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freebsd-ports/biology
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Rene Ladan 66fee90926 KDE3 and QT3 expired on 2013-07-01, remove these ports. 
Unfortunately, this also affects some ports using QT3 as a GUI toolkit.

Changes to infrastructure files:
- bsd.kde.mk : obsolete, remove
- bsd.qt.mk : note that a CONFLICTS_BUILD line can probably go after a while
- CHANGES : document the removals from bsd.port.mk
- KNOBS : remove KDE and QT (KDE4 and QT4 should be used instead)
- MOVED : add the removed ports

PR:		ports/180745
Submitted by:	rene
Approved by:	portmgr (bapt)
Exp-run by:	bapt
2013-07-26 19:19:20 +00:00
..
adun - reset MAINTAINER 2012-06-26 05:44:19 +00:00
ariadne . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 14:10:02 +00:00
artemis Decommissioning java 1.5 (EOLed since October 2009): 2012-12-10 11:25:27 +00:00
avida - Fix build with clang 2013-06-04 08:26:03 +00:00
babel . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 19:01:47 +00:00
biococoa - cleanup comments 2012-10-13 13:39:56 +00:00
biojava Remove hardcoded extract dependency on diablo-jdk16, directly use USE_ZIP 2012-12-11 07:26:38 +00:00
blast - Take maintainership 2012-10-01 14:55:55 +00:00
blat . remove pkg-plist (along with the previous commit). 2013-06-19 18:44:32 +00:00
boinc-simap Use bsd.port.options.mk instead of bsd.port.{pre|post}.mk 2013-04-29 12:20:35 +00:00
chemeq . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 20:01:30 +00:00
clustalw
consed
crux - adoption of optionsNG 2013-03-18 06:48:55 +00:00
dotter - Mark broken checksum mismatch 2013-03-25 01:41:31 +00:00
embassy Convert from USE_MOTIF to USES=motif 2013-07-09 21:49:35 +00:00
emboss Convert from USE_MOTIF to USES=motif 2013-07-09 21:49:35 +00:00
fasta Fix some PORT_OPTIONS conversions 2013-06-30 20:53:06 +00:00
fasta3 - Update to 36.3.6 2013-07-19 14:08:02 +00:00
fastdnaml . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 13:35:55 +00:00
finchtv - Reassign to the heap at maintainer's request 2012-10-01 14:45:16 +00:00
fluctuate . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 12:43:28 +00:00
garlic Fix typos in COMMENT 2012-07-25 06:32:06 +00:00
genpak - update png to 1.5.10 2012-06-01 05:26:28 +00:00
gff2ps . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 18:56:37 +00:00
gmap
gperiodic . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 19:05:47 +00:00
grappa
hmmer - Update to 3.0 2013-07-20 15:08:45 +00:00
iolib - Update to 7.31.0 2013-07-11 16:26:26 +00:00
jalview Decommissioning java 1.5 (EOLed since October 2009): 2012-12-10 11:25:27 +00:00
lagan - Update to version 2.0 2012-11-15 07:04:29 +00:00
lamarc . trim Makefile headers; 2013-06-19 15:39:18 +00:00
libgenome . add license (GPLv2); 2013-06-19 18:53:54 +00:00
libsbml - adoption of optionsNG 2013-03-18 06:50:12 +00:00
linux-foldingathome
mafft Mark as broken on sparc64: depends on thread-local storage, which is not 2012-09-08 08:30:39 +00:00
mapm3
migrate - Update to 3.5.1 2013-05-26 07:49:47 +00:00
molden - Update to 5.0.6 2013-04-26 06:57:37 +00:00
mopac . NOPORTEXAMPLES -> PORT_OPTIONS:MEXAMPLES; 2013-06-19 18:38:46 +00:00
mrbayes
mummer - Update to 3.23 2012-01-17 00:51:39 +00:00
muscle Fix typos in COMMENT 2012-07-24 07:19:21 +00:00
