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* - 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)
* Update to 1.92pgollucci2008-12-242-4/+4
| | | | | | Changes http://search.cpan.org/src/LDS/AcePerl-1.92/ChangeLog Approved by: gabor (mentor)
* - Mark as brokenwxs2008-12-171-0/+2
| | | | | PR: ports/129597 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)
* - update to 1.10leeym2008-12-113-14/+21
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* Reset nemoliu due to maintainer-timeouts and no response to email.linimon2008-12-081-1/+1
| | | | Hat: portmgr
* - Roll back to 4.6 as 4.7 is the development version and is constantly beingwxs2008-11-115-110/+117
| | | | | | | | re-rolled. - Move post-patch target into files/patch-xwin.c to remove sed invocation. - Respect NOPORTDATA and DATADIR. - Bring files/patch-aa back (to preserve history) and retire patch-makefile. - Fixup files/patch-xwin.c so it applies cleanly to this version.
* Mark as broken since it has been re-rolled for the 4th(?) time.wxs2008-11-081-0/+2
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* Distfile was re-rolled. The changes were to fix some bugs in the code.wxs2008-11-073-10/+13
| | | | While I'm here, make it respect NOPORTDOCS.
* Update to 4.7wxs2008-11-058-140/+309
| | | | | PR: ports/128476 Submitted by: fulvio ciriaco <oivulf@gmail.com>
* - Update to 2.8.1amdmi32008-10-234-150/+40
| | | | | PR: 128057 Submitted by: Christian Sturm <athaba at inode dot at>
* - Unbreakrafan2008-10-213-7/+42
| | | | | PR: ports/128193 Submitted by: Mauricio Herrera Cuadra <mauricio at arareko.net> (maintainer)
* - Update to 1.48miwi2008-10-113-19/+16
| | | | | | PR: 127776 Submitted by: Wen heping <wenheping@gmail.com> Approved by: maintainer
* - Update to 4.1miwi2008-09-303-8/+13
| | | | | | | - Pass maintainership to submitter PR: 127683 Submitted by: Wen heping <wenheping@gmail.com>
* - Respect PORTDOCS/PORTEXAMPLESgahr2008-09-092-188/+186
| | | | | Reported by: QA Tindie Approved by: portmgr
* Reset sf@slappy.org due to maintainer-timeouts and no response to email.linimon2008-09-031-1/+1
| | | | Hat: portmgr
* - Fix buildgahr2008-08-281-2/+2
| | | | Reported by: QA Tindie
* - Update to 3.68gahr2008-08-272-6/+5
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* Add -lf2c, this is the correct dependency. Bump portrevision.maho2008-08-232-0/+9
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* Update CONFIGURE_ARGS for how we pass CONFIGURE_TARGET to configure script.rafan2008-08-214-5/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 - Remove CONFIGURE_TARGET hack in various bsd.*.mk - USE_GNOME=gnometarget is now an no-op Changes to individual ports, other than removing the CONFIGURE_TARGET hack: = pkg-plist changed (due to the ugly CONFIGURE_TARGET prefix in * executables) - comms/gnuradio - science/abinit - science/elmer-fem - science/elmer-matc - science/elmer-meshgen2d - science/elmerfront - science/elmerpost = use x86_64 as ARCH - devel/g-wrap = other changes - print/magicfilter GNU_CONFIGURE -> HAS_CONFIGURE since it's not generated by autoconf Total # of ports modified: 1,027 Total # of ports affected: ~7,000 (set GNU_CONFIGURE to yes) PR: 126524 (obsoletes 52917) Submitted by: rafan Tested on: two pointyhat 7-amd64 exp runs (by pav) Approved by: portmgr (pav)
* Unbreak building for 8-x.bsam2008-08-162-4/+114
| | | | Submitted by: Steve Kargl <sgk at troutmask.apl.washington.edu> at ports@ ML
* - update PORTSCOUTdinoex2008-08-131-1/+3
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* - Update to 1.47miwi2008-08-123-53/+92
| | | | | | PR: 125912 Submitted by: Wen heping <wenheping@gmail.com> Approved by: maintainer timeout
* - Update to 2.1.3pgollucci2008-08-013-4/+5
| | | | Approved by: gabor (mentor)
