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2cf4c1e2c8
freebsd-ports/biology
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Philip M. Gollucci 2cf4c1e2c8 - Remove ports that only work with < perl 5.12 (devel/p5-B-Size, devel/p5-Devel-Arena) 
- Remove conditionals for PERL_LEVEL < 501200
- Remove regression-test targets b/c this will be centralized in Mk/bsd.perl.mk
- Other minor cleanups
  RUN_DEPENDS = ${BUILD_DEPENDS} -> RUN_DEPENDS:= ${BUILD_DEPENDS}

PR:             ports/165605
Submitted by:   pgollucci (myself)
Approved by:    portmgr (linimon)
Exp Run by:     linimon
Tested by:      make index
2012-03-08 18:45:38 +00:00
..
adun - fix build with gcc46 2012-02-07 05:36:27 +00:00
ariadne - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
artemis Now that the Java 1.3 and Java 1.4 ports are deprecated and will expire soon, 2011-07-21 05:03:02 +00:00
avida Change maintainer address to my FreeBSD address 2011-09-15 12:33:27 +00:00
babel - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
belvu - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
biococoa - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
biojava - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
blast - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
blat - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
boinc-simap - Fix fetch and update WWW 2011-11-04 20:39:12 +00:00
chemeq Remove WWW entries from unmaintained ports that return 404 or where the domain 2011-08-02 20:58:23 +00:00
clustalw Remove USE_GNOME=gnometarget from ports. It has been a empty keyword since 2011-08-11 19:20:17 +00:00
consed - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
crux Does not build on powerpc-9: error in pthreads. 2011-11-10 14:30:51 +00:00
dna-qc - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
dotter - Updated WWW: to a working link 2011-04-22 18:59:11 +00:00
embassy - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) 2011-09-23 22:26:39 +00:00
emboss - remove maintainer tags from pkg-descr 2011-10-22 23:50:23 +00:00
fasta - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
fasta3 - remove maintainer tags from pkg-descr 2011-10-22 23:50:23 +00:00
fastdnaml - Fix MASTER_SITES and WWW: line 2011-08-26 00:24:48 +00:00
finchtv - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
fluctuate - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
garlic Update to 1.6. Web site has been moved. 2011-05-11 05:55:27 +00:00
genpak - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
gff2ps - Update MASTER_SITES and WWW: line 2012-02-19 23:24:52 +00:00
gmap - fix fetch: wget is not required for fetching 2010-12-12 08:10:05 +00:00
gperiodic - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
grappa Update to GNU make 3.82 after numerous -exp runs. 2011-04-11 19:54:35 +00:00
hmmer - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
iolib - Remove WITH_FBSD10_FIX, is no longer needed 2011-11-09 15:26:04 +00:00
jalview Now that the Java 1.3 and Java 1.4 ports are deprecated and will expire soon, 2011-07-21 05:03:02 +00:00
lagan - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
lamarc - The proper acronym for Apache Software License 2 is really AL2 2012-01-09 15:41:08 +00:00
libgenome - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
libsbml - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
linux-foldingathome - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
mafft - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
mapm3 - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
migrate - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
molden The vast majority of pkg-descr files had the following format when they 2011-10-24 09:11:38 +00:00
mopac - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) 2011-09-23 22:26:39 +00:00
mrbayes - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
mummer - Update to 3.23 2012-01-17 00:51:39 +00:00
muscle - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
ncbi-toolkit - remove maintainer tags from pkg-descr 2011-10-22 23:50:23 +00:00
njplot Bump PORTREVISION after open-mofit update 2011-05-02 12:44:53 +00:00
ortep3 - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
p5-AcePerl - remove maintainer tags from pkg-descr 2011-10-22 23:50:23 +00:00
p5-Bio-ASN1-EntrezGene - remove maintainer tags from pkg-descr 2011-10-22 23:50:23 +00:00
p5-Bio-Das - Remove ports that only work with < perl 5.12 (devel/p5-B-Size, devel/p5-Devel-Arena) 2012-03-08 18:45:38 +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 0.7 2011-10-10 02:33:51 +00:00
p5-Bio-Glite At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450 2012-01-21 17:40:15 +00:00
p5-Bio-Graphics - Update to 2.26 2012-02-11 02:04:24 +00:00
p5-Bio-MAGETAB - Update to 1.22 2012-02-09 03:28:51 +00:00
p5-Bio-NEXUS - Update to 0.78 2012-02-11 02:04:41 +00:00
p5-Bio-Phylo - Update to 0.46 2012-03-05 08:22:46 +00:00
p5-Bio-SCF At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450 2012-01-21 17:40:15 +00:00
p5-bioperl At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450 2012-01-21 17:40:15 +00:00
p5-bioperl-run At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450 2012-01-21 17:40:15 +00:00
paml - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
phd2fasta - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
phrap - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
phred - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
phylip - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
phyml - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
platon The vast majority of pkg-descr files had the following format when they 2011-10-24 09:11:38 +00:00
povchem Switch dependency on povray to povray-meta port. 2011-06-20 22:32:03 +00:00
primer3 - Respect CC 2012-01-27 17:41:00 +00:00
protomol - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) 2011-09-23 22:26:39 +00:00
psi88 - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
py-biopython - Update to 1.59 2012-03-06 06:40:50 +00:00
pycogent - Update to 1.5.1 2011-08-11 11:37:18 +00:00
pyfasta - Update to 0.4.5 2012-02-23 13:43:25 +00:00
pymol update to 1.5.0.1. 2012-02-16 02:30:10 +00:00
python-nexus - Update to 0.87 2011-12-23 08:05:00 +00:00
rasmol - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
recombine - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
ruby-bio - Fix pkg-plist, got the wrong version before 2010-12-30 23:08:47 +00:00
seaview Chase pdflib.so version and bump PORTREVISION accordingly. 2012-01-10 11:41:37 +00:00
seqio - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
sim4 - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
ssaha - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
t_coffee - remove maintainer tags from pkg-descr 2011-10-22 23:50:23 +00:00
tinker - ${FFLAGS} might contain commas 2011-10-10 20:17:22 +00:00
treepuzzle - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
treeviewx - remove maintainer tags from pkg-descr 2011-10-22 23:50:23 +00:00
tRNAscan-SE - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
velvet Update to 1.1.04 2011-06-09 16:33:21 +00:00
wise - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
xdrawchem - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) 2011-09-23 22:26:39 +00:00
xmolwt The vast majority of pkg-descr files had the following format when they 2011-10-24 09:11:38 +00:00
Makefile Bye bye abandonwares (part 2) 2011-08-01 04:29:44 +00:00