emboss (6.6.0+dfsg-6) unstable; urgency=medium * debhelper 10 * d/watch: version=4 * Build-Depends: default-libmysqlclient-dev Closes: #845838 -- Andreas Tille Sat, 03 Dec 2016 08:40:10 +0100 emboss (6.6.0+dfsg-5) unstable; urgency=medium * Make sure manpage links will not end up in archindep packages Closes: #834013 -- Andreas Tille Fri, 12 Aug 2016 16:48:46 +0200 emboss (6.6.0+dfsg-4) unstable; urgency=medium [ Canberk Koç ] * Team upload. * Autopkgtest added [ Andreas Tille ] * hardening+=all * Fix some minor spelling issues inside packaging * Secure Vcs-Git * Bumped Standards-Version -- Canberk Koç Tue, 09 Aug 2016 07:27:29 +0300 emboss (6.6.0+dfsg-3) unstable; urgency=medium * Make sure we will not delete documentation files from new upstream version * Enable build on hurd Closes: #762673 * cme fix dpkg-control * incorporate changes from biolinux (see below) * Make sure data are really in th directory where they will be copied from Closes: #806022 * Ignore false lintian positives about package-contains-timestamped-gzip * Cleanup debian/copyright from not existing files and not DEP5 conform issues * d/watch: add version mangling -- Andreas Tille Tue, 01 Dec 2015 16:03:42 +0100 emboss (6.6.0+dfsg-2biolinux1) trusty; urgency=medium * Current package builds jemboss from source but then installs the pre-built jemboss.jar from the tarball - not good!! Add ant dep and ensure that jemboss.jar really builds * Include image for icon and edit .desktop file * Add /usr/bin/jemboss * Clean ./jemboss/runJemboss.sh which is created on build * Clean various other files that blocked debuild -S (but note we are still using some convenience copies of JARs) * Remove makeJar.csh, and thus remove jemboss dep on csh * Remove activation.jar which does not seem to be used at all -- Tim Booth Wed, 08 Apr 2015 19:06:09 +0100 emboss (6.6.0+dfsg-1) unstable; urgency=medium [ Andreas Tille ] * debian/copyright: Add Upstream-Contact to report bugs [ Gert Wollny ] * Add patch to pad Hershey_to_Unicode_table consistently (Closes: #748395) [ Andreas Tille ] * cme fix dpkg-control: - drop very old library versions from conflicts / replaces list * remove explicite quilt dependency which is not needed * debian/copyright: Exclude invariant GFDL 1.1 files which are related to quite outdated EMBOSS 2.5.0 * debian/emboss-doc.doc-base.emboss-admin: removed * debian/patches/remove_non-free_doc.patch: Cleanup Makefile.am from non-free docs -- Andreas Tille Mon, 19 May 2014 20:52:12 +0200 emboss (6.6.0-1) unstable; urgency=low [ Charles Plessy ] ec024a3 Imported Upstream version 6.5.7 78ef855 Removed upstream patch (for version 6.4.0). 2f66060 Clarified the license of the packaging. [ Andreas Tille ] * Imported Upstream version 6.6.0 (+adapt quilt patches) Closes: #558852 (at least the regexp dpkg-shlibdeps: warning: symbol.*found in none of the libraries does not appear in the build log any more - feel free to reopen with more info) * Clarified copyright and licenses for: - emboss/data/OBO/chebi.obo [b60238c] - emboss/data/OBO/gene_ontology*.obo [dc91819] - emboss/data/OBO/software.obo [3c8b4bf] - emboss/data/OBO/*.obo [8c34d40] - emboss/data/OBO/pathway.obo [1b3bbcf][1ff8ab9] - emboss/data/OBO/eco.obo [95aa795] - emboss/data/OBO/ro.obo [2865596] * debian/control: - Standards-Version: 3.9.4 (no changes needed) - Provide real package evince in addition to virtual package pdf-viewer * debian/rules: - Remove some remainings from CVS from emboss-test package * debian/{jemboss.desktop,jemboss.menu}: - runJemboss.sh is now POSIX shell instead of csh * debian/source/format: 3.0 (quilt) * debian/patches/bashism.patch: Avoid bashism Closes: #690651 -- Andreas Tille Mon, 09 Sep 2013 14:48:22 +0200 emboss (6.4.0-4) unstable; urgency=low * use autoreconf to enable latest changes -- Andreas Tille Fri, 10 Aug 2012 22:46:33 +0200 emboss (6.4.0-3) unstable; urgency=low * Import patches prepared by Felix Geyer to cope with the --as-needed issue when linking against database clients (thanks to Felix) Closes: #650237 * Fix typo to build emboss including PostgreSQL support (Thanks to Felix Geyer for the patch) Closes: #683190 -- Andreas Tille Thu, 09 Aug 2012 16:01:07 +0200 emboss (6.4.0-2) unstable; urgency=low * Separate architecture-dependant and independant targets in debian/rules. This makes the package buildable again on our build farm. -- Charles Plessy Thu, 21 Jun 2012 14:31:59 +0900 emboss (6.4.0-1) unstable; urgency=low [ Charles Plessy ] * New upstream release. * Removed calls to dh_makeshlibs in debian/rules (closes: #595613). * Build on libpng-dev instead of libpng12-dev (closes: #662313). * Breaks: EMBASSY <= 6.3.1 (debian/control). [ Andreas Tille ] * debian/upstream: separate reference section * debian/rules: - Make sure every binary package has a changelog file - enable hardening - do not clean backup file which is part of upstream tarball - remove executable flag from some test data - restore executable flag of some jemboss utils which seems to be removed by install target * debian/control: - remove article from description - Standards-Version: 3.9.3 (no changes needed) * debian/emboss.menu: delete - chances that users will pick command line programs from longish menu entries are pretty low * debian/emboss-lib.lintian-overrides: Adapted string of lintian warning -- Charles Plessy Wed, 20 Jun 2012 18:55:16 +0900 emboss (6.3.1-6) unstable; urgency=low * All EMBOSS libraries are to be considered private. The libajax* and libnucleus* are merged in the emboss-lib package, which is moved from the ‘libs’ to the ‘science’ section. Closes: #595613. * Added a Lintian override for the convenience copy of the PCRE library (debian/emboss-lib.lintian-overrides). * Build-depend on libhpdf-dev for PDF support, removed erroneous build dependance on libpcre3-dev (debian/control). * Added dependance on emboss to jemboss (debian/control). -- Charles Plessy Thu, 16 Sep 2010 21:06:14 +0900 emboss (6.3.1-5) unstable; urgency=low * New upstream patch, version 1-4. * Restore original config.* files in the clean target if the unpacked source package is a git repository (debian/rules). -- Charles Plessy Thu, 12 Aug 2010 08:00:58 +0900 emboss (6.3.1-4) unstable; urgency=low * New upstream patch, version 1-2. * Unset LS_COLORS in debian/rules (see #592089). -- Charles Plessy Sat, 07 Aug 2010 23:03:10 +0900 emboss (6.3.1-3) unstable; urgency=low * Use default Java instead of OpenJDK (debian/control, debian/rules, closes: #590553, thanks to Petr Salinger). * Incremented Standards-Version in debian/control to reflect conformance with Debian Policy 3.9.1 (no changes needed). -- Charles Plessy Wed, 28 Jul 2010 23:42:31 +0900 emboss (6.3.1-2) unstable; urgency=low * First upstream patch for version 6.3.1 (debian/series, debian/patches/official-upstream-patch.patch). * Moved openjdk-6-jdk to Build-Depends (debian/control, closes: #589897). -- Charles Plessy Fri, 23 Jul 2010 10:51:50 +0900 emboss (6.3.1-1) unstable; urgency=low * New upstream release. - Dropped debian/patches/official-upstream-patch.patch. - Refreshed the manual pages (debian/*manpages*). * Incremented Standards-Version in debian/control to reflect conformance with Debian Policy 3.9.0 (no changes needed). * Keep and restore a clean copy of the test directory, closes: #587170. * Build against Debian's zlib and expat libraries (debian/rules, debian/control, deleted debian/libajax6.lintian-overrides). * Added support for MySQL