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Port details
libgenome Toolkit for developing bioinformatic related software in C++
0.5.2_2 biology Deleted 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 0.5.2_2Version of this port present on the latest quarterly branch.
Deprecated DEPRECATED: Unmaintained since 2002
Expired This port expired on: 2014-04-17
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: 2002-07-30 10:57:35
Last Update: 2014-04-18 11:17:45
SVN Revision: 351531
License: GPLv2
WWW:
http://pages.cs.wisc.edu/~darling/libgenome/
Description:
libGenome is a freely available toolkit for developing bioinformatic related software in C++. It is intended to take the hassle out of performing common tasks on genetic sequence and annotation data. Among other things, libGenome can help you: - Read and write Multi-FastA format files - Read and write GenBank flat file database entries - Append, chop, truncate, reverse, complement, translate, and otherwise mangle sequence data - Access annotation in GenBank flat files WWW: http://pages.cs.wisc.edu/~darling/libgenome/
Homepage    cgit ¦ GitHub ¦ GitHub ¦ GitLab ¦ SVNWeb

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:
  • libgenome>0:biology/libgenome
No installation instructions:
This port has been deleted.
PKGNAME: libgenome
Flavors: there is no flavor information for this port.
distinfo:
There is no distinfo for this port.

No package information for this port in our database
Sometimes this happens. Not all ports have packages.
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. libtool>=2.4 : devel/libtool
There are no ports dependent upon this port

Configuration Options:
===> The following configuration options are available for libgenome-0.5.2_2: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings
Options name:
N/A
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (2 items)
Collapse this list.
  1. ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/
  2. http://pages.cs.wisc.edu/~darling/libgenome/releases/
Collapse this list.

Number of commits found: 33

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.5.2_2
18 Apr 2014 11:17:45
Revision:351531Original commit files touched by this commit
rene search for other commits by this committer
Remove expired ports:
2014-04-16 ports-mgmt/pkgsearch: Upstream disappeared
2014-04-17 science/flounder: Unmaintained since 2002
2014-04-17 security/nbaudit: Unmaintained since 2002
2014-04-17 security/saint: Unmaintained since 2002
2014-04-17 graphics/gozer: Unmaintained since 2002
2014-04-17 misc/pdfmap: Unmaintained since 2002
2014-04-17 devel/showgrammar: Unmaintained since 2002
2014-04-17 biology/libgenome: Unmaintained since 2002
2014-04-17 deskutils/narval: Unmaintained since 2002
2014-04-17 devel/fampp: Unmaintained since 2002
2014-04-17 net-p2p/py-fngrab: Unmaintained since 2002
2014-04-17 misc/wmfirew: Unmaintained since 2002
2014-04-17 x11-wm/e16utils: Unmaintained since 2002
2014-04-17 misc/salias: Unmaintained since 2002
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.5.2_2
11 Mar 2014 21:21:15
Revision:347934Original commit files touched by this commit
antoine search for other commits by this committer
Deprecate a few old unmaintained ports
0.5.2_2
05 Feb 2014 23:47:48
Revision:342906Original commit files touched by this commit
marino search for other commits by this committer
biology/libgenome: Fix build on dragonfly
0.5.2_2
21 Jan 2014 23:18:05
Revision:340671Original commit files touched by this commit
bapt search for other commits by this committer
Fix properties on pkg-plist
0.5.2_2
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)
0.5.2_2
14 Aug 2013 09:53:39
Revision:324692Original commit files touched by this commit
marino search for other commits by this committer
biology/libgenome: Mark jobs unsafe

Approved by: 	bapt/culot (mentors, implicit)
0.5.2_2
19 Jun 2013 18:53:55
Revision:321307Original commit files touched by this commit
bsam search for other commits by this committer
. add license (GPLv2);
. bump PORTREVISION;
. NOPORTDOCS -> PORT_OPTIONS:MDOCS;
. trim Makefile headers.
0.5.2_1
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
0.5.2_1
04 Dec 2010 07:34:27
Original commit files touched by this commit
ade search for other commits by this committer
Sync to new bsd.autotools.mk
0.5.2_1
02 Aug 2009 19:36:34
Original commit files touched by this commit
mezz search for other commits by this committer
-Repocopy devel/libtool15 -> libtool22 and libltdl15 -> libltdl22.
-Update libtool and libltdl to 2.2.6a.
-Remove devel/libtool15 and devel/libltdl15.
-Fix ports build with libtool22/libltdl22.
-Bump ports that depend on libltdl22 due to shared library version change.
-Explain what to do update in the UPDATING.

