Author: philipp Date: 2011-11-02 20:46:11 +0000 (Wed, 02 Nov 2011) New Revision: 8397
Added: trunk/packages/mcl/tags/1:11-294-1/ trunk/packages/mcl/tags/1:11-294-1/debian/changelog trunk/packages/mcl/tags/1:11-294-1/debian/control trunk/packages/mcl/tags/1:11-294-1/debian/rules Removed: trunk/packages/mcl/tags/1:11-294-1/debian/changelog trunk/packages/mcl/tags/1:11-294-1/debian/control trunk/packages/mcl/tags/1:11-294-1/debian/rules Log: [svn-buildpackage] Tagging mcl 1:11-294-1 Deleted: trunk/packages/mcl/tags/1:11-294-1/debian/changelog =================================================================== --- trunk/packages/mcl/trunk/debian/changelog 2011-01-24 16:58:10 UTC (rev 5699) +++ trunk/packages/mcl/tags/1:11-294-1/debian/changelog 2011-11-02 20:46:11 UTC (rev 8397) @@ -1,336 +0,0 @@ -mcl (1:10-201-21) UNRELEASED; urgency=low - - * New upstream version - * debian/control: - - Added myself to uploaders - - Fixed spelling of Debian Med - - Standards-Version: 3.9.1 (no changes needed) - - debhelper 7 - - removed versioned conflicts for mcl-doc from quite old mcl version - which seems to be useless these days - * debian/source/format: 3.0 (quilt) - * debian/rules, debian/patches/01-manpage-errors.patch: - Use sed on installed packages to get the same effect as the patch but - there is no need to change the patch for new versions - - -- Andreas Tille <[email protected]> Mon, 24 Jan 2011 15:58:07 +0100 - -mcl (1:10-148-1) unstable; urgency=low - - * New upstream release - - -- Philipp Benner <[email protected]> Tue, 01 Jun 2010 10:44:22 +0200 - -mcl (1:09-308-1) unstable; urgency=low - - * New upstream release - * Moved repository to debian-med - - -- Philipp Benner <[email protected]> Tue, 24 Nov 2009 20:43:56 +0000 - -mcl (1:09-261-1) unstable; urgency=low - - * New upstream release - - -- Philipp Benner <[email protected]> Wed, 30 Sep 2009 10:54:28 +0000 - -mcl (1:09-182-1) unstable; urgency=low - - * New upstream release - * New maintainer e-mail address - * Removed DMUA - - -- Philipp Benner <[email protected]> Fri, 24 Jul 2009 08:15:19 +0000 - -mcl (1:09-149-1) unstable; urgency=low - - * New upstream release. - * Standards version 3.8.2. - - -- Philipp Benner <[email protected]> Sat, 27 Jun 2009 20:33:54 +0000 - -mcl (1:08-312-1) unstable; urgency=low - - * New upstream release. - * Added debian/patches/manpages-whatis-fix.patch. - * Added debian/patches/perl-interpreter-path.patch - * Build-depends on zoem and tidy to regenerate manuals. - - -- Philipp Benner <[email protected]> Sun, 25 Jan 2009 12:29:28 +0000 - -mcl (1:06-058-2) unstable; urgency=low - - * New maintainer e-mail address. - * debian/control: Added DM-Upload-Allowed: yes. - * debian/mcl-doc.doc-base.mcxio: fixed typo. - * Changed the doc-base section according to the new policy. - - -- Philipp Benner <[email protected]> Mon, 31 Mar 2008 11:04:53 +0200 - -mcl (1:06-058-1) unstable; urgency=low - - * Adopting package (Closes: #452405). - * Standards version 3.7.2. - * Added Vcs-Browser and Vcs-Svn field to debian/control. - * Machine interpretable copyright file. - * Improved config.{guess,sub} handling. - * New upstream release. - - -- Philipp Benner <[email protected]> Mon, 26 Nov 2007 14:37:21 +0100 - -mcl (1:06-021-2) unstable; urgency=low - - * Orphaning this package (per Bug #452405). Set maintainer to Debian - QA Group. - * Move Homepage to control field. - - -- Joost van Baal <[email protected]> Sat, 24 Nov 2007 00:35:03 +0100 - -mcl (1:06-021-1) unstable; urgency=low - - * New stable upstream release: Analysis and cache modes have been improved. - This mcl binary in this release displays a citation reference on STDERR. - Of course we honor upstream's wishes here, and do not suppress this - helpful reminder. See the comments in debian/rules for hints on how to - operate if you disagree. - * debian/control: found out how to add Homepage pseudo-field (finally!) - * debian/control: we no longer ship plain text manpages in mcl-doc, adjust - description. - - -- Joost van Baal <[email protected]> Tue, 07 Feb 2006 21:05:31 +0100 - -mcl (1:05-321-1) unstable; urgency=low - - * New stable upstream release. (Missed 05-272, 05-300, 05-314.) - Some rephrased snippets from the announcement messages: - + mcl-05-321: - This mainly adds 'transformation' functionality, which complements the - label-value streaming stuff. It means you can apply quite complex - transformations on values, albeit only context-insensive transformations. - + mcl-05-314: - MCL can now read in label input in a simple line based format where - each lines contains two labels and an optional value separated by - whitespace. Output clusters are returned as lines of tab-separated - labels. The BLAST parser can stream this format directly to mcl - creating a very concise and easy to manage sequence clustering - pipeline. The mcl(1) manual now has a 'getting started' section - with some examples. New utility mcxload(1) with many custom options for - reading in label data and transforming the associated numerical values, - storing mappings in tab files and saving a graph in native mcl input - format. - + mcl-05-300: - Important for mcxassemble users: Changed mcxassemble to pick the maximum - between repeated entries by default. Other noteworthy changes: mcxdump - can now also be used to restrict