and PostgreSQL (debian/control, debian/rules). * Added symbols files for emboss-libs, libajax6 and libnucleus6. This will prevent mixing incompatible binary packages (LP: 526356). -- Charles Plessy Wed, 21 Jul 2010 15:24:07 +0900 emboss (6.2.0-2) unstable; urgency=low * Updated debian/patches/official-upstream-patch.patch to version 1-19. -- Charles Plessy Tue, 22 Jun 2010 17:01:44 +0900 emboss (6.2.0-1) unstable; urgency=low * New upstream release. * Dropped useless dependency on csh | c-shell for emboss (LP: 525662). * Incremented Standards-Version in debian/control to reflect conformance with Policy 3.8.4 (no changes needed). * Detected a zlib convenience copy; added debian/emboss.lintian-overrides until Upstream confirms that EMBOSS can build on latest pristine zlib (See http://lists.open-bio.org/pipermail/emboss/2010-May/003915.html). -- Charles Plessy Mon, 31 May 2010 15:13:09 +0900 emboss (6.1.0-5) unstable; urgency=low * The source package is now managed with Git (debian/control). - VCS URLs updated in debian/control. * debian/changelog: corrected an error on a program name (vectorstrip). * debian/patches/transient-vectorstrip.patch: keep quality scores. * Two new patches not yet officialised: - debian/patches/transient-vectorstrip.patch: retain quality scores. - debian/patches/tfm-html.patch: corrects path to HTML documentation. * Added Debian and FreeDesktop menu entries for Jemboss. * Do not create a makefile when there is not at clean time (debian/rules). * Documented how the package is tested in README.debian. * Added various informations about Upstream in debian/upstream-metadata.yaml -- Charles Plessy Mon, 09 Nov 2009 20:39:28 +0900 emboss (6.1.0-4) unstable; urgency=low * New upstream patch (patch-1-2): - Fix string extension so that pointers in lists remain valid. - This fixes a bug in processing SwissProt complex descriptions. - Fix definition of AJRESIZE0 macro. - Fix processing of first match in a profile alignment (prophet). * Delete /usr/share/EMBOSS/doc/programs/text/frestdist.txt, that should belong to embassy-phylip (PHYLIPNEW). (debian/rules) * Incremented Standards-Version in debian/control to reflect conformance with Policy 3.8.3 (no changes needed). * Removed the libtool libraries from the development packages (debian/rules). -- Charles Plessy Tue, 25 Aug 2009 23:19:10 +0900 emboss (6.1.0-2) unstable; urgency=low * New upstream patch (patch-1-1): - Fix feature specification problems in Jemboss. - Use version number to point to documentation URLs - Remove standalone option from server script. - Correct FASTQ input searching for '@' to start next sequence - Standardize FASTQ sequence formats with other OpenBio projects - Correct issues in igstrict, genpept and refseqp formats * debian/control: - Incremented Standards-Version to reflect conformance with Policy 3.8.2 (no changes needed). * debian/copyright.introduction: - Use symbolic links to refer to relevant versions of the GNU licenses. -- Charles Plessy Sat, 01 Aug 2009 10:26:26 +0900 emboss (6.1.0-1) unstable; urgency=low * New upstream release (Closes: #530112). * Dropped patch against previous release. * Created or refreshed the manpages. -- Charles Plessy Wed, 15 Jul 2009 23:15:26 +0900 emboss (6.0.1-11) unstable; urgency=low * New upstream patch (patch-1-12): - Remove the 'aligned' attribute that was added in Fix 4. - Fix crash if maxfragl > 40 selected. - Update Entrez retrieval to cope with an extra line added in the NCBI results. - For phylogenetic applications (PHYLIPNEW) reading distance matrix files failed for some formats written by other applications. Distance matrix input now works for multiple matrices in square, upper-triangular and lower-triangular formats. -- Charles