* - Remove USE_GCC where it can be satisfied with base compiler on followingpav2008-07-252-2/+0
| | | | FreeBSD versions: 5.3 and up, 6.x, 7.x, 8-CURRENT
* - Remove duplicates from MAKE_ENV after inclusion of CC and CXX in default ↵pav2008-07-253-3/+5
| | | | MAKE_ENV
* - Delete biology/nab port after being marked DEPRECATED for three monthspav2008-07-2415-1093/+0
| | | | | PR: ports/125891 Submitted by: M. L. Dodson <mldodson@comcast.net> (maintainer)
* Update my ports to my freebsd addresspgollucci2008-07-232-2/+2
| | | | Approved by: araujo (mentor)
* - respect NOPORTEXAMPLES/NOPORTDOCS and fix plistitetcu2008-07-122-14/+15
| | | | | | - bump PORTREVISION Prompted by: QA Tindy run
* - Update to 2.1.2c.araujo2008-07-122-5/+5
| | | | | | | - Pass maintainership to submitter. PR: ports/125497 Submitted by: Philip M. Gollucci <pgollucci@p6m7g8.com>
* - extened PORTSCOUTdinoex2008-07-091-1/+1
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* - Mark BROKEN: missing cpan dependency (interactive loop)pav2008-07-081-0/+2
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* - Bump portrevision after openbabel updatebeech2008-07-071-1/+1
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* - Update to 1.5.2.lippe2008-07-074-1355/+1063
| | | | | | | PR: ports/124648 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer) Reviewed by: lippe Approved by: gabor (mentor, implicit)
* - Update to 1.45beech2008-07-043-26/+79
| | | | | | PR: ports/125134 Submitted by: Wen heping <wenheping@gmail.com> Approved by: Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)
* - extend PORTSCOUTdinoex2008-06-241-1/+1
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* - Fix plist files installation.lippe2008-06-211-1/+2
| | | | | | | - Bump PORTREVISION. Reported by: QA Tindy Approved by: gabor (mentor, implicit)
* SSAHA is a software tool for very fast matching and alignment of DNAlippe2008-06-2136-0/+1362
| | | | | | | | | | | | | sequences. It stands for Sequence Search and Alignment by Hashing Algorithm. It achieves its fast search speed by converting sequence information into a `hash table' data structure, which can then be searched very rapidly for matches. WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/ PR: ports/124525 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Approved by: gabor (mentor, implicit)
* - Fix fetch, update WWWpav2008-06-192-2/+2
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* - Fix build dependsgahr2008-06-091-0/+3
| | | | | | - Bump port revision Reported by: pointyhat via pav
* Bump portrevision due to upgrade of devel/gettext.edwin2008-06-0613-11/+13
| | | | | | | | | | 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)
* - Update to 3.67gahr2008-06-042-12/+7
| | | | - Sanitize Makefile a little bit
* - cleanup FreeBSD 5.xdinoex2008-06-021-7/+1
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* - Update to 1.09miwi2008-05-312-4/+4
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* Teach the building cluster that these ports are not to be buildedwin2008-05-264-0/+12
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* New port: biology/consed viewing and editing workbench for sequenceedwin2008-05-249-0/+221
| | | | | | | | | | | | | | | | | | | | | | | | | | | assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* New port: biology/consed viewing and editing workbench for sequenceedwin2008-05-244-0/+22
| | | | | | | | | | | | | | | | | | | | | | | | | | | assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* New port: biology/consed viewing and editing workbench for sequenceedwin2008-05-242-0/+49
| | | | | | | | | | | | | | | | | | | | | | | | | | | assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* New port: biology/consed viewing and editing workbench for sequenceedwin2008-05-249-0/+1174