tab files, and: Fixed mcxsubs bug, - introduced in last release, where selections never materialize unless one - mysteriously specifies --rand-merge. No changes in mcl, only stuff done - to the graph manipulation programs. - + mcl-05-272: - Major changes in clmimac, a noticeable change in mclblastline, a minor - addition to mcxdeblast, improved dump functionality in mcl. If you just - use mcl there is little need for upgrading. - mcl-05-272 adds some extra stuff to doc/mcl/examples/ . - As always, read changelog for details. - * debian/mcl-doc.doc-base.mcxload: added - * debian/{compat,control,rules}: move from debhelper compatibility level 3 - to 4 (add ${misc:Depends} to Depends) - * debian/copyright: new snailmail address of FSF. - * debian/watch: make sure it doesn't match the symlink mcl-latest.tar.gz. - * debian/rules, debian/mcl-doc.install: no longer install upstream TODO file: - it's not useful for users. - * debian/control: fix versioned conflicts syntax - * debian/rules: make proper use of comments: don't clobber build output. - * debian/control: Standards Version bumped from 3.6.1.0 to 3.6.2.0 (no - changes needed). - - -- Joost van Baal <[email protected]> Wed, 23 Nov 2005 16:36:39 +0100 - -mcl (1:05-118-1) unstable; urgency=low - - * New stable upstream release: a lot faster on large graphs because a - clunky input routine was fixed. - * debian/rules: Make sure config.{guess,sub} are up to date. (Upstream - _does_ ship these.) - * debian/mcl-doc.doc-base.mcl, debian/mcl-doc.doc-base.mclfaq: We are no - longer shipping documentation in txt format. - - -- Joost van Baal <[email protected]> Wed, 25 May 2005 08:09:54 +0200 - -mcl (1:05-096-1) unstable; urgency=low - - * New upstream development release. (Missed mcl-04-314, mcl-05-090.) - The only difference between mcl 05-096 and the official 05-090 release is - the addition of a clmorder(1) manpage. Here's a rephrased snippet from - the 05-090 announcement message: - Nothing changed in the core clustering algorithm. But: - - Better support for diagnostics: mcl can now dump iterand submatrices. - - Helper applications for analyzing cluster structure added: clxdo, - clxcoarse (primitive hierarchical clustering, undocumented shell - scripts, installed in /usr/share/doc/mcl/scripts) and clmorder. - - Improvement of sibling applications: large mcxsubs rewrite - cleaner - specification language and new modes and options. Also, rewrite of - the IO library (umpteenth). - Read changelog for details. - * Install upstream TODO file. - * Removed maintainer scripts: not needed for this package. - * mcl-doc.doc-base.clmdist: fixed typo. - - -- Joost van Baal <[email protected]> Wed, 06 Apr 2005 09:50:10 +0200 - -mcl (1:04-250-2) unstable; urgency=medium - - * control: Fixed embarrasing typo in description (closes: #285424). - This is the reason urgency=medium rather than high: it'd be very - nice if this package made it to sarge, so that not too many people - get exposed to this ugly typo: s/computer sciense/computer science/. - * mcl 04-314 is out, but might not get packaged: it has no shocking - improvements, and a new upstream is likely to get published soon. - - -- Joost van Baal <[email protected]> Sun, 16 Jan 2005 16:27:12 +0100 - -mcl (1:04-250-1) unstable; urgency=low - - * New upstream release. (Missed mcl-04-230.) - * watch: added, so that - http://qa.debian.org/developer.php?gpg_key=969457F0 looks even - more spiffy. - - -- Joost van Baal <[email protected]> Wed, 08 Sep 2004 15:04:32 +0200 - -mcl (1:04-189-1) unstable; urgency=low - - * New upstream release. (Missed mcl-04-174, 04-185, 04-187.) - However, beware! mcl-04-103 might be considered non-free by some. - LICENSE in this release is more clear, and free. debian/copyright - updated accoringly. - Furthermore, zoem >= 04-173 is needed for parsing cmlformat(1)'s - zoem output. Such a zoem release is not yet packaged for Debian. - * control: added Enhances: blast2, ncbi-tools-bin, bioperl. - - -- Joost van Baal <[email protected]> Thu, 08 Jul 2004 12:13:30 +0200 - -mcl (1:04-103-1) unstable; urgency=low - - * New upstream development release. (Upstream has published six other - development releases since 03-277.) - * Splitted in mcl and mcl-doc binary packages. - * No longer installs HTML documentation in plain text too. - * Some manpages no longer register via doc-base; just the "major" ones - do now. - * Debian Policy compliance: bumped from Standards Version 3.5.9 to - Standards-Version: 3.6.1.0: debian/rules now honors DEB_BUILD_OPTIONS. - - -- Joost van Baal <[email protected]> Tue, 13 Apr 2004 07:59:47 +0200 - -mcl (1:03-277-1) unstable; urgency=low - - * New upstream release. This is the same as - http://micans.org/mcl/src/mcl-03-276.tar.gz, the version number is - the only thing which differs. - * doc-base.clmmate: added. Upstream ships a clmmate manpage now: our - package is lintian clean again. - - -- Joost van Baal <[email protected]> Sun, 05 Oct 2003 12:27:53 +0200 - -mcl (1:03-276-1) unstable; urgency=low - - * New upstream _development_ release (missed formal releases 03-154, - 03-178, 03-185, 03-245). - * copyright: added note on citations when using the software in writing - scientific papers. - * rules: build and install BLAST parsing scripts. Do not build tribe - stuff. See README for details. - * doc-base.