Debian Bug report logs - #857454
qtltools: 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: qtltools: please make the build reproducible

Date: Sat, 11 Mar 2017 13:49:49 +0000

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

Source: qtltools
Version: 1.1+dfsg-1
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 qtltools could not be built reproducibly.

This is because the examples.tar.xz can contain itself:

├── ./usr/share/doc/qtltools/examples/examples.tar.xz
├── 6-content
├── file list
│ │ │ │ │ │ @@ -1,7 +1,8 @@
│ │ │ │ │ │ +-rw-r--r--   0        0        0        0 2018-03-21 07:15:07.000000 ./examples.tar.xz

Patch attached; we should be removing this file in the clean target anyway.

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


Regards,

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

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

Message #12 received at 857454-close@bugs.debian.org (full text, mbox, reply):

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

To: 857454-close@bugs.debian.org

Subject: Bug#857454: fixed in qtltools 1.1+dfsg-2

Date: Fri, 11 Aug 2017 19:53:53 +0000

Source: qtltools
Source-Version: 1.1+dfsg-2

We believe that the bug you reported is fixed in the latest version of
qtltools, 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 857454@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 qtltools 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: Wed, 19 Jul 2017 23:54:14 +0200
Source: qtltools
Binary: qtltools qtltools-example
Architecture: source amd64 all
Version: 1.1+dfsg-2
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:
 qtltools   - Tool set for molecular QTL discovery and analysis
 qtltools-example - Tool set for molecular QTL discovery and analysis - example
Closes: 857454
Changes:
 qtltools (1.1+dfsg-2) unstable; urgency=medium
 .
   [ Dylan Aïssi ]
   * Remove examples.tar.xz during dh_auto_clean in order
      to improve reproducible builds. (Closes: #857454)
      (Thanks to Chris Lamb)
   * Add OMICtools ref.
 .
   [ Andreas Tille ]
   * cme fix dpkg-control
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 52c61ba768639d19dbfbcc902226522b89ea9a98 2215 qtltools_1.1+dfsg-2.dsc
 8c00faa64e51e1b63dd035067998502a8fc0e548 13556192 qtltools_1.1+dfsg-2.debian.tar.xz
 60d549abecbdbab035ef07d8ce58b41adde7b873 136926914 qtltools-dbgsym_1.1+dfsg-2_amd64.deb
 0eff48fba128d18dfc0b74286b8d2ef59ca83ff1 13556378 qtltools-example_1.1+dfsg-2_all.deb
 c9a41754dc397dbfa6adf8598a7bbc6baadfc758 7595 qtltools_1.1+dfsg-2_amd64.buildinfo
 15f13b7397dfdd8005321edb4ae926dea1d459ea 658176 qtltools_1.1+dfsg-2_amd64.deb
Checksums-Sha256:
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 ef7829c4fcdc74f238dafc343fc949fe9c766a1c6c4cf9300fd1c5eedb160c6d 13556192 qtltools_1.1+dfsg-2.debian.tar.xz
 88427c8626da6b7860e4010fb98c552cc2090e5416bf2b313437e4328d4afa02 136926914 qtltools-dbgsym_1.1+dfsg-2_amd64.deb
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 61a8459893cb7f5f544dc9f6bea5254f99566554ae85d73dc8afea188439adb0 7595 qtltools_1.1+dfsg-2_amd64.buildinfo
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Files:
 c8925b62cf7058fc89a2edf24b2aee74 2215 science optional qtltools_1.1+dfsg-2.dsc
 d0ca74237398a52ed3a44fabaca1b6df 13556192 science optional qtltools_1.1+dfsg-2.debian.tar.xz
 91f045790ebe73f791b2ecb800020501 136926914 debug extra qtltools-dbgsym_1.1+dfsg-2_amd64.deb
 9986dc8d6501c5b2e66a91ad405db0f6 13556378 doc optional qtltools-example_1.1+dfsg-2_all.deb
 1610bfa94869f89a635374fdf8904267 7595 science optional qtltools_1.1+dfsg-2_amd64.buildinfo
 5ddc19d99a3326e40452e39248189a40 658176 science optional qtltools_1.1+dfsg-2_amd64.deb

