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* silent updates of archives:maho2003-12-283-4/+8
| | | | | | | | | a) program: Draw the hydrophobicity function F5 b) documentation: add very minor description not related FreeBSD. 1) bump portrevision 2) several clean ups for Makefile
* - Fix MASTER_SITESkrion2003-12-201-1/+1
| | | | | PR: 60417 Submitted by: maintainer
* Mark as broken on 5.x due to the usual gcc terminating-character hassles.linimon2003-12-191-1/+7
| | | | Notified mainatainer.
* - Update to last snapshotpav2003-12-072-9/+6
| | | | | PR: ports/58511 (based on) Submitted by: Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp> (maintainer)
* - Update checksum again, seems author removes .ps version of documentationpav2003-11-224-467/+31
| | | | | | | from tarball - Unmark broken, it builds for me just fine Approved by: adamw (mentor)
* Define USE_PERL5_BUILD, not erroneous USE_PERL.trevor2003-11-202-2/+2
| | | | Submitted by: Oliver Eikemeier
* Define USE_PERL to make Perl available for (mostly deprecated)trevor2003-11-202-0/+2
| | | | "perl -pi -e" construction.
* - Unbreak on 5.xpav2003-11-203-7/+54
| | | | Approved by: adamw (mentor)
* - Update to new version 2003.11.17krion2003-11-176-66/+17
| | | | - Unbreak this port
* unPERLify by using REINPLACE_CMD and SED where appropriate.marcus2003-11-162-3/+1
| | | | | PR: 47654 Submitted by: Simon 'portlint' Schubert <corecode@corecode.ath.cx>
* Switch to wxgtk2.fjoe2003-11-141-1/+2
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* Use the FIND and XARGS macros introduced in bsd.port.mk 1.391.trevor2003-11-133-3/+3
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* Remove my e-mail address from comment blocks of portstrevor2003-11-131-1/+1
| | | | I have contributed, in hopes of attracting less spam.
* wxgtk-devel -> wxgtkfjoe2003-11-101-1/+2
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* - Switch to wxgtk2fjoe2003-11-101-7/+9
| | | | - USE_MESA -> USE_GL
* LIB_DEPENDS on libglut for libglut rather than soon-to-disappear Mesa3.anholt2003-11-081-1/+1
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* Update to 2.0.7.adamw2003-11-083-4/+7
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* Mark BROKEN: distfile has changed.anholt2003-11-071-0/+2
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* ${MASTER_SITES} are slow. This patch adds a mirror site to helpjeh2003-11-061-1/+2
| | | | | | | | fetch work more frequently. This patch patches the Makefile from PORTSDIR}/biology PR: 58130 Submitted by: MAINTAINER
* Make this port use wxgtk 2.4.2.fjoe2003-11-053-7/+19
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* Chase wxgtk library name (and version) change.fjoe2003-11-051-1/+1
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* Pet portlint.linimon2003-11-041-1/+1
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* Date: Tue, 04 Nov 2003 00:42:55 +0900edwin2003-11-041-1/+1
| | | | | | | | | | | | | | | | From: Motomichi Matsuzaki <mzaki@e-mail.ne.jp> Subject: Re: question about FreeBSD ports you maintain Briefly, I have no time for maintaining ports. So I wish to leave the maintainer position of these ports: biology/fastdnaml textproc/wv Thanks you for maintaining the FreeBSD system. Best regards, Motomichi Matsuzaki
* Mark BROKEN (see bento logs). These ports are scheduled for removalkris2003-11-031-1/+1
| | | | | after Feb 2 2004 if they are still broken at that time and no fixes have been submitted by PR.
* ports with possibly unreachable MAINTAINERsedwin2003-11-022-2/+2
| | | | | | | *** addresses that seem to be dead: PR: ports/58694 Submitted by: Oliver Eikemeier <eikemeier@fillmore-labs.com>
* Chased new mastersite per distfile survey. Notified maintainer.linimon2003-10-261-1/+1
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* utilize SITE_PERLijliao2003-10-244-387/+385
| | | | | PR: 58166 Submitted by: Cheng-Lung Sung <clsung@dragon2.net>
* Respect CC and CFLAGSkris2003-10-231-5/+11
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* Cosmetic fix: use %%DOCSDIR%% macro.osa2003-10-2231-1259/+1259
| | | | | | | No functionally changes. Submitted by: Oleg Karachevtsev <ok@etrust.ru> A part of PR: 57992
* - Update to 0.5.2krion2003-10-213-297/+298
| | | | | PR: 58304 Submitted by: Clement Laforet <sheepkiller@cultdeadsheep.org>
* Don't remove share/java/classes system directory.kris2003-10-191-1/+0
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* Fixes the checksum problem, but doesn't fix the port; adds a BROKENlinimon2003-10-162-2/+3
| | | | | | | line about how it fails. Some other interested person will have to take it from here. PR: 56882
* Update to 0.5.3.knu2003-10-153-2/+4
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* update biology/nab: 4.5.1 -> 4.5.2daichi2003-10-145-20/+38
| | | | | PR: 57970 Submitted by: M. L. Dodson <bdodson@scms.utmb.edu> (maintainer)
* BROKEN: Broken pkg-plistkris2003-10-131-0/+2
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* BROKEN: Does not fetchkris2003-10-131-0/+2
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* Port update (maintainer): biology/wiseedwin2003-09-242-2/+2
