mcl (1:22-282+ds-3) unstable; urgency=medium * Move external code in a separate subdirectory * Save backup of changed docs to restore it in clean target Closes: #1046152 * Standards-Version: 4.7.0 (routine-update) -- Andreas Tille Mon, 23 Dec 2024 16:14:18 +0100 mcl (1:22-282+ds-2) unstable; urgency=medium * Team Upload. * Re-vendor mcxdeblast back (Closes: #1024170) -- Nilesh Patra Wed, 16 Nov 2022 17:51:43 +0530 mcl (1:22-282+ds-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.6.1 (routine-update) * Remove trailing whitespace in debian/copyright (routine-update) * Build-Depends: libtingea-dev * Deactivate OCaml patch * There is no minimcl doc any more, but install the script anyway * Drop some doc-base files where doc was removed * lintian-overrides for script-with-language-extension -- Andreas Tille Wed, 02 Nov 2022 13:57:43 +0100 mcl (1:14-137+ds-9) unstable; urgency=medium * Fix FTBFS when using gcc-10 (Closes: #957525) -- Shayan Doust Wed, 22 Jul 2020 14:32:45 +0100 mcl (1:14-137+ds-8) unstable; urgency=medium * Add myself as an uploader * Modify patch to fix missing scripts' installation (Closes: #963774) -- Shayan Doust Mon, 29 Jun 2020 10:54:16 +0100 mcl (1:14-137+ds-7) unstable; urgency=medium * Team upload. [ Andreas Tille ] * Add missing Build-Depends: bsdextrautils * Enable backports [ Shayan Doust ] * Install missing library -- Shayan Doust Sun, 21 Jun 2020 19:27:10 +0100 mcl (1:14-137+ds-6) unstable; urgency=medium * Source-only upload -- Andreas Tille Wed, 17 Jun 2020 12:25:00 +0200 mcl (1:14-137+ds-5) unstable; urgency=medium * Team upload. [ Steffen Moeller ] * d/u/metadata: yamllint [ Shayan Doust ] * Patch for mcl OCaml support * OCaml headers are not compatible with c89, so change to c99 * Add rules for *.ml files to build ...fails for some reason * Add build depends for OCaml * Add oasis as build dependency and run oasis setup in rules * Disable dh_auto_build as we do this manually due to OCaml * Use --with ocaml but invoke autoreconf manually within overridden dh_auto_build * New package libmcl-ocaml-dev providing the mcl / ocaml bindings * install ocaml libs within libmcl-ocaml-dev.install * Install META file * Set directory = "^" for ocamlfind to find the libs * Revert "Set directory = "^" for ocamlfind to find the libs" * Use XMETAExtraLines in _oasis to add directory = "^" for ocamlfind to find the libs [ Andreas Tille ] * Add Build-Depends to work with "--with ocaml" * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Use secure URI in Homepage field. * Set field Upstream-Name in debian/copyright. * dh_missing of debhelper compat=13 claims missing installation of docs * install mcl's own examples in one dir and autopkgtest in other dir * Section: ocaml -- Shayan Doust Thu, 11 Jun 2020 19:18:39 +0100 mcl (1:14-137+ds-4) unstable; urgency=medium [ Saira Hussain ] * Team upload. * Provide autopkgtest [ Andreas Tille ] * Standards-Version: 4.4.0 * debhelper 12 -- Saira Hussain Thu, 11 Jul 2019 14:30:55 +0200 mcl (1:14-137+ds-3) unstable; urgency=medium * Philipp Benner has retired - thanks for your work on this package Closes: #913462 -- Andreas Tille Thu, 06 Dec 2018 10:07:17 +0100 mcl (1:14-137+ds-2) unstable; urgency=medium * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 * Remove trailing whitespace in debian/copyright * Fix Perl interpreter path -- Andreas Tille Mon, 29 Oct 2018 09:51:31 +0100 mcl (1:14-137+ds-1) unstable; urgency=medium * Do not save copies of docs in d/rules Closes: #887829 * Remove files from upstream tarball which will be recreated and prevent building the package twice in a row * Standards-Version: 4.1.3 * debhelper 11 * Fix further spelling issues -- Andreas Tille Mon, 22 Jan 2018 13:00:52 +0100 mcl (1:14-137-2) unstable; urgency=medium * DEP5 * Moved packaging from SVN to Git * debhelper 10 * Standards-Version: 4.1.1 * Secure watch file * DEP3 * hardening=+all * Fix spelling * Fix whatis entry in manpages -- Andreas Tille Tue, 28 Nov 2017 11:08:18 +0100 mcl (1:14-137-1) unstable; urgency=medium * New upstream version * Moved debian/upstream to debian/upstream/metadata * debian/control: - cme fix dpkg-control - debhelper 9 * debian/rules: short dh * html docs are now installed into html subdirectory -- Andreas Tille Tue, 20 May 2014 15:50:29 +0200 mcl (1:12-135-2) unstable; urgency=low * Added mayhem bugfixes. * Standards version 3.9.4. -- Philipp Benner Sun, 07 Jul 2013 15:01:08 +0200 mcl (1:12-135-1) unstable; urgency=low [ Andreas Tille ] * debian/upstream: Add citation information [ Philipp Benner ] * New upstream release * Hardening flags * Renamed variables with name 'restricted' in src/impala/matrix.c (Closes: #688655) -- Philipp Benner Sun, 27 Jan 2013 15:49:50 +0100 mcl (1:12-068-1) unstable; urgency=low * New upstream version * debian/control: Standards version 3.9.2 -- Philipp Benner Fri, 09 Mar 2012 15:15:48 +0000 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 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 Mon, 24 Jan 2011 15:58:07 +0100 mcl (1:10-148-1) unstable; urgency=low * New upstream release -- Philipp Benner 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 Tue, 24 Nov 2009 20:43:56 +0000 mcl (1:09-261-1) unstable; urgency=low * New upstream release -- Philipp Benner 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Sat, 10 May 2003 10:29:04 +0200 mcl (1:02-277-1) unstable; urgency=low * New upstream release. -- Joost van Baal 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 Mon, 24 Jun 2002 14:44:11 +0200 mcl (1:02-116-1) unstable; urgency=low * New upstream release. -- Joost van Baal 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 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 Wed, 6 Feb 2002 10:20:17 +0100 mcl (1:02-034-1) unstable; urgency=low * New upstream release. -- Joost van Baal 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 Wed, 30 Jan 2002 22:46:28 +0100 mcl (20020116-1) unstable; urgency=low * Snapshot build from CVS. -- Joost van Baal 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 Tue, 11 Dec 2001 20:19:42 +0100 mcl (20011012-1) unstable; urgency=low * Initial Release. -- Joost van Baal Fri, 12 Oct 2001 22:43:08 +0200