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* - Update to 0.5wen2011-06-102-3/+3
| | | | ChangeLog: http://cpansearch.perl.org/src/RBUELS/Bio-GFF3-0.5/Changes
* Update to 1.1.04jlaffaye2011-06-105-126/+35
| | | | | | PR: ports/157527 Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> Approved by: bapt (mentor)
* deprecate and set expiration date:bapt2011-06-091-0/+3
| | | | it is an abandonware and it is unmaintain for very long
* - Update to 0.4.3wen2011-06-022-3/+3
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* - update to 2.24bapt2011-06-023-3/+10
| | | | | - add licenses - changes: http://cpansearch.perl.org/src/LDS/Bio-Graphics-2.24/Changes
* - Update to 1.57wen2011-05-243-111/+18
| | | | | | PR: ports/156329 Submitted by: Wen Heping (myself) Approved by: maintainer
* Update to 1.6. Web site has been moved.maho2011-05-114-10/+11
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* Update math/gsl to 1.15, and adjust PORTREVISIONbf2011-05-101-1/+2
| | | | and LIB_DEPENDS of dependent ports
* - Update to 0.4wen2011-05-092-3/+3
| | | | http://cpansearch.perl.org/src/RBUELS/Bio-GFF3-0.4/Changes
* update to 1.4.1maho2011-05-093-8/+41
| | | | Notified by: Alvin Oga
* - Update to 2.11swills2011-05-092-3/+3
| | | | Changes: http://cpansearch.perl.org/dist/Bio-Das-Lite/Changes
* Bump PORTREVISION after open-mofit updatemakc2011-05-024-2/+4
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* Fix build with open-motif-2.3.3makc2011-05-023-7/+72
| | | | | | PR: ports/154044 Submitted by: Mikhail Tsatsenko <m.tsatsenko at gmail.com> Exp-runs by: pav
* - Updated WWW: to a working linkglarkin2011-04-231-14/+17
| | | | | | | - Copied unbranded distfile (dotter.LIN) to LOCAL/glarkin for mirroring to MASTER_SITE_LOCAL and prevention of fetch checksum error. [1] Reported by: pointyhat (via miwi)
* Bio::GFF3 are low-level, fast functions for parsing GFF version 3 files.wen2011-04-225-0/+49
| | | | | | | All they do is convert back and forth between low-level Perl data structures and GFF3 text. WWW: http://search.cpan.org/dist/Bio-GFF3/
* - Update to 0.4.2wen2011-04-132-3/+3
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* Update to GNU make 3.82 after numerous -exp runs.ade2011-04-121-0/+11
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* - Update to 0.36wen2011-04-013-4/+14
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* - Get Rid MD5 supportmiwi2011-03-1983-110/+0
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* - Take maintainershipwen2011-03-141-1/+1
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* - Reassign to the heaptabthorpe2011-03-131-1/+1
| | | | PR: ports/155507 ports/155508
* - Update to 0.35wen2011-02-282-3/+4
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* - Move over to python2.5 or highermiwi2011-02-252-2/+2
| | | | - While here kick md5
* - Update to 0.8wen2011-02-152-4/+3
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* - Update to 1.12.5culot2011-02-113-4/+4
| | | | Changes: http://sourceforge.net/news/?group_id=100316&id=297223
* - Update to 5.1.09miwi2011-01-317-470/+508
| | | | | | PR: 154359 Submitted by: Ruslan Mahmatkhanov <cvs-src@yandex.ru> Feature safe: yes
* - Unbreak the port; I'm not sure how it could possibly work beforepav2011-01-282-12/+3
| | | | | Reported by: pointyhat Feature safe: yes
* - Change depobj for fasta3 to something that does not change on fasta updatespav2011-01-281-1/+1
| | | | | Reported by: pointyhat Feature safe: yes
* - Update to 36.3.2 to fix distfile fetching on pointyhatbeat2011-01-273-16/+13
| | | | | | PR: ports/154267 Submitted by: Fernan Aguero <fernan AT iib.unsam.edu.ar> (maintainer) Feature safe: yes
* - Fix fetchpav2011-01-251-1/+1
| | | | | Reported by: pointyhat Feature safe: yes
* - Fix pkg-plist, got the wrong version beforepgollucci2010-12-311-0/+9
| | | | Reported by: pointyhat via pav
* - DISTNAME= ${PORTNAME}-${PORTVERSION} is the default and not needed.pgollucci2010-12-301-1/+0
| | | | | | | PR: ports/153292 Submitted by: myself (pgollucci) Tested by: -exp run by pav Approved by: portmgr (pav)
* - Update to 1.4.1pgollucci2010-12-273-149/+143
| | | | | | | | | - Remove MD5 PR: ports/153394 Submitted by: myself (pgollucci) Approved by: mauricio@arareko.net (maintainer) Sponsored by: RideCharge Inc. / TaxiMagic
