notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Want a good monitor light? See my photosAll times are UTC
Ukraine
This referral link gives you 10% off a Fastmail.com account and gives me a discount on my Fastmail account.

Get notified when packages are built

A new feature has been added. FreshPorts already tracks package built by the FreeBSD project. This information is displayed on each port page. You can now get an email when FreshPorts notices a new package is available for something on one of your watch lists. However, you must opt into that. Click on Report Subscriptions on the right, and New Package Notification box, and click on Update.

FInally, under Watch Lists, click on ABI Package Subscriptions to select your ABI (e.g. FreeBSD:14:amd64) & package set (latest/quarterly) combinatio for a given watch list. This is what FreshPorts will look for.

Port details
biococoa Bioinformatics framework
2.2.2_8 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 View this port on Repology. pkg-fallout 2.2.2_8Version of this port present on the latest quarterly branch.
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: 2006-12-30 09:21:22
Last Update: 2023-04-25 15:17:15
Commit Hash: feb1fa3
Also Listed In: gnustep
License: LGPL21
WWW:
http://bioinformatics.org/biococoa/
Description:
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
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (71 items)
Collapse this list.
  1. /usr/local/share/licenses/biococoa-2.2.2_8/catalog.mk
  2. /usr/local/share/licenses/biococoa-2.2.2_8/LICENSE
  3. /usr/local/share/licenses/biococoa-2.2.2_8/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. @owner
  70. @group
  71. @mode
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, run one of these commands:
  • pkg install biology/biococoa
  • pkg install biococoa
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: biococoa
Flavors: 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

Packages (timestamps in pop-ups are UTC):
biococoa
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.2.2_82.2.2_8--2.2.2_8---
FreeBSD:13:quarterly2.2.2_82.2.2_8--2.2.2_8-2.2.2_82.2.2_8
FreeBSD:14:latest2.2.2_82.2.2_8--2.2.2_8--2.2.2_8
FreeBSD:14:quarterly2.2.2_82.2.2_8--2.2.2_8-2.2.2_82.2.2_8
FreeBSD:15:latest2.2.2_82.2.2_8n/a-n/a-2.2.2_82.2.2_8
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : 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
  1. x11/gnustep-app

Configuration Options:
No options to configure
Options name:
biology_biococoa
USES:
gnustep
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. http://bioinformatics.org/biococoa/downloads/
Collapse this list.

Number of commits found: 31

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.2.2_8
25 Apr 2023 15:17:15
commit hash: feb1fa34f58ea796656b86a81c2a2996b0b03c96commit hash: feb1fa34f58ea796656b86a81c2a2996b0b03c96commit hash: feb1fa34f58ea796656b86a81c2a2996b0b03c96commit hash: feb1fa34f58ea796656b86a81c2a2996b0b03c96 files touched by this commit
Christian Weisgerber (naddy) search for other commits by this committer
audio/opus: bump consumers after update to 1.4
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
2.2.2_7
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.2.2_7
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
2.2.2_7
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
2.2.2_7
14 Feb 2021 23:21:03
Revision:565273Original commit files touched by this commit
nc search for other commits by this committer
Update a few GNUstep ports:

 * devel/gnustep-make: Update to 2.8.0
 * lang/gnustep-base: Update to 1.27.0
 * x11-toolkits/gnustep-back: update to 0.28.0
 * x11-toolkits/gnustep-gui: update to 0.28.0

Also bump PORTREVISION on dependent ports.
2.2.2_6
05 Mar 2020 20:49:06
Revision:527847Original commit files touched by this commit
rene search for other commits by this committer
Return theraven's ports to the pool after safekeeping his commit bit.
2.2.2_6
03 Feb 2019 15:37:58
Revision:492056Original commit files touched by this commit
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)
2.2.2_5
26 Sep 2018 15:23:37
Revision:480741Original commit files touched by this commit
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
2.2.2_4
03 Dec 2017 12:23:54
Revision:455401Original commit files touched by this commit
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
Revision:451982Original commit files touched by this commit Sanity Test Failure Refresh
bapt search for other commits by this committer
Mark as broken ports with no public distfiles
21 Aug 2017 13:26:29
Revision:448472Original commit files touched by this commit Sanity Test Failure Refresh
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.
2.2.2_2
19 Sep 2015 10:33:36
Revision:397315Original commit files touched by this commit
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
2.2.2_1
14 May 2015 10:15:09
Revision:386312Original commit files touched by this commit
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
Revision:383626Original commit files touched by this commit Sanity Test Failure Refresh
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
2.2.2_1
20 Oct 2014 07:10:48
Revision:371237Original commit files touched by this commit
bapt search for other commits by this committer
Cleanup plist
2.2.2_1
10 Sep 2014 20:50:37
Revision:367888Original commit files touched by this commit
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)
2.2.2
08 Oct 2013 18:34:45
Revision:329819Original commit files touched by this commit
theraven search for other commits by this committer
Update BioCocoa to the latest release.

Approved by:	bapt (mentor)
2.2.1
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)
2.2.1
28 Aug 2013 18:26:01
Revision:325546Original commit files touched by this commit
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
1.6.0_2
13 Oct 2012 13:39:59
Revision:305832Original commit files touched by this commit
dinoex search for other commits by this committer
- cleanup comments
Feature safe: yes
1.6.0_2
26 Jun 2012 05:43:33
Original commit files touched by this commit
dinoex search for other commits by this committer
- reset MAINTAINER
1.6.0_2
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
1.6.0_2
05 Jun 2010 06:14:28
Original commit files touched by this commit
dinoex search for other commits by this committer
LICENSE LGPL21
1.6.0_2
30 May 2010 12:28:39
Original commit files touched by this commit
dinoex search for other commits by this committer
- drop USE_GNUSTEP_PREFIX
1.6.0_2
16 Jan 2009 16:01:05
Original commit files touched by this commit
dinoex search for other commits by this committer
- add LICENSE:
1.6.0_2
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)
1.6.0_1
25 May 2007 05:55:36
Original commit files touched by this commit
dinoex search for other commits by this committer
- update for gnustep-make-2.0.0
1.6.0_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}.
1.6.0
31 Jan 2007 18:18:14
Original commit files touched by this commit
dinoex search for other commits by this committer
- add category gnustep
PR:             103931
Approved by:    pav
1.6.0
30 Dec 2006 09:20:54
Original commit files touched by this commit
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: 31