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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 - Fix fetch 2010-12-21 00:12:22 +00:00
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 - Update to 36.3.2 to fix distfile fetching on pointyhat 2011-01-26 20:26:36 +00:00
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 - 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 - 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 - Use canonical format for FreeBSD.org MAINTAINER addresses 2010-12-25 16:55:41 +00:00
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 - Fix pkg-plist, got the wrong version before 2010-12-30 23:08:47 +00:00
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 - Update to 5.1.09 2011-01-31 11:45:44 +00:00
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