* - Use canonical format for FreeBSD.org MAINTAINER addressessunpoet2010-12-262-2/+1
| | | | | | | | - Remove obsolete MD5 checksum while I'm here PR: ports/152844 Submitted by: sunpoet (myself) Approved by: miwi (with portmgr hat)
* - Update to 2.18wen2010-12-232-3/+3
| | | | ChangeLog: http://cpansearch.perl.org/src/LDS/Bio-Graphics-2.18/Changes
* - Update to 0.34wen2010-12-232-3/+3
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* - Fix fetchwen2010-12-212-2/+3
| | | | Reported by: QAT@
* - Update to 0.33wen2010-12-163-4/+4
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* - Update to 0.32pgollucci2010-12-133-3/+11
| | | | | With Hat: perl@ Changes: http://search.cpan.org/dist/Bio-Phylo/Changes
* - fix fetch: wget is not required for fetchingpgollucci2010-12-122-6/+0
| | | | Reported by: QAT
* Sync to new bsd.autotools.mkade2010-12-045-5/+5
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* - Update to 0.4.1wen2010-12-022-4/+3
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* Improve port description.danfe2010-11-291-7/+15
| | | | Approved by: maintainer timeout since December 2009
* - Also remove them from pkg-plist lists not from me that crept inpgollucci2010-11-241-1/+0
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* - Update to 0.31wen2010-11-223-3/+7
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* - Update to 2.1wen2010-11-222-4/+3
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* - Update to 0.30wen2010-11-172-75/+76
| | | | | PR: ports/152205 Submitted by: Gea-Suan Lin <gslin@gslin.org>
* Fix plist.skreuzer2010-11-171-1/+1
| | | | Reported by: QAT
* - Update to 2.15wen2010-11-163-196/+201
| | | | | | | Changelog: http://search.cpan.org/src/LDS/Bio-Graphics-2.15/Changes PR: ports/152189 Submitted by: Gea-Suan Lin <gslin@gslin.org>
* - Update to 1.5.0wen2010-11-103-4/+41
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* - Update to 0.28jadawin2010-11-093-7/+3
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* - Unbreak build: CPP is now part of MAKE_ENVpav2010-11-081-1/+1
| | | | Reported by: pointyhat
* - Update to 2.10wen2010-11-042-7/+6
| | | | Changelog: http://search.cpan.org/src/RPETTETT/Bio-Das-Lite-2.10/Changes
* - Unbreak by removing some old and adding some new master sitesrene2010-10-311-5/+4
| | | | | | - Bump PORTREVISION PR: ports/151733 Submitted by: Chris Petrik [c.petrik.sosa gmail.com]
* - Update to 0.4.0wen2010-10-262-4/+4
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* - Update to 0.26wen2010-10-253-5/+8
| | | | - Reset maintainer to perl@
* - Update to 0.22wen2010-10-223-20/+20
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* Update my MAINTAINER address to culot@FreeBSD.org.culot2010-10-201-1/+1
| | | | Approved by: sahil@ (mentor)
* - Update to 2.14wen2010-10-192-4/+4
| | | | ChangeLog: http://search.cpan.org/src/LDS/Bio-Graphics-2.14/Changes
* Punt autoconf267->autoconf268ade2010-10-161-1/+1
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* - Update to 4.2.0wen2010-10-083-5/+6
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* Round one migration of ports from automake{19,110} to automake111ade2010-10-062-2/+2
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* - Add an additional MASTER_SITESsunpoet2010-10-011-1/+2
| | | | | | PR: ports/151112 Submitted by: gjb (maintainer) Approved by: pgollucci (mentor)
* Mark BROKEN: does not fetch.erwin2010-09-301-0/+1
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* - Update to 2.13wen2010-09-263-4/+5
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* - Update to 0.76wen2010-09-252-4/+4
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* Change dependency on old p5-Compress-Zlib, p5-IO-Compress-Base,mm2010-09-211-1/+2
| | | | | | p5-IO-Compress-Zlib and p5-IO-Compress-Bzip2 modules to p5-IO-Compress. Explicitly depend on p5-IO-Compress only if PERL_LEVEL < 500903 Bump PORTREVISION
* Also broken on sparc64 (and, by implication, ia64).linimon2010-09-171-2/+2
| | | | Hat: portmgr
* Update to 1.3r1.3913.maho2010-09-174-636/+699
| | | | | | Actually the version number is from SVN, and maho@ manually checked out from SVN. The source archive is not distributed as tar ball.
