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Port details
biococoa Bioinformatics framework
2.2.2_2 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: 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 : Homepage : Distfiles Availability : PortsMon

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

PKGNAME: biococoa


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

Build dependencies:
  1. gmake : devel/gmake
  2. gnustep-make>0 : devel/gnustep-make
  3. gnustep-back>0 : x11-toolkits/gnustep-back
Runtime dependencies:
  1. gnustep-back>0 : x11-toolkits/gnustep-back
Library dependencies:
  1. libobjc.so.4.6 : lang/libobjc2

This port is required by:

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...
Configuration Options
     No options to configure

USES:
gnustep

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

Number of commits found: 19

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
19 Sep 2015 10:33:36
Original commit files touched by this commit  2.2.2_2
Revision:397315
theraven search for other commits by this committer
Make all GNUstep ports install into the System domain so that the Local domain
is available for stuff built from source.

Some ports were already installing in the System domain, for these just remove
the Makefile lines explicitly specifying the install domain.

The rest are installed in the Local domain, remove any overrides, update their
pkg-plists and any explicit paths in the Makefiles and then bump port revision.

Approved by:	bapt (mentor)
Differential Revision:	https://reviews.freebsd.org/D2977
14 May 2015 10:15:09
Original commit files touched by this commit  2.2.2_1
Revision:386312
mat search for other commits by this committer
MASTER_SITES cleanup.

- Replace ${MASTER_SITE_FOO} with FOO.
- Merge MASTER_SITE_SUBDIR into MASTER_SITES when possible. (This means 99.9%
  of the time.)
- Remove occurrences of MASTER_SITE_LOCAL when no subdirectory was present and
  no hint of what it should be was present.
- Fix some logic.
- And generally, make things more simple and easy to understand.

While there, add magic values to the FESTIVAL, GENTOO, GIMP, GNUPG, QT and
SAMBA macros.

Also, replace some EXTRACT_SUFX occurences with USES=tar:*.

Checked by:	make fetch-urlall-list
With hat:	portmgr
Sponsored by:	Absolight
09 Apr 2015 07:44:42
Refresh Original commit files touched by this commit
Revision:383626  Sanity Test Failure
bapt search for other commits by this committer
Convert bsd.gnustep.mk to USES=gnustep

Simplify gnustep ports
Hook into the regular ports framework:
- LIB_DEPENDS for library dependencies
- Use regular USE_LDCONFIG

Reuse USES=objc (automatic)
USE_GNUSTEP is now a macro to set the dependencies and build feature needed.
Accepted arguments: back base build gui

Merge deskutils/preferencepanes into deskutils/systempreferences
20 Oct 2014 07:10:48
Original commit files touched by this commit  2.2.2_1
Revision:371237
bapt search for other commits by this committer
Cleanup plist
10 Sep 2014 20:50:37
Original commit files touched by this commit  2.2.2_1
Revision:367888
gerald search for other commits by this committer
Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)
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: 19

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