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to debian-bugs-dist@lists.debian.org, reproducible-bugs@lists.alioth.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>: Bug#961494; Package src:bowtie2.
(Mon, 25 May 2020 09:48:04 GMT) (full text, mbox, link).
Acknowledgement sent
to "Chris Lamb" <lamby@debian.org>:
New Bug report received and forwarded. Copy sent to reproducible-bugs@lists.alioth.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>.
(Mon, 25 May 2020 09:48:04 GMT) (full text, mbox, link).
Subject: bowtie2: please make the build reproducible
Date: Mon, 25 May 2020 10:43:39 +0100
Source: bowtie2
Version: 2.4.1-4
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
bowtie2 could not be built reproducibly.
Whilst you do patch out -fdebug-prefix-map in debian/patches/reproducible.patch,
you al
Patch attached.
[0] https://reproducible-builds.org/
Regards,
--
,''`.
: :' : Chris Lamb
`. `'` lamby@debian.org / chris-lamb.co.uk
`-
Information forwarded
to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>: Bug#961494; Package src:bowtie2.
(Mon, 25 May 2020 10:00:04 GMT) (full text, mbox, link).
Acknowledgement sent
to "Chris Lamb" <lamby@debian.org>:
Extra info received and forwarded to list. Copy sent to Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>.
(Mon, 25 May 2020 10:00:04 GMT) (full text, mbox, link).
Subject: Re: bowtie2: please make the build reproducible
Date: Mon, 25 May 2020 10:49:28 +0100
Hi,
> […]
This should have read:
Whilst you do patch out -fdebug-prefix-map in
debian/patches/reproducible.patch, you also need to filter
-ffile-prefix-map.
Regards,
--
,''`.
: :' : Chris Lamb
`. `'` lamby@debian.org / chris-lamb.co.uk
`-
Information forwarded
to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>: Bug#961494; Package src:bowtie2.
(Mon, 25 May 2020 10:00:05 GMT) (full text, mbox, link).
Acknowledgement sent
to "Chris Lamb" <lamby@debian.org>:
Extra info received and forwarded to list. Copy sent to Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>.
(Mon, 25 May 2020 10:00:05 GMT) (full text, mbox, link).
Subject: Re: bowtie2: please make the build reproducible
Date: Mon, 25 May 2020 10:49:28 +0100
Hi,
> […]
This should have read:
Whilst you do patch out -fdebug-prefix-map in
debian/patches/reproducible.patch, you also need to filter
-ffile-prefix-map.
Regards,
--
,''`.
: :' : Chris Lamb
`. `'` lamby@debian.org / chris-lamb.co.uk
`-
Information forwarded
to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>: Bug#961494; Package src:bowtie2.
(Mon, 25 May 2020 10:00:06 GMT) (full text, mbox, link).
Acknowledgement sent
to "Chris Lamb" <lamby@debian.org>:
Extra info received and forwarded to list. Copy sent to Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>.
(Mon, 25 May 2020 10:00:07 GMT) (full text, mbox, link).
Subject: Re: bowtie2: please make the build reproducible
Date: Mon, 25 May 2020 10:49:28 +0100
Hi,
> […]
This should have read:
Whilst you do patch out -fdebug-prefix-map in
debian/patches/reproducible.patch, you also need to filter
-ffile-prefix-map.
Regards,
--
,''`.
: :' : Chris Lamb
`. `'` lamby@debian.org / chris-lamb.co.uk
`-
Information forwarded
to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>: Bug#961494; Package src:bowtie2.
(Mon, 25 May 2020 12:42:02 GMT) (full text, mbox, link).
Acknowledgement sent
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(Mon, 25 May 2020 12:42:02 GMT) (full text, mbox, link).
Subject: Re: Bug#961494: bowtie2: please make the build reproducible
Date: Mon, 25 May 2020 14:39:40 +0200
Hi Chris,
On Mon, May 25, 2020 at 10:49:28AM +0100, Chris Lamb wrote:
> This should have read:
>
> Whilst you do patch out -fdebug-prefix-map in
> debian/patches/reproducible.patch, you also need to filter
> -ffile-prefix-map.
I've tried this in Git[1] but the resulting bowtie2 package fails the
autopkgtest in my pbuilder environment. I remember issues with
autopkgtest in pbuilder before and I suspect this might be the case
here as well. However, before I really upload I'd invite others to
have a look.
Kind regards
Andreas.
[1] https://salsa.debian.org/med-team/bowtie2/-/commit/97052bc2de1b271f368dd8415cfafde5356e2fe8
--
http://fam-tille.de
Information forwarded
to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>: Bug#961494; Package src:bowtie2.
(Mon, 25 May 2020 15:21:04 GMT) (full text, mbox, link).
Acknowledgement sent
to Nilesh Patra <npatra974@gmail.com>:
Extra info received and forwarded to list. Copy sent to Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>.
(Mon, 25 May 2020 15:21:04 GMT) (full text, mbox, link).
On Mon, 25 May 2020 at 20:10, Andreas Tille <tille@debian.org> wrote:
> Hi Chris,
>
> On Mon, May 25, 2020 at 10:49:28AM +0100, Chris Lamb wrote:
> > This should have read:
> >
> > Whilst you do patch out -fdebug-prefix-map in
> > debian/patches/reproducible.patch, you also need to filter
> > -ffile-prefix-map.
