Emanuel Haupt 5005b67362 According to the Porter's Handbook (5.12.2.3.) default options must be added to ... OPTIONS_DEFINE. This policy has been implemented only recently that's why we have many ports violating this policy. This patch adds the default options specified in the Porter's Handbook to OPTIONS_DEFINE where they are being used. Ports maintained by gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded. Approved by: portmgr (bapt)		2014-02-10 13:54:26 +00:00
..
ariadne
artemis	Support stage	2014-01-20 23:06:48 +00:00
avida
babel	Support stage	2014-01-15 22:44:13 +00:00
biococoa
biojava	According to the Porter's Handbook (5.12.2.3.) default options must be added to	2014-02-10 13:54:26 +00:00
blast	Convert biology to MDOCS and MEXAMPLES	2014-01-03 15:46:52 +00:00
blat
boinc-simap	Drop maintainership BOINC ports, old machine running them gave up.	2014-02-04 17:54:29 +00:00
chemeq	Stage support	2014-01-18 15:55:42 +00:00
clustalw	- Fix build with clang/libc++.	2013-12-20 15:29:07 +00:00
consed	According to the Porter's Handbook (5.12.2.3.) default options must be added to	2014-02-10 13:54:26 +00:00
crux	Fix properties on pkg-plist	2014-01-21 23:18:05 +00:00
embassy	Reduce over inclusion of bsd.port.mk	2014-01-15 22:48:32 +00:00
emboss	In preparation for making libtool generate libraries with a sane name, fix all	2013-12-11 14:43:51 +00:00
fasta	Reduce over inclusion of bsd.port.mk	2014-01-15 22:50:18 +00:00
fasta3	Mark as broken: Invalid checksum, seems like the software was rerolled	2014-01-03 19:46:05 +00:00
fastdnaml
finchtv	According to the Porter's Handbook (5.12.2.3.) default options must be added to	2014-02-10 13:54:26 +00:00
fluctuate
garlic
genpak	According to the Porter's Handbook (5.12.2.3.) default options must be added to	2014-02-10 13:54:26 +00:00
gff2ps
gmap
gperiodic
grappa	- Respect CC/CFLAGS	2013-12-20 13:27:13 +00:00
hmmer	Stage support	2013-12-30 18:08:14 +00:00
iolib	Support stage	2014-01-20 17:02:11 +00:00
jalview	Fix properties on pkg-plist	2014-01-21 23:18:05 +00:00
lagan
lamarc	- rename AL2 to APACHE20 in Mk/bsd.licenses.db.mk	2013-12-30 20:55:18 +00:00
libgenome	biology/libgenome: Fix build on dragonfly	2014-02-05 23:47:48 +00:00
libsbml	Reduce over inclusion of bsd.port.mk	2014-01-15 22:50:50 +00:00
linux-foldingathome
mafft	Convert biology to MDOCS and MEXAMPLES	2014-01-03 15:46:52 +00:00
mapm3	- Fix build with clang	2014-01-12 19:07:28 +00:00
migrate	- Stagify; cleanup Makefile and reorder the knobs a bit	2014-01-29 12:08:29 +00:00
molden	- USES=fortran gmake.	2013-12-29 14:30:20 +00:00
mopac	In preparation for making libtool generate libraries with a sane name, fix all	2013-12-11 14:43:51 +00:00
mrbayes	Support stage	2013-12-10 17:54:12 +00:00
mummer	According to the Porter's Handbook (5.12.2.3.) default options must be added to	2014-02-10 13:54:26 +00:00
muscle
ncbi-toolkit
njplot	According to the Porter's Handbook (5.12.2.3.) default options must be added to	2014-02-10 13:54:26 +00:00