It has been tested with GNOME2, XFCE4, KDE3, KDE4 and other many wm/desktop
and applications in the runtime.

With help:      marcus and kwm
Pointyhat-exp:  a few times by pav
Tested by:      pgollucci, "Romain Tartière" <romain@blogreen.org>, and
                a few MarcusCom CVS users. Also, I might have missed a few.
Repocopy by:    marcus
Approved by:    portmgr
0.5.2_1
21 Aug 2008 06:18:49
Original commit files touched by this commit
rafan search for other commits by this committer
Update CONFIGURE_ARGS for how we pass CONFIGURE_TARGET to configure script.
Specifically, newer autoconf (> 2.13) has different semantic of the
configure target. In short, one should use --build=CONFIGURE_TARGET
instead of CONFIGURE_TARGET directly. Otherwise, you will get a warning
and the old semantic may be removed in later autoconf releases.

To workaround this issue, many ports hack the CONFIGURE_TARGET variable
so that it contains the ``--build='' prefix.

To solve this issue, under the fact that some ports still have
configure script generated by the old autoconf, we use runtime detection
in the do-configure target so that the proper argument can be used.

Changes to Mk/*:
 - Add runtime detection magic in bsd.port.mk
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.5.2_1
18 Jun 2008 19:08:46
Original commit files touched by this commit
pav search for other commits by this committer
- Fix fetch, update WWW
0.5.2_1
01 Feb 2007 02:42:06
Original commit files touched by this commit
kris search for other commits by this committer
Use libtool port instead of included version to avoid objformat a.out botch
0.5.2_1
14 Aug 2006 10:08:25
Original commit files touched by this commit
clsung search for other commits by this committer
- s,INSTALLS_SHLIB,USE_LDCONFIG,g
- these include astro/ audio/ biology/ chinese/ maintained by ports@

PR:             ports/101916
Submitted by:   Gea-Suan Lin <gslin_AT_gslin dot org>
0.5.2_1
03 May 2006 23:26:35
Original commit files touched by this commit
edwin search for other commits by this committer
Remove USE_REINPLACE from all categories starting with B
0.5.2_1
23 Feb 2006 10:40:45
Original commit files touched by this commit
ade search for other commits by this committer
Conversion to a single libtool environment.

Approved by:    portmgr (kris)
0.5.2
24 Nov 2005 00:04:00
Original commit files touched by this commit
pav search for other commits by this committer
- Add SHA256
0.5.2
15 Nov 2005 06:52:12
Original commit files touched by this commit
ade search for other commits by this committer
Mass-conversion to the USE_AUTOTOOLS New World Order.  The code present
in bsd.autotools.mk essentially makes this a no-op given that all the
old variables set a USE_AUTOTOOLS_COMPAT variable, which is parsed in
exactly the same way as USE_AUTOTOOLS itself.

Moreover, USE_AUTOTOOLS has already been extensively tested by the GNOME
team -- all GNOME 2.12.x ports use it.

Preliminary documentation can be found at:
        http://people.FreeBSD.org/~ade/autotools.txt

which is in the process of being SGMLized before introduction into the
Porters Handbook.