* - Update to 4.1.0wen2010-09-163-5/+28
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* Autotools update. Read ports/UPDATING 20100915 for details.ade2010-09-161-1/+2
| | | | | Approved by: portmgr (for Mk/bsd.port.mk part) Tested by: Multiple -exp runs
* - Update to 4.4cwen2010-09-082-4/+4
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* - Update to 0.75wen2010-09-073-6/+12
| | | | - Reset maintainer to perl@
* - Update to 1.13wen2010-09-072-4/+4
| | | | | PR: ports/150317 Submitted by: Frederic Culot <frederic@culot.org>
* - Update MAINTAINER to submitters new mail addressdecke2010-09-041-1/+1
| | | | | | PR: ports/150274 Submitted by: Glen Barber <glen dot j dot barber at gmail dot com> (maintainer) Approved by: beat (co-mentor, implicit)
* - Update to 2.10.0sahil2010-08-215-29/+13
| | | | | | | | | | | - Add LICENSE - Mark MAKE_JOBS_SAFE - Eliminate unnecessary patch - Note new homepage in pkg-descr - Pass maintainership to submitter PR: ports/149827 Submitted by: C-S <c-s@c-s.li>
* - Update USE_PYTHON in Makefile to reflect upstream Pythonglarkin2010-08-181-1/+1
| | | | | | | | dependency version requirement PR: ports/149251 Submitted by: glarkin Approved by: wen (via email)
* Update to 1.12:az2010-08-182-5/+5
| | | | | | | | - dependency on MooseX::FollowPBP added - dependency on Moose::Policy removed PR: ports/149612 Submitted by: Frederic Culot <frederic@culot.org>
* - Update to 2.1.5lwhsu2010-08-042-7/+12
| | | | | | | - Pass maintainership to submitter PR: ports/149247 Submitted by: C-S <c-s AT c-s.li>
* Fix typo in maintainer mail addressbapt2010-08-031-1/+1
| | | | | Submitted by: Frederic Culot <frederic _at_ culot.org> (maintainer) Approved by: jadawin@ (co-mentor)
* - Update to 1.12.4bapt2010-08-022-6/+11
| | | | | | | | | - Add libcurl as dependency - Submitter is now maintainer PR: ports/149079 Submitted by: Frederic Coulot <frederic _at_ coulot.org> (maintainer) Approved by: jadawin@ (co-mentor)
* - Update the libmap instructions for amd64/8pav2010-07-292-4/+14
| | | | Submitted by: Rick van der Zwet <info@rickvanderzwet.nl>
* - Update to 1.54wen2010-07-023-49/+146
| | | | | | | PR: ports/148274 Submitted by: Ju Pengfei <jupengfei@gmail.com> Approved by: maintainer Feature safe: yes
* - Update to 2.11wen2010-06-302-4/+4
| | | | Feature safe: yes
* - Update to 1.17wen2010-06-302-4/+4
| | | | Feature safe: yes
* - Update to 1.16wen2010-06-242-4/+4
| | | | Feature safe: yes
* - Update to 2.04wen2010-06-223-7/+6
| | | | | - Pass maintainership to perl@ Feature safe: yes
* BROKEN should not be quoted.erwin2010-06-131-1/+1
| | | | No functional change.
* - Update to 1.15wen2010-06-122-5/+4
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* Update to 1.10.tobez2010-06-112-7/+6
| | | | Changes: http://search.cpan.org/dist/Bio-MAGETAB/Changes
* - Update to 1.4.0pgollucci2010-06-083-75/+188
| | | | | - Sort pkg-plist - seperate NOPORTDOCS and NOPORTEXAMPLES
* LICENSE GPLv2dinoex2010-06-062-1/+3
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* LICENSE LGPL21dinoex2010-06-051-0/+2
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* - Update to 1.4.1wen2010-06-013-4/+25
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* Bounce PORTREVISION for gettext-related ports. Have fun, ya'll.ade2010-05-311-1/+1
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* - Update to 3.1.6sylvio2010-05-313-5/+5
| | | | | PR: ports/147194 Submitted by: Glen Barber <glen.j.barber@gmail.com> (maintainer)
* - drop USE_GNUSTEP_PREFIXdinoex2010-05-304-320/+318
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* - Update to 4.0.1wen2010-05-242-4/+4
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* - fix build for gnustep-base 1.21.0dinoex2010-05-241-2/+3
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* - Update to 1.12.2wen2010-05-213-6/+7
| | | | - Reset maintainer
* - Update to 2.09wen2010-05-182-4/+4
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* - Update to 2.0.8wen2010-05-143-5/+4
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* - Update to 2.0.7wen2010-05-102-5/+5
| | | | - Set maintainer to perl@
* - Update to 3.1.4sylvio2010-05-093-11/+18
| | | | | PR: ports/146411 Submitted by: Glen Barber <glen.j.barber@gmail.com> (maintainer)
* - Update to 1.00wen2010-05-082-5/+6
| | | | - Set maintainer to perl@
* - Removed BROKEN because file fetches and checksums correctlyglarkin2010-04-291-3/+2
| | | | | | | - Added another MASTER_SITES for redundancy PR: ports/144733 Submitted by: Fernan Aguero <fernan.aguero@gmail.com> (maintainer)
* - Update to 2.04wen2010-04-202-4/+5
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* - Update to 4.4awen2010-04-202-7/+7
| | | | - Update my mail address to FreeBSD
* - update to 0.81dinoex2010-04-143-10/+32
| | | | - fix build on amd64
* - Update to 6.2.0wen2010-04-076-75/+232
| | | | | Submitted by: Wen Heping(myself) Approved by: maintainer(via Email)
* - Update to 2.03wen2010-04-022-4/+4
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* Mark various ports as broken or ignore on powerpc.linimon2010-04-013-3/+21
| | | | While here, remove remnants of alpha.
