[med-svn] [Git][med-team/mcl][master] 6 commits: d/watch: version=5
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Sep 23 09:30:21 BST 2026
Andreas Tille pushed to branch master at Debian Med / mcl
Commits:
99b3fd66 by Andreas Tille at 2026-09-23T10:03:38+02:00
d/watch: version=5
- - - - -
91dbef49 by Andreas Tille at 2026-09-23T10:23:19+02:00
d/upstream/metadata: Take over valid citation from d/copyright into machine readable format
- - - - -
d3a01e00 by Andreas Tille at 2026-09-23T10:25:10+02:00
d/copyright: rcl/* is only GPL-3
- - - - -
87a3f2c1 by Andreas Tille at 2026-09-23T10:27:28+02:00
Fix debian/mcl_14-137_scripts/mcxdeblast
- - - - -
f8f7dcb6 by Andreas Tille at 2026-09-23T10:27:56+02:00
Add d/lrc.config
- - - - -
cdc9a70a by Andreas Tille at 2026-09-23T10:30:06+02:00
i386 is explicitly excluded by Build-Depends: architecture-is-64-bit
- - - - -
6 changed files:
- debian/changelog
- debian/copyright
- + debian/lrc.config
- debian/salsa-ci.yml
- debian/upstream/metadata
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -6,6 +6,12 @@ mcl (1:22-282+ds-5) UNRELEASED; urgency=medium
* Install the OCaml findlib package into the versioned multiarch OCaml
stdlib directory (@OCamlStdlibDir@) instead of the hardcoded
/usr/lib/ocaml
+ * d/watch: version=5
+ * d/upstream/metadata: Take over valid citation from d/copyright into
+ machine readable format
+ * d/copyright: rcl/* is only GPL-3
+ * Add d/lrc.config
+ * i386 is explicitly excluded by Build-Depends: architecture-is-64-bit
-- Andreas Tille <tille at debian.org> Mon, 21 Sep 2026 00:00:00 +0200
=====================================
debian/copyright
=====================================
@@ -9,36 +9,12 @@ Upstream-Name: mcl
Files: *
Copyright: © 1999-2014 Stijn van Dongen <stijn at micans.org>
License: GPL-3+
-Comment: Citation
- If you use MCL software in your scientific research, please cite it
- appropriately as you would cite a journal or a book. This includes papers
- published in regular or electronic journals, usage of MCL as a back-end to a
- database that is accessible via a web interface, or inclusion of MCL in a
- larger framework of software that is distributed for other people for
- scientific use. Include one of the following citations:
- .
- Stijn van Dongen, Graph Clustering by Flow Simulation.
- PhD thesis, University of Utrecht, May 2000.
- ( http://www.library.uu.nl/digiarchief/dip/diss/1895620/inhoud.htm )
- .
- Stijn van Dongen. A cluster algorithm for graphs. Technical Report
- INS-R0010, National Research Institute for Mathematics and Computer
- Science in the Netherlands, Amsterdam, May 2000.
- ( http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z )
- .
- and proper attributions to mcl's home http://micans.org/mcl/
- and its author, Stijn van Dongen.
- The publications listed above can be retrieved from the preceding URL.
- .
- If you are using some wrapper around mcl such as the blast module or the
- tribe module, you are asked to act likewise.
- .
- For biological applications, it is appropriate to cite, additionally,
- the reference article for the first application of mcl to biological data:
- .
- Enright A.J., Van Dongen S., Ouzounis C.A.
- An efficient algorithm for large-scale detection of protein families,
- Nucleic Acids Research 30(7):1575-1584 (2002).
+
+Files: rcl/*
+Copyright: © 202 Stijn van Dongen <stijn at micans.org>
+License: GPL-3
+ On Debian systems you can find the full text of the GNU General Public
+ License version 3 at /usr/share/common-licenses/GPL-3.
Files: debian/*
Copyright: © 2001-2007 Joost van Baal <joostvb at debian.org>,
@@ -46,7 +22,7 @@ Copyright: © 2001-2007 Joost van Baal <joostvb at debian.org>,
© 2014-2017 Andreas Tille <tille at debian.org>
License: GPL-3+
-Files: debian/mcxdeblast
+Files: debian/mcl_14-137_scripts/mcxdeblast
Copyright: © 2002-2009 Stijn van Dongen,
© 2004 Jason Stajich
License: GPL-3+
=====================================
debian/lrc.config
=====================================
@@ -0,0 +1,3 @@
+aclocal.m4
+autofoo/install-sh
+configure
=====================================
debian/salsa-ci.yml
=====================================
@@ -1,4 +1,7 @@
---
include:
- - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
- - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/recipes/debian.yml
+
+variables:
+# i386 is explicitly excluded by Build-Depends: architecture-is-64-bit
+ SALSA_CI_DISABLE_BUILD_PACKAGE_I386: 1
=====================================
debian/upstream/metadata
=====================================
@@ -10,6 +10,18 @@ Reference:
URL: http://www.springerlink.com/content/u5380k70754v8017
ePrint: >
http://www.springerlink.com/content/u5380k70754v8017/fulltext.pdf
+ - Author: Enright, A. J. and Van Dongen, S and Ouzounis, C. A.
+ Title: An efficient algorithm for large-scale detection of protein families
+ Journal: Nucleic Acids Res
+ Year: 2002
+ Volume: 30
+ Pages: 7
+ DOI: 10.1093/nar/30.7.1575
+ PMID: 11917018
+ PMCID: PMC101833
+ URL: https://academic.oup.com/nar/article/30/7/1575/2376029
+ ePrint: >
+ https://academic.oup.com/nar/article-pdf/30/7/1575/7039591/gkf245.pdf
Registry:
- Name: bio.tools
Entry: mcl
=====================================
debian/watch
=====================================
@@ -1,4 +1,6 @@
-version=4
+Version: 5
-opts="repacksuffix=+ds,dversionmangle=s/\+ds//g,repack,compression=xz" \
- https://micans.org/mcl/src/mcl-(..-.*)\.tar\.gz
+Source: https://micans.org/mcl/src/
+Matching-Pattern: mcl-(..-.*)\.tar\.gz
+Dversionmangle: auto
+Repacksuffix: +ds
View it on GitLab: https://salsa.debian.org/med-team/mcl/-/compare/47f23e3757c7f14cae66a28ce9762a910a037ee7...cdc9a70a77b0656943e714fa6d465be29b0dacf1
--
View it on GitLab: https://salsa.debian.org/med-team/mcl/-/compare/47f23e3757c7f14cae66a28ce9762a910a037ee7...cdc9a70a77b0656943e714fa6d465be29b0dacf1
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