Mark Linimon 06e6677793 Now that the Java 1.3 and Java 1.4 ports are deprecated and will expire soon, ... remove support for them from bsd.java.mk. As Jikes is not available in Java 1.5 or higher, remove it from bsd.java.mk too (suggested by hq@) and from the ports which used it (only occurences were USE_JIKES=no). Support for the Blackdown VM is also removed, as it is not available in Java 1.5 and higher. Also remove the mapping from Java 1.1-1.4 to Java 1.5+ in bsd.java.mk to detect old, broken ports; therefore bump the minimal value of JAVA_VERSION to 1.5. While here, replace static values of JAVA_VERSION in files/*.in by %%JAVA_VERSION%% . PR: ports/158969 Submitted by: rene Tested on: pointyhat-west -exp		2011-07-21 05:03:02 +00:00
..
adun	Update math/gsl to 1.15, and adjust PORTREVISION	2011-05-09 16:42:27 +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	- Get Rid MD5 support	2011-03-19 12:38:54 +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	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
chemeq	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
clustalw
consed	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
crimap	Another bunch of deprecation: no more public distfiles and/or abandonware	2011-06-16 10:43:58 +00:00
crux	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
distribfold	- Use USERS and GROUPS	2011-06-27 17:50:37 +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	Bump PORTREVISION after open-mofit update	2011-05-02 12:44:53 +00:00
emboss	- kick MD5	2011-07-02 11:33:17 +00:00
fasta	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
fasta3
fastdnaml	- Get Rid MD5 support	2011-03-19 12:38:54 +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	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
gmap
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	- Update to 1.12.5	2011-02-11 13:11:45 +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
kinemage	Another bunch of deprecation: no more public distfiles and/or abandonware	2011-06-16 17:33:07 +00:00
L-Breeder	Another bunch of deprecation: no more public distfiles and/or abandonware	2011-06-16 10:43:58 +00:00
lagan	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
lamarc	- Get Rid MD5 support	2011-03-19 12:38:54 +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
lsysexp	Another bunch of deprecation: no more public distfiles and/or abandonware	2011-06-16 10:43:58 +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	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
mopac	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
mrbayes	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
mummer	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
muscle	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
ncbi-toolkit	Fix build with open-motif-2.3.3	2011-05-02 12:41:44 +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	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
p5-Bio-ASN1-EntrezGene	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
p5-Bio-Das	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
p5-Bio-Das-Lite	- Update to 2.11	2011-05-08 17:06:15 +00:00
p5-Bio-GFF3	- Update to 0.5	2011-06-10 08:12:40 +00:00
p5-Bio-Glite	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
p5-Bio-Graphics	- update to 2.24	2011-06-01 20:21:51 +00:00
p5-Bio-MAGETAB	- Update to 1.20	2011-07-13 06:48:25 +00:00
p5-Bio-NEXUS
p5-Bio-Phylo	- Update to 0.38	2011-07-16 06:08:34 +00:00
p5-Bio-SCF	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
p5-bioperl	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
p5-bioperl-run	- Get Rid MD5 support	2011-03-19 12:38:54 +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	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
povchem	Switch dependency on povray to povray-meta port.	2011-06-20 22:32:03 +00:00
primer3	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
protomol	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
psi88	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
py-biopython	- Update to 1.57	2011-05-24 09:06:29 +00:00
pycogent	- Fix *_DEPENDS after the repocopy of databases/py-sqlalchemy	2011-06-25 07:21:20 +00:00
pyfasta	- Update to 0.4.3	2011-06-02 01:38:55 +00:00
pymol	update to 1.4.1	2011-05-09 04:36:54 +00:00
python-nexus	- Update to 0.8	2011-02-15 01:59:12 +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
seaview	- Get Rid MD5 support	2011-03-19 12:38:54 +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	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
tinker
treepuzzle	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
treeviewx	- Get Rid MD5 support	2011-03-19 12:38:54 +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	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
xmolwt	- Get Rid MD5 support	2011-03-19 12:38:54 +00:00
Makefile	Bio::GFF3 are low-level, fast functions for parsing GFF version 3 files.	2011-04-22 08:51:24 +00:00