Debian Bug report logs - #993304
samtools: 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: samtools: please make the build reproducible

Date: Mon, 30 Aug 2021 14:55:21 +0100

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

Source: samtools
Version: 1.13-1
Severity: wishlist
Tags: patch
User: reproducible-builds@lists.alioth.debian.org
Usertags: buildpath
X-Debbugs-Cc: reproducible-bugs@lists.alioth.debian.org

Hi,

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

This is because it includes the build flags in the binary to include
in --version output, but this will encode the buildpath due to
dpkg-buildflags(1) embedding (for example) -ffile-prefix-map.

Patch attached that normalises these paths to a placeholder entry
using sed(1).

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


Regards,

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

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

Message #10 received at 993304-close@bugs.debian.org (full text, mbox, reply):

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

To: 993304-close@bugs.debian.org

Subject: Bug#993304: fixed in samtools 1.13-2

Date: Mon, 30 Aug 2021 15:03:53 +0000

Source: samtools
Source-Version: 1.13-2
Done: Andreas Tille <tille@debian.org>

We believe that the bug you reported is fixed in the latest version of
samtools, 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 993304@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated samtools 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: Mon, 30 Aug 2021 16:32:37 +0200
Source: samtools
Architecture: source
Version: 1.13-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Closes: 993304
Changes:
 samtools (1.13-2) unstable; urgency=medium
 .
   [ Étienne Mollier ]
   * d/control: bump B-D libhts-dev (>= 1.13~); builds otherwise break against
     older htslib versions.
 .
   [ Andreas Tille ]
   * make the build reproducible (Thanks for the patch to Chris Lamb)
     Closes: #993304
Checksums-Sha1:
 3583faa3cfb03a9424b2d2efb58583c300ae1762 2290 samtools_1.13-2.dsc
 83d77dce5c46721c7e15686aa06f5a57f910f46a 20600 samtools_1.13-2.debian.tar.xz
 15191f28cd20a04fc884131f046d1c352b81a3ef 7199 samtools_1.13-2_amd64.buildinfo
Checksums-Sha256:
 bb17e35ecad1711feace7392c3a67d000116866433b6b1765ca306621ad55499 2290 samtools_1.13-2.dsc
 c032291accc4201d51dbffd3af6fba038522fc9102b6558de1700fcbd4920842 20600 samtools_1.13-2.debian.tar.xz
 c71f3bebe84833d7e0d968ab1098ec710c27f592abdb48f6b03c6ae5651cd06e 7199 samtools_1.13-2_amd64.buildinfo
Files:
 d8ef89e3c7fe6983d5c0c9c0d2e63c2b 2290 science optional samtools_1.13-2.dsc
 51058b7f72bb9ce3f16b510b17e280d2 20600 science optional samtools_1.13-2.debian.tar.xz
 7bcaf6fbc54debcc3d4a0945a1ff424f 7199 science optional samtools_1.13-2_amd64.buildinfo

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