>
> I've tried this in Git[1] but the resulting bowtie2 package fails the
> autopkgtest in my pbuilder environment. I remember issues with
> autopkgtest in pbuilder before and I suspect this might be the case
> here as well. However, before I really upload I'd invite others to
> have a look.
>
I can confirm that this passes for me.
autopkgtest [20:46:44]: test binary-run: [-----------------------
autopkgtest [20:46:45]: test binary-run: -----------------------]
autopkgtest [20:46:45]: test binary-run: - - - - - - - - - - results - - -
- - - - - - -
binary-run PASS
autopkgtest [20:46:45]: @@@@@@@@@@@@@@@@@@@@ summary
check-wo-arguments PASS
indexing-ref-genome PASS
binary-run PASS
Just maybe, this is a false positive again, at your end.
[1]
> https://salsa.debian.org/med-team/bowtie2/-/commit/97052bc2de1b271f368dd8415cfafde5356e2fe8
Kind regards,
Nilesh
Information forwarded
to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>: Bug#961494; Package src:bowtie2.
(Mon, 25 May 2020 17:36:03 GMT) (full text, mbox, link).
Acknowledgement sent
to Pranav Ballaney <ballaneypranav@gmail.com>:
Extra info received and forwarded to list. Copy sent to Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>.
(Mon, 25 May 2020 17:36:03 GMT) (full text, mbox, link).
Hi everyone,
The tests pass for me as well.
autopkgtest [22:46:32]: test binary-run: - - - - - - - - - - results - - -
- - - - - - -
binary-run PASS
autopkgtest [22:46:32]: @@@@@@@@@@@@@@@@@@@@ summary
check-wo-arguments PASS
indexing-ref-genome PASS
binary-run PASS
Regards,
Pranav
ᐧ
On Mon, May 25, 2020 at 8:49 PM Nilesh Patra <npatra974@gmail.com> wrote:
>
>
> On Mon, 25 May 2020 at 20:10, Andreas Tille <tille@debian.org> wrote:
>
>> Hi Chris,
>>
>> On Mon, May 25, 2020 at 10:49:28AM +0100, Chris Lamb wrote:
>> > This should have read:
>> >
>> > Whilst you do patch out -fdebug-prefix-map in
>> > debian/patches/reproducible.patch, you also need to filter
>> > -ffile-prefix-map.
>>
>> I've tried this in Git[1] but the resulting bowtie2 package fails the
>> autopkgtest in my pbuilder environment. I remember issues with
>> autopkgtest in pbuilder before and I suspect this might be the case
>> here as well. However, before I really upload I'd invite others to
>> have a look.
>>
>
> I can confirm that this passes for me.
>
> autopkgtest [20:46:44]: test binary-run: [-----------------------
> autopkgtest [20:46:45]: test binary-run: -----------------------]
> autopkgtest [20:46:45]: test binary-run: - - - - - - - - - - results - -
> - - - - - - - -
> binary-run PASS
> autopkgtest [20:46:45]: @@@@@@@@@@@@@@@@@@@@ summary
> check-wo-arguments PASS
> indexing-ref-genome PASS
> binary-run PASS
>
> Just maybe, this is a false positive again, at your end.
>
> [1]
>> https://salsa.debian.org/med-team/bowtie2/-/commit/97052bc2de1b271f368dd8415cfafde5356e2fe8
>
>
> Kind regards,
> Nilesh
>
Information forwarded
to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>: Bug#961494; Package src:bowtie2.
(Mon, 25 May 2020 19:24:06 GMT) (full text, mbox, link).
Acknowledgement sent
to Andreas Tille <andreas@an3as.eu>:
Extra info received and forwarded to list. Copy sent to Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>.
(Mon, 25 May 2020 19:24:06 GMT) (full text, mbox, link).
To: Pranav Ballaney <ballaneypranav@gmail.com>, 961494@bugs.debian.org
Cc: Nilesh Patra <npatra974@gmail.com>
Subject: Re: Bug#961494: bowtie2: please make the build reproducible
Date: Mon, 25 May 2020 21:22:21 +0200
On Mon, May 25, 2020 at 11:02:38PM +0530, Pranav Ballaney wrote:
> Hi everyone,
> The tests pass for me as well.
Thanks to you both for checking, Andreas.
--
http://fam-tille.de
Reply sent
to Andreas Tille <tille@debian.org>:
You have taken responsibility.
(Mon, 25 May 2020 19:51:11 GMT) (full text, mbox, link).
Notification sent
to "Chris Lamb" <lamby@debian.org>:
Bug acknowledged by developer.
(Mon, 25 May 2020 19:51:11 GMT) (full text, mbox, link).
Source: bowtie2
Source-Version: 2.4.1-5
Done: Andreas Tille <tille@debian.org>
We believe that the bug you reported is fixed in the latest version of
bowtie2, 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 961494@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 bowtie2 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: SHA256
Format: 1.8
Date: Mon, 25 May 2020 14:14:23 +0200
Source: bowtie2
Architecture: source
Version: 2.4.1-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Closes: 961494
Changes:
bowtie2 (2.4.1-5) unstable; urgency=medium
.
* Reproducible builds: filter out -ffile-prefix-map
Closes: #961494
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Bug archived.
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(Tue, 23 Jun 2020 07:33:36 GMT) (full text, mbox, link).
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