profphd (1.0.42-2) unstable; urgency=medium [ Tatiana Malygina ] * Team upload. * cme fix dpkg-control * cme fix dpkg-copyright * add hardening in d/rules * add patches 1-4 to use latest perl 5.22 (UNFINISHED! checking if this works) * add debian/tests (unfinished too) * remove autopkgtest-perl commands - they actually do nothing - and replaced them with syntax check for all .pm files inside src dir (which is run with command 'perl -c .pm') * update comments in debian/tests/profphd-install-test * add header to debian/patches/5_fix_regex_warning.patch * cleaned up debian/patches/3_fix_indexing.patch [ Andreas Tille ] * Moved packaging from SVN to Git * debhelper 10 * d/rules: do not parse d/changelog * Standards-Version: 4.1.1 -- Tatiana Malygina Thu, 16 Nov 2017 15:10:34 +0100 profphd (1.0.42-1) unstable; urgency=medium * Moved debian/upstream to debian/upstream/metapackages * remove redundant stuff from d/watch * debhelper 9 * Priority: optional * short dh instead of cdbs * cme fix dpkg-control * DEP5 fix -- Andreas Tille Fri, 31 Jul 2015 19:29:28 +0200 profphd (1.0.40-1) unstable; urgency=low [ Laszlo Kajan ] * New upstream release. [ Gregor Herrmann ] * Fix "FTBFS with perl 5.18: POD failure": add patch to fix POD (Closes: #720497) [ Andreas Tille ] * cme fix dpkg-control * anonscm in Vcs fields -- Andreas Tille Thu, 29 Aug 2013 08:52:49 +0200 profphd (1.0.39-1) unstable; urgency=low [ Andreas Tille ] * debian/upstream: Make author field BibTeX compliant [ Laszlo Kajan ] * New upstream release. (Closes: #684857) -- Laszlo Kajan Tue, 14 Aug 2012 19:50:34 +0200 profphd (1.0.38-1) unstable; urgency=low [ Laszlo Kajan ] * New upstream release [ Andreas Tille ] * debian/control: Added rsync to Build-Depends Closes: #646662 * debian/watch: Stripped unneeded comments * debian/patches: Deleted empty dir -- Andreas Tille Wed, 26 Oct 2011 08:09:27 +0200 profphd (1.0.37-1) unstable; urgency=low * Initial release in Debian (Closes: #643324) * New upstream release -- Laszlo Kajan Wed, 28 Sep 2011 14:51:19 +0200 profphd (1.0.36-1) UNRELEASED; urgency=low * New upstream release -- Laszlo Kajan Wed, 28 Sep 2011 12:31:43 +0200 profphd (1.0.35-1) UNRELEASED; urgency=low * added Replaces and Conflicts to control file for profphd-perl and profphd-data -- Laszlo Kajan Tue, 27 Sep 2011 11:05:27 +0200 profphd (1.0.34) unstable; urgency=low * fixed "HTMTOP_RID :-10.942" bug in src/prof/scr/lib/lib-prof.pl -- Laszlo Kajan Fri, 20 May 2011 21:09:41 +0200 profphd (1.0.33) unstable; urgency=low * use warnings in phd.pl -- Laszlo Kajan Tue, 01 Mar 2011 16:00:23 +0100 profphd (1.0.32) unstable; urgency=low * copyright corrected to GPL -- Laszlo Kajan Fri, 26 Nov 2010 16:49:36 +0100 profphd (1.0.31) unstable; urgency=low * Makefile update - works now on Ubuntu as well (/bin/sh bug) -- Laszlo Kajan Fri, 26 Nov 2010 16:49:36 +0100 profphd (1.0.29) * [A-Z.~_!] in src/prof/scr/lib/lib-col.pl -- Laszlo Kajan Wed, 20 Oct 2010 14:28:49 +0200 profphd (1.0.28) * provide NORM_EXP for Selenocysteine: $NORM_EXP{"U"} = $NORM_EXP{"C"}; # U - Selenocysteine # lkajan quick hack -- Laszlo Kajan Wed, 20 Oct 2010 13:54:03 +0200 profphd (1.0.27) * fasta AA pattern now [A-Z.~_!] -- Laszlo Kajan Wed, 20 Oct 2010 11:54:27 +0200 profphd (1.0.26) * Documented `optJury' * prof in debug mode now dumps final parameter values before starting actual work * Proper error reporting when input file is empty -- Laszlo Kajan Thu, 07 Oct 2010 08:48:44 +0200 profphd (1.0.25) * work dir now automatically set to temp dir when not given * introduced translate-jobid-in-param-values param to suppress unexpected file name (and other) conversions - now you have to explicitly ask for this behaviour -- Laszlo Kajan Fri, 27 Aug 2010 17:33:30 +0200 profphd (1.0.24) * Man page syntax corrected * Better debugging output -- Laszlo Kajan Fri, 27 Aug 2010 17:33:30 +0200 profphd (1.0.23) * Now the default is to no change nice level * Documented para3 paraBoth paraSec paraAcc numresMin nresPerLineAli