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Port details
biojava Open-source Java tools for processing biological data
1.7,1 biology Deleted on this many watch lists=2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.7,1Version of this port present on the latest quarterly branch.
Broken BROKEN: Does not build
Deprecated DEPRECATED: Broken for more than 6 months
Expired This port expired on: 2017-08-23
Ignore IGNORE: is marked as broken: Does not build
There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2000-10-10 08:14:04
Last Update: 2017-08-23 11:33:26
SVN Revision: 448603
People watching this port, also watch:: jdictionary
Also Listed In: java
License: not specified in port
WWW:
http://www.biojava.org/
Description:
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/
Homepage    cgit ¦ GitHub ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
There is no configure plist information for this port.
Dependency lines:
  • biojava>0:biology/biojava
No installation instructions:
This port has been deleted.
PKGNAME: biojava
Flavors: there is no flavor information for this port.
distinfo:
SHA256 (biojava-1.7-all.jar) = 5c5e7fc66bc79a07494fb7d935164ec2aab50dc2effb7644f89bfa4fc907bb3f SIZE (biojava-1.7-all.jar) = 28062592

No package information for this port in our database
Sometimes this happens. Not all ports have packages.
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. java : java/openjdk8
  2. ant : devel/apache-ant
Runtime dependencies:
  1. java : java/openjdk8
There are no ports dependent upon this port

Configuration Options:
===> The following configuration options are available for biojava-1.7,1: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings
Options name:
N/A
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. http://www.biojava.org/download/bj17/all/
Collapse this list.

Number of commits found: 39

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.7,1
23 Aug 2017 11:33:26
Revision:448603Original commit files touched by this commit
rene search for other commits by this committer
Remove expired ports:
2017-08-23 games/plee-the-bear: Broken for more than 6 months
2017-08-23 x11-themes/kde-icons-umicons: Broken for more than 6 months
2017-08-23 lang/bigloo: Broken for more than 6 months
2017-08-23 audio/linux-neroaaccodec: Broken for more than 6 months
2017-08-23 x11-themes/kde-icons-dark-glass: Broken for more than 6 months
2017-08-23 misc/fortune-mod-ferengi_rules_of_acquisition: Broken for more than 6
months
2017-08-23 misc/fortune-mod-culmea-culmilor: Broken for more than 6 months
2017-08-23 misc/xyzcmd: Broken for more than 6 months
2017-08-23 russian/fortuneru: Broken for more than 6 months
2017-08-23 security/bdc: Broken for more than 6 months
2017-08-23 x11-themes/kde-icons-icosx: Broken for more than 6 months
2017-08-23 devel/insight: Broken for more than 6 months
2017-08-23 devel/gdb66: Broken for more than 6 months
2017-08-23 biology/biojava: Broken for more than 6 months
2017-08-23 games/xroach: Broken for more than 6 months
1.7,1
22 Jul 2017 11:01:38
Revision:446387Original commit files touched by this commit
antoine search for other commits by this committer
Deprecate ports BROKEN for more than 6 months
1.7,1
28 Oct 2016 01:49:40
Revision:424800Original commit files touched by this commit
wen search for other commits by this committer
- Mark it BROKEN
- Reset maintainer to ports@
1.7,1
19 Jul 2016 11:04:14
Revision:418767Original commit files touched by this commit
mat search for other commits by this committer
When there is a do-install target, do not use a post-install target, do
everything at once.  Sometime, rename post-install into a options helper
target.

I did not fix ports that were such a mess that I could not figure out
what they really wanted to do.  I also did not change ports that had
some version of an auto-plist code in post-install, for the same reason.

With hat:	portmgr
Sponsored by:	Absolight
1.7,1
19 May 2016 10:21:25
Revision:415498Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Fix trailing whitespace in pkg-descrs, categories [a-f]*

Approved by:	portmgr blanket
1.7,1
01 Jun 2014 10:37:23
Revision:356092Original commit files touched by this commit
ohauer search for other commits by this committer
- add stage support
1.7,1
08 Mar 2014 16:39:01
Revision:347521Original commit files touched by this commit
antoine search for other commits by this committer
Unbreak
1.7,1
07 Mar 2014 15:52:40
Revision:347402Original commit files touched by this commit
bapt search for other commits by this committer
Convert b* to USES=zip
1.7,1
21 Feb 2014 13:35:26
Revision:345397Original commit files touched by this commit
ehaupt search for other commits by this committer
Remove trailing whitespaces from category biology
1.7,1
10 Feb 2014 13:54:28
Revision:343634Original commit files touched by this commit
ehaupt search for other commits by this committer
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)
1.7,1
03 Jan 2014 15:46:52
Revision:338550Original commit files touched by this commit
adamw search for other commits by this committer
Convert biology to MDOCS and MEXAMPLES
1.7,1
20 Sep 2013 15:55:44
Revision:327709Original commit files touched by this commit
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
1.7,1
11 Dec 2012 07:26:39
Revision:308665Original commit files touched by this commit
bapt search for other commits by this committer
Remove hardcoded extract dependency on diablo-jdk16, directly use USE_ZIP
instead given that jar files are just zip files, remove hardcoded do extract
target.