*: new docs: clmformat, mclblastline, mclpipeline, mcxassemble, - mcxdeblast, mcxio. removed docs: clmconf, mcxformat. - - -- Joost van Baal <[email protected]> Fri, 03 Oct 2003 11:48:46 +0200 - -mcl (1:03-010-2) unstable; urgency=low - - * Removed bogus mcximac doc-base file: mcximac does not exist. Tnx - Laurent Bonnaud. (closes: #193058) - - -- Joost van Baal <[email protected]> Thu, 15 May 2003 10:58:17 +0200 - -mcl (1:03-010-1) unstable; urgency=low - - * New upstream release. - * Registered new docs using doc-base: clmimac, clmresidue, mcxmap. mcl - and mclfaq now get installed in plain text format too. - * debian/control: Standards 3.5.2 -> 3.5.9 (no changes needed). - - -- Joost van Baal <[email protected]> Sat, 10 May 2003 10:29:04 +0200 - -mcl (1:02-277-1) unstable; urgency=low - - * New upstream release. - - -- Joost van Baal <[email protected]> Fri, 25 Oct 2002 11:31:34 +0200 - -mcl (1:02-172-1) unstable; urgency=low - - * New upstream release. - * debian/rules: no longer uses touch-hack to work around timeskew - problems: upstreams uses AM_MAINTAINER_MODE now. - - -- Joost van Baal <[email protected]> Mon, 24 Jun 2002 14:44:11 +0200 - -mcl (1:02-116-1) unstable; urgency=low - - * New upstream release. - - -- Joost van Baal <[email protected]> Sat, 27 Apr 2002 22:59:49 +0200 - -mcl (1:02-113-cvs-1) unstable; urgency=low - - * build from current cvs, pre-release - * debian/rules: set configure flags based on check equality of - DEB_BUILD_GNU_TYPE and DEB_HOST_GNU_TYPE, cf current autotools-dev ideas. - * debian/control, debian/copyright: MCL found a new home on the www. - * debian/copyright: added note on contrib/tribe/ copyright holder. - * doc-base.*: added doc-base.mclfaq and doc-base.mcximac - - -- Joost van Baal <[email protected]> Tue, 23 Apr 2002 23:30:37 +0200 - -mcl (1:02-035-1) unstable; urgency=low - - * First release for the Debian archive (closes: #132283). - * copyright: new download location, refer to /usr/share/common-licenses/GPL . - * rules: applied some of Henrique de Moraes Holschuh's autotools-dev voodoo, - got rid of some NOP dh_ calls. - * docs: no longer installs NEWS; this file is not yet maintained upstream. - - -- Joost van Baal <[email protected]> Wed, 6 Feb 2002 10:20:17 +0100 - -mcl (1:02-034-1) unstable; urgency=low - - * New upstream release. - - -- Joost van Baal <[email protected]> Mon, 4 Feb 2002 08:33:36 +0100 - -mcl (1:02-030-1) unstable; urgency=low - - * Snapshot build from CVS. - * Use epoch in version numbering, since upstream made order-breaking - version numbering policy change. - * Use docbase for all .ps and .html manpages. - - -- Joost van Baal <[email protected]> Wed, 30 Jan 2002 22:46:28 +0100 - -mcl (20020116-1) unstable; urgency=low - - * Snapshot build from CVS. - - -- Joost van Baal <[email protected]> Wed, 16 Jan 2002 21:08:22 +0100 - -mcl (20011211-1) unstable; urgency=low - - * New upstream release. Now registers documentation using doc-base. - - -- Joost van Baal <[email protected]> Tue, 11 Dec 2001 20:19:42 +0100 - -mcl (20011012-1) unstable; urgency=low - - * Initial Release. - - -- Joost van Baal <[email protected]> Fri, 12 Oct 2001 22:43:08 +0200 Copied: trunk/packages/mcl/tags/1:11-294-1/debian/changelog (from rev 8396, trunk/packages/mcl/trunk/debian/changelog) =================================================================== --- trunk/packages/mcl/tags/1:11-294-1/debian/changelog (rev 0) +++ trunk/packages/mcl/tags/1:11-294-1/debian/changelog 2011-11-02 20:46:11 UTC (rev 8397) @@ -0,0 +1,344 @@ +mcl (1:11-294-1) unstable; urgency=low + + * New upstream version + * debian/rules: Added targets build-indep and build-arch + * debian/control: Standards version 3.9.2 + + -- Philipp Benner <[email protected]> Wed, 02 Nov 2011 20:23:52 +0000 + +mcl (1:10-201-21) unstable; urgency=low + + * New upstream version + * debian/control: + - Added myself to uploaders + - Fixed spelling of Debian Med + - Standards-Version: 3.9.1 (no changes needed) + - debhelper 7 + - removed versioned conflicts for mcl-doc from quite old mcl version + which seems to be useless these days + * debian/source/format: 3.0 (quilt) + * debian/rules, debian/patches/01-manpage-errors.patch: + Use sed on installed packages to get the same effect as the patch but + there is no need to change the patch for new versions + + -- Andreas Tille <[email protected]> Mon, 24 Jan 2011 15:58:07 +0100 + +mcl (1:10-148-1) unstable; urgency=low + + * New upstream release + + -- Philipp Benner <[email protected]> Tue, 01 Jun 2010 10:44:22 +0200 + +mcl (1:09-308-1) unstable; urgency=low + + * New upstream release + * Moved repository to debian-med + + -- Philipp Benner <[email protected]> Tue, 24 Nov 2009 20:43:56 +0000 + +mcl (1:09-261-1) unstable; urgency=low + + * New upstream release + + -- Philipp Benner <[email protected]> Wed, 30 Sep 2009 10:54:28 +0000 + +mcl (1:09-182-1) unstable; urgency=low + + * New upstream release + * New maintainer e-mail address + * Removed DMUA + + -- Philipp Benner <[email protected]> Fri, 24 Jul 2009 08:15:19 +0000 + +mcl (1:09-149-1) unstable; urgency=low + + * New upstream release. + * Standards version 3.8.2. + + -- Philipp Benner <[email protected]> Sat, 27 Jun 2009 20:33:54 +0000 + +mcl (1:08-312-1) unstable; urgency=low + + * New upstream release. + * Added debian/patches/manpages-whatis-fix.patch. + * Added debian/patches/perl-interpreter-path.patch + * Build-depends on zoem and tidy to regenerate manuals. + + -- Philipp Benner <[email protected]> Sun, 25 Jan 2009 12:29:28 +0000 + +mcl (1:06-058-2) unstable; urgency=low + + * New maintainer e-mail address. + * debian/control: Added DM-Upload-Allowed: yes. + * debian/mcl-doc.doc-base.mcxio: fixed typo. + * Changed the doc-base section according to the new policy. + + -- Philipp Benner <[email protected]> Mon, 31 Mar 2008 11:04:53 +0200 + +mcl (1:06-058-1) unstable; urgency=low + + * Adopting package (Closes: #452405). + * Standards version 3.7.2. + * Added Vcs-Browser and Vcs-Svn field to debian/control. + * Machine interpretable copyright file. + * Improved config.