riSubSec riSubAcc riSubSym -- Laszlo Kajan Mon, 23 Aug 2010 20:48:29 +0200 profphd (1.0.22) * Documented a phd.pl call * Fixed overzealous ID substitution in src/prof/embl/scr/lib-phd.pl -- Laszlo Kajan Mon, 05 Jul 2010 12:25:14 +0200 profphd (1.0.21) * Fixed verbosity bug that lead to incorrect call to hssp_filter.pl -- Laszlo Kajan Thu, 24 Jun 2010 14:54:11 +0200 profphd (1.0.20) * Changed default to silent mode from verbose -- Laszlo Kajan Thu, 24 Jun 2010 11:56:26 +0200 profphd (1.0.19) * Added param dirWork to prof/scr/lib/lib-prof.pl exeCopf call * Markus' failing sequence now works ('ARCH' in file name problem) * Weird prof/scr/lib/lib-prof.pl $fileOut{1,$kwd} constructs eliminated * Resolved bug 9 'prof creates tmp files into current directory (where it is run from)' -- Laszlo Kajan Sat, 15 May 2010 13:38:56 +0200 profphd (1.0.18) * resolved bug #10 html formatting of ouput -- Guy Yachdav Sun, 02 May 2010 13:28:27 +0200 profphd (1.0.17) * Much more efficient install Makefile target * Produces gold standard for tsnap_query.fasta * Able to use dirWork now: read-only input file dir is now OK * Command line options now correctly documented: no leading - * sed --in-place -> -i, --in-place is not understood by Mac sed -- Laszlo Kajan Sat, 15 May 2010 13:38:41 +0200 profphd (1.0.16) * corrected faulty file name extension matching: escapes '.' now -- Laszlo Kajan Tue, 09 Feb 2010 18:18:43 +0100 profphd (1.0.15) * removed pub blast - it was not in use -- Laszlo Kajan Sat, 16 Jan 2010 11:03:59 +0100 profphd (1.0.14) * moved ./src/prof/scr/safFilterRed.pl to librg-utils-perl -- Laszlo Kajan Fri, 15 Jan 2010 16:00:43 +0100 profphd (1.0.13) * Modifications now allow usage of RG::Utils::* modules -- Laszlo Kajan Thu, 14 Jan 2010 21:10:39 +0100 profphd (1.0.12) * added debugging for system()-like calls to scr/pack/hssp_filter.pm * added more examples: DMD_HUMAN.hssp is huge; PSA2_HUMAN.safFil has xxxx_a and xxxx_A sequences; * increased MAXCORE to 16777216 in filter_hssp.f in order to allow a big alignment to fit (DMD_HUMAN.hssp example) * Made sequence names case sensitive for READ_MSF routine - solves bug with 3h4p_A and 3h4p_a chains mistaken for the same thing -- Laszlo Kajan Tue, 12 Jan 2010 11:52:56 +0100 profphd (1.0.11) * Fixed hssp_filter 'gyachdav' path bug -- Laszlo Kajan Fri, 08 Jan 2010 12:49:19 +0100 profphd (1.0.10) * Removed faulty executable checks that did not take PATH into account -- Laszlo Kajan Thu, 07 Jan 2010 18:24:46 +0100 profphd (1.0.9) * Removed bin dependency of make all target because the binary utilities are distributed in a separate package -- Laszlo Kajan Thu, 07 Jan 2010 15:06:40 +0100 profphd (1.0.8) * Removed $ARCH extension from src/prof/scr/pack/copf.pm exeConvertSeq and exeConvertSeqBig -- Laszlo Kajan Thu, 07 Jan 2010 10:18:44 +0100 profphd (1.0.7) * Fixed saf issue due to copf path problem -- Laszlo Kajan Wed, 06 Jan 2010 17:01:59 +0100 profphd (1.0.6) * Changed prof to the gold-standard: the prof from SNAP (now snapfun) * Introduces __PREFIX__ where necessary -- Laszlo Kajan Tue, 05 Jan 2010 21:51:16 +0100 profphd (1.0.5) * Moved prof and phd fortran sources to profnet package * Added facilities for making a Debian source package out of src-lib * Changed prof to the gold-standard: the prof from SNAP (now snapfun) * Introduces __PREFIX__ where necessary -- Laszlo Kajan Tue, 05 Jan 2010 21:51:16 +0100 profphd (1.0.4) * Added -fbounds-check to Fortran compilation options * Removed .LINUX from binary names * Fixed string bounds problem at line 327 of file lib-phd.f -- Laszlo Kajan Tue, 15 Dec 2009 23:57:05 +0100 profphd (1.0.3) * Adjusted buffer size for reading in network data. Allows for analysis of large (>2000 residues) sequences -- Guy Yachdav Tue, 24 Nov 2009 12:22:17 +0200 profphd (1.0.2) * Compilation failure when profphd is installed on system issue resolved. * Man page example changed to work in default installation scenario. -- Laszlo Kajan Fri, 20 Nov 2009 08:15:04 +0100