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Port details
biojava 1.5.b2_2,1 biology on this many watch lists=2 search for ports that depend on this port
Open-source java tools for processing biological data
Maintained by: nemoliu@FreeBSD.org search for ports maintained by this maintainer
Port Added: 10 Oct 2000 09:14:04
Also Listed In: java


The BioJava Project is an open-source project dedicated to providing Java
tools for processing biological data. This will include objects for
manipulating sequences, file parsers, CORBA interoperability, access to
ACeDB, dynamic programming, and simple statistical routines. 

The BioJava library is useful for automating those daily and mundane
bioinformatics tasks. As the library matures, the BioJava libraries will
provide a foundation upon which both free software and commercial packages
can be developed.

WWW: http://www.biojava.org/
CVSWeb : Sources : Main Web Site : Distfiles Availability : PortsMon
Required To Build: databases/hsqldb, textproc/xerces-j, java/jakarta-regexp, java/jakarta-commons-cli, java/jakarta-commons-dbcp, java/jakarta-commons-pool, java/jakarta-commons-collections, java/junit, java/diablo-jdk15, devel/apache-ant
Required To Run: databases/hsqldb, textproc/xerces-j, java/jakarta-regexp, java/jakarta-commons-cli, java/jakarta-commons-dbcp, java/jakarta-commons-pool, java/jakarta-commons-collections, java/diablo-jdk15

To install the port: cd /usr/ports/biology/biojava/ && make install clean
To add the package: pkg_add -r biojava


Configuration Options
     No options to configure

Master Sites:
ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/

Number of commits found: 21

Commit History - (may be incomplete: see CVSWeb link above for full details)
DateByDescription
06 Jun 2008 14:08:29
Original commit files touched by this commit  1.5.b2_2,1
edwin search for other commits by this committer
Bump portrevision due to upgrade of devel/gettext.

The affected ports are the ones with gettext as a run-dependency
according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT
in Makefile (29 of them).

PR:             ports/124340
Submitted by:   edwin@
Approved by:    portmgr (pav)
19 May 2007 21:32:57
Original commit files touched by this commit  1.5.b2_1,1
flz search for other commits by this committer
- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
30 Apr 2007 07:27:41
Original commit files touched by this commit  1.5.b2,1
nemoliu search for other commits by this committer
Use my @FreeBSD.org address.

Approved by:    delphij (mentor)
27 Mar 2007 09:01:54
Original commit files touched by this commit  1.5.b2,1
miwi search for other commits by this committer
- Update to 1.5-beta2
- Pass maintainership to submitter

PR:             110621
Submitted by:   Nemo Liu<nemoliu@gmail.com>
11 Feb 2007 01:23:35
Original commit files touched by this commit  1.5.b,1
kris search for other commits by this committer
Schedule these broken ports for removal on 2007-04-10 if they are still
broken at that time and no fix has been submitted.
05 Feb 2007 00:08:52
Original commit files touched by this commit  1.5.b,1
kris search for other commits by this committer
BROKEN: Does not build
13 Dec 2006 12:56:01
Original commit files touched by this commit  1.5.b,1
linimon search for other commits by this committer
Reset whitekid@gmail.com after timeouts and no response to email.

Hat:            portmgr
21 Nov 2006 22:35:28
Original commit files touched by this commit  1.5.b,1
thierry search for other commits by this committer
- Upgrade to the latest beta and unbreak;

- Add a regression-test target;

- Fix plist for WITHOUT_SAMPLES.

PR:             ports/104685
Approved by:    maintainer's time-out (1 month)
02 Sep 2006 17:51:10
Original commit files touched by this commit  1.30
kris search for other commits by this committer
Schedule these broken ports for termination on 2006-12-01
22 Apr 2006 23:09:45
Original commit files touched by this commit  1.30
kris search for other commits by this committer
BROKEN: Does not compile
22 Jan 2006 08:20:34
Original commit files touched by this commit  1.30
edwin search for other commits by this committer
SHA256ify

Approved by:    krion@
22 Nov 2004 15:47:58
Original commit files touched by this commit  1.30
vs search for other commits by this committer
- Update biology/biojava to 1.30
- Install javadoc and example files
- Assign maintainership to submitter

PR:             ports/73391
Submitted by:   Cheng-Dae Choe
Add. reviewing: hq@
27 Jan 2004 20:51:07
Original commit files touched by this commit  1.01
trevor search for other commits by this committer
Add SIZE.
02 Nov 2003 02:48:09
Original commit files touched by this commit  1.01
edwin search for other commits by this committer
ports with possibly unreachable MAINTAINERs
*** addresses that seem to be dead:

PR:             ports/58694
Submitted by:   Oliver Eikemeier <eikemeier@fillmore-labs.com>
22 Oct 2003 10:29:55
Original commit files touched by this commit  1.01
osa search for other commits by this committer
Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.

Submitted by:   Oleg Karachevtsev <ok@etrust.ru>
A part of PR:   57992
19 Oct 2003 03:26:52
Original commit files touched by this commit  1.01
kris search for other commits by this committer
Don't remove share/java/classes system directory.
21 Feb 2003 11:01:38
Original commit files touched by this commit  1.01
knu search for other commits by this committer
De-pkg-comment.
16 Jun 2002 02:08:49
Original commit files touched by this commit  1.01
glewis search for other commits by this committer
Unbreak this port:

. Fix dependencies to be in sync with the recent JDK ports renaming.
. Replace MASTER_SITES with a location that actually contains the
  source.
. Fix the packing list.

Note that there is a much newer version of this application available,
but that is beyond the scope of what I was trying to do (just fix the
JDK dependency), as is the last two items.
20 Nov 2001 23:29:38
files touched by this commit
lioux search for other commits by this committer
Style police: WWW tags should either end in a file/script or TRAILING /; Fix the
later case    
08 Jul 2001 20:15:34
files touched by this commit
ijliao search for other commits by this committer
Add NOPORTDOCS support to pkg-plist    
10 Oct 2000 13:14:04
files touched by this commit
jeh search for other commits by this committer
Initial import of biology/biojava    

Number of commits found: 21

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