943956">

Debian Bug report logs - #943956
snakemake: please make the build reproducible

version graph

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

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

Date: Fri, 1 Nov 2019 18:33:02 UTC

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

Severity: wishlist

Tags: fixed-upstream, patch

Found in versions snakemake/5.9.1-1, snakemake/5.7.4-1

Fixed in version 5.10.0-2

Done: "Rebecca N. Palmer" <rebecca_palmer@zoho.com>

Bug is archived. No further changes may be made.

Forwarded to https://github.com/snakemake/snakemake/pull/80

View this report as an mbox folder, status mbox, maintainer mbox


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#943956; Package src:snakemake. (Fri, 01 Nov 2019 18:33:05 GMT) (full text, mbox, link).


Acknowledgement sent to "Chris Lamb" <chris@chris-lamb.co.uk>:
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>. (Fri, 01 Nov 2019 18:33:05 GMT) (full text, mbox, link).


Message #5 received at submit@bugs.debian.org (full text, mbox, wrote: > Source: snakemake > Version: 5.7.4-1 > 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 > snakemake could still not be built reproducibly. This is because my > previous patch did not cover quite everything. Do excuse the patch-to- > a-patch but please apply the following: > > --- a/debian/patches/0012-reproducible-build.patch > +++ b/debian/patches/0012-reproducible-build.patch > @@ -22,6 +22,15 @@ Last-Update: 2019-07-15 > raise ValueError("Path to report output has to be an HTML file.") > --- snakemake.orig/snakemake/utils.py > +++ snakemake/snakemake/utils.py > +@@ -202,7 +202,7 @@ def makedirs(dirnames): > + def report( > + text, > + path, > +- stylesheet=os.path.join(os.path.dirname(__file__), "report.css"), > ++ stylesheet=None, > + defaultenc="utf8", > + template=None, > + metadata=None, > > ... and this should cover it. :) > > [0] https://reproducible-builds.org/ > > > Best wishes, > > -- > ,''`. > : :' : Chris Lamb > `. `'` lamby@debian.org / chris-lamb.co.uk > `- > > ">reply):

From: "Chris Lamb" <chris@chris-lamb.co.uk>
To: submit@bugs.debian.org
Subject: snakemake: please make the build reproducible
Date: Fri, 01 Nov 2019 11:30:11 -0700
Source: snakemake
Version: 5.7.4-1
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
snakemake could still not be built reproducibly. This is because my
previous patch did not cover quite everything. Do excuse the patch-to-
a-patch but please apply the following:

  --- a/debian/patches/0012-reproducible-build.patch
  +++ b/debian/patches/0012-reproducible-build.patch
  @@ -22,6 +22,15 @@ Last-Update: 2019-07-15
            raise ValueError("Path to report output has to be an HTML file.")
   --- snakemake.orig/snakemake/utils.py
   +++ snakemake/snakemake/utils.py
  +@@ -202,7 +202,7 @@ def makedirs(dirnames):
  + def report(
  +     text,
  +     path,
  +-    stylesheet=os.path.join(os.path.dirname(__file__), "report.css"),
  ++    stylesheet=None,
  +     defaultenc="utf8",
  +     template=None,
  +     metadata=None,
  
... and this should cover it. :)

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


Best wishes,

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



Owner recorded as "Chris Lamb" <lamby@debian.org>. Request was from "Chris Lamb" <lamby@debian.org> to control@bugs.debian.org. (Fri, 01 Nov 2019 18:39:03 GMT) (full text, mbox, link).


Set Bug forwarded-to-address to 'https://github.com/snakemake/snakemake/pull/80'. Request was from "Chris Lamb" <lamby@debian.org> to control@bugs.debian.org. (Fri, 01 Nov 2019 22:33:03 GMT) (full text, mbox, link).


Information forwarded to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>:
Bug#943956; Package src:snakemake. (Fri, 01 Nov 2019 22:39:06 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>. (Fri, 01 Nov 2019 22:39:06 GMT) (full text, mbox, link).


Message #14 received at 943956@bugs.debian.org (full text, mbox, wrote: > forwarded 943956 https://github.com/snakemake/snakemake/pull/80 > thanks > > I've forwarded this upstream here: > > https://github.com/snakemake/snakemake/pull/80 > > > Regards, > > -- > ,''`. > : :' : Chris Lamb > `. `'` lamby@debian.org / chris-lamb.co.uk > `- > > ">reply):

From: "Chris Lamb" <lamby@debian.org>
To: 943956@bugs.debian.org
Subject: Re: snakemake: please make the build reproducible
Date: Fri, 01 Nov 2019 15:28:47 -0700
forwarded 943956 https://github.com/snakemake/snakemake/pull/80
thanks

I've forwarded this upstream here:

  https://github.com/snakemake/snakemake/pull/80


Regards,

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



Added tag(s) fixed-upstream. Request was from debian-bts-link@lists.debian.org to control@bugs.debian.org. (Thu, 07 Nov 2019 17:45:04 GMT) (full text, mbox, link).


Reply sent to Alexandre Mestiashvili <mestia@debian.org>:
You have taken responsibility. (Sun, 09 Feb 2020 15:51:02 GMT) (full text, mbox, link).


Notification sent to "Chris Lamb" <chris@chris-lamb.co.uk>:
Bug acknowledged by developer. (Sun, 09 Feb 2020 15:51:02 GMT) (full text, mbox, link).


