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mirror of https://git.FreeBSD.org/ports.git synced 2024-11-24 00:45:52 +00:00
freebsd-ports/biology
Koop Mast 5aa7246575 Switch from libglut to freeglut and retire libglut. Libglut hasn't been
developed in years and has been dropped from the MESA 8.0 distribution.
Freeglut is a rewrite of glut and is actively developed and is used by
many linux distributions instead of libglut.

Bump all ports that directly depend on libglut because of the shlib version
change.

There are some extra items in this patch.

*) Because freeglut doesn't have the same dependancies as libglut, some ports
	need extra dependencies added to USE_XORG to make them build.
*) Mark graphics/f90gl broken, f90gl depends on a header that is only shipped
	with libglut.
*) Remove option for libglut/freeglut selection in games/cake, only freeglut
	remains now.
*) While here fix a png related build issue games/vegastrike.

Thanks to miwi for running the exp-run.

Approved by:	portmgr (miwi)

Collaboration with:	zeising@
Obtained from:	xorg-dev staging area.
2012-08-04 22:52:02 +00:00
..
adun - reset MAINTAINER 2012-06-26 05:44:19 +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 - Update to version 2.12.3 2012-06-17 20:04:32 +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 - reset MAINTAINER 2012-06-26 05:44:19 +00:00
biojava Fix typos in COMMENT 2012-07-29 11:17:02 +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 - Adjust BOINC_* variables to be consistent with new system in boinc-client 2012-05-16 13:46:30 +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 - update png to 1.5.10 2012-06-01 05:26:28 +00:00
emboss - update png to 1.5.10 2012-06-01 05:26:28 +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 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 - 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 - update png to 1.5.10 2012-06-01 05:26:28 +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 - Update to version 2.1.8 2012-06-17 20:22:32 +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 Switch from libglut to freeglut and retire libglut. Libglut hasn't been 2012-08-04 22:52:02 +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 Fix typos in COMMENT 2012-07-24 07:19:21 +00:00
ncbi-toolkit - remove maintainer tags from pkg-descr 2011-10-22 23:50:23 +00:00
njplot s/X11BASE/LOCALBASE/, or equivalent. 2012-06-24 21:53:38 +00:00
ortep3 - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
p5-AcePerl - Convert all remaining instances of BUILD_DEPENDS=${RUN_DEPENDS} or 2012-06-10 18:42:48 +00:00
p5-Bio-ASN1-EntrezGene - remove maintainer tags from pkg-descr 2011-10-22 23:50:23 +00:00
p5-Bio-Das - Convert all remaining instances of BUILD_DEPENDS=${RUN_DEPENDS} or 2012-06-10 18:42:48 +00:00
p5-Bio-Das-Lite - Fix missing DEPENDS to silence build warnings 2011-09-24 20:45:23 +00:00
p5-Bio-GFF3 Fix typos in COMMENT 2012-07-25 06:32:06 +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 2.29 2012-06-18 09:30:35 +00:00
p5-Bio-MAGETAB - Update to 1.23 2012-07-19 16:42:55 +00:00
p5-Bio-NEXUS - Update to 0.78 2012-02-11 02:04:41 +00:00
p5-Bio-Phylo - Update to 0.50 2012-06-12 18:55:28 +00:00
p5-Bio-SCF At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450 2012-01-21 17:40:15 +00:00
p5-bioperl - Remove SITE_PERL from *_DEPENDS 2012-06-30 05:23:19 +00:00
p5-bioperl-run - Remove SITE_PERL from *_DEPENDS 2012-06-30 14:53:22 +00:00
paml - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
phd2fasta - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
phrap - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
phred - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
phylip - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
phyml - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
platon The vast majority of pkg-descr files had the following format when they 2011-10-24 09:11:38 +00:00
povchem - update png to 1.5.10 2012-06-01 05:26:28 +00:00
primer3 - Respect CC 2012-01-27 17:41:00 +00:00
protomol Switch from libglut to freeglut and retire libglut. Libglut hasn't been 2012-08-04 22:52:02 +00:00
psi88 - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
py-biopython - Update to 1.59 2012-03-06 06:40:50 +00:00
pycogent - Convert all remaining instances of BUILD_DEPENDS=${RUN_DEPENDS} or 2012-06-10 18:42:48 +00:00
pyfasta - Update to 0.4.5 2012-02-23 13:43:25 +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 - 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 - update png to 1.5.10 2012-06-01 05:26:28 +00:00
seqan Replace USE_GCC=4.4+ by USE_GCC=4.6+ since GCC 4.4 is on its way out. 2012-07-21 22:20:32 +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 - Convert all remaining instances of BUILD_DEPENDS=${RUN_DEPENDS} or 2012-06-10 18:42:48 +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 - update png to 1.5.10 2012-06-01 05:26:28 +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 - update png to 1.5.10 2012-06-01 05:26:28 +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 SeqAn is an open source C++ library of efficient algorithms 2012-06-06 17:51:33 +00:00