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Port details
biococoa 2.2.2 biology on this many watch lists=0 search for ports that depend on this port
Bioinformatics framework
Maintained by: theraven@FreeBSD.org search for ports maintained by this maintainer
Port Added: 30 Dec 2006 09:21:22
Also Listed In: gnustep
License: LGPL21


The BioCocoa framework provides developers with the opportunity to add
support for reading and writing BEAST, Clustal, EMBL, Fasta, GCG-MSF, GDE,
Hennig86, NCBI, NEXUS, NONA, PDB, Phylip, PIR, Plain/Raw, Swiss-Prot and
TNT files by writing only three lines of code.
The framework is written in Cocoa (Objective-C).

LICENSE: LGPL2 or later

WWW: http://bioinformatics.org/biococoa/
SVNWeb : Main Web Site : Distfiles Availability : PortsMon

NOTE: FreshPorts displays only required dependencies information. Optional dependencies are not covered.

Required To Build:
  1. devel/gnustep-make
  2. lang/clang33
  3. x11-toolkits/gnustep-back
  4. devel/gmake
Required To Run:
  1. devel/gnustep-make
  2. x11-toolkits/gnustep-back

This port is required by:

for Build for Run * - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...

To install the port: cd /usr/ports/biology/biococoa/ && make install clean
To add the package: pkg install biology/biococoa


Configuration Options
     No options to configure

Master Sites:
  1. ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/
  2. ftp://ftp.acc.umu.se/debian/pool/main/b/biococoa.app/
  3. ftp://ftp.au.debian.org/debian/pool/main/b/biococoa.app/
  4. ftp://ftp.bg.debian.org/debian/pool/main/b/biococoa.app/
  5. ftp://ftp.br.debian.org/debian/pool/main/b/biococoa.app/
  6. ftp://ftp.cl.debian.org/debian/pool/main/b/biococoa.app/
  7. ftp://ftp.cz.debian.org/debian/pool/main/b/biococoa.app/
  8. ftp://ftp.de.debian.org/debian/pool/main/b/biococoa.app/
  9. ftp://ftp.df.lth.se/pub/debian/pool/main/b/biococoa.app/
  10. ftp://ftp.ee.debian.org/debian/pool/main/b/biococoa.app/
  11. ftp://ftp.es.debian.org/debian/pool/main/b/biococoa.app/
  12. ftp://ftp.fi.debian.org/debian/pool/main/b/biococoa.app/
  13. ftp://ftp.fr.debian.org/debian/pool/main/b/biococoa.app/
  14. ftp://ftp.hk.debian.org/debian/pool/main/b/biococoa.app/
  15. ftp://ftp.hr.debian.org/debian/pool/main/b/biococoa.app/
  16. ftp://ftp.hu.debian.org/debian/pool/main/b/biococoa.app/
  17. ftp://ftp.ie.debian.org/debian/pool/main/b/biococoa.app/
  18. ftp://ftp.is.debian.org/debian/pool/main/b/biococoa.app/
  19. ftp://ftp.it.debian.org/debian/pool/main/b/biococoa.app/
  20. ftp://ftp.jp.debian.org/debian/pool/main/b/biococoa.app/
  21. ftp://ftp.nl.debian.org/debian/pool/main/b/biococoa.app/
  22. ftp://ftp.no.debian.org/debian/pool/main/b/biococoa.app/
  23. ftp://ftp.pl.debian.org/debian/pool/main/b/biococoa.app/
  24. ftp://ftp.ru.debian.org/debian/pool/main/b/biococoa.app/
  25. ftp://ftp.se.debian.org/debian/pool/main/b/biococoa.app/
  26. ftp://ftp.si.debian.org/debian/pool/main/b/biococoa.app/
  27. ftp://ftp.sk.debian.org/debian/pool/main/b/biococoa.app/
  28. ftp://ftp.snt.utwente.nl/pub/linux/debian/pool/main/b/biococoa.app/
  29. ftp://ftp.uk.debian.org/debian/pool/main/b/biococoa.app/
  30. ftp://ftp.us.debian.org/debian/pool/main/b/biococoa.app/
  31. ftp://ftp.wa.au.debian.org/debian/pool/main/b/biococoa.app/
  32. ftp://ftp2.de.debian.org/debian/pool/main/b/biococoa.app/
  33. ftp://mirror.symnds.com/debian/pool/main/b/biococoa.app/
  34. http://bioinformatics.org/biococoa/downloads/
  35. http://ring.nict.go.jp/archives/linux/debian/debian/pool/main/b/biococoa.app/
  36. http://www.gtlib.gatech.edu/pub/debian/pool/main/b/biococoa.app/

Number of commits found: 14

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
08 Oct 2013 18:34:45
Original commit files touched by this commit  2.2.2
Revision:329819
theraven search for other commits by this committer
Update BioCocoa to the latest release.

Approved by:	bapt (mentor)
20 Sep 2013 15:55:44
Original commit files touched by this commit  2.2.1
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
28 Aug 2013 18:26:01
Original commit files touched by this commit  2.2.1
Revision:325546
theraven (src committer) search for other commits by this committer
Update to latest GNUstep core libraries.
Update dependent packages with more recent releases.
Remove old and bit-rotted ones.
Switch to using clang 3.3 and libobjc2 1.7 by default, so modern Objective-C
features work out of the box and remove a lot of configurable options for
sub-optimal (and, often, unsupported / deprecated upstream) configurations.
Take maintainership of GNUstep-related ports.

Several of the ports left in have scary warnings which mean that they are likely
broken in lots of cases.  Future commits will fix them.

Approved by:	bapt
13 Oct 2012 13:39:59
Original commit files touched by this commit  1.6.0_2
Revision:305832
dinoex search for other commits by this committer
- cleanup comments
Feature safe: yes
26 Jun 2012 05:43:33
Original commit files touched by this commit  1.6.0_2
dinoex search for other commits by this committer
- reset MAINTAINER
19 Mar 2011 12:38:54
Original commit files touched by this commit  1.6.0_2
miwi search for other commits by this committer
- Get Rid MD5 support
05 Jun 2010 06:14:28
Original commit files touched by this commit  1.6.0_2
dinoex search for other commits by this committer
LICENSE LGPL21
30 May 2010 12:28:39
Original commit files touched by this commit  1.6.0_2
dinoex search for other commits by this committer
- drop USE_GNUSTEP_PREFIX
16 Jan 2009 16:01:05
Original commit files touched by this commit  1.6.0_2
dinoex search for other commits by this committer
- add LICENSE:
06 Jun 2008 13:08:29
Original commit files touched by this commit  1.6.0_2
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)
25 May 2007 05:55:36
Original commit files touched by this commit  1.6.0_1
dinoex search for other commits by this committer
- update for gnustep-make-2.0.0
19 May 2007 20:32:57
Original commit files touched by this commit  1.6.0_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}.
31 Jan 2007 18:18:14
Original commit files touched by this commit  1.6.0
dinoex search for other commits by this committer
- add category gnustep
PR:             103931
Approved by:    pav
30 Dec 2006 09:20:54
Original commit files touched by this commit  1.6.0
dinoex search for other commits by this committer
The BioCocoa framework provides developers with the opportunity to add
support for reading and writing BEAST, Clustal, EMBL, Fasta, GCG-MSF, GDE,
Hennig86, NCBI, NEXUS, NONA, PDB, Phylip, PIR, Plain/Raw, Swiss-Prot and
TNT files by writing only three lines of code.
The framework is written in Cocoa (Objective-C).

WWW: http://bioinformatics.org/biococoa/

Number of commits found: 14

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