2009
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 progam 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 <plessy@debian.org> 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 <plessy@debian.org> 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 <plessy@debian.org> Sat, 01 Aug 2009 10:26:26 +0900
emboss (6.1.0-1) unstable; urgency=low
* New upstream relase (Closes: #530112). * Dropped patch against previous release. * Created or refreshed the manpages.
-- Charles Plessy <plessy@debian.org> 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 <plessy@debian.org> 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 <plessy@debian.org> 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 <plessy@debian.org> 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 <plessy@debian.org> 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 <plessy@debian.org> 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 <plessy@debian.org> 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 <plessy@debian.org> 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 <plessy@debian.org> Sun, 22 Feb 2009 22:53:55 +0900
2008
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 <plessy@debian.org> 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 <plessy@debian.org> 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 <plessy@debian.org> 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 <plessy@debian.org> 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 <charles-debian-nospam@plessy.org> 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 <charles-debian-nospam@plessy.org> 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 <charles-debian-nospam@plessy.org> 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:
- Swiched 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 disapperared from
the documentation; the edialign program is still there.
- -dev packages now depend on their corresponding libraries.
- Replaced occurences 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 <charles-debian-nospam@plessy.org> Thu, 10 Jan 2008 21:27:31 +0900
2007
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.
* Temporarly incorporates a relicenced version of the EMBOSS Quick
Guide, until it becomes part of the original tarball. Its sources
are shipped uuencoded, therfore emboss now build-depends on sharutils.
[ Nelson A. de Oliveira ]
* Checked and fixed clean target. (Closes: #442554).
-- Charles Plessy <charles-debian-nospam@plessy.org> 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 befor invoking the clean rule.
* Added /etc/emboss/embossrc.d directory for future modular
configuration.
* Swiched 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 includion of debian/manpages.
* Removing the entries in the Debian menu until we agree that we
want them.
-- Charles Plessy <charles-debian-nospam@plessy.org> Thu, 19 Jul 2007 13:56:11 +0900
emboss (4.1.0-1) experimental; urgency=low
* New maintainer and uploaders * First official relase (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 <charles-debian-nospam@plessy.org> Mon, 12 Mar 2007 08:26:15 +0900
2004
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 <dopey@debian.org> Fri, 21 May 2004 12:47:47 +1000
2003
emboss (2.8.0-1) unstable; urgency=low
* New upstream release
-- Matt Hope <dopey@debian.org> 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 <matth@bioinformatics.unsw.edu.au> Mon, 7 Jul 2003 14:36:14 +1000
emboss (2.6.0-1) unstable; urgency=low
* New upstream release
-- Matt Hope <matth@bioinformatics.unsw.edu.au> Fri, 7 Apr 2003 21:41:12 +1000
2002
emboss (2.4.1-1) unstable; urgency=low
* Initial package.
Thanks for the feedback from everyone.
(Closes: Bug#156276 ITP)
-- Matt Hope <matth@bioinformatics.unsw.edu.au> Sat, 6 Jul 2002 01:11:17 +1000