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mirror of https://git.FreeBSD.org/ports.git synced 2024-11-23 00:43:28 +00:00
freebsd-ports/biology
Niclas Zeising 39fc32e828 The FreeBSD x11@ and graphics team proudly presents
a zeising, kwm production, with help from dumbbell, bdrewery:

NEW XORG ON FREEBSD 9-STABLE AND 10-STABLE

This update switches over to use the new xorg stack by default on FreeBSD 9
and 10 stable, on osversions where vt(9) is available.
It is still possible to use the old stack by specifying WITHOUT_NEW_XORG in
/etc/make.conf .
FreeBSD 8-STABLE and released versions of FreeBSD still use
the old version.
A package repository with binary packages for new xorg will
be available soon.

This patch also contains updates of libxcb and related ports, pixman, as well
as some drivers and utilities.

Bump portrevisions for xf86-* ports, as well as virtualbox-ose-additions due
to xserver version change.

Apart from these updates, the way shared libraries are handled has been
changed for all xorg ports, as well as libxml2 and freetype, which means
ltverhack is gone and as a consequence shared libraries have been bumped.
The plan is that this change will make library bumps less likely in the
future.
All affected ports have had their portrevisions bumped as a consequence of
this.

Fix some issues where WITH_NEW_XORG weren't detected properly on CURRENT.

Update instructions, hardware support, and more notes can be found on
https://wiki.freebsd.org/Graphics

Thanks to:	all testers, bdrewery and the FreeBSD x11@ team
exp-run by:	bdrewery [1]
PR:		ports/187602 [1]
Approved by:	portmgr (bdrewery), core (jhb)
2014-04-16 18:28:47 +00:00
..
ariadne
artemis
avida
babel
biococoa
biojava Unbreak 2014-03-08 16:39:01 +00:00
blast
blat Convert b* to USES=zip 2014-03-07 15:52:40 +00:00
boinc-simap
chemeq
clustalw
consed Remove trailing whitespaces from category biology 2014-02-21 13:35:26 +00:00
crux Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
embassy
emboss
fasta - Add staging support 2014-03-24 09:01:39 +00:00
fasta3 biology/fasta3: Checked new distfile and regenerated distinfo to unbreak 2014-03-02 10:58:50 +00:00
fastdnaml
finchtv Deprecate: Broken for more than 6 months 2014-03-18 18:10:25 +00:00
fluctuate
garlic - Convert USE_GMAKE to USES 2014-03-13 07:41:34 +00:00
gff2ps Add staging support 2014-03-23 17:43:41 +00:00
gmap
gperiodic Add staging support 2014-03-23 18:09:23 +00:00
grappa
hmmer
iolib - Back to the heap, I don't use this port anymore 2014-04-12 07:42:33 +00:00
jalview
lagan
lamarc
libgenome Deprecate a few old unmaintained ports 2014-03-11 21:21:14 +00:00
libsbml The FreeBSD x11@ and graphics team proudly presents 2014-04-16 18:28:47 +00:00
linux-foldingathome
mafft - Convert USE_GMAKE to USES 2014-03-13 07:41:34 +00:00
mapm3
migrate
molden Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
mopac - Add staging support 2014-03-23 18:10:41 +00:00
mrbayes
mummer - Convert USE_GMAKE to USES 2014-03-13 07:41:34 +00:00
muscle - Convert USE_GMAKE to USES 2014-03-13 07:41:34 +00:00
ncbi-toolkit Add staging support 2014-03-23 20:50:54 +00:00
njplot Remove trailing whitespaces from category biology 2014-02-21 13:35:26 +00:00
ortep3 Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
p5-AcePerl
p5-Bio-ASN1-EntrezGene
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-GFF3 - Fix PLIST 2014-03-26 14:23:09 +00:00
p5-Bio-Glite
p5-Bio-Graphics Mark as broken unstaged perl ports 2014-04-09 09:49:02 +00:00
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF
p5-bioperl Mark as broken unstaged perl ports 2014-04-09 09:49:02 +00:00
p5-bioperl-run Remove trailing whitespaces from category biology 2014-02-21 13:35:26 +00:00
paml - Update to 4.8 2014-04-05 10:56:52 +00:00
phd2fasta
phrap
phred
phylip The FreeBSD x11@ and graphics team proudly presents 2014-04-16 18:28:47 +00:00
phyml
platon Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
plink Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
plinkseq Convert to dos2unix 2014-03-07 11:37:35 +00:00
povchem
primer3 - Update to 2.3.6 2014-04-06 03:56:03 +00:00
protomol The FreeBSD x11@ and graphics team proudly presents 2014-04-16 18:28:47 +00:00
psi88 Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
py-biopython Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
pycogent Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
pyfasta - Update to 0.5.2 2014-04-06 04:05:43 +00:00
pymol The FreeBSD x11@ and graphics team proudly presents 2014-04-16 18:28:47 +00:00
python-nexus
recombine - Support staging 2014-02-16 11:39:42 +00:00
ruby-bio Support stage 2014-04-07 13:01:26 +00:00
seaview - Stage support 2014-02-27 08:46:42 +00:00
seqan Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
seqio Support staging 2014-02-16 11:42:09 +00:00
seqtools
sim4 Support staging 2014-02-16 11:43:07 +00:00
ssaha biology/ssaha: undeprecate, this port fetches and builds fine. 2014-03-09 09:39:50 +00:00
t_coffee Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
tinker Update the default version of GCC used in the Ports Collection from 2014-03-10 20:55:20 +00:00
treepuzzle
treeviewx Unbreak 2014-03-28 00:08:03 +00:00
tRNAscan-SE
ugene Update to version 1.13.1. 2014-03-07 07:39:20 +00:00
velvet - Convert USE_GMAKE to USES 2014-03-13 07:41:34 +00:00
wise - Add staging support 2014-03-24 10:46:35 +00:00
xmolwt Add staging support 2014-03-24 11:06:56 +00:00
Makefile Remove expired ports: 2014-04-13 10:55:38 +00:00