{guess,sub} handling. + * New upstream release. + + -- Philipp Benner <[email protected]> Mon, 26 Nov 2007 14:37:21 +0100 + +mcl (1:06-021-2) unstable; urgency=low + + * Orphaning this package (per Bug #452405). Set maintainer to Debian + QA Group. + * Move Homepage to control field. + + -- Joost van Baal <[email protected]> Sat, 24 Nov 2007 00:35:03 +0100 + +mcl (1:06-021-1) unstable; urgency=low + + * New stable upstream release: Analysis and cache modes have been improved. + This mcl binary in this release displays a citation reference on STDERR. + Of course we honor upstream's wishes here, and do not suppress this + helpful reminder. See the comments in debian/rules for hints on how to + operate if you disagree. + * debian/control: found out how to add Homepage pseudo-field (finally!) + * debian/control: we no longer ship plain text manpages in mcl-doc, adjust + description. + + -- Joost van Baal <[email protected]> Tue, 07 Feb 2006 21:05:31 +0100 + +mcl (1:05-321-1) unstable; urgency=low + + * New stable upstream release. (Missed 05-272, 05-300, 05-314.) + Some rephrased snippets from the announcement messages: + + mcl-05-321: + This mainly adds 'transformation' functionality, which complements the + label-value streaming stuff. It means you can apply quite complex + transformations on values, albeit only context-insensive transformations. + + mcl-05-314: + MCL can now read in label input in a simple line based format where + each lines contains two labels and an optional value separated by + whitespace. Output clusters are returned as lines of tab-separated + labels. The BLAST parser can stream this format directly to mcl + creating a very concise and easy to manage sequence clustering + pipeline. The mcl(1) manual now has a 'getting started' section + with some examples. New utility mcxload(1) with many custom options for + reading in label data and transforming the associated numerical values, + storing mappings in tab files and saving a graph in native mcl input + format. + + mcl-05-300: + Important for mcxassemble users: Changed mcxassemble to pick the maximum + between repeated entries by default. Other noteworthy changes: mcxdump + can now also be used to restrict tab files, and: Fixed mcxsubs bug, + introduced in last release, where selections never materialize unless one + mysteriously specifies --rand-merge. No changes in mcl, only stuff done + to the graph manipulation programs. + + mcl-05-272: + Major changes in clmimac, a noticeable change in mclblastline, a minor + addition to mcxdeblast, improved dump functionality in mcl. If you just + use mcl there is little need for upgrading. + mcl-05-272 adds some extra stuff to doc/mcl/examples/ . + As always, read changelog for details. + * debian/mcl-doc.doc-base.mcxload: added + * debian/{compat,control,rules}: move from debhelper compatibility level 3 + to 4 (add ${misc:Depends} to Depends) + * debian/copyright: new snailmail address of FSF. + * debian/watch: make sure it doesn't match the symlink mcl-latest.tar.gz. + * debian/rules, debian/mcl-doc.install: no longer install upstream TODO file: + it's not useful for users. + * debian/control: fix versioned conflicts syntax + * debian/rules: make proper use of comments: don't clobber build output. + * debian/control: Standards Version bumped from 3.6.1.0 to 3.6.2.0 (no + changes needed). + + -- Joost van Baal <[email protected]> Wed, 23 Nov 2005 16:36:39 +0100 + +mcl (1:05-118-1) unstable; urgency=low + + * New stable upstream release: a lot faster on large graphs because a + clunky input routine was fixed. + * debian/rules: Make sure config.{guess,sub} are up to date. (Upstream + _does_ ship these.) + * debian/mcl-doc.doc-base.mcl, debian/mcl-doc.doc-base.mclfaq: We are no + longer shipping documentation in txt format. + + -- Joost van Baal <[email protected]> Wed, 25 May 2005 08:09:54 +0200 + +mcl (1:05-096-1) unstable; urgency=low + + * New upstream development release. (Missed mcl-04-314, mcl-05-090.) + The only difference between mcl 05-096 and the official 05-090 release is + the addition of a clmorder(1) manpage. Here's a rephrased snippet from + the 05-090 announcement message: + Nothing changed in the core clustering algorithm. But: + - Better support for diagnostics: mcl can now dump iterand submatrices. + - Helper applications for analyzing cluster structure added: clxdo, + clxcoarse (primitive hierarchical clustering, undocumented shell + scripts, installed in /usr/share/doc/mcl/scripts) and clmorder. + - Improvement of sibling applications: large