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Port details
biococoa Bioinformatics framework
2.2.2_6 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
2.2.2Version of this port present on the latest quarterly branch.
Maintainer: theraven@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2006-12-30 09:21:22
Last Update: 2019-02-03 15:37:58
SVN Revision: 492056
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
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (68 items)
  1. /usr/local/share/licenses/biococoa-2.2.2_6/catalog.mk
  2. /usr/local/share/licenses/biococoa-2.2.2_6/LICENSE
  3. /usr/local/share/licenses/biococoa-2.2.2_6/LGPL21
  4. GNUstep/System/Library/Frameworks/BioCocoa.framework/BioCocoa
  5. GNUstep/System/Library/Frameworks/BioCocoa.framework/Headers
  6. GNUstep/System/Library/Frameworks/BioCocoa.framework/Resources
  7. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/BioCocoa
  8. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCAminoAcid.h
  9. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCAnnotation.h
  10. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCAtom.h
  11. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCCachedFastaFile.h
  12. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCCachedSequenceFile.h
  13. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCChain.h
  14. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCCodon.h
  15. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCCodonDNA.h
  16. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCCodonRNA.h
  17. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCDataMatrix.h
  18. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCFoundation.h
  19. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCFoundationDefines.h
  20. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCGeneticCode.h
  21. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCMCP.h
  22. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCNucleotide.h
  23. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCNucleotideDNA.h
  24. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCNucleotideRNA.h
  25. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCPairwiseAlignment.h
  26. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCParseSOFT.h
  27. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCPlatform.h
  28. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCPreferences.h
  29. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCProteinStructure.h
  30. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCResidue.h
  31. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSample.h
  32. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCScoreMatrix.h
  33. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSecondaryStructure.h
  34. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSequence.h
  35. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSequenceAlignment.h
  36. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSequenceArray.h
  37. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSequenceCodon.h
  38. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSequenceReader.h
  39. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSequenceStructure.h
  40. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSequenceTool.h
  41. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSequenceWriter.h
  42. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSeries.h
  43. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCStringDefinitions.h
  44. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSuffixArray.h
  45. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSymbol.h
  46. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCSymbolSet.h
  47. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCToolComplement.h
  48. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCToolDigest.h
  49. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCToolHydropathyCalculator.h
  50. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCToolMassCalculator.h
  51. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCToolSequenceFinder.h
  52. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCToolSymbolCounter.h
  53. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCToolTranslator.h
  54. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCToolTranslatorDNA.h
  55. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCUtilData.h
  56. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Headers/BCUtilStrings.h
  57. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Resources/Info-gnustep.plist
  58. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Resources/aminoacids.plist
  59. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/Resources/nucleotides.plist
  60. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so
  61. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so.2
  62. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/2/libBioCocoa.so.2.2.2
  63. GNUstep/System/Library/Frameworks/BioCocoa.framework/Versions/Current
  64. GNUstep/System/Library/Frameworks/BioCocoa.framework/libBioCocoa.so
  65. GNUstep/System/Library/Headers/BioCocoa
  66. GNUstep/System/Library/Libraries/libBioCocoa.so
  67. GNUstep/System/Library/Libraries/libBioCocoa.so.2
  68. GNUstep/System/Library/Libraries/libBioCocoa.so.2.2.2
  69. Collapse this list.
Dependency lines:
  • biococoa>0:biology/biococoa

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

PKGNAME: biococoa

There is no flavor information for this port.

distinfo:

SHA256 (biococoa-2.2.2-src.tgz) = 383eea4e04ca584ecf5bc06507996acf193d3b1df9afecaca6fb58cbe41df384
SIZE (biococoa-2.2.2-src.tgz) = 358850


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. clang70 : devel/llvm70
  4. 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
Configuration Options
     No options to configure

USES:
gnustep

Master Sites:
  1. http://bioinformatics.org/biococoa/downloads/

Number of commits found: 24

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
03 Feb 2019 15:37:58
Original commit files touched by this commit  2.2.2_6
Revision:492056
theraven search for other commits by this committer
Move Objective-C ports to the v2 GNUstep ABI.

 * Bump the LLVM revision used for GNUstep to 7, the minimum to support
   the new ABI.
 * GNUstep-back does not work with lld, so mark it to use Gold (BFD LD
   doesn't seem able to link Objective-C things).
 * Turn off some annoying debug logs in GNUstep back, which generate
   several messages per second when you move the mouse.  These should
   never have been enabled in a release build anyway.
 * Downgrade Cenon to 4.0.2.  This was the last version to actually work
   with GNUstep (the later ones use XCode >= 5 .xib files, which GNUstep
   can't parse).
 * Update gorm to git head. The current release doesn't work with the
   new Objective-C ABI, but -head has the patches to fix it.
 * Update PikoPixel and add it to the gnustep-app meta-package.
 * Update the three core GNUstep packages to the latest release.
 * Update gnumail and pantomime to the latest release and fix a linking
   error with the new ABI.
 * Update GNUstep FTP to the latest version.

Reviewed by:	bapt (previous version)
26 Sep 2018 15:23:37
Original commit files touched by this commit  2.2.2_5
Revision:480741
brooks search for other commits by this committer
Update Objective-C LLVM version to 6.0.

Fixes aarch64 build.  Reduces depends on obsolete LLVM 4.0.

PR:		230116
Submitted by:	mikael.urankar@gmail.com
Approved by:	theraven (prior version)
Sponsored by:	DARPA, AFRL
03 Dec 2017 12:23:54
Original commit files touched by this commit  2.2.2_4
Revision:455401
theraven search for other commits by this committer
Fix configure options for gnustep-make

We were not setting the flag to select the GNUstep ABI, so were defaulting to
using the GCC-compatible version, which was likely to trigger a lot of subtle
bugs.  This was noticed when C++ exceptions thrown through Objective-C stack
frames caused segfaults.
13 Oct 2017 11:14:53
Refresh Original commit files touched by this commit
Revision:451982  Sanity Test Failure
bapt search for other commits by this committer
Mark as broken ports with no public distfiles
21 Aug 2017 13:26:29
Refresh Original commit files touched by this commit
Revision:448472  Sanity Test Failure
theraven search for other commits by this committer
Update GNUstep core libraries.

Update the default Objective-C compiler.

Fix various build failures in GNUstep ports from newer versions of the GNUstep
core libraries and from changes to GNUstep Make.

Update various ports that use GNUstep and bump the portrevision of the ones
that haven't had a new release.
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: 24

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