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Message #27 received at 857454@bugs.debian.org (full text, mbox, reply):

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

To: 857454@bugs.debian.org

Subject: Re: qtltools: please make the build reproducible

Date: Sun, 29 Dec 2019 11:44:35 +0000

reopen 857454 
found 857454 1.2+dfsg-1 
thanks

Hi,

This appears to have reoccured:

│ │ │ ├── ./usr/share/doc/qtltools/examples/examples.tar.xz
│ │ │ │ ├── examples.tar
│ │ │ │ │ ├── file list
│ │ │ │ │ │ @@ -1,8 +1,7 @@
│ │ │ │ │ │ --rw-r--r--   0        0        0        0 2019-12-28 13:56:00.000000 ./examples.tar.xz
│ │ │ │ │ │  -rw-r--r--   0        0        0  1230243 2019-09-30 21:26:57.000000 ./genes.50percent.chr22.bed.gz
│ │ │ │ │ │  -rw-r--r--   0        0        0     4634 2019-09-30 21:26:57.000000 ./genes.50percent.chr22.bed.gz.tbi

ie. the examples.tar.xz can include itself. My previous patch has still
been applied so I wonder what has changed upstream (or in the toolchain)
that could have caused this regression.


Regards,

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

Message #32 received at 857454-done@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: Chris Lamb <lamby@debian.org>, 857454-done@bugs.debian.org

Subject: Re: Bug#857454: qtltools: please make the build reproducible

Date: Sat, 11 Jan 2020 23:05:21 +0100

On Sun, Dec 29, 2019 at 11:44:35AM +0000, Chris Lamb wrote:
> 
> This appears to have reoccured:
> 
> │ │ │ ├── ./usr/share/doc/qtltools/examples/examples.tar.xz
> │ │ │ │ ├── examples.tar
> │ │ │ │ │ ├── file list
> │ │ │ │ │ │ @@ -1,8 +1,7 @@
> │ │ │ │ │ │ --rw-r--r--   0        0        0        0 2019-12-28 13:56:00.000000 ./examples.tar.xz
> │ │ │ │ │ │  -rw-r--r--   0        0        0  1230243 2019-09-30 21:26:57.000000 ./genes.50percent.chr22.bed.gz
> │ │ │ │ │ │  -rw-r--r--   0        0        0     4634 2019-09-30 21:26:57.000000 ./genes.50percent.chr22.bed.gz.tbi
> 
> ie. the examples.tar.xz can include itself. My previous patch has still
> been applied so I wonder what has changed upstream (or in the toolchain)
> that could have caused this regression.

As Michael explained this is not the case in his recent upload
any more.  I also added in Git[1] some

    | grep -v examples.tar.xz

before the tar command to make really sure it should not happen again
in the next upload.

Thus closing the bug.

Kind regards

     Andreas.

[1] https://salsa.debian.org/med-team/qtltools/blob/master/debian/rules#L22

-- 
http://fam-tille.de

Message #37 received at 857454@bugs.debian.org (full text, mbox, reply):

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

To: "Andreas Tille" <tille@debian.org>, 857454@bugs.debian.org

Subject: Re: Bug#857454: qtltools: please make the build reproducible

Date: Sat, 11 Jan 2020 23:57:04 -0000

Hi Andreas,

> > This appears to have reoccured:
[…]
> As Michael explained this is not the case in his recent upload
> any more.

Thanks for fixing. However, I think I'm missing something as I do not
see this aforementioned explanation on #857454?