Plessy Sun, 17 May 2009 14:51:05 +0900 emboss (6.0.1-10) unstable; urgency=low * New upstream patch (patch-1-8): Incorrect information was often given in the subsidiary table listing REs that would cut a greater number of times than an optional user-supplied maximum number. The main role of the program was unaffected. -- Charles Plessy Tue, 21 Apr 2009 13:01:38 +0900 emboss (6.0.1-9) unstable; urgency=low * New upstream patch (patch-1-7): - Corrections on syntax using the master qualifier name as a suffix. - Better support of the --without-x (not used in this package). - Bug corrected for needle and water using the -nobrief option. * debian/rules - Corrected again the targets to avoid calling them when it is not necessary. - Defines emboss_acdroot, emboss_docroot and emboss_data in order to run the tests. -- Charles Plessy Wed, 08 Apr 2009 20:20:58 +0900 emboss (6.0.1-8) unstable; urgency=low * debian/rules: - Do not pass java options to the configure script if openjdk is not installed (Closes: #521996, thanks to Peter Green). - Recursive removal of emboss_tmp (to build the package twice in a row). - Removed one `dh binary-indep` instance that strangely sneaked in after running `svn update`. * debian/control: - Moved again openjdk-6-jdk to Build-Depends-Indep. - Added debhelper's ${misc:Depends} substitution variable to the packages that did not already depend on it. -- Charles Plessy Tue, 31 Mar 2009 14:26:55 +0900 emboss (6.0.1-7) unstable; urgency=low * debian/control: moved openjdk-6-jdk to Build-Depends. Apologies to buildd administrators. (Closes: #521912). -- Charles Plessy Tue, 31 Mar 2009 08:34:59 +0900 emboss (6.0.1-6) unstable; urgency=low * debian/rules: - Build arch all packages only when binary-indep is called (Closes: #521398) - Corrected stamping gymnastics. * debian/control: moved openjdk-6-jdk to Build-Depends-Indep -- Charles Plessy Mon, 30 Mar 2009 13:02:11 +0900 emboss (6.0.1-5) unstable; urgency=low * New upstream patch (patch-1-6): correction for large pairwise alignments. * debian/control: - Incremented Standards-Version to reflect conformance with Policy 3.8.1 (no changes needed). - Moved the bibliographic reference from the description of the EMBOSS package to the file debian/reference. -- Charles Plessy Wed, 25 Mar 2009 11:44:30 +0900 emboss (6.0.1-4) unstable; urgency=low * New upstream patch (patch-1-5): - removes unnecessary whitespaces in edialign.acd. - saves Citations and comments in EMBL/GenBank formats for each new entry processed. * debian/control: - Uses the official homepage URL as confirmed by Upstream. - Redundant section field removed for jemboss. - Description corrected for libnucleus6-dev. * debian/rules: - Pass --bindir=/usr/lib/emboss directly instead of moving files. - Hardcode AJAX_FIXED_ROOT to /usr/share/EMBOSS (Closes: #487539). - Replaced `dh_clean -k', deprecated, by dh_prep. * debian/emboss.dir, debian/emboss.install: simplified after reworking the installation of the binaries and their symbolic links. -- Charles Plessy Sun, 22 Feb 2009 22:53:55 +0900 emboss (6.0.1-3) experimental; urgency=low * New upstream patch (patch-1-3). - fixes segmentation fault in vectorstrip when -auto is used with empty vectorsfile. - adds '.' trailer to the OS line in SwissProt output. * debian/rules: corrected the section of the manual pages of the renamed programs from 1 to 1e (Closes: #503733). * Preliminary support for jEMBOSS: - Build-Depend on openjdk-6-jdk (debian/control). - New package "jemboss", depending on openjdk-6-jre (debian/control). - The jemboss package contains everything installed by the command `make -C jemboss install' (debian/rules). -- Charles Plessy Wed, 26 Nov 2008 08:57:20 +0900 emboss (6.0.1-2) experimental; urgency=low * New upstream patch (patch-1-1). - jaspscan can now scan multiple sequences. - "digest -allpartials" now reports all C-term fragments. -- Charles Plessy Wed, 27 Aug 2008 22:11:45 +0900 emboss (6.0.1-1) experimental; urgency=low * New upstream release: - New applications: aligncopy, aligncopypair, consambig, density, featcopy, featreport, infobase, inforesidue, jaspextract, jaspscan, maskambignuc, maskambigprot, nohtml, nospace, notab, sizeseq, skipredundant, trimspace. - See `/usr/share/doc/emboss/changelog.gz' for more details. * debian/patches: - Removed the patches that are obsoleted by the new release. - Documented the local patch on `tfm' that changes default pager. * debian/README.source added to document how to patch and unpatch the sources. * debian/emboss-doc.doc-base.{apps/groups} corrected for new file locations. * debian/control: - Replaced build dependency on deprecated x-dev by x11proto-core-dev. - Uses debhelper 7. - Incremented the soname of the AJAX and NUCLEUS libraries (conflict and replace the previous versions). - Incremented Standards-Version to 3.8.0 after adding README.Sources. - Added a new package, emboss-test, that contains test data. - Build-Depends: tcsh | csh | c-shell to run the tests. * debian/rules: - Implemented build-time tests. - Updated the instructions to build manpages. -- Charles Plessy Thu, 17 Jul 2008 14:07:40 +0900 emboss (5.0.0-7) unstable; urgency=low * Changed the doc-base section according to the new policy. * Updated my email address. * Updated the contact address in the manpages. -- Charles Plessy Fri, 16 May 2008 19:58:37 +0900 emboss (5.0.0-6) unstable; urgency=low * New bugfixes released upstream: - Fixes failure on some databases if the PAGESIZE was set large and the CACHESIZE was set small. - Platform-independence modifications added. * debian/README.Debian: described the change of default pager for tfm. -- Charles Plessy Fri, 07 Mar 2008 10:15:31 +0900 emboss (5.0.0-5) unstable; urgency=low * New bugfixes released upstream. - Fixes changed ID format in GCG databases. - Fixes reading from PIR databases. - Fixes a problem with O in protein sequences for pyrrolysine. - Fixes a problem in GENBANK output format. - Fixes a problem in reading protein sequences from Staden "spin" interface. - Fixes tokens that are longer than the maximum length. - debian/patches now uses the monolithic upstream patch instead of file-per-file fixes. You can find longer explanations in the header of debian/patches/patch-1-3. -- Charles Plessy Sat, 01 Mar 2008 11:46:26 +0900 emboss (5.0.0-4) unstable; urgency=low * debian/patches: - using-pager-in-tfm.patch: Patching tfm so that it uses the alternatives system `/usr/bin/pager' if the `PAGER' environment variable is not defined. - embindex-fix-2008-01-19.patch: Official fix 3. EMBOSS-5.0.0/nucleus/embindex.c 18 Jan 2008. Order and fill fixes to sort out potential problems with kw/de/tx indexes. -- Charles Plessy Wed, 23 Jan 2008 20:56:22 +0900 emboss (5.0.0-3) unstable; urgency=low [ Nelson A. de Oliveira ] * Using bzip2 compression for packages. This saves about 832KB of space. [ Charles Plessy ] * debian/patches/ajindex-fix-2008-01-09.patch: - Fixes rare secondary index problem with input files over 2Gb. * debian/control: - Switched maintainership to the Debian-Med packaging team. - Relocated the package to the Debian-Med Subversion repository. - Allowed upload by Debian Maintainers. - Checked that the package is compliant to Policy 3.7.3 - Added dialign again to the Recommends: field. It only disappeared from the documentation; the edialign program is still there. - -dev packages now depend on their corresponding libraries. - Replaced occurrences of $(source:Version} by ${binary:Version} to make the packages binNMU safe. - emboss-data and emboss-doc do not Suggest: emboss anymore. - Changed the description of libajax5 and libnucleus5 so that they are not identical. - Removed the XS- prefix in the Vcs fields. - Build-depends on autotools-dev. * debian/rules: - Removes Makefiles ignored by make distclean in the test directory. - Uses config.