mcxsubs rewrite - cleaner + specification language and new modes and options. Also, rewrite of + the IO library (umpteenth). + Read changelog for details. + * Install upstream TODO file. + * Removed maintainer scripts: not needed for this package. + * mcl-doc.doc-base.clmdist: fixed typo. + + -- Joost van Baal <[email protected]> Wed, 06 Apr 2005 09:50:10 +0200 + +mcl (1:04-250-2) unstable; urgency=medium + + * control: Fixed embarrasing typo in description (closes: #285424). + This is the reason urgency=medium rather than high: it'd be very + nice if this package made it to sarge, so that not too many people + get exposed to this ugly typo: s/computer sciense/computer science/. + * mcl 04-314 is out, but might not get packaged: it has no shocking + improvements, and a new upstream is likely to get published soon. + + -- Joost van Baal <[email protected]> Sun, 16 Jan 2005 16:27:12 +0100 + +mcl (1:04-250-1) unstable; urgency=low + + * New upstream release. (Missed mcl-04-230.) + * watch: added, so that + http://qa.debian.org/developer.php?gpg_key=969457F0 looks even + more spiffy. + + -- Joost van Baal <[email protected]> Wed, 08 Sep 2004 15:04:32 +0200 + +mcl (1:04-189-1) unstable; urgency=low + + * New upstream release. (Missed mcl-04-174, 04-185, 04-187.) + However, beware! mcl-04-103 might be considered non-free by some. + LICENSE in this release is more clear, and free. debian/copyright + updated accoringly. + Furthermore, zoem >= 04-173 is needed for parsing cmlformat(1)'s + zoem output. Such a zoem release is not yet packaged for Debian. + * control: added Enhances: blast2, ncbi-tools-bin, bioperl. + + -- Joost van Baal <[email protected]> Thu, 08 Jul 2004 12:13:30 +0200 + +mcl (1:04-103-1) unstable; urgency=low + + * New upstream development release. (Upstream has published six other + development releases since 03-277.) + * Splitted in mcl and mcl-doc binary packages. + * No longer installs HTML documentation in plain text too. + * Some manpages no longer register via doc-base; just the "major" ones + do now. + * Debian Policy compliance: bumped from Standards Version 3.5.9 to + Standards-Version: 3.6.1.0: debian/rules now honors DEB_BUILD_OPTIONS. + + -- Joost van Baal <[email protected]> Tue, 13 Apr 2004 07:59:47 +0200 + +mcl (1:03-277-1) unstable; urgency=low + + * New upstream release. This is the same as + http://micans.org/mcl/src/mcl-03-276.tar.gz, the version number is + the only thing which differs. + * doc-base.clmmate: added. Upstream ships a clmmate manpage now: our + package is lintian clean again. + + -- Joost van Baal <[email protected]> Sun, 05 Oct 2003 12:27:53 +0200 + +mcl (1:03-276-1) unstable; urgency=low + + * New upstream _development_ release (missed formal releases 03-154, + 03-178, 03-185, 03-245). + * copyright: added note on citations when using the software in writing + scientific papers. + * rules: build and install BLAST parsing scripts. Do not build tribe + stuff. See README for details. + * doc-base.*: new docs: clmformat, mclblastline, mclpipeline, mcxassemble, + mcxdeblast, mcxio. removed docs: clmconf, mcxformat. + + -- Joost van Baal <[email protected]> Fri, 03 Oct 2003 11:48:46 +0200 + +mcl (1:03-010-2) unstable; urgency=low + + * Removed bogus mcximac doc-base file: mcximac does not exist. Tnx + Laurent Bonnaud. (closes: #193058) + + -- Joost van Baal <[email protected]> Thu, 15 May 2003 10:58:17 +0200 + +mcl (1:03-010-1) unstable; urgency=low + + * New upstream release. + * Registered new docs using doc-base: clmimac, clmresidue, mcxmap. mcl + and mclfaq now get installed in plain text format too. + * debian/control: Standards 3.5.2 -> 3.5.9 (no changes needed). + + -- Joost van Baal <[email protected]> Sat, 10 May 2003 10:29:04 +0200 + +mcl (1:02-277-1) unstable; urgency=low + + * New upstream release. + + -- Joost van Baal <[email protected]> Fri, 25 Oct 2002 11:31:34 +0200 + +mcl (1:02-172-1) unstable; urgency=low + + * New upstream release. + * debian/rules: no longer uses touch-hack to work around timeskew + problems: upstreams uses AM_MAINTAINER_MODE now. + + -- Joost van Baal <[email protected]> Mon, 24 Jun 2002 14:44:11 +0200 + +mcl (1:02-116-1) unstable; urgency=low + + * New upstream release. + + -- Joost van Baal <[email protected]> Sat, 27 Apr 2002 22:59:49 +0200 + +mcl (1:02-113-cvs-1) unstable; urgency=low + + * build from current cvs, pre-release + * debian/rules: set configure flags based on check equality of + DEB_BUILD_GNU_TYPE and DEB_HOST_GNU_TYPE, cf current autotools-dev ideas. + * debian/control, debian/copyright: MCL found a new home on the www. + * debian/copyright: added note on contrib/tribe/ copyright holder. + * doc-base.