Debian Bug report logs - #842356
bio-eagle: 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: bio-eagle: please make the build reproducible

Date: Fri, 28 Oct 2016 13:01:08 +0100

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

Source: bio-eagle
Version: 2.3-2
Severity: wishlist
Tags: patch
User: reproducible-builds@lists.alioth.debian.org
Usertags: fileordering
X-Debbugs-Cc: reproducible-builds@lists.alioth.debian.org

Hi,

Whilst working on the Reproducible Builds effort [0], we noticed
that bio-eagle could not be built reproducibly.

Whilst you correctly pass --sort=name, the wildcard is already expanded
in a locale-specific manner.

Patch attached.

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


Regards,

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

[bio-eagle.diff.txt (text/plain, attachment)]

Message #10 received at 842356@bugs.debian.org (full text, mbox, reply):

From: Chris Lamb <lamby@debian.org>

To: 842356@bugs.debian.org

Subject: Re: bio-eagle: please make the build reproducible

Date: Fri, 28 Oct 2016 19:07:36 +0100

Hi,

> Patch attached

Do note that his slightly changes the directory structure of the
.tar.xz. If you care (enough!), you can probably use tar -C instead;
what I was trying to avoid was an ugly:

  cd examples && find -type f | LC_ALL=C sort | tar … -T -

.. call :) Will leave it up to your judgement as maintaner.


Regards,

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

Message #15 received at 842356@bugs.debian.org (full text, mbox, reply):

From: Dylan <bob.dybian@gmail.com>

To: 842356@bugs.debian.org

Cc: lamby@debian.org

Date: Mon, 31 Oct 2016 00:07:28 +0100

Hi Chris,
Thanks for your bug report and your patch.

I did not apply it but I have removed the (autopkg)test which causes
troubles in Continuous Integration and by the way in reproducibility.

Best regards,
Dylan

Message #20 received at 842356@bugs.debian.org (full text, mbox, reply):

From: Chris Lamb <lamby@debian.org>

To: Dylan <bob.dybian@gmail.com>, 842356@bugs.debian.org

Subject: Re:

Date: Mon, 31 Oct 2016 09:35:17 +0000

Dyland wrote:

> I did not apply it but I have removed the (autopkg)test which causes
> troubles in Continuous Integration and by the way in reproducibility.

Hm? I did not think it was the tests that was causing reproucibility
issues; it was the creation of the examples.tar.gz.


Regards,

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

Message #25 received at 842356@bugs.debian.org (full text, mbox, reply):

From: Dylan <bob.dybian@gmail.com>

To: Chris Lamb <lamby@debian.org>

Cc: 842356@bugs.debian.org

Subject: Re:

Date: Mon, 31 Oct 2016 22:41:59 +0100

Hi,

2016-10-31 10:35 GMT+01:00 Chris Lamb <lamby@debian.org>:
>
> Hm? I did not think it was the tests that was causing reproucibility
> issues; it was the creation of the examples.tar.gz.
>

Oops, sorry I took a shortcut. I simplified the tests by removing one
which cause trouble, so I removed the creation of the examples.tar.gz
in the rule file. It should not be anymore reproducibility issues in
this way.


Best regards,
Dylan

Message #30 received at 842356-close@bugs.debian.org (full text, mbox, reply):

From: Dylan Aïssi <bob.dybian@gmail.com>

To: 842356-close@bugs.debian.org

Subject: Bug#842356: fixed in bio-eagle 2.3-3

Date: Wed, 02 Nov 2016 21:18:28 +0000

Source: bio-eagle
Source-Version: 2.3-3

We believe that the bug you reported is fixed in the latest version of
bio-eagle, 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 842356@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Dylan Aïssi <bob.dybian@gmail.com> (supplier of updated bio-eagle 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, 30 Oct 2016 23:26:33 +0100
Source: bio-eagle
Binary: bio-eagle bio-eagle-examples
Architecture: source
Version: 2.3-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Dylan Aïssi <bob.dybian@gmail.com>
Description:
 bio-eagle  - Haplotype phasing within a genotyped cohort or using a phased ref
 bio-eagle-examples - Examples for bio-eagle
Closes: 842356
Changes:
 bio-eagle (2.3-3) unstable; urgency=medium
 .
   * Remove the test which creates a false positive in the autopkgtest
     by emitting some warnings. (Closes: #842356)
Checksums-Sha1:
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 9766f83ba17a8cf3c4f39d95f0dfe6e6f7495f5c 6548 bio-eagle_2.3-3.debian.tar.xz
Checksums-Sha256:
 d421e678c85ea39217b0f81273e306b173130dc06dc36f9d1981f79ddf9beada 2126 bio-eagle_2.3-3.dsc
 63479516647de87a1bb34b8bea4d05424095f508b3c67e715eb8f4091daf3d00 6548 bio-eagle_2.3-3.debian.tar.xz
Files:
 340196cdbe3112422f6d3508688a1a9c 2126 science optional bio-eagle_2.3-3.dsc
 6b3e7b7ab87b6160ca2cd965ef97235b 6548 science optional bio-eagle_2.3-3.debian.tar.xz

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From: "Quatif Group of Companies" <sefca@fca.unam.mx>

Subject: Business Proposal

Date: Sat, 21 Jan 2017 01:24:53 -0600

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