(sub|guess) from the autotools-dev package. -- Charles Plessy Thu, 10 Jan 2008 21:27:31 +0900 emboss (5.0.0-2) unstable; urgency=low [ Charles Plessy ] * Using a emboss/psiphi.c file fixed by upstream ftp://emboss.open-bio.org/pub/EMBOSS/fixes/psiphi.c * Documentation: - Building the manpages offline to save buildd time, therefore not depending anymore on the XML toolchain. - Added a "e" suffix to the manpages, to avoid conflicts. (Closes: #427439) - Linked /usr/share/emboss-doc/doc/ to /usr/share/EMBOSS/docs, and registered documentation in doc-base. (Closes: #423941) * Gave their own packages to the AJAX and NUCLEUS libraries. - Header files are in /usr/include/ajax and /usr/include/nucleus. - The private pcre files are kept under /usr/include/ajax. (Closes: #433316) * Packaging: - Removed the extra Tag field in debian/control. - Removed the recommendation on dialign, as edialign disappeared. - Tightened the Depends: relationship between emboss and emboss-lib (Closes: #435232). - Removed inactive developer from the uploaders list. - Suggests: embassy. * Temporarily incorporates a relicenced version of the EMBOSS Quick Guide, until it becomes part of the original tarball. Its sources are shipped uuencoded, therefore emboss now build-depends on sharutils. [ Nelson A. de Oliveira ] * Checked and fixed clean target. (Closes: #442554). -- Charles Plessy Sat, 13 Oct 2007 15:05:53 +0900 emboss (5.0.0-1) unstable; urgency=low * New upstream version * Renaming cons and pscan to em_cons and em_pscan, see README.Debian for more information. * Moved all the binaries to /usr/lib/emboss. /usr/bin contains only symbolic links (Closes : #427439, #427440). * Makes sure that there is a Makefile before invoking the clean rule. * Added /etc/emboss/embossrc.d directory for future modular configuration. * Switched from dpatch to quilt (no patches for the moment). * Build-depend on libemboss-acd-perl to generate manpages with acd2docbook.pl, written especially for this package (Closes: #423938). * Adding a placeholder file to force the inclusion of debian/manpages. * Removing the entries in the Debian menu until we agree that we want them. -- Charles Plessy Thu, 19 Jul 2007 13:56:11 +0900 emboss (4.1.0-1) experimental; urgency=low * New maintainer and uploaders * First official release (Closes: #156276) * Xlib transition. * Using dpatch and /usr/share/dpatch/dpatch.make to manage patches. * Added XS-Vcs entries in debian/changelog. * Removed the pcre includes from the emboss-libs package. * Fixed watch file. * Emboss Recommends:dialign and Suggests:clustalw. -- Charles Plessy Mon, 12 Mar 2007 08:26:15 +0900 emboss (2.8.0-2) unstable; urgency=low * Fixed manpages being in both emboss and emboss-lib * Removed circ.dep. emboss <-> emboss-lib -- Matt Hope Fri, 21 May 2004 12:47:47 +1000 emboss (2.8.0-1) unstable; urgency=low * New upstream release -- Matt Hope Fri, 5 Dec 2003 15:08:54 +1100 emboss (2.7.1-1) unstable; urgency=low * New upstream release * emboss-lib - Fixed the shlibs. -- Matt Hope Mon, 7 Jul 2003 14:36:14 +1000 emboss (2.6.0-1) unstable; urgency=low * New upstream release -- Matt Hope Fri, 7 Apr 2003 21:41:12 +1000 emboss (2.4.1-1) unstable; urgency=low * Initial package. Thanks for the feedback from everyone. (Closes: Bug#156276 ITP) -- Matt Hope Sat, 6 Jul 2002 01:11:17 +1000