*: added doc-base.mclfaq and doc-base.mcximac + + -- Joost van Baal <[email protected]> Tue, 23 Apr 2002 23:30:37 +0200 + +mcl (1:02-035-1) unstable; urgency=low + + * First release for the Debian archive (closes: #132283). + * copyright: new download location, refer to /usr/share/common-licenses/GPL . + * rules: applied some of Henrique de Moraes Holschuh's autotools-dev voodoo, + got rid of some NOP dh_ calls. + * docs: no longer installs NEWS; this file is not yet maintained upstream. + + -- Joost van Baal <[email protected]> Wed, 6 Feb 2002 10:20:17 +0100 + +mcl (1:02-034-1) unstable; urgency=low + + * New upstream release. + + -- Joost van Baal <[email protected]> Mon, 4 Feb 2002 08:33:36 +0100 + +mcl (1:02-030-1) unstable; urgency=low + + * Snapshot build from CVS. + * Use epoch in version numbering, since upstream made order-breaking + version numbering policy change. + * Use docbase for all .ps and .html manpages. + + -- Joost van Baal <[email protected]> Wed, 30 Jan 2002 22:46:28 +0100 + +mcl (20020116-1) unstable; urgency=low + + * Snapshot build from CVS. + + -- Joost van Baal <[email protected]> Wed, 16 Jan 2002 21:08:22 +0100 + +mcl (20011211-1) unstable; urgency=low + + * New upstream release. Now registers documentation using doc-base. + + -- Joost van Baal <[email protected]> Tue, 11 Dec 2001 20:19:42 +0100 + +mcl (20011012-1) unstable; urgency=low + + * Initial Release. + + -- Joost van Baal <[email protected]> Fri, 12 Oct 2001 22:43:08 +0200 Deleted: trunk/packages/mcl/tags/1:11-294-1/debian/control =================================================================== --- trunk/packages/mcl/trunk/debian/control 2011-01-24 16:58:10 UTC (rev 5699) +++ trunk/packages/mcl/tags/1:11-294-1/debian/control 2011-11-02 20:46:11 UTC (rev 8397) @@ -1,37 +0,0 @@ -Source: mcl -Section: math -Priority: optional -Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Philipp Benner <[email protected]>, - Andreas Tille <[email protected]> -Build-Depends: debhelper (>= 7), autotools-dev, quilt, zoem, tidy -Standards-Version: 3.9.1 -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mcl/ -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mcl/ -Homepage: http://micans.org/mcl/ - -Package: mcl -Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends} -Suggests: mcl-doc -Enhances: blast2, ncbi-tools-bin, bioperl-run -Description: the Markov Cluster algorithm - The MCL package is an implementation of the MCL algorithm, and offers - utilities for manipulating sparse matrices (the essential data - structure in the MCL algorithm) and conducting cluster experiments. - . - MCL is currently being used in sciences like biology (protein family - detection, genomics), computer science (node clustering in - Peer-to-Peer networks), and linguistics (text analysis). - -Package: mcl-doc -Architecture: all -Depends: ${misc:Depends} -Section: doc -Suggests: mcl -Description: documentation for mcl - The MCL package is an implementation of the Markov Cluster algorithm, - for manipulating sparse matricess and conducting cluster experiments. - . - This is documention for mcl: the MCL FAQ, some examples as well as manpages - in HTML and PostScript format. Copied: trunk/packages/mcl/tags/1:11-294-1/debian/control (from rev 8396, trunk/packages/mcl/trunk/debian/control) =================================================================== --- trunk/packages/mcl/tags/1:11-294-1/debian/control (rev 0) +++ trunk/packages/mcl/tags/1:11-294-1/debian/control 2011-11-02 20:46:11 UTC (rev 8397) @@ -0,0 +1,37 @@ +Source: mcl +Section: math +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Philipp Benner <[email protected]>, + Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 7), autotools-dev, quilt, zoem, tidy +Standards-Version: 3.9.2 +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mcl/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mcl/ +Homepage: http://micans.org/mcl/ + +Package: mcl +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Suggests: mcl-doc +Enhances: blast2, ncbi-tools-bin, bioperl-run +Description: Markov Cluster algorithm + The MCL package is an implementation of the MCL algorithm, and offers + utilities for manipulating sparse matrices (the essential data + structure in the MCL algorithm) and conducting cluster experiments. + . + MCL is currently being used in sciences like biology (protein family + detection, genomics), computer science (node clustering in + Peer-to-Peer networks), and linguistics (text analysis). + +Package: mcl-doc +Architecture: all +Depends: ${misc:Depends} +Section: doc +Suggests: mcl +Description: documentation for mcl + The MCL package is an implementation of the Markov Cluster algorithm, + for manipulating sparse matricess and conducting cluster experiments. + . + This is documention for mcl: the MCL FAQ, some examples as well as manpages + in HTML and PostScript format. Deleted: trunk/packages/mcl/tags/1:11-294-1/debian/rules =================================================================== --- trunk/packages/mcl/trunk/debian/rules 2011-01-24 16:58:10 UTC (rev 5699) +++ trunk/packages/mcl/tags/1:11-294-1/debian/rules 2011-11-02 20:46:11 UTC (rev 8397) @@ -1,194 +0,0 @@ -#!