ortep3	USES=fortran, fix LDFLAGS, staging.	2013-12-17 21:24:17 +00:00
p5-AcePerl	- Stage support	2014-02-10 06:56:52 +00:00
p5-Bio-ASN1-EntrezGene	- add stage support	2014-01-06 09:57:19 +00:00
p5-Bio-Das	- support stage	2014-01-05 12:07:20 +00:00
p5-Bio-Das-Lite	- fix pkg-plist	2014-01-30 07:34:25 +00:00
p5-Bio-GFF3	- Update to 1.9	2014-01-23 03:28:37 +00:00
p5-Bio-Glite	- support stage	2014-01-05 12:07:20 +00:00
p5-Bio-Graphics
p5-Bio-MAGETAB
p5-Bio-NEXUS	- Stage support	2014-01-31 12:47:06 +00:00
p5-Bio-Phylo	- support stage	2014-01-05 12:07:20 +00:00
p5-Bio-SCF	- add stage support	2014-01-06 09:44:19 +00:00
p5-bioperl	According to the Porter's Handbook (5.12.2.3.) default options must be added to	2014-02-10 13:54:26 +00:00
p5-bioperl-run	According to the Porter's Handbook (5.12.2.3.) default options must be added to	2014-02-10 13:54:26 +00:00
paml	According to the Porter's Handbook (5.12.2.3.) default options must be added to	2014-02-10 13:54:26 +00:00
phd2fasta	Convert biology to MDOCS and MEXAMPLES	2014-01-03 15:46:52 +00:00
phrap	Convert biology to MDOCS and MEXAMPLES	2014-01-03 15:46:52 +00:00
phred	Convert biology to MDOCS and MEXAMPLES	2014-01-03 15:46:52 +00:00
phylip
phyml	- Stage support	2014-01-31 12:32:55 +00:00
platon	Version 2013.12.12, USES=fortran, staging.	2013-12-17 21:55:24 +00:00
plink	Fix the build with more standards-compliant compilers such as GCC 4.7. [1]	2013-12-13 09:34:40 +00:00
plinkseq	- Stage support	2014-01-31 12:33:11 +00:00
povchem
primer3
protomol	Reduce over inclusion of bsd.port.mk	2014-01-15 22:51:26 +00:00
psi88	USES=fortran, staging, miscellaneous cleanups.	2013-12-18 16:23:08 +00:00
py-biopython	Python cleanup:	2014-01-13 21:00:02 +00:00
pycogent
pyfasta	- Convert to PYDISTUTILS_AUTOPLIST	2014-01-31 12:31:24 +00:00
pymol	In preparation for making libtool generate libraries with a sane name, fix all	2013-12-11 14:43:51 +00:00
python-nexus	- Convert to PYDISTUTILS_AUTOPLIST	2014-01-31 12:30:39 +00:00
rasmol
recombine
ruby-bio	Reduce over inclusion of bsd.port.mk	2014-01-15 22:52:28 +00:00
seaview	In preparation for making libtool generate libraries with a sane name, fix all	2013-12-11 14:43:51 +00:00
seqan
seqio
seqtools	biology/seqtools: update to 4.24	2013-12-24 17:23:23 +00:00
sim4
ssaha	Deprecate ports unmaintained for which distillator is not able to find public distfiles	2014-02-07 18:50:30 +00:00
t_coffee	USES=fortran, staging.	2013-12-18 17:24:51 +00:00
tinker	- biology/tinker: USES=fortran, staging.	2013-12-18 18:27:04 +00:00
treepuzzle
treeviewx	Stage support	2013-12-30 18:27:32 +00:00
tRNAscan-SE	biology/tRNAscan-SE: Fix hardcoded perl path	2014-02-05 23:44:50 +00:00
ugene	Unbreak the fetch: one of the documentation PDF files was rerolled.	2014-01-30 13:38:26 +00:00
velvet	According to the Porter's Handbook (5.12.2.3.) default options must be added to	2014-02-10 13:54:26 +00:00
wise	biology/wise: Add dragonfly support	2014-02-05 23:42:06 +00:00
xmolwt
Makefile