| | | | | | | | | | | | | | | | | | | | | | | | | | assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* Update to 1.08mat2008-05-232-4/+4
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* - Update MASTER_SITES and WWW: linemiwi2008-05-224-61/+46
| | | | | | | | - Support CC/CFLAGS properly - Strip binary PR: 123866 Submitted by: Ports Fury
* - Include some ports in perl5 category.araujo2008-05-191-1/+1
| | | | | | | PR: ports/123530 Submitted by: Philip M. Gollucci <pgollucci@p6m7g8.com> Reworked by: araujo (myself) Approved by: flz (portmgr)
* - Update maintainer's email addresspav2008-05-183-3/+3
| | | | Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
* - Try to fix fetchpav2008-05-181-0/+2
| | | | Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
* Update to 1.23erwin2008-05-152-4/+4
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* NJplot is a tree drawing program able to draw any phylogenetic tree expressedpav2008-05-145-0/+145
| | | | | | | | | | | | | | | | | | | | | | in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods. The package contains the following programs: njplot - draw phylogenetic trees and interactively modify them newicktops - non-interactive version rendering into a PostScript file newicktotxt - non-interactive version rendering into a text file unrooted - draw unrooted circular trees If you use NJplot in a published work, please cite the following reference: Perriere, G. and Gouy, M. (1996) WWW-Query: An on-line retrieval system for biological sequence banks. Biochimie, 78, 364-369. WWW: http://pbil.univ-lyon1.fr/software/njplot.html PR: ports/118438 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* MUSCLE is multiple alignment software for protein and nucleotide sequences.pav2008-05-147-0/+232
| | | | | | | | | | | | | | | | | | | | | | | | | | | The name stands for multiple sequence comparison by log-expectation. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. Default parameters are those that give the best average accuracy in the published tests. MUSCLE can achieve both better average accuracy and better speed than CLUSTALW or T-Coffee, depending on the chosen options. Citation: Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5): 1792-1797. Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5(1): 113. The NAR paper gives only a brief overview of the algorithm and implementation details. For a full discussion of the method and many of the non-default options that it offers, please see the BMC paper. WWW: http://www.drive5.com/muscle/ PR: ports/118460 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* - add PORTSCOUTdinoex2008-05-041-0/+2
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* Update to version 34.okazaki2008-05-012-11/+5
| | | | | | | Remove BROKEN. PR: 123218 Submitted by: maintainer
* - update to 0.8.2dinoex2008-04-309-456/+205
| | | | | - take maintainership Approved by: maintainer
* - Update to 2.0.6miwi2008-04-292-5/+5
| | | | | | | - Pass maintainership to submitter PR: 123193 Submitted by: Wen heping <wenheping@gmail.com>
* Reset aaron's port maintainerships due to many maintainer-timeouts.linimon2008-04-291-1/+1
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* - Mark BROKEN on -CURRENT: error: 'linkat' redeclared as different kind of ↵pav2008-04-261-0/+4
| | | | | | symbol Reported by: pointyhat
* - Remove unneeded dependency from gtk12/gtk20 [1]miwi2008-04-2019-50/+43
| | | | | | | | | | | | | | | - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG - Remove X11BASE support in favor of LOCALBASE or PREFIX - Use USE_LDCONFIG instead of INSTALLS_SHLIB - Remove unneeded USE_GCC 3.4+ Thanks to all Helpers: Dmitry Marakasov, Chess Griffin, beech@, dinoex, rafan, gahr, ehaupt, nox, itetcu, flz, pav PR: 116263 Tested on: pointyhat Approved by: portmgr (pav)