Light blue touch-paper.  Run.
0.5.2
31 May 2005 16:34:45
Original commit files touched by this commit
oliver search for other commits by this committer
change the libtool version to use from 1.3 to 1.5
0.5.2
12 Apr 2005 03:26:57
Original commit files touched by this commit
obrien search for other commits by this committer
At Kris's request, back out the MACHINE_ARCH spelling correction until
after 5.4-RELEASE.
0.5.2
11 Apr 2005 08:04:41
Original commit files touched by this commit
obrien search for other commits by this committer
Assist getting more ports working on AMD64 by obeying the
Ports Collection documentation and use 'ARCH' rather than 'MACHINE_ARCH'.
0.5.2
09 Jul 2004 17:43:11
Original commit files touched by this commit
marcus search for other commits by this committer
Apply a big libtool patch to allow porters to use the libtool installed by
the libtoolX ports instead of the one included with each port.  Ports that
set USE_LIBTOOL_VER=X will now use the ports version of libtool instead of
the included version.  To restore previous behavior, use the new macro,
USE_INC_LIBTOOL_VER.  Both macros accept the same argument: a libtool version.

For example, to use the ports version of libtool-1.5, add the following to
your Makefile:

USE_LIBTOOL_VER=        15

To use the included version of libtool with extra hacks provided by
libtool-1.5, add the following to your Makefile:

USE_INC_LIBTOOL_VER=    15

With this change, ports that had to add additional libtool hacks to prevent
.la files from being installed or to fix certain threading issues can now
delete those hacks (after appropriate testing, of course).

PR:             63944
Based on work by:eik and marcus
Approved by:    ade (autotools maintainer)
Tested by:      kris on pointyhat
Bound to be hidden problems:    You bet
0.5.2
22 May 2004 07:29:47
Original commit files touched by this commit
krion search for other commits by this committer
- Update MASTER_SITES and WWW: line

PR:             ports/67015
Submitted by:   Roman Neuhauser <neuhauser@chello.cz>
0.5.2
14 Mar 2004 06:17:56
Original commit files touched by this commit
ade search for other commits by this committer
Whoa there, boy, that's a mighty big commit y'all have there...

Begin autotools sanitization sequence by requiring ports to explicitly
specify which version of {libtool,autoconf,automake} they need, erasing
the concept of a "system default".

For ports-in-waiting:

        USE_LIBTOOL=YES         ->      USE_LIBTOOL_VER=13
        USE_AUTOCONF=YES        ->      USE_AUTOCONF_VER=213
        USE_AUTOMAKE=YES        ->      USE_AUTOMAKE_VER=14

Ports attempting to use the old style system after June 1st 2004 will be
sorely disappointed.
0.5.2
27 Jan 2004 20:51:07
Original commit files touched by this commit
trevor search for other commits by this committer
Add SIZE.
0.5.2
20 Oct 2003 22:41:04
Original commit files touched by this commit
krion search for other commits by this committer
- Update to 0.5.2

PR:             58304
Submitted by:   Clement Laforet <sheepkiller@cultdeadsheep.org>
0.5.1
18 Feb 2003 14:09:17
Original commit files touched by this commit
naddy search for other commits by this committer
Fix install and packaging list.

Reported by:    kris
0.5.1
11 Feb 2003 18:13:27
Original commit files touched by this commit
naddy search for other commits by this committer
Update to version 0.5.1.

PR:             48047
Submitted by:   Ports Fury
0.5.0_1
29 Dec 2002 04:44:13
Original commit files touched by this commit
ijliao search for other commits by this committer
add missing include

PR:             46584
Submitted by:   Ports Fury
0.5.0_1
22 Dec 2002 12:51:20
Original commit files touched by this commit
ijliao search for other commits by this committer
fix build on -current

PR:             46459
Submitted by:   Ports Fury
0.5.0_1
07 Nov 2002 03:10:58
Original commit files touched by this commit
adamw search for other commits by this committer
Fix PORTCOMMENTs that were killing INDEX builds.

105 pointy hats to:     me
Approved by:            pat
0.5.0_1
17 Aug 2002 19:16:55
Original commit files touched by this commit
naddy search for other commits by this committer
- Support CXXFLAGS properly.
- Do not install .la file.

PR:             41732
Submitted by:   Ports Fury
0.5.0
30 Jul 2002 10:57:06
Original commit files touched by this commit
ijliao search for other commits by this committer
add libgenome 0.5.0
Toolkit for developing bioinformatic related software in C++

Number of commits found: 33