/usr/bin/make -f - -# based upon sample debian/rules that uses debhelper. -# GNU copyright 1997 to 1999 by Joey Hess. - -# Uncomment this to turn on verbose mode. -# export DH_VERBOSE=1 - -include /usr/share/quilt/quilt.make - -pkg=mcl - -# allow bashism's in commandlines -SHELL = /bin/bash - -# Debian Policy 10.1 -CFLAGS = -g -Wall -ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) -CFLAGS += -O0 -else -CFLAGS += -O2 -endif -INSTALL = install -INSTALL_PROGRAM = $(INSTALL) -p -o root -g root -m 755 -ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS))) -INSTALL_PROGRAM += -s -endif - -# variables to be used in configure invocation. see -# autotools-dev/README.Debian.gz -export DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE) -export DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE) - -# use autoconf 2.52 or newer -ifeq ($(DEB_BUILD_GNU_TYPE), $(DEB_HOST_GNU_TYPE)) - confflags += --build $(DEB_HOST_GNU_TYPE) -else - confflags += --build $(DEB_BUILD_GNU_TYPE) --host $(DEB_HOST_GNU_TYPE) -endif - -## Build BLAST parsing script mcxdeblast and the pipeline script mclblastline -## (sources in src/alien/oxygen). It encapsulates all the stages of parsing, -## matrix creation, running mcl, and formatting the result -## into a single application. -confflags += --enable-blast - -## add --enable-tribe to confflags to add the upstreams supplied tribe tools -## (protein clustering stuff). This builds and installs the tools -## -## tribe-families tribe-matrix tribemcl tribe-parse -## -## We're not doing it since tribe-matrix segfaults, and the tools lackproper -## manpages. Furthermore, the BLAST parsing scripts can be used in place of -## the tribe module. - -# confflags += --enable-tribe - -## If you really want to suppress the citation reference printed by MCL (the -## one which looks like -## -## Please cite: -## Stijn van Dongen, Graph Clustering by Flow Simulation. PhD thesis, -## University of Utrecht, May 2000. -## ( http://www.library.uu.nl/digiarchief/dip/diss/1895620/full.pdf -## or http://micans.org/mcl/lit/svdthesis.pdf.gz) -## OR -## 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 -## or http://micans.org/mcl/lit/INS-R0010.ps.Z) -## -## ), then this is the place to do it. Of course we honor the choice of -## upstream here, and build as suggested by upsteam. - -# confflags += --disable-helpful-reminder - -config: config-stamp -config-stamp: - dh_testdir - -# # Make sure we have fresh config.{sub,guess}, in order to make life -# # more easy for porters to new architectures. See -# # autotools-dev/README.Debian.gz - if [ -r /usr/share/misc/config.sub ] && [ ! -f autofoo/config.sub.backup ]; then \ - mv -v autofoo/config.sub autofoo/config.sub.backup; \ - cp -f /usr/share/misc/config.sub autofoo/config.sub; \ - fi - - if [ -r /usr/share/misc/config.guess ] && [ ! -f autofoo/config.guess.backup ]; then \ - mv -v autofoo/config.guess autofoo/config.guess.backup; \ - cp -f /usr/share/misc/config.guess autofoo/config.guess; \ - fi - - touch $@ - -config-clean: - dh_testdir - dh_testroot - - if [ -f autofoo/config.sub.backup ]; then \ - mv -fv autofoo/config.sub.backup autofoo/config.sub; \ - fi - - if [ -f autofoo/config.guess.backup ]; then \ - mv -fv autofoo/config.guess.backup autofoo/config.guess; \ - fi - - $(RM) config-stamp - - -configure: config configure-stamp -configure-stamp: - dh_testdir - - ./configure \ - $(confflags) \ - --prefix=/usr \ - --mandir=\$${prefix}/share/man \ - --infodir=\$${prefix}/share/info - - touch configure-stamp - -build: patch configure build-stamp -build-stamp: $(QUILT_STAMPFN) - dh_testdir - - $(MAKE) - - touch build-stamp - -clean: unpatch config-clean - dh_testdir - dh_testroot - $(RM) -f build-stamp configure-stamp - - [ ! -f Makefile ] || $(MAKE) distclean - - dh_clean - -install: build - dh_testdir - dh_testroot - dh_clean -k - dh_installdirs - - $(MAKE) install DESTDIR=$(CURDIR)/debian/mcl -# # install some extra stuff not installed by upstream - install -c -m 644 $(CURDIR)/{AUTHORS,README,THANKS} $(CURDIR)/debian/mcl/usr/share/doc/mcl/ - mkdir $(CURDIR)/debian/mcl/usr/share/doc/mcl/scripts - install -c -m 644 $(CURDIR)/scripts/clx* $(CURDIR)/debian/mcl/usr/share/doc/mcl/scripts/ -# # clean up unneeded docs - $(RM) $(CURDIR)/debian/mcl/usr/share/doc/mcl/*txt -# # process mcl-doc.install - dh_install --sourcedir=debian/mcl - dh_installdocs -# # clean up files just copied to mcl-doc - $(RM) $(CURDIR)/debian/mcl/usr/share/doc/mcl/{AUTHORS,README,THANKS} - $(RM) $(CURDIR)/debian/mcl/usr/share/doc/mcl/*{html,ps,minimcl} - $(RM) -r $(CURDIR)/debian/mcl/usr/share/doc/mcl/examples - $(RM) -r $(CURDIR)/debian/mcl/usr/share/man/man[5,7] - -binary-indep: build install - dh_installman - # Fix broken manpages instead - sed -i -e 's/^\(.TH "[cm][lc][mx]\) \+\(\w\)/\1\2/' \ - -e 's/^\([cm][lc][mx]\) \+\(\w\+ \\-\)/\1\2/' \ - $(CURDIR)/debian/$(pkg)/usr/share/man/man1/[cm]*.1 - dh_installchangelogs ChangeLog - dh_compress - dh_fixperms - dh_installdeb - dh_shlibdeps - dh_gencontrol - dh_md5sums - dh_builddeb -pmcl-doc - - -binary-arch: build install -# no need to call dh_installexamples: upstream takes care of -# this in 'make install' - dh_installman - dh_installchangelogs ChangeLog - dh_strip - dh_compress - dh_fixperms - dh_installdeb - dh_shlibdeps - dh_gencontrol - dh_md5sums - dh_builddeb -pmcl - -binary: binary-indep binary-arch -.PHONY: build clean binary-indep binary-arch binary install configure config config-clean Copied: trunk/packages/mcl/tags/1:11-294-1/debian/rules (from rev 8396, trunk/packages/mcl/trunk/debian/rules) =================================================================== --- trunk/packages/mcl/tags/1:11-294-1/debian/rules (rev 0) +++ trunk/packages/mcl/tags/1:11-294-1/debian/rules 2011-11-02 20:46:11 UTC (rev 8397) @@ -0,0 +1,196 @@ +#!