version of
pigx-rnaseq, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 985144@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Nilesh Patra <nilesh@debian.org> (supplier of updated pigx-rnaseq package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Thu, 16 Sep 2021 02:16:16 +0530
Source: pigx-rnaseq
Architecture: source
Version: 0.0.19-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Closes: 985144
Changes:
 pigx-rnaseq (0.0.19-1) unstable; urgency=medium
 .
   * Team Upload.
   [ Steffen Moeller ]
   * New upstream version 0.0.19
   * Bumped policy to 4.6.0
   * New dependencies
     - hisat2 - upstream changed default genomic aligner
     - fastp - fastq file processing
     - r-cran-gprofiler2
   * d/u/metadata: Added ref to SciCrunch RRID:SCR_016476
   * overriding dh_fixperms on permissions in /usr/libexec
   * Added ref to guix
 .
   [ Nilesh Patra ]
   * Remove d/p/salmon_sa.bin2pos.bin.patch: Merged upstream
   * Pass gunzip and sed paths during configure
     so it builds reproducible on usrmerge system
     (Closes: #985144)
   * Add d/common: The pigx-rnaseq is a submodule needed by this package,
     But this has no code, and does not look worth it to package.
     Since its size is very less, it has been added in debian/ dir
     Changes have also been mentioned in d/copyright
   * Add B-D on r-cran-ggpubr and r-cran-gprofiler2
Checksums-Sha1:
 cff2c6485c5556e036b60d85250dcd6cb295df13 2851 pigx-rnaseq_0.0.19-1.dsc
 ea3821f683285bae6e6b7f3d5383c9844f6dc000 4418300 pigx-rnaseq_0.0.19.orig.tar.xz
 45c077eb6c5cfbd168a06aa4af1d5582165686f2 12280 pigx-rnaseq_0.0.19-1.debian.tar.xz
 b48253fcd028dbf28fcf6eb1bed42854df1036cf 27754 pigx-rnaseq_0.0.19-1_amd64.buildinfo
Checksums-Sha256:
 7426d2d7c4a5b348708a9f20628fb62aa6a7019776701a7243cc4592becd2e68 2851 pigx-rnaseq_0.0.19-1.dsc
 e3e603110b354b2c3a901908e4fc32580245dfb6335d1cf27d0f7c06af75b6ef 4418300 pigx-rnaseq_0.0.19.orig.tar.xz
 2677ee5a6dac784ef02c9cba36485120e33b890b9d138843cc43e20bd1c60656 12280 pigx-rnaseq_0.0.19-1.debian.tar.xz
 41637b85548ac0a18ad720e0fb968e68db3eb122fb75a17f71efe6a49974cbf7 27754 pigx-rnaseq_0.0.19-1_amd64.buildinfo
Files:
 686782ff242a125c138a2efca9d2c576 2851 science optional pigx-rnaseq_0.0.19-1.dsc
 5d58c6d9634a7c3086a357759938b840 4418300 science optional pigx-rnaseq_0.0.19.orig.tar.xz
 7117be8e7204bc9f1a2b7d3711377f8b 12280 science optional pigx-rnaseq_0.0.19-1.debian.tar.xz
 3c5731f3534c30cbfd5857f7871fb227 27754 science optional pigx-rnaseq_0.0.19-1_amd64.buildinfo

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