ncbi-toolkit Convert from USE_MOTIF to USES=motif 2013-07-09 21:49:35 +00:00
njplot Convert from USE_MOTIF to USES=motif 2013-07-10 07:33:24 +00:00
ortep3 . introdice optionsNG to the port; 2013-06-19 20:06:59 +00:00
p5-AcePerl - Convert all remaining instances of BUILD_DEPENDS=${RUN_DEPENDS} or 2012-06-10 18:42:48 +00:00
p5-Bio-ASN1-EntrezGene - remove maintainer tags from pkg-descr 2011-10-22 23:50:23 +00:00
p5-Bio-Das Cleanup supporting perl version 5.8 and 5.10, 2012-12-17 15:39:36 +00:00
p5-Bio-Das-Lite - Fix missing DEPENDS to silence build warnings 2011-09-24 20:45:23 +00:00
p5-Bio-GFF3 - Update to 1.5 2012-12-16 04:22:15 +00:00
p5-Bio-Glite For perl@ owned ports: 2013-03-29 00:44:53 +00:00
p5-Bio-Graphics - Update to 2.37 2013-07-20 10:03:10 +00:00
p5-Bio-MAGETAB For perl@ owned ports: 2013-03-29 00:44:53 +00:00
p5-Bio-NEXUS For perl@ owned ports: 2013-03-29 00:44:53 +00:00
p5-Bio-Phylo - Update to 0.56 2013-07-20 10:04:32 +00:00
p5-Bio-SCF - Trim Makefile headers 2013-06-01 14:22:35 +00:00
p5-bioperl - Avoid of using SITE_PERL 2013-06-07 06:51:42 +00:00
p5-bioperl-run - Remove SITE_PERL from *_DEPENDS 2012-06-30 14:53:22 +00:00
paml - Trim Makefile headers 2013-06-01 14:22:35 +00:00
phd2fasta Remove unneeded escaping 2013-04-26 16:23:13 +00:00
phrap
phred
phylip Fix some screw ups introduced in r319847. 2013-06-24 18:09:52 +00:00
phyml - Update to 20121109. 2013-02-04 10:07:30 +00:00
platon The vast majority of pkg-descr files had the following format when they 2011-10-24 09:11:38 +00:00
plink Add new ports biology/plink [1] and biology/plinkseq [2]: 2012-09-27 09:59:25 +00:00
plinkseq Fix build with protobuf-2.5.0 2013-03-21 14:09:22 +00:00
povchem - remove empty files 2013-02-15 08:57:19 +00:00
primer3 - Take maintainership 2012-10-01 14:55:55 +00:00
protomol - adoption of optionsNG 2013-03-18 06:54:39 +00:00
psi88 . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 19:54:13 +00:00
py-biopython - update to 1.60 2012-09-25 08:06:42 +00:00
pycogent - Update to 1.5.3 2012-10-08 03:17:02 +00:00
pyfasta - Trim Makefile headers 2013-06-01 14:22:35 +00:00
pymol Switch from libglut to freeglut and retire libglut. Libglut hasn't been 2012-08-04 22:52:02 +00:00
python-nexus - Update to 0.87 2011-12-23 08:05:00 +00:00
rasmol Convert to USES=imake 2013-06-28 18:32:25 +00:00
recombine . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 19:15:14 +00:00
ruby-bio - adoption of optionsNG 2013-03-18 06:55:42 +00:00
seaview - Update to 4.4.2 2013-07-15 14:49:02 +00:00
seqan - convert USE_CMAKE to USES 2013-03-22 20:06:14 +00:00
seqio Remove stale (since r321246) pkg-plist file. 2013-06-19 21:04:36 +00:00
sim4 . add license (GPLv2); 2013-06-19 16:36:53 +00:00
ssaha - Reassign to the heap at maintainer's request 2012-10-01 14:45:16 +00:00
t_coffee - Update to 9.03. 2013-01-14 08:04:38 +00:00
tinker - Update to 6.2.06 2013-07-15 14:50:22 +00:00
treepuzzle
treeviewx - Reassign to the heap at maintainer's request 2012-10-01 14:45:16 +00:00
tRNAscan-SE . NOPORTDOCS -> PORT_OPTIONS:MDOCS; 2013-06-19 19:20:25 +00:00
ugene Unbreak on 7.X and i386 systems. 2013-02-25 13:00:15 +00:00
velvet
wise Fix build by adding an explicit dep on pkgconf 2013-05-03 20:48:34 +00:00
xmolwt Use optionsNG for DOCS. 2013-06-19 19:07:35 +00:00
Makefile KDE3 and QT3 expired on 2013-07-01, remove these ports. 2013-07-26 19:19:20 +00:00