Debian Bug report logs - #997000
snakemake: please make the build reproducible

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

From: "Chris Lamb" <lamby@debian.org>

To: submit@bugs.debian.org

Subject: snakemake: please make the build reproducible

Date: Fri, 22 Oct 2021 09:26:46 +0100

[Message part 1 (text/plain, inline)]

Source: snakemake
Version: 6.9.1+dfsg1-3
Severity: wishlist
Tags: patch
User: reproducible-builds@lists.alioth.debian.org
Usertags: randomness
X-Debbugs-Cc: reproducible-bugs@lists.alioth.debian.org

Hi,

Whilst working on the Reproducible Builds effort [0] we noticed that
snakemake could not be built reproducibly.

This is because it generates and ships a Graphviz .dot file during the
tests and this file has a non-deterministic ordering. Also, the PDF
file generated from this very .dot file contains a created date in its
headers.

Patch attached that fixes the non-determinism in the .dot file
generation and prevents the Debian packaging from shipping the
non-deterministic PDF version.

 [0] https://reproducible-builds.org/


Regards,

-- 
      ,''`.
     : :'  :     Chris Lamb
     `. `'`      lamby@debian.org / chris-lamb.co.uk
       `-

[snakemake.diff.txt (text/plain, attachment)]

Message #10 received at 997000@bugs.debian.org (full text, mbox, reply):

From: Nilesh Patra <nilesh@onenetbeyond.org>

To: Chris Lamb <lamby@debian.org>, 997000@bugs.debian.org, submit@bugs.debian.org

Subject: Re: [Debian-med-packaging] Bug#997000: snakemake: please make the build reproducible

Date: Fri, 22 Oct 2021 18:14:07 +0530

[Message part 1 (text/plain, inline)]

On 10/22/21 1:56 PM, Chris Lamb wrote:
> Source: snakemake
> Version: 6.9.1+dfsg1-3
> Severity: wishlist
> Tags: patch
> User: reproducible-builds@lists.alioth.debian.org
> Usertags: randomness
> X-Debbugs-Cc: reproducible-bugs@lists.alioth.debian.org
> 
> Hi,
> 
> Whilst working on the Reproducible Builds effort [0] we noticed that
> snakemake could not be built reproducibly.
> 
> This is because it generates and ships a Graphviz .dot file during the
> tests and this file has a non-deterministic ordering. Also, the PDF
> file generated from this very .dot file contains a created date in its
> headers.
> 
> Patch attached that fixes the non-determinism in the .dot file
> generation and prevents the Debian packaging from shipping the
> non-deterministic PDF version.

Thanks, I will upload with this patch in the next couple of days (by sunday night)

Nilesh

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Message #15 received at 997000-close@bugs.debian.org (full text, mbox, reply):

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

To: 997000-close@bugs.debian.org

Subject: Bug#997000: fixed in snakemake 6.9.1+dfsg1-4

Date: Sat, 23 Oct 2021 19:35:10 +0000

Source: snakemake
Source-Version: 6.9.1+dfsg1-4
Done: Nilesh Patra <nilesh@debian.org>

We believe that the bug you reported is fixed in the latest version of
snakemake, 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 997000@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 snakemake 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: Sun, 24 Oct 2021 00:18:19 +0530
Source: snakemake
Architecture: source
Version: 6.9.1+dfsg1-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Closes: 997000
Changes:
 snakemake (6.9.1+dfsg1-4) unstable; urgency=medium
 .
   * Team Upload.
   * Add patch to make build reproducible (Closes: #997000)
     + Thanks to Chris Lamb!
Checksums-Sha1:
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 116a709c01eb74b78b6143fd4b9e76f2884e170e 24864 snakemake_6.9.1+dfsg1-4.debian.tar.xz
 344fe3467346405eab668b8005c859dec99791ca 16193 snakemake_6.9.1+dfsg1-4_amd64.buildinfo
Checksums-Sha256:
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Files:
 b86bd819ff01706bef36bc74a3e67964 3266 science optional snakemake_6.9.1+dfsg1-4.dsc
 b2f134c978a7cb7c69b3f6eeba073f33 24864 science optional snakemake_6.9.1+dfsg1-4.debian.tar.xz
 ade9bccbd9965a5f03da125505a243cd 16193 science optional snakemake_6.9.1+dfsg1-4_amd64.buildinfo

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