* - Update to 2.02wen2010-03-303-5/+6
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* - Bump PORTREVISION to chase the update of math/gslwen2010-03-291-2/+2
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* - update to 1.4.1dinoex2010-03-2818-20/+22
| | | | | Reviewed by: exp8 run on pointyhat Supported by: miwi
* - Update to 3.1.3wen2010-03-242-5/+5
| | | | | | | - Pass maintainership to submitter PR: ports/144992 Submitted by: Glen Barber <glen.j.barber@gmail.com>
* - Chase x11-toolkits/fltk updategahr2010-03-242-5/+5
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* - Update to 3.22sylvio2010-03-222-4/+4
| | | | Approved by: itetcu (mentor)
* - Update to 0.3.9wen2010-03-192-4/+4
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* - Update to 2.01wen2010-03-102-4/+4
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* - Update to 0.21wen2010-03-093-47/+41
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* - Update to 0.18wen2010-03-033-35/+72
| | | | | | - Adopt Feature safe: yes
* p5-Bio-Das-Lite is an implementation of a client for the DAS protocol (XMLwen2010-03-015-0/+42
| | | | | | | | over HTTP primarily for biological-data). WWW: http://search.cpan.org/dist/Bio-Das-Lite/ Feature safe: yes
* - Update to 0.7wen2010-02-243-9/+8
| | | | Feature safe: yes
* - Reset more ports I don't use anymorepgollucci2010-02-111-1/+1
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* Update to 3.1.2edwin2010-02-102-4/+4
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* - Update to 2.00wen2010-02-103-5/+5
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* - update to jpeg-8dinoex2010-02-0518-18/+19
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* - Update to 0.99wen2010-02-032-5/+5
| | | | - Update my mail address to FreeBSD
* - Update to 3.1.1miwi2010-02-035-88/+40
| | | | | PR: 143437 Submitted by: Ports Fury
* - use $SUB_FILES to dynamically adjust pkg-messagepgollucci2010-01-311-2/+1
| | | | | | PR: ports/142408 Submitted by: Sevan Janiyan <venture37@geeklan.co.uk> Approved by: fernan@iib.unsam.edu.ar (maintainer)
* - Remove unneeded dependencies which is in perl-5.8.9 distkuriyama2010-01-294-11/+7
| | | | | | (part 19; last!). Approved by: portmgr (itetcu)
* - actually remove old patchpgollucci2010-01-171-31/+0
| | | | Reported by: QAT
* - Fix on amd64pgollucci2010-01-174-0/+60
| | | | | PR: ports/142472 Submitted by: Edmund Sumbar <esumbar@ualberta.ca>
* - Remove unneeded dependencies which is in perl-5.8.9 dist from portskuriyama2010-01-161-2/+2
| | | | | | | | maintained by (perl|ports|kuriyama)@FreeBSD.org. - Targets are: Test::Simple, Digest::MD5, Locale-Maketext, ExtUtils::MakeMaker, ExtUtils::ParseXS, File::Temp, Getopt::Long, Encode, Digest, Pod::Parser, File::Spec.
* - SUB_FILES += pkg-messagepgollucci2010-01-101-4/+1
| | | | | | PR: ports/142407 Submitted by: Sevan Janiyan <venture37@geeklan.co.uk> Approved by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Update to 1.03wen2010-01-092-5/+5
| | | | - Update my mail address to FreeBSD
* - SBU_FILES += pkg-messagepgollucci2010-01-084-56/+54
| | | | | PR: ports/142409 Submitted by: Sevan Janiyan <venture37@geeklan.co.uk>
* - Update to 1.995wen2010-01-072-4/+4
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* - Update to 1.53wen2010-01-063-99/+39
| | | | | | PR: ports/142221 Submitted by: Wen Heping (myself) Approved by: maintainer
* python-nexus is a generic nexus (phylogenetics) file format(.nex, .trees)wen2009-12-295-0/+35
| | | | | | reader for python. WWW: http://simon.net.nz/articles/python-nexus
* - Fix fetch errorwen2009-12-271-2/+2
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* - Update to 0.3.7wen2009-12-242-4/+4
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* - Update to 7.1.11miwi2009-12-224-41/+49
| | | | | PR: 141812 Submitted by: Ports Fury
* - Update to 0.3.5wen2009-12-212-4/+4
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* For ports maintained by ports@FreeBSD.org, remove names and/ordougb2009-12-2111-22/+0
| | | | | | | | e-mail addresses from the pkg-descr file that could reasonably be mistaken for maintainer contact information in order to avoid confusion on the part of users looking for support. As a pleasant side effect this also avoids confusion and/or frustration for people who are no longer maintaining those ports.
