Debian Bug report logs - #995259
python-pybedtools: please make the build reproducible

Package: src:python-pybedtools; Maintainer for src:python-pybedtools is Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>;

Reported by: "Chris Lamb" <lamby@debian.org>

Date: Tue, 28 Sep 2021 15:57:04 UTC

Severity: wishlist

Tags: fixed-upstream, patch

Found in version python-pybedtools/0.8.0-5

Done: Sascha Steinbiss <satta@debian.org>

Bug is archived. No further changes may be made.

Forwarded to https://github.com/daler/pybedtools/pull/349

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Report forwarded 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#995259; Package src:python-pybedtools. (Tue, 28 Sep 2021 15:57:06 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>. (Tue, 28 Sep 2021 15:57:06 GMT) (full text, mbox, link).

Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

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

Source: python-pybedtools
Version: 0.8.0-5
Severity: wishlist
Tags: patch
User: reproducible-builds@lists.alioth.debian.org
Usertags: filesystem
X-Debbugs-Cc: reproducible-bugs@lists.alioth.debian.org

Hi,

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

This is because it includes output inherited from non-deterministic
filesystem ordering:

/usr/lib/python3/dist-packages/pybedtools/cbedtools.cpp:

│ │ │ │ @@ -16,17 +16,17 @@
│ │ │ │              "z"
│ │ │ │          ],
│ │ │ │          "name": "pybedtools.cbedtools",
│ │ │ │          "sources": [
│ │ │ │              "pybedtools/cbedtools.pyx",
│ │ │ │ -            "pybedtools/include/fileType.cpp",
│ │ │ │              "pybedtools/include/bedFile.cpp",
│ │ │ │ -            "pybedtools/include/gzstream.cpp"
│ │ │ │ +            "pybedtools/include/gzstream.cpp",
│ │ │ │ +            "pybedtools/include/fileType.cpp"
│ │ │ │          ]
│ │ │ │      },
│ │ │ │      "module_name": "pybedtools.cbedtools"
│ │ │ │  }

Patch attached that sorts these entries in setup.py.

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


Regards,

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

[python-pybedtools.diff.txt (text/plain, attachment)]

Information forwarded to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>:
Bug#995259; Package src:python-pybedtools. (Tue, 28 Sep 2021 16:24:02 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>. (Tue, 28 Sep 2021 16:24:02 GMT) (full text, mbox, link).

Message #10 received at 995259@bugs.debian.org (full text, mbox, reply):

forwarded 995259 https://github.com/daler/pybedtools/pull/349
thanks

I've forwarded this upstream here:

  https://github.com/daler/pybedtools/pull/349


Regards,

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

Set Bug forwarded-to-address to 'https://github.com/daler/pybedtools/pull/349'. Request was from "Chris Lamb" <lamby@debian.org> to control@bugs.debian.org. (Tue, 28 Sep 2021 16:24:03 GMT) (full text, mbox, link).

Added tag(s) fixed-upstream. Request was from debian-bts-link@lists.debian.org to control@bugs.debian.org. (Mon, 04 Oct 2021 17:21:05 GMT) (full text, mbox, link).

Reply sent to Sascha Steinbiss <satta@debian.org>:
You have taken responsibility. (Sat, 19 Feb 2022 14:18:03 GMT) (full text, mbox, link).

Notification sent to "Chris Lamb" <lamby@debian.org>:
Bug acknowledged by developer. (Sat, 19 Feb 2022 14:18:03 GMT) (full text, mbox, link).

Message #19 received at 995259-done@bugs.debian.org (full text, mbox, reply):

AFAICS this is done by updating the package to the latest version 0.9.0
which contains the fixes upstreamed by Chris. This version seems to
build reproducibly now everywhere.

Cheers
Sascha

Bug archived. Request was from Debbugs Internal Request <owner@bugs.debian.org> to internal_control@bugs.debian.org. (Sun, 20 Mar 2022 07:27:19 GMT) (full text, mbox, link).

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Debian Bug report logs - #995259 python-pybedtools: please make the build reproducible

Debian Bug report logs - #995259
python-pybedtools: please make the build reproducible