Message #21 received at 943956-close@bugs.debian.org (full text, mbox, reply):

From: Debian FTP Masters <ftpmaster@ftp-master.debian.org>
To: 943956-close@bugs.debian.org
Subject: Bug#943956: fixed in snakemake 5.10.0-1
Date: Sun, 09 Feb 2020 15:49:28 +0000
Source: snakemake
Source-Version: 5.10.0-1

We believe that the bug you reported is fixed in the latest version of
snakemake, 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 943956@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Alexandre Mestiashvili <mestia@debian.org> (supplier of updated snakemake 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, 09 Feb 2020 11:57:42 +0100
Source: snakemake
Architecture: source
Version: 5.10.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Alexandre Mestiashvili <mestia@debian.org>
Closes: 943956
Changes:
 snakemake (5.10.0-1) unstable; urgency=medium
 .
   * Team upload.
   * New upstream version 5.10.0
     Closes: #943956
   * Refresh python3 patch, drop 0012-reproducible-build.patch
   * d/control: add python3-nbformat, python3-toposort to Build-Depends,
     bump Policy to 4.5.0
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 12b2f0a6eff8fabc44eb7c0d5df49f5dc9408649cb082f945e5e503c9126ca6f 2705 snakemake_5.10.0-1.dsc
 8f7a80ff5eca347c28699aec383519219f178834e7d734e5a7751ddb1b114185 4039590 snakemake_5.10.0.orig.tar.gz
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 053e848d7d4dd7712cb72b5b3c8d9b3ca31fab503334a32fe67917aafeaad79d 15040 snakemake_5.10.0-1_amd64.buildinfo
Files:
 0fa2f1d61a16dfad6055eb43f1200e4a 2705 science optional snakemake_5.10.0-1.dsc
 92a9897e8ec2c46a945215a5f2e23ebb 4039590 science optional snakemake_5.10.0.orig.tar.gz
 0517e702c9227cea380f801d5afb54d4 268760 science optional snakemake_5.10.0-1.debian.tar.xz
 29747c844e28c19dd9f85707406881ab 15040 science optional snakemake_5.10.0-1_amd64.buildinfo

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Changed Bug submitter to '"Chris Lamb" <lamby@debian.org>' from '"Chris Lamb" <chris@chris-lamb.co.uk>'. Request was from "Chris Lamb" <lamby@debian.org> to control@bugs.debian.org. (Sun, 09 Feb 2020 16:00:04 GMT) (full text, mbox, link).


Bug reopened Request was from Alex Mestiashvili <amestia@rsh2.donotuse.de> to control@bugs.debian.org. (Tue, 11 Feb 2020 09:36:07 GMT) (full text, mbox, link).


No longer marked as fixed in versions snakemake/5.10.0-1. Request was from Alex Mestiashvili <amestia@rsh2.donotuse.de> to control@bugs.debian.org. (Tue, 11 Feb 2020 09:36:08 GMT) (full text, mbox, link).


Information forwarded to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>:
Bug#943956; Package src:snakemake. (Tue, 11 Feb 2020 10:09:03 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, 11 Feb 2020 10:09:03 GMT) (full text, mbox, link).


Message #32 received at 943956@bugs.debian.org (full text, mbox, wrote: > found 943956 5.9.1-1 > tags 943956 + patch > thanks > > > > still FTBR... > > New patch attached. > > > Regards, > > -- > ,''`. > : :' : Chris Lamb > `. `'` lamby@debian.org 🍥 chris-lamb.co.uk > `-">reply):

From: "Chris Lamb" <lamby@debian.org>
To: "Debian Bug Tracking System" <943956@bugs.debian.org>, "Alex Mestiashvili" <amestia@rsh2.donotuse.de>
Cc: "Debian Med Packaging Team" <debian-med-packaging@lists.alioth.debian.org>
Subject: Re: snakemake: please make the build reproducible
Date: Tue, 11 Feb 2020 10:04:43 +0000
[Message part 1 (text/plain, inline)]
found 943956 5.9.1-1
tags 943956 + patch
thanks

> > still FTBR...

New patch attached.


Regards,

-- 
      ,''`.
     : :'  :     Chris Lamb
     `. `'`      lamby@debian.org 🍥 chris-lamb.co.uk
       `-
[snakemake.diff.txt (text/plain, attachment)]

Marked as found in versions snakemake/5.9.1-1. Request was from "Chris Lamb" <lamby@debian.org> to control@bugs.debian.org. (Tue, 11 Feb 2020 10:09:09 GMT) (full text, mbox, link).


Reply sent to "Rebecca N. Palmer" <rebecca_palmer@zoho.com>:
You have taken responsibility. (Sun, 26 Apr 2020 13:51:07 GMT) (full text, mbox, link).


Notification sent to "Chris Lamb" <lamby@debian.org>:
Bug acknowledged by developer. (Sun, 26 Apr 2020 13:51:07 GMT) (full text, mbox, link).


Message #39 received at 943956-done@bugs.debian.org (full text, mbox, wrote: > Version: 5.10.0-2 > > https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/snakemake.html > > &References=&subject=Re: appears to be fixed&In-Reply-To=">reply):

From: "Rebecca N. Palmer" <rebecca_palmer@zoho.com>
To: 943956-done@bugs.debian.org
Subject: appears to be fixed
Date: Sun, 26 Apr 2020 14:48:00 +0100
Version: 5.10.0-2

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



Bug archived. Request was from Debbugs Internal Request <owner@bugs.debian.org> to internal_control@bugs.debian.org. (Sun, 16 Aug 2020 07:29:54 GMT) (full text, mbox, link).


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