Bug#961494: bowtie2: please make the build reproducible

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Bug#961494: bowtie2: please make the build reproducible

Chris Lamb -2
Source: bowtie2
Version: 2.4.1-4
Severity: wishlist
Tags: patch
User: [hidden email]
Usertags: buildpath
X-Debbugs-Cc: [hidden email]

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,

--
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     : :'  :     Chris Lamb
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Bug#961494: bowtie2: please make the build reproducible

Chris Lamb -2
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
     `. `'`      [hidden email] / chris-lamb.co.uk
       `-

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Bug#961494: bowtie2: please make the build reproducible

Chris Lamb -2
In reply to this post by Chris Lamb -2
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
     `. `'`      [hidden email] / chris-lamb.co.uk
       `-

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Bug#961494: bowtie2: please make the build reproducible

Chris Lamb -2
In reply to this post by Chris Lamb -2
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
     `. `'`      [hidden email] / chris-lamb.co.uk
       `-

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Bug#961494: bowtie2: please make the build reproducible

Andreas Tille-2
In reply to this post by Chris Lamb -2
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

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Bug#961494: bowtie2: please make the build reproducible

Nilesh Patra


On Mon, 25 May 2020 at 20:10, Andreas Tille <[hidden email]> 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
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Bug#961494: bowtie2: please make the build reproducible

Pranav Ballaney
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

On Mon, May 25, 2020 at 8:49 PM Nilesh Patra <[hidden email]> wrote:


On Mon, 25 May 2020 at 20:10, Andreas Tille <[hidden email]> 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
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Bug#961494: bowtie2: please make the build reproducible

Andreas Tille-5
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.

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