* - Update to 1.1.4wen2009-12-182-11/+11
| | | | | Submitted by: Wen Heping (myself) Approved by: maintainer (via Email)
* - Update to 1.4wen2009-12-173-30/+126
| | | | - Update my mail address to FreeBSD
* - Update to 0.3.4wen2009-12-162-4/+4
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* - Turn over a bunch of p5- ports that change infrequently to perl@pgollucci2009-12-141-1/+1
| | | | so more people can look at them.
* - Update to 1.994wen2009-12-113-4/+6
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* - Update to 0.3.3wen2009-12-063-7/+7
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* - Update to 1.993wen2009-12-042-4/+4
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* - Update to 1.6.1wen2009-12-045-912/+939
| | | | Approved by: maintainer (via Email)
* Chase math/gsl update,makc2009-12-021-2/+2
| | | | bump PORTREVISION
* - Update to 2.0.12wen2009-11-292-6/+5
| | | | - Update my mail address to FreeBSD
* - Update my mail address to FreeBSDsylvio2009-11-281-1/+1
| | | | Approved by: miwi (mentor)
* - Mark MAKE_JOBS_UNSAFEpav2009-11-212-0/+2
| | | | Reported by: pointyhat
* - Update to 1.992wen2009-11-202-5/+5
| | | | - Update my mail address to FreeBSD
* - broken checksum mismatchmiwi2009-11-191-0/+2
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* - Mark MAKE_JOBS_UNSAFEpav2009-11-191-0/+1
| | | | Reported by: pointyhat
* pyfasta is a python module for fast, memory-efficient, pythonicwen2009-11-185-0/+52
| | | | | | access to fasta sequence files. WWW: http://bitbucket.org/brentp/biostuff/src/
* - Update to 21.1.1wen2009-11-184-29/+17
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* Velvet is a de novo genomic assembler specially designed for short readamdmi32009-11-077-0/+244
| | | | | | | | | | | | | | | sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI). Citation: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008) WWW: http://www.ebi.ac.uk/~zerbino/velvet/ PR: 140147 Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
* - Annotate that 8.x no longer needs libmap hackpav2009-10-011-1/+1
| | | | Reported by: rene
* - Update to 4.0.0wen2009-09-234-13/+23
| | | | | | | | | - Update my mail address to FreeBSD PR: ports/137652 Submitted by: wenheping@gmail.com(myself) Approved by: miwi(mentor) Feature safe: yes
* Update to Crux 1.2.0.jasone2009-09-203-26/+29
| | | | Feature safe: yes
* UNBREAK: Probably was a temporary failure, checksums are ok now.garga2009-09-161-2/+0
| | | | Feature safe: yes
* -Update to 3.69miwi2009-09-162-14/+10
| | | | | | PR: 138813 Submitted by: Ports Fury Feature safe: yes
* Bump PORTREVISION for everything that sets USE_FORTRAN=yes which nowgerald2009-09-136-5/+6
| | | | | | implies lang/gcc44 up from lang/gcc43. Approved by: portmgr
* - Update to 1.14jadawin2009-09-082-4/+4
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* - Update to 138038miwi2009-09-054-444/+152
| | | | | | PR: 138038 Submitted by: Wen Heping <wenheping@gmail.com> Approved by: maintainer
* - Update to 0.982miwi2009-08-292-5/+5
| | | | | PR: 138264 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
* Bio::SCF module allows you to read and update (in a restrictedmiwi2009-08-295-0/+46
| | | | | | | | | | | way) SCF chromatographic sequence files. It is an interface to Roger Staden's io-lib. See the installation directions for further instructions. WWW: http://search.cpan.org/dist/Bio-SCF/ PR: ports/138263 Submitted by: Wen Heping <wenheping at gmail.com>
* Io_lib is a library of file reading and writing code to provide amiwi2009-08-295-0/+107
| | | | | | | | | | | | general purpose trace file (and Experiment File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" C structure with the data loaded into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows. WWW: http://staden.sourceforge.net/ PR: ports/138254 Submitted by: Wen Heping <wenheping at gmail.com>
* - Update to 3.21.araujo2009-08-282-5/+5
| | | | | | | - Reset maintainer to submitter. PR: ports/138192 Submitted by: Sylvio Cesar <scjamorim@bsd.com.br>
* - Update to 1.12miwi2009-08-282-5/+4
| | | | | PR: 138230 Submitted by: Wen Heping <wenheping@gmail.com>
* Update to 35.4.9makc2009-08-232-4/+4
| | | | | PR: ports/137991 Submitted by: Fernan Aguero (maintainer)