* implement @dirrmtry macro for the pkg-plistedwin2008-04-191-1/+1
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* - Update mastersite.jmelo2008-04-181-1/+2
| | | | | PR: ports/122130 Submitted by: Ganael Laplanche <ganael.laplanche@martymac.com>
* - Replace SF with second working master sitepav2008-04-181-1/+1
| | | | Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Take advantage of CPAN macro from bsd.sites.mk, change ↵araujo2008-04-176-10/+6
| | | | | | | | | ${MASTER_SITE_PERL_CPAN} to CPAN. PR: ports/122674 Submitted by: Philip M. Gollucci <pgollucci@p6m7g8.com> Reworked by: araujo (myself) Approved by: portmgr (pav)
* - It seems that upstream removes their distfiles from sourceforge, so addrafan2008-04-171-1/+2
| | | | | | the download site pointed by their webpage as first choice. Noticed by: pointyhat via pav
* - Update to 5.0.0rafan2008-04-1317-6851/+707
| | | | | PR: ports/122437 Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
* - Sort pkg-plist before updating to 5.0.0rafan2008-04-131-888/+888
| | | | | PR: ports/122437 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* Change maintainers e-mail address.ehaupt2008-04-111-2/+2
| | | | Requested over: IRC
* - Update to 35.3.6clsung2008-04-102-5/+5
| | | | | PR: ports/122607 Submitted by: maintainer (Fernan Aguero)
* - Chase the gsl shared lib bump.jadawin2008-04-081-2/+2
| | | | Approved by: thierry (mentor)
* - Update maintainer's emailrafan2008-04-061-3/+5
| | | | | | | - Mark as deprecated PR: ports/122474 Submitted by: M. L. Dodson <mldodson at comcast.net> (maintainer with another email)
* MAPMAKER/EXP is a linkage analysis package designed to help construct primaryrafan2008-04-0628-0/+1101
| | | | | | | | | | | | | | | | | | linkage maps of markers segregating in experimental crosses. MAPMAKER/EXP performs full multipoint linkage analysis (simultaneous estimation of all recombination fractions from the primary data) for dominant, recessive, and co- dominant (e.g. RFLP-like) markers. MAPMAKER/EXP is an experimental-cross-only successor to the original MAPMAKER program. MAPMAKER/QTL is a companion program to MAPMAKER/EXP which allows one to map genes controlling polygenic quantitative traits in F2 intercrosses and BC1 backcrosses relative to a genetic linkage map. More information on MAPMAKER/QTL can be found in the technical report (included with MAPMAKER/QTL). WWW: http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/ PR: ports/122452 Submitted by: Tassilo Philipp <tphilipp at potion-studios.com>
* - Update to 5.68rafan2008-04-053-10/+10
| | | | | | | - Remove gcc version restriction PR: ports/122435 Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
* - Update to 1.1.3pav2008-04-053-185/+203
| | | | | | PR: ports/122374 Submitted by: Wen heping <wenheping@gmail.com> Patch revised: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Chase fasta3 updatepav2008-04-021-1/+1
| | | | Reported by: pointyhat
* - Update to 35.3.5rafan2008-03-303-53/+49
| | | | | | | | | | - Switch to .tar.gz distfile so that we don't define our do-extract - While I'm here, using substitution for version numbers in pkg-plist for easier upgrade PR: ports/121690 Submitted by: Wen heping <wenheping at gmail.com> Approved by: maintainer timeout (2 weeks)
* - Fix build with GCC 4.2gahr2008-03-292-5/+18
| | | | Approved by: miwi (mentor)
* - Add missing dependensmiwi2008-03-271-1/+3
| | | | | | - Bump PORTREVISION Submitted by: pointyhat via pav
* - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORGmiwi2008-03-261-2/+1
| | | | | | - Bump PORTREVISION Approved by: portmgr (xorg cleanup)
* - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORGmiwi2008-03-241-2/+2
| | | | | | - Bump PORTREVISION Approved by: portmgr (xorg cleanup)
* - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORGmiwi2008-03-241-2/+1