Reported by:	linimon, matthew
1.7,1
10 Dec 2012 13:18:29
Revision:308604Original commit files touched by this commit
bapt search for other commits by this committer
Decommissioning java 1.5 (EOLed since October 2009):
suppress any reference to JAVA_VERSION=	1.5+ (part2)
1.7,1
29 Jul 2012 11:17:04
Original commit files touched by this commit
cs search for other commits by this committer
Fix typos in COMMENT

Approved by:	portmgr@ (implicit)
1.7,1
19 Mar 2011 12:38:54
Original commit files touched by this commit
miwi search for other commits by this committer
- Get Rid MD5 support
1.7,1
01 May 2009 09:33:42
Original commit files touched by this commit
miwi search for other commits by this committer
- Update to 1.7
- Pass maintainership to submitter

PR:             134056
Submitted by:   Wen Heping <wenheping@gmail.com>
1.5.b2_2,1
08 Dec 2008 06:43:50
Original commit files touched by this commit
linimon search for other commits by this committer
Reset nemoliu due to maintainer-timeouts and no response to email.

Hat:    portmgr
1.5.b2_2,1
06 Jun 2008 13:08:29
Original commit files touched by this commit
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)
1.5.b2_1,1
19 May 2007 20:32:57
Original commit files touched by this commit
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}.
1.5.b2,1
30 Apr 2007 06:27:41
Original commit files touched by this commit
nemoliu search for other commits by this committer
Use my @FreeBSD.org address.

Approved by:    delphij (mentor)
1.5.b2,1
27 Mar 2007 08:01:54
Original commit files touched by this commit
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>
1.5.b,1
11 Feb 2007 01:23:35
Original commit files touched by this commit
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.
1.5.b,1
05 Feb 2007 00:08:52
Original commit files touched by this commit
kris search for other commits by this committer
BROKEN: Does not build
1.5.b,1
13 Dec 2006 12:56:01
Original commit files touched by this commit
linimon search for other commits by this committer
Reset whitekid@gmail.com after timeouts and no response to email.

Hat:            portmgr
1.5.b,1
21 Nov 2006 22:35:28
Original commit files touched by this commit
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)
1.30
02 Sep 2006 16:51:10
Original commit files touched by this commit
kris search for other commits by this committer
Schedule these broken ports for termination on 2006-12-01
1.30
22 Apr 2006 22:09:45
Original commit files touched by this commit
kris search for other commits by this committer
BROKEN: Does not compile
1.30
22 Jan 2006 08:20:34
Original commit files touched by this commit
edwin search for other commits by this committer
SHA256ify

Approved by:    krion@
1.30
22 Nov 2004 15:47:58
Original commit files touched by this commit
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@
1.01
27 Jan 2004 20:51:07
Original commit files touched by this commit
trevor search for other commits by this committer
Add SIZE.
1.01
02 Nov 2003 02:48:09
Original commit files touched by this commit
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>
1.01
22 Oct 2003 09:29:55
Original commit files touched by this commit
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
1.01
19 Oct 2003 02:26:52
Original commit files touched by this commit
kris search for other commits by this committer
Don't remove share/java/classes system directory.
1.01
21 Feb 2003 11:01:38
Original commit files touched by this commit
knu search for other commits by this committer
De-pkg-comment.
1.01
16 Jun 2002 01:08:49
Original commit files touched by this commit
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
commit hash: fp1.20977@dev.null.freshports.orgcommit hash: fp1.20977@dev.null.freshports.orgcommit hash: fp1.20977@dev.null.freshports.orgcommit hash: fp1.20977@dev.null.freshports.org 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 19:15:34
commit hash: fp1.15991@dev.null.freshports.orgcommit hash: fp1.15991@dev.null.freshports.orgcommit hash: fp1.15991@dev.null.freshports.orgcommit hash: fp1.15991@dev.null.freshports.org files touched by this commit
ijliao search for other commits by this committer
Add NOPORTDOCS support to pkg-plist    
10 Oct 2000 12:14:04
commit hash: fp1.4935@dev.null.freshports.orgcommit hash: fp1.4935@dev.null.freshports.orgcommit hash: fp1.4935@dev.null.freshports.orgcommit hash: fp1.4935@dev.null.freshports.org files touched by this commit
jeh search for other commits by this committer
Initial import of biology/biojava    

Number of commits found: 39