Port details |
- biojava Open-source Java tools for processing biological data
- 1.7,1 biology
=2 1.7,1Version of this port present on the latest quarterly branch. BROKEN: Does not build
DEPRECATED: Broken for more than 6 months
This port expired on: 2017-08-23
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
 - 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/
cgit ¦ GitHub ¦ GitHub ¦ GitLab ¦ 
- 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. Perhaps there is a build error. Check the fallout link:

- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- java : java/openjdk8
- ant : devel/apache-ant
- Runtime dependencies:
-
- 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:
|
Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
Commit | Credits | Log message |
1.7,1 23 Aug 2017 11:33:26
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rene  |
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
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antoine  |
Deprecate ports BROKEN for more than 6 months |
1.7,1 28 Oct 2016 01:49:40
  |
wen  |
- Mark it BROKEN
- Reset maintainer to ports@ |
1.7,1 19 Jul 2016 11:04:14
  |
mat  |
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
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amdmi3  |
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
Approved by: portmgr blanket |
1.7,1 01 Jun 2014 10:37:23
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ohauer  |
- add stage support |
1.7,1 08 Mar 2014 16:39:01
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antoine  |
Unbreak |
1.7,1 07 Mar 2014 15:52:40
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bapt  |
Convert b* to USES=zip |
1.7,1 21 Feb 2014 13:35:26
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ehaupt  |
Remove trailing whitespaces from category biology |
1.7,1 10 Feb 2014 13:54:28
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ehaupt  |
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
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adamw  |
Convert biology to MDOCS and MEXAMPLES |
1.7,1 20 Sep 2013 15:55:44
  |
bapt  |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
1.7,1 11 Dec 2012 07:26:39
  |
bapt  |
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
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bapt  |
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
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cs  |
Fix typos in COMMENT
Approved by: portmgr@ (implicit) |
1.7,1 19 Mar 2011 12:38:54
 |
miwi  |
- Get Rid MD5 support |
1.7,1 01 May 2009 09:33:42
 |
miwi  |
- 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
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linimon  |
Reset nemoliu due to maintainer-timeouts and no response to email.
Hat: portmgr |
1.5.b2_2,1 06 Jun 2008 13:08:29
 |
edwin  |
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
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flz  |
- 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
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nemoliu  |
Use my @FreeBSD.org address.
Approved by: delphij (mentor) |
1.5.b2,1 27 Mar 2007 08:01:54
 |
miwi  |
- 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
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kris  |
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
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kris  |
BROKEN: Does not build |
1.5.b,1 13 Dec 2006 12:56:01
 |
linimon  |
Reset whitekid@gmail.com after timeouts and no response to email.
Hat: portmgr |
1.5.b,1 21 Nov 2006 22:35:28
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thierry  |
- 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
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Schedule these broken ports for termination on 2006-12-01 |
1.30 22 Apr 2006 22:09:45
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BROKEN: Does not compile |
1.30 22 Jan 2006 08:20:34
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edwin  |
SHA256ify
Approved by: krion@ |
1.30 22 Nov 2004 15:47:58
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vs  |
- 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
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trevor  |
Add SIZE. |
1.01 02 Nov 2003 02:48:09
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edwin  |
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
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osa  |
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
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kris  |
Don't remove share/java/classes system directory. |
1.01 21 Feb 2003 11:01:38
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knu  |
De-pkg-comment. |
1.01 16 Jun 2002 01:08:49
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glewis  |
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
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lioux  |
Style police: WWW tags should either end in a file/script or TRAILING /; Fix the
later case |
08 Jul 2001 19:15:34
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ijliao  |
Add NOPORTDOCS support to pkg-plist |
10 Oct 2000 12:14:04
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jeh  |
Initial import of biology/biojava |