| | | | | | - Bump PORTREVISION Approved by: portmgr (xorg cleanup)
* - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORGmiwi2008-03-243-6/+3
| | | | | | - Bump PORTREVISION Approved by: portmgr (xorg cleanup)
* - Remove USE_X_PREFIXbeech2008-03-222-4/+2
| | | | | | - Bump portrevision Approved by: David Yeske <dyeske@gmail.com> (maintainer, implicit)
* - Update to 2.0.5jadawin2008-03-191-5/+10
| | | | | | | | - Add RESTRICTED due to non-commercial use licence. PR: ports/121794 Submitted by: KATO Tsuguru <tkato432@yahoo.com> Approved by: thierry and tabthorpe (mentors)
* - Update to version 2.0.5jadawin2008-03-192-21/+10
| | | | | | | | - Add RESTRICTED due to a non-commercial use licence. PR: ports/121794 Submitted by: KATO Tsuguru <tkato432@yahoo.com> Approved by: thierry and tabthorpe (mentors)
* - Update to 1.07miwi2008-03-122-4/+4
|
* Fix pkg-plistmaho2008-03-101-0/+142
| | | | Submitted by: pav
* Update to 1.0r2.maho2008-03-076-955/+636
|
* - File was rerolled for a small bugfix.miwi2008-02-273-3/+16
| | | | Submitted by: pointyhat via pav/erwin
* - Restore clustalw symlink, other ports rely on itpav2008-02-271-1/+5
| | | | | Reported by: pointyhat Pointy hat to: pav
* - Update to 2.4.3miwi2008-02-262-4/+4
| | | | Submitted by: Ports Fury
* - Update to 2.0.3pav2008-02-266-61/+8
|
* Umark BROKEN, stale distfile removed from ftp-master.erwin2008-01-271-2/+0
|
* - Update to 2.4.2 (fix fetch problems)miwi2008-01-262-4/+4
| | | | Submitted by: pointyhat via pav
* Mark BROKEN: does not fetcherwin2008-01-261-0/+2
|
* - Update to 2.4.1miwi2008-01-214-15/+46
| | | | | PR: 119719 Submitted by: KATO Tsuguru <tkato432@yahoo.com>
* Fix build on !i386arved2008-01-041-9/+5
| | | | | | PR: 118922 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> Approved by: Fernan Aguero <fernan@iib.unsam.edu.ar>
* - Update to 2.0pav2007-12-1615-406/+60
| | | | | PR: ports/117713 Submitted by: Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
* MrBayes is a program for the Bayesian estimation of phylogeny.miwi2007-12-155-0/+60
| | | | | | | | | | | | | | | Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. WWW: http://mrbayes.csit.fsu.edu/ PR: ports/118542 Submitted by: mzaki at biol.s.u-tokyo.ac.jp
* MUMmer is a modular system for the rapid whole genome alignment of finishedmiwi2007-12-155-0/+79
| | | | | | | | | | | or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. WWW: http://mummer.sourceforge.net/ PR: ports/118142 Submitted by: Tony Maher
* - Mark BROKEN outside i386: does not compilepav2007-12-051-0/+4
| | | | | Reported by: pointyhat Approved by: portmgr (hat)
* - Allow build with AMD64miwi2007-10-292-2/+5
| | | | | | | | - Fix pkg-plist - Bump PORTREVISION PR: 117435 Submitted by: "M. L. Dodson" <mldodson@comcast.net> (maintainer)
* - Update to 1.1.0clsung2007-10-243-74/+86
| | | | | | PR: ports/117369 Submitted by: Motomichi Matsuzaki <mzaki_AT_e-mail dot ne dot jp> Approved by: maintainer (Mauricio Herrera Cuadra)
* - Update to 2.1.2bmiwi2007-10-245-37/+20
| | | | | PR: 117336 Submitted by: KATO Tsuguru <tkato432@yahoo.com>
* Migration from bison 1.x to 2.xade2007-10-171-1/+2
| | | | | PR: 117086 Tested by: -exp runs
* - Update to 2.1miwi2007-10-087-18/+196
| | | | | PR: 116017 Submitted by: KATO Tsuguru <tkato432@yahoo.com>
* - Sort category Makefilessat2007-10-061-2/+2
| | | | | Inspired by: Jason Harris <jharris@widomaker.com> Howto: http://twiki.cenkes.org/Cenkes/SortingCategoryMakefiles
* - Fix typo in WWWpav2007-10-041-1/+1
|
* Remove always-false/true conditions based on OSVERSION 500000edwin2007-10-041-1/+1
|
* Mark as broken on gcc4.2.linimon2007-10-021-1/+7
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* Mark as broken with gcc4.2.linimon2007-10-021-0/+4
|