Regards,

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

Message #46 received at 857454@bugs.debian.org (full text, mbox, reply):

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

To: 857454@bugs.debian.org

Subject: Re: qtltools: please make the build reproducible

Date: Mon, 13 Jul 2020 12:16:40 +0100

reopen 857454 
found 857454 1.2+dfsg-2
thanks

Hi,

I'm afraid this has regressed again (or I forgot to properly re-open):

│ ├── data.tar.xz
│ │ ├── data.tar
│ │ │ ├── file list
│ │ │ │ @@ -1,14 +1,14 @@
│ │ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2019-12-25 21:27:16.000000 ./
│ │ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2019-12-25 21:27:16.000000 ./usr/
│ │ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2019-12-25 21:27:16.000000 ./usr/share/
│ │ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2019-12-25 21:27:16.000000 ./usr/share/doc/
│ │ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2019-12-25 21:27:16.000000 ./usr/share/doc/qtltools/
│ │ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2019-12-25 21:27:16.000000 ./usr/share/doc/qtltools/examples/
│ │ │ │ --rw-r--r--   0 root         (0) root         (0) 13549832 2019-12-25 21:27:16.000000 ./usr/share/doc/qtltools/examples/examples.tar.xz
│ │ │ │ +-rw-r--r--   0 root         (0) root         (0) 13550168 2019-12-25 21:27:16.000000 ./usr/share/doc/qtltools/examples/examples.tar.xz
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     1675 2019-09-16 09:56:58.000000 ./usr/share/doc/qtltools/examples/plotTrans.R
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     1317 2019-12-25 14:43:38.000000 ./usr/share/doc/qtltools/examples/run-sample-analysis
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     1020 2019-09-16 09:56:58.000000 ./usr/share/doc/qtltools/examples/runFDR_atrans.R
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     2780 2019-09-16 09:56:58.000000 ./usr/share/doc/qtltools/examples/runFDR_cis.R
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)      787 2019-09-16 09:56:58.000000 ./usr/share/doc/qtltools/examples/runFDR_ftrans.R
│ │ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2019-12-25 21:27:16.000000 ./usr/share/doc/qtltools-example/
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)      770 2019-12-25 21:27:16.000000 ./usr/share/doc/qtltools-example/changelog.Debian.gz
│ │ │ ├── ./usr/share/doc/qtltools/examples/examples.tar.xz
│ │ │ │ ├── examples.tar
│ │ │ │ │ ├── file list
│ │ │ │ │ │ @@ -1,7 +1,8 @@
│ │ │ │ │ │ +-rw-r--r--   0        0        0        0 2020-07-11 21:44:22.000000 ./examples.tar.xz
│ │ │ │ │ │  -rw-r--r--   0        0        0  1230243 2019-12-25 14:43:38.000000 ./genes.50percent.chr22.bed.gz

ie. the examples.tar.xz can contain "itself" in the second build.

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/qtltools.html


Regards,

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

Message #55 received at 857454@bugs.debian.org (full text, mbox, reply):

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

To: 857454@bugs.debian.org, reproducible-bugs@lists.alioth.debian.org

Subject: Re: Bug#857454: qtltools: please make the build reproducible

Date: Mon, 12 Oct 2020 16:58:03 -0000

Chris Lamb wrote:

> [..]

Friendly ping on this?


Regards,

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

Message #60 received at 857454@bugs.debian.org (full text, mbox, reply):

From: Dylan Aïssi <daissi@debian.org>

To: 857454@bugs.debian.org, Chris Lamb <lamby@debian.org>

Subject: qtltools: please make the build reproducible

Date: Tue, 20 Oct 2020 10:53:43 +0200

Hi Chris,

On Mon, 12 Oct 2020 16:58:03 -0000 "Chris Lamb" <lamby@debian.org> wrote:
>
> Friendly ping on this?
>

This package seems now reproducible. Could you confirm?

Best,
Dylan

Message #65 received at 857454-done@bugs.debian.org (full text, mbox, reply):

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

To: Dylan Aïssi <daissi@debian.org>, 857454-done@bugs.debian.org

Subject: Re: qtltools: please make the build reproducible

Date: Tue, 20 Oct 2020 10:45:21 +0100

Version: 1.3.1+dfsg-1

Hi Dylan,

> > Friendly ping on this?
>
> This package seems now reproducible. Could you confirm?

Ah yes, it looks like it was fixed in 1.3.1+dfsg-1 but this bug was
not referenced:

    qtltools (1.3.1+dfsg-1) unstable; urgency=medium

      * Team upload.

      [ Andreas Tille ]
      * Make really sure examples.tar.xz will not contain itself
      * debhelper-compat 12
      […]

(Closing this bug accordingly.)


Regards,

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

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