* Bio::NEXUS package provides an object-oriented, Perl-basedmiwi2009-08-235-0/+91
| | | | | | | | | | | | | | | | | | | applications programming interface (API) to the NEXUS file format of Maddison, et al., 1997 (Syst. Biol. 46:590-621). NEXUS is a powerful and extensible format designed for use in evolutionary analysis, including the analysis of molecular sequence data as well as classical morphological and life-history data. NEXUS is the input or output format for software such as PAUP*, MacClade, Mesquite, SIMMAP, MrBayes, Nexplorer, and so on. This package also contains the demonstration applications nexplot.pl (plot character data with a tree) and nextool.pl (allowing programmatic editing, e.g., selecting particular clades or subsets of data). WWW: http://search.cpan.org/dist/Bio-NEXUS/ PR: ports/137983 Submitted by: Wen Heping <wenheping at gmail.com>
* - BROKEN checksum mismatchmiwi2009-08-221-0/+2
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* - Switch SourceForge ports to the new File Release System: categories ↵amdmi32009-08-225-8/+5
| | | | starting with B,C
* - Fix fetchmiwi2009-08-171-1/+1
| | | | | PR: 137840 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Update MASTER_SITESmiwi2009-08-142-4/+2
| | | | | PR: 137750 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Update to 4.3miwi2009-08-142-6/+6
| | | | | PR: 137625 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
* Fix PKGORIGINerwin2009-08-081-1/+1
| | | | Submitted by: pointyhat
* - Relax check on bioperl version; people keep forgetting to update this checkpav2009-08-031-1/+1
| | | | | | when updating bioperl port Reported by: pointyhat
* - Unbreak fetchpav2009-08-031-1/+1
| | | | Submitted by: maintainer
* -Repocopy devel/libtool15 -> libtool22 and libltdl15 -> libltdl22.mezz2009-08-032-2/+2
| | | | | | | | | | | | | | | | | | -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
* - bump all port that indirectly depends on libjpeg and have not yet been ↵dinoex2009-07-3114-7/+14
| | | | | | bumped or updated Requested by: edwin
* Utilize %%SITE_PERL%% and %%PERL_ARCH%% in pkg-plistspgollucci2009-07-311-3/+3
| | | | | | PR: ports/136771 Exp Run by: pav Approved by: portmgr (pav)
* - lang/perl5.6 is dead, remove PERL_LEVEL/PERL_VERSION < 500801 checkspgollucci2009-07-232-14/+1
| | | | | | PR: ports/135398 Tested by: 2 -exp runs by pav Approved by: portmgr (pav)
* PhyML is a software that estimates maximum likelihood phylogenies fromamdmi32009-07-216-0/+75
| | | | | | | | | | | | | | | | | | | | | | | alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the "comfort zone" for PhyML generally lies around 3 to 500 sequences less than 2,000 character long. WWW: http://code.google.com/p/phyml/ PR: 136877 Submitted by: Ben Allen <ben@sysadminschronicles.com>
* - update to jpeg7dinoex2009-07-181-2/+2
| | | | Tested by: pav on pointyhat
* - Flip MAKE_JOBS_SAFE to MAKE_JOBS_UNSAFEpav2009-07-081-1/+1
| | | | Reported by: pointyhat
* - fix PORTSCOUTdinoex2009-07-061-1/+1
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* - Update to 1.97miwi2009-07-063-4/+14
| | | | | PR: 136310 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
* - cleanup ADDITIONAL_LIB_DIRSdinoex2009-07-051-1/+1
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* p5-Bio-MAGETAB contains the core MAGE-TAB Utilities Perl modules. Thismiwi2009-07-015-0/+177
| | | | | | | | | | | | | is a beta release. All functions have now been implemented and most have test suites; the exceptions include the modules involved in export of MAGE-TAB documents, which are still a little experimental in nature. The API is mostly finalised (and fully documented), but some details may yet change where necessary to improve usability. WWW: http://search.cpan.org/dist/Bio-MAGETAB/ PR: ports/136021 Submitted by: Wen Heping <wenheping at gmail.com>
* PyCogent is a software library for genomic biology. It is a fully integratedmiwi2009-06-225-0/+887
| | | | | | | | | | | | | | and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics. It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data. WWW: http://pycogent.sourceforge.net/ PR: ports/135863 Submitted by: Wen Heping <wenheping at gmail.com>
* Update to Crux 1.1.0.jasone2009-06-213-9/+7
| | | | Fix the ATLAS/LAPACK build option.