* biology/linux-foldingathome needs to run as root?edwin2007-09-233-6/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | (also: update to 5.0.4) Upon installing FoldingAtHome I ran the software from a user account only to find that I was stuck in a loop of trying to enter configuration options. Shortly thereafter I realized that it was trying to write to /usr/local/share/foldingathome, and therefore requires being run as root to write there unless one changes permissions there. Seing as this isn't installed with a startup script for daemonization, and running as root seems a little excessive for this application, should this be adapted to run from a user account or set up to be able to start at boot? And from maintainer: This diff updates the port to version 5.04, and adds support to running as normal user using ~/.fah directory. PR: ports/113335 Submitted by: James Snyder <jbsnyder@fanplastic.org> Approved by: maintainer
* Welcome bsd.perl.mk. Add support for constructs such as USE_PERL5=5.8.0+.linimon2007-09-087-39/+5
| | | | | | | | Drop support for antique perl. Work done by: gabor Sponsored by: Google Summer of Code 2007 Hat: portmgr
* - Update to 1.06miwi2007-09-072-12/+5
| | | | - Remove 4.X cruft
* - Update to version 2.3itetcu2007-09-034-46/+57
| | | | | PR: ports/116019 Submitted by: KATO Tsuguru
* - Chase x11-toolkits/pmw renamed to x11-toolkits/py-Pmwrafan2007-09-021-2/+2
| | | | PR: 115302
* Replace IGNORE with ONLY_FOR_ARCHS for this binary port.kris2007-08-091-9/+2
| | | | Submitted by: maintainer
* Fix pkg-plistlme2007-08-031-0/+1
| | | | | Spotted by: pav Approved by: miwi (mentor)
* Update to 2.0.10lme2007-08-014-22/+22
| | | | | | PR: 114738 Submitted by: KATO Tsuguru <tkato432 (AT) yahoo.com> Approved by: miwi (mentor)
* - cleanup after gnustep-make-2.0.1dinoex2007-07-231-1/+0
| | | | Approved by: maintainer (implicit)
* Now we use USE_FORTRAN=yes to use FORTRAN compiler.maho2007-07-141-7/+2
|
* Now we use USE_FORTRAN=yes to use FORTRAN compiler.maho2007-07-121-4/+2
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* Now we use USE_FORTRAN=yes to use FORTRAN compiler.maho2007-07-122-9/+2
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* Now we use USE_FORTRAN=yes to use FORTRAN compiler.maho2007-07-121-5/+1
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* - Runs on 7.0-CURRENT with compat6xpav2007-07-081-0/+4
| | | | Reported by: Rene Ladan <r.c.ladan@gmail.com>
* - Update to version 9rafan2007-07-083-1313/+1505
| | | | | | | | | - Don't install CVS directories which are going to be removed in next release PR: ports/113831 Submitted by: Thomas Abthorpe <thomas at goodking.ca> Approved by: maintainer timeout (20 days)
* dyeske at yahoo dot com -> dyeske at gmail dot comedwin2007-07-064-6/+6
|
* chase math/gsl lib versionijliao2007-06-291-2/+2
|
* Bump to v0.16.aaron2007-06-203-6/+53
| | | | | PR: 111719 Submitted by: araujo@bsdmail.org
* - Fix the build with GCC 4.2danfe2007-06-192-7/+32
| | | | | | - Remove BROKEN tag Reported by: pointyhat (logs)
* - Fix typos.miwi2007-05-311-3/+3
| | | | Reported by: stas@
* - Update to 1.43miwi2007-05-304-92/+167
| | | | | | PR: 111817 Submitted by: "P.BandieraPaiva" <paiva@unifesp.br> Approved by: maintainer
* BROKEN: Unfetchablekris2007-05-271-0/+2
|
* BROKEN with gcc 4.2kris2007-05-271-1/+7
|
* - update for gnustep-make-2.0.0dinoex2007-05-252-71/+79
| | | | Approved by: gurkan (maintainer)
* - update for gnustep-make-2.0.0dinoex2007-05-251-1/+1
|
* swap MASTER_SITES to improve fetchiness on pointyhat which is blocked from ↵edwin2007-05-251-4/+2
| | | | dasher.wustl.edu
* BROKEN: Unfetchablekris2007-05-251-0/+2
|
* - Chase openbabel updatepav2007-05-251-2/+2
|
* - Welcome X.org 7.2 \o/.flz2007-05-2035-20/+40
| | | | | - Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}. - Bump PORTREVISION for ports intalling files in ${X11BASE}.