/usr/bin/make -f + +# based upon sample debian/rules that uses debhelper. +# GNU copyright 1997 to 1999 by Joey Hess. + +# Uncomment this to turn on verbose mode. +# export DH_VERBOSE=1 + +include /usr/share/quilt/quilt.make + +pkg=mcl + +# allow bashism's in commandlines +SHELL = /bin/bash + +# Debian Policy 10.1 +CFLAGS = -g -Wall +ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) +CFLAGS += -O0 +else +CFLAGS += -O2 +endif +INSTALL = install +INSTALL_PROGRAM = $(INSTALL) -p -o root -g root -m 755 +ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS))) +INSTALL_PROGRAM += -s +endif + +# variables to be used in configure invocation. see +# autotools-dev/README.Debian.gz +export DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE) +export DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE) + +# use autoconf 2.52 or newer +ifeq ($(DEB_BUILD_GNU_TYPE), $(DEB_HOST_GNU_TYPE)) + confflags += --build $(DEB_HOST_GNU_TYPE) +else + confflags += --build $(DEB_BUILD_GNU_TYPE) --host $(DEB_HOST_GNU_TYPE) +endif + +## Build BLAST parsing script mcxdeblast and the pipeline script mclblastline +## (sources in src/alien/oxygen). It encapsulates all the stages of parsing, +## matrix creation, running mcl, and formatting the result +## into a single application. +confflags += --enable-blast + +## add --enable-tribe to confflags to add the upstreams supplied tribe tools +## (protein clustering stuff). This builds and installs the tools +## +## tribe-families tribe-matrix tribemcl tribe-parse +## +## We're not doing it since tribe-matrix segfaults, and the tools lackproper +## manpages. Furthermore, the BLAST parsing scripts can be used in place of +## the tribe module. + +# confflags += --enable-tribe + +## If you really want to suppress the citation reference printed by MCL (the +## one which looks like +## +## Please cite: +## Stijn van Dongen, Graph Clustering by Flow Simulation. PhD thesis, +## University of Utrecht, May 2000. +## ( http://www.library.uu.nl/digiarchief/dip/diss/1895620/full.pdf +## or http://micans.org/mcl/lit/svdthesis.pdf.gz) +## OR +## 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 +## or http://micans.org/mcl/lit/INS-R0010.ps.Z) +## +## ), then this is the place to do it. Of course we honor the choice of +## upstream here, and build as suggested by upsteam. + +# confflags += --disable-helpful-reminder + +config: config-stamp +config-stamp: + dh_testdir + +# # Make sure we have fresh config.{sub,guess}, in order to make life +# # more easy for porters to new architectures. See +# # autotools-dev/README.Debian.gz + if [ -r /usr/share/misc/config.sub ] && [ ! -f autofoo/config.sub.backup ]; then \ + mv -v autofoo/config.sub autofoo/config.sub.backup; \ + cp -f /usr/share/misc/config.sub autofoo/config.sub; \ + fi + + if [ -r /usr/share/misc/config.guess ] && [ ! -f autofoo/config.guess.backup ]; then \ + mv -v autofoo/config.guess autofoo/config.guess.backup; \ + cp -f /usr/share/misc/config.guess autofoo/config.guess; \ + fi + + touch $@ + +config-clean: + dh_testdir + dh_testroot + + if [ -f autofoo/config.sub.backup ]; then \ + mv -fv autofoo/config.sub.backup autofoo/config.sub; \ + fi + + if [ -f autofoo/config.guess.backup ]; then \ + mv -fv autofoo/config.guess.backup autofoo/config.guess; \ + fi + + $(RM) config-stamp + + +configure: config configure-stamp +configure-stamp: + dh_testdir + + ./configure \ + $(confflags) \ + --prefix=/usr \ + --mandir=\$${prefix}/share/man \ + --infodir=\$${prefix}/share/info + + touch configure-stamp + +build: build-arch build-indep +build-arch: build-stamp +build-indep: build-stamp +build-stamp: patch configure $(QUILT_STAMPFN) + dh_testdir + + $(MAKE) + + touch build-stamp + +clean: unpatch config-clean + dh_testdir + dh_testroot + $(RM) -f build-stamp configure-stamp + + [ ! -f Makefile ] || $(MAKE) distclean + + dh_clean + +install: build + dh_testdir + dh_testroot + dh_clean -k + dh_installdirs + + $(MAKE) install DESTDIR=$(CURDIR)/debian/mcl +# # install some extra stuff not installed by upstream + install -c -m 644 $(CURDIR)/{AUTHORS,README,THANKS} $(CURDIR)/debian/mcl/usr/share/doc/mcl/ + mkdir $(CURDIR)/debian/mcl/usr/share/doc/mcl/scripts + install -c -m 644 $(CURDIR)/scripts/clx* $(CURDIR)/debian/mcl/usr/share/doc/mcl/scripts/ +# # clean up unneeded docs + $(RM) $(CURDIR)/debian/mcl/usr/share/doc/mcl/*txt +# # process mcl-doc.install + dh_install --sourcedir=debian/mcl + dh_installdocs +# # clean up files just copied to mcl-doc + $(RM) $(CURDIR)/debian/mcl/usr/share/doc/mcl/{AUTHORS,README,THANKS} + $(RM) $(CURDIR)/debian/mcl/usr/share/doc/mcl/*{html,ps,minimcl} + $(RM) -r $(CURDIR)/debian/mcl/usr/share/doc/mcl/examples + $(RM) -r $(CURDIR)/debian/mcl/usr/share/man/man[5,7] + +binary-indep: build install + dh_installman + # Fix broken manpages instead + sed -i -e 's/^\(.TH "[cm][lc][mx]\) \+\(\w\)/\1\2/' \ + -e 's/^\([cm][lc][mx]\) \+\(\w\+ \\-\)/\1\2/' \ + $(CURDIR)/debian/$(pkg)/usr/share/man/man1/[cm]*.1 + dh_installchangelogs ChangeLog + dh_compress + dh_fixperms + dh_installdeb + dh_shlibdeps + dh_gencontrol + dh_md5sums + dh_builddeb -pmcl-doc + + +binary-arch: build install +# no need to call dh_installexamples: upstream takes care of +# this in 'make install' + dh_installman + dh_installchangelogs ChangeLog + dh_strip + dh_compress + dh_fixperms + dh_installdeb + dh_shlibdeps + dh_gencontrol + dh_md5sums + dh_builddeb -pmcl + +binary: binary-indep binary-arch +.PHONY: build clean binary-indep binary-arch binary install configure config config-clean _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