* - Update to 6.0.0amdmi32009-06-173-406/+438
| | | | | | | - Unbreak PR: 135376 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* Change CONFIGURE_ENV --> USE_CSTD. [1]jasone2009-06-102-2/+6
| | | | | | | | | Add missing pkg-plist entry for Parsing.so. [2] Change RUN_DEPENDS --> LIB_DEPENDS for optional math/atlas dependency. Submitted by: [1] erwin Reported by: [2] QAT
* Convert most of remaining ports that depend on xorg-libraries toamdmi32009-06-092-2/+4
| | | | | | | | | | | | | modular xorg. - supply corresponding USE_XORG for all imake-using ports that need it - USE_IMAKE no longer implies USE_XLIB in absence of USE_XORG - retire USE_X_PREFIX which is not really used anywhere after the above change - a few minor nits like whitespace and SF macro Tested by: 2 tinderbox runs by pav Approved by: portmgr (pav)
* - Update to 35.4.7 [1]itetcu2009-06-094-8/+27
| | | | | | | - Obey PREFIX [2] Submitted by: maintainer [1] [2] Reported by: QATty [2]
* Add the biology/crux port.jasone2009-06-095-0/+131
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* - Update lang/python26 and make Python 2.6.2 to the default Python versionmiwi2009-06-092-4/+3
| | | | | Tested by: 3 pointyhat runs Thanks to: pav, gahr, lwhsu, mva, amdmi3
* - Update to 1.11jadawin2009-06-082-4/+4
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* 2009-05-31 biology/p5-bioperl-devel: no longer under developmentmiwi2009-06-0611-3118/+0
| | | | | | 2009-05-31 biology/p5-bioperl-run-devel: no longer under development 2009-06-01 net-p2p/deluge05: use net-p2p/deluge instead 2009-06-03 textproc/gmat: failed to build for a long time, no maintainer and apparently no users either
* - Update to 1.95miwi2009-06-032-4/+4
| | | | | PR: 135141 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
* - fix build for custom LOCALBASE in UL subdirdinoex2009-06-021-1/+1
| | | | Reported by: QAT
* - fix build for custom LOCALBASEdinoex2009-06-011-0/+2
| | | | Reported by: QAT
* LibSBML is an open-source programming library to help you read, write,miwi2009-05-296-0/+343
| | | | | | | | | | | | | | | | manipulate, translate, and validate SBML files and data streams. It is not an application itself (though it does come with example programs), but rather a library you can embed in your own applications. LibSBML understands all Levels and Versions of SBML, as well as the SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in ISO C and C++ but can be used from all the languages listed in the right-hand box. WWW: http://www.sbml.org/ PR: ports/135022 Submitted by: Wen Heping <wenheping at gmail.com>
* - fix build with gnustep-make-2.2.0dinoex2009-05-211-2/+4
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* - Mark most of my ports MAKE_JOBS_SAFE=yespgollucci2009-05-162-0/+4
| | | | Tested by: several builds in P6 TB
* Fix LIB_DEPENDS on devel/readline: its sh lib version was bumped recently fromitetcu2009-05-121-1/+2
| | | | | | | 5 to 6. Forgotten by: araujo@ Reported by: QAT
* - Update to 1.94miwi2009-05-012-4/+4
| | | | Approved by: maintainer implicit
* - Update to 1.7miwi2009-05-014-281/+29
| | | | | | | - Pass maintainership to submitter PR: 134056 Submitted by: Wen Heping <wenheping@gmail.com>
* - Update to 1.93miwi2009-04-052-4/+4
| | | | | PR: 133342 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
* Bio::Glite is an interface to G-language Genome Analysis Environmentmiwi2009-04-035-0/+52
| | | | | | | | | | | | | | | | | | | | | | | through its REST web service (http://www.g-language.org). This module allows almost everything G-language GAE can do, without installing all necessary tookits and modules. Advantage of this module over the standard installation of G-language GAE package is: 1. Easy installation from CPAN 2. Extremely light-weight (less than 1000 lines of code) 3. Does not require much CPU/RAM (all calculation is done on the cloud) Disadvantages includes: 1. Slower analysis speed 2. Internet connection is required 3. No other software interfaces such as the G-language Shell WWW: http://search.cpan.org/dist/Bio-Glite/ PR: ports/133273 Submitted by: Wen Heping <wenheping at gmail.com>
* - Update to 2009.03.01miwi2009-03-293-30/+93
| | | | | | PR: 133099 Submitted by: Fernan Aguero <fernan.aguero@gmail.com> Approved by: maintainer
* - Update to 1.91miwi2009-03-263-4/+5
| | | | | PR: 133065 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