* [patch] cleanup non-supported FreeBSD versionsedwin2007-05-021-7/+2
| | | | | | PR: ports/111728 Submitted by: Edwin Groothuis <edwin@mavetju.org> Approved by: maintainer timeout
* [patch] cleanup non-supported FreeBSD versionsedwin2007-05-021-7/+1
| | | | | | PR: ports/111726 Submitted by: Edwin Groothuis <edwin@mavetju.org> Approved by: maintainer timeout
* [patch] cleanup non-supported FreeBSD versionsedwin2007-05-021-6/+2
| | | | | | PR: ports/111725 Submitted by: Edwin Groothuis <edwin@mavetju.org> Approved by: maintainer timeout
* [patch] cleanup non-supported FreeBSD versionsedwin2007-05-021-7/+1
| | | | | | PR: ports/111724 Submitted by: Edwin Groothuis <edwin@mavetju.org> Approved by: maintainer timeout
* Use my @FreeBSD.org address.nemoliu2007-04-301-1/+1
| | | | Approved by: delphij (mentor)
* - Update to 4.5clsung2007-04-243-14/+13
|
* - Unbreakmiwi2007-04-211-3/+3
| | | | | | | - Add backup MASTER_SITES PR: 111963 Submitted by: Jason Harris <jharris@widomaker.com>
* BROKEN: Unfetchablekris2007-04-201-0/+2
|
* [patch] cleanup non-supported FreeBSD versionsedwin2007-04-173-41/+1
| | | | | | PR: ports/111727 Submitted by: Edwin Groothuis <edwin@mavetju.org> Approved by: Bob Zimmermann <rpz@cse.wustl.edu>
* Remove always-true condition due to OSVERSIONedwin2007-04-161-1/+1
|
* - Remove unreachable OSVERSION code.edwin2007-04-161-13/+9
| | | | - Make portlint happier
* - Fix after objformat removalpav2007-03-291-0/+3
| | | | Reported by: pointyhat
* - Update to 1.5-beta2miwi2007-03-273-13/+14
| | | | | | | - Pass maintainership to submitter PR: 110621 Submitted by: Nemo Liu<nemoliu@gmail.com>
* - MASTER_SITE is back, remove BROKENgabor2007-03-171-2/+0
| | | | | PR: ports/109954 Submitted by: Tsurutani Naoki <turutani@scphys.kyoto-u.ac.jp>
* Reset razi@genet.sickkids.on.ca due to maintainer-timeouts and no response tolinimon2007-03-141-1/+1
| | | | | | email. Hat: portmgr
* Reset dbader@eece.unm.edu due to maintainer-timeouts.linimon2007-03-111-1/+1
| | | | Hat: portmgr
* Reset dbader@eece.unm.edu due to maintainer-timeout. While here, fix fetch.linimon2007-03-111-2/+2
|
* Reset chuynh@biolateral.com.au: address bounces.linimon2007-03-112-2/+2
| | | | Hat: portmgr
* - Update to 4.96miwi2007-03-093-10/+143
| | | | | PR: 110080 Submitted by: Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
* - Update to 34.26.2miwi2007-03-092-8/+6
| | | | | PR: 110079 Submitted by: Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
* - Release distfile was renamed.miwi2007-03-082-5/+5
| | | | | PR: 110078 Submitted by: Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
* BROKEN: Unfetchablekris2007-02-271-0/+2
|
* - mark ignore on FreeBSD 5.xdinoex2007-02-191-1/+7
| | | | Approved by: maintainer
* Schedule these broken ports for removal on 2007-04-10 if they are stillkris2007-02-111-0/+2
| | | | broken at that time and no fix has been submitted.
* Update to 0.99rc6.maho2007-02-092-5/+5
| | | | | PR: 108940 Submitted by: CHAO Shin
* BROKEN: Does not buildkris2007-02-051-0/+2
|
* Use libtool port instead of included version to avoid objformat a.out botchkris2007-02-011-0/+1
|
* - add category gnustepdinoex2007-02-012-2/+2
| | | | | PR: 103931 Approved by: pav
* Build fix.maho2007-01-291-1/+2
| | | | Submitted by: kris via pointyhat and pav.
* Update to 3.66itetcu2007-01-282-4/+4
| | | | | PR: ports/108434 Submitted by: Marcelo Araujo
* Fix master sites, un-deprecate and update biology/recombine to 1.41.vd2007-01-254-86/+19
|
* Remove expired leaf port:vd2007-01-256-78/+0
| | | | | | | | | 2007-01-07 biology/coalesce: distfile disappeared from homepage Actually the software is still available at: http://evolution.gs.washington.edu/lamarc/coalesce.html, but it is not supported by the authors. Last version is from 1995 and biology/fluctuate can be used instead.