* bump PORTREVISION after cmake updatemakc2009-03-251-0/+1
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* - Mark BROKEN does not compilemiwi2009-03-241-0/+2
| | | | Submitted by: maintainer via private mail
* - Update to 1.6.1miwi2009-03-203-683/+216
| | | | | | PR: 132122 Submitted by: Wen Heping <wenheping@gmail.com> Approved by: maintainer
* - Mark DEPRECATED (no longer under development)miwi2009-03-202-0/+6
| | | | | PR: 132122 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)
* Welcome to the new linux ports infrastructure which allows usingbsam2009-03-201-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | both current (fc4) and future linux (f8) distributions at one ports tree. The patch contains full changes to ports/Mk files and all ports involved. But only infrastructure is changed. The resulting packages are the same as before. Hence no need to bump PORTREVISIONs. The idea was taken from bsd.gnome.mk and others. More than 130 ports are switched to follow a new linux infrastructure introduced by changes to bsd.port.mk, bsd.linux-rpm.mk and a new bsd.linux-apps.mk. Thanks for all who was involved and helped me with this work. And help from Alexander Leidinger was incredible. Other changes are coming. Stay tuned! PR: ports/132510 Submitted by: bsam (me) Exp-run by: portmgr (pav)
* - Update to 1.90miwi2009-03-203-6/+9
| | | | | PR: 132659 Submitted by: Wen heping <wenheping@gmail.com> (maintainer)
* - Update to 0.1.24miwi2009-03-143-485/+571
| | | | | | PR: 132527 Submitted by: Wen Heping <wenheping@gmail.com> Approved by: maintainer
* p5-Bio-Graphics is a simple GD-based renderer (diagram drawer)miwi2009-03-115-0/+222
| | | | | | | | | for DNA and protein sequences. WWW: http://search.cpan.org/dist/Bio-Graphics/ PR: ports/132088 Submitted by: Wen Heping <wenheping at gmail.com>
* Rename PERL_VER to PERL_VERSION.skv2009-03-081-2/+2
| | | | Pointed by: pav
* Remove variable PERL_VER from the ports tree at all - becauseskv2009-03-061-2/+2
| | | | it is obsolete since Perl 5.6.0.
* - Update to 4.2bmiwi2009-03-032-6/+6
| | | | | PR: 132249 Submitted by: Wen Heping <wenheping@gmail.com>
* - Update to 1.6.0garga2009-02-246-1082/+1559
| | | | | PR: ports/131989 Submitted by: maintainer
* - Add forgotten patchamdmi32009-02-241-0/+11
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* - Update to 35.4.4amdmi32009-02-243-25/+47
| | | | | PR: 132007 Submitted by: Fernan Aguero <fernan at iib dot unsam dot edu dot ar> (maintainer)
* - update PORTSCOUTdinoex2009-02-161-1/+1
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* - Update download locations, update WWWpgollucci2009-02-042-3/+2
| | | | Reported by: -fetch-original pointyhat run
* Reset dyeske@gmail.com at his request.linimon2009-02-034-8/+2
| | | | Hat: portmgr
* - Update download locations, update WWWpgollucci2009-02-012-2/+2
| | | | Reported by: -fetch-original pointyhat run
* - Update download locationpav2009-02-011-2/+2
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* - Update X.org ports to 7.4+ (few ports are more recent than the katamari).flz2009-01-244-5/+6
| | | | | | | | - Bump PORTREVISION for all ports depending on libglut since the shlib version number went from 4 to 3. - Bump PORTREVISION for all ports depending on libXaw as libXaw.so.8 isn't installed anymore. - Couple of ports fixes (mostly missing xorg components added to USE_XORG).
* - add LICENSE:dinoex2009-01-172-0/+4
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* - Unbreak after p5-bioperl changed portrevisionpav2009-01-161-1/+1
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* - Update to 3.0.3miwi2009-01-156-57/+122
| | | | | PR: 130459 Submitted by: KATO Tsuguru <tkato432@yahoo.com>
* Fix plist with perl 5.8.9.tobez2009-01-141-1/+2
| | | | Approved by: portmgr (pav, implicit)
* - Chase math/gsl slib bumpmiwi2009-01-131-2/+2
| | | | Reported by: pavbot
* - Unbreak distinfo after portrevision bumppav2009-01-102-4/+3
| | | | Reported by: pointyhat
* Bump PORTREVISION due to change of USE_FORTRAN=yes to GCC 4.3.gerald2009-01-085-4/+5
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* - Remove conditional checks relevant only on FreeBSD 5.x and olderpav2009-01-066-31/+1
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* - Update to 4.2miwi2008-12-262-4/+4
| | | | | PR: 129895 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
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