* Get rid of biology/coalesce dependency, it is deprecated and will be removedvd2007-01-251-2/+2
| | | | shortly.
* Fix master site and un-deprecatevd2007-01-251-4/+1
|
* - Fix typomiwi2007-01-231-1/+1
|
* - Project moves to a new home. Change MASTER_SITES and WWWrafan2007-01-232-2/+2
| | | | | | PR: ports/108214 Submitted by: Thomas Abthorpe <thomas at goodking.ca> Approved by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
* Fix build.maho2007-01-191-1/+1
| | | | Submitted by: kris via pointyhat.
* Forgot to commit a patch. Fixes build.maho2007-01-191-0/+20
| | | | Submitted by: kris via pointyhat.
* * Migrate to gfortran.maho2007-01-172-13/+11
| | | | * Bump port revision.
* . change dependencies: shells/bash2 -> shells/bash;bsam2007-01-171-1/+2
| | | | | | | | | | | | | | | . bump PORTREVISION (RUN_DEPENDS changes); . for converters/konwert: - introduce PATCHLEVEL to be used instead of PORTREVISION at filenames; - update to new PATCHLEVEL=11. PR: 107000 [1], 107046 [2], 107106 [3], 107114 [4] Submitted by: bsam (me) Approved by: all maintainers timeout three and a half week: mij at bitchx.it [1] j.koopmann at seceidos.de [2] chuynh at biolateral.com.au [3] alexs at snark.rinet.ru [4]
* * Migrate to gfortran.maho2007-01-161-5/+4
| | | | | | | * Bump port revision. * fix build [1]. Submitted by: kris [1]
* - update to use new bsd.gnustep.mkdinoex2007-01-131-4/+3
| | | | Approved by: gurkan@linuks.mine.nu
* * Migrate to gfortran.maho2007-01-122-2/+7
| | | | * Bump port revision.
* Using gfortran42 only. not using gcc42.maho2007-01-121-3/+5
| | | | Bump portrevision.
* Using only gfortran42. not gcc42.maho2007-01-122-6/+10
| | | | Bump portrevision.
* * Add dummy knob WANT_FORTRAN for future gfortranmaho2007-01-092-127/+147
| | | | | migration. currently it is not buildable with gfrotran42. * Honor FC and FFLAGS.
* migrated to gfortran.maho2007-01-091-0/+3
|
* Migrated to gfortran.maho2007-01-093-6/+13
|
* The BioCocoa framework provides developers with the opportunity to adddinoex2006-12-305-0/+45
| | | | | | | | | 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/
* - Update to 1.0.1miwi2006-12-303-97/+98
| | | | | | | | - Update MASTER_SITES - Pass maintainership to submitter PR: ports/107246 Submitted by: Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
* Update to v0.15aaron2006-12-283-40/+40
|
* Reset tonymaher@optusnet.com.au due to maintainer-timeouts and no responselinimon2006-12-265-5/+5
| | | | | | to email. Hat: portmgr
* - Update to 5.1.2miwi2006-12-2411-236/+308
| | | | | | | - Update maintainer mail adresse PR: ports/107118 Submitted by: M. L. Dodson <bdodson@houston.rr.com> (maintainer)
* - Update to 1.03rafan2006-12-193-105/+42
| | | | | | PR: ports/106300 Submitted by: chinsan Approved by: maintainer timeout (15 days)
* Reset dbader@ece.unm.edu due to timeouts and no response to email.linimon2006-12-132-2/+2
| | | | Hat: portmgr
* Reset whitekid@gmail.com after timeouts and no response to email.linimon2006-12-131-1/+1
| | | | Hat: portmgr
* - Update to 2.1.3gabor2006-12-104-33/+19
| | | | | | | | - Fix fetching - Remove old patch and use MAKE_ARGS instead - portlint(1) and whitespace Approved by: erwin (mentor)
* - Deprecategabor2006-12-103-0/+9
| | | | | | - Set EXPIRATION_DATE Approved by: erwin (mentor)
generated by cgit (git 2.34.1) at 2024-12-02 16:12:31 +0800