| | | | | | | | | Fenner's porsurvey show wise no longer available at original site. Original site readme shows it has moved so update the MASTER_SITES accordingly. PR: ports/57154 Submmited by: Tony Maher <tonymaher@optushome.com.au>
* Make portlint(1) happy by changing strip to ${STRIP_CMD}osa2003-09-242-2/+2
| | | | | Submitted by: Oleg Karachevtsev <ok@etrust.ru> PR: 56998
* Update port: biology/gperiodic to 2.0.6edwin2003-09-083-4/+5
| | | | | | | - Update to version 2.0.6 PR: ports/56522 Submitted by: KATO Tsuguru <tkato@prontomail.com>
* new port:biology/lsysexpedwin2003-09-035-0/+71
| | | | | | | | | | | | | | | | | | L-system Explorer is a program used for viewing and creating L-system fractals. The following features are supported: - Over 500 builtin L-systems, arranged into about 20 groups. - Ability to create and save custom L-systems and L-system groups. - Abilty to save images of L-systems (in PNG or JPEG format). - Multiple L-systems can be viewed at the same time. - Able to use custom colors and gradients. - Can also generate random gradients, or completely random colors. - Able to draw using lines, points, or a random combination of both. PR: iports/51400 Submitted by: David Yeske <dyeske@yahoo.com>
* Silent changes to the port distfile which *not* have significantmaho2003-09-021-2/+2
| | | | | | | | functional differences. just changing very minor change of documatation, adding very minor functionality and some cleanup for coding Submitted by: bento's log
* - Add an end-of-string to each line of the inputkrion2003-08-281-7/+7
| | | | | | | when parsing the input files PR: 56043 Submitted by: maintainer
* Update to 0.5.2.knu2003-08-233-2/+13
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* Fix build on python2.3perky2003-08-201-1/+6
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* o Main modificationnork2003-08-192-9/+7
| | | | | | | | | | | | | | | | | | graphics/gd(based on 1.8.4) -> graphics/gd1 graphics/gd2(based on 2.0.15) -> graphics/gd graphics/p5-GD(based on 1.41) -> graphics/p5-GD1 graphics/p5-GD2(based on 2.07) -> graphics/p5-GD japanese/gd -> japanese/gd1 japanese/gd2 -> japanese/gd o Include some feature WITH_XPM(w/, w/o WITHOUT_X11) o Chase this modification o Fix build error [1] PR: ports/54540 Submitted by: Ports Fury Approved by: maintainer (blanket) Reported by: bento via kris [1]
* As announced on May 6, remove the broken p5-bioperl-devel port.kris2003-08-088-686/+0
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* BROKEN: Checksum mismatchkris2003-08-071-0/+2
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* Fix python version detection routines to cope with python 2.3'sperky2003-08-021-1/+1
| | | | boolean representation.
* Somehow pkg-plist is removed...maho2003-08-011-0/+128
| | | | Pointy hat to: myself
* a) Update to 1.7.3maho2003-08-013-84/+18
| | | | | | | | | b) Maintainer timeout: This PR is submitted by Thu May 08 07:30:18 PDT 2003 but no reply from the maintainer. PR: 51971 Submitted by: KATO Tsuguru <tkato@prontomail.com> aka Ports Fury
* Add USE_XLIB=yes to compilemaho2003-07-311-0/+1
| | | | Submitted by: kris via bento
* Update to 0.5.1.knu2003-07-292-2/+2
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* A new port garlic, free molecular viewer and editor, free molecularmaho2003-07-286-0/+399
| | | | | visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule.
* - Update to version 2.0.5krion2003-07-285-41/+25
| | | | | | PR: 54899 Submitted by: KATO Tsuguru <tkato@prontomail.com> Approved by: fjoe (mentor) (implicit)
* Some clean-up.maho2003-07-261-17/+14
| | | | | | a) ECHO-> ECHO_CMD b) place of WITH_OPTIMIZED_FLAGS seems to be wrong. c) fix errors reported from freshports.org
* Duplicated the `pre-extract:' and `post-build:'maho2003-07-261-9/+0
| | | | | Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov> Pointy hat to: myself
* a) Some corrupts with Makefile and pkg-plist.maho2003-07-252-12/+26
| | | | | | | b) forgot to notice that drop maintainership to ports@ Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov> Pointy hat to: myself
* a) Forgot to update distinfo 52498maho2003-07-255-33/+69
| | | | | | | | | b) added LEGAL. author requests no distribution except from his FTP site c) clean-ups for compiler optimization Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov> Pointy hat to: maho; partially :)
* Update to 0.90maho2003-07-244-309/+328
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* enhancement, build and install the opengl viewer, moldenogl.maho2003-07-194-74/+64
| | | | | | | | | | update to 3.9, not 3.8, which is newer :) Committed by maintainer timeout: > Sat Apr 5 17:46:57 EST 2003 - edwin - informed maintainer PR: 47177 Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov>
* honor CFLAGS and FFLAGSmaho2003-07-192-3/+4
| | | | | PR: 54396 Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov>
* Maintainer update of biology/tinker port to version 4.0.maho2003-07-195-20/+42
| | | | | PR: 52498 Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov>
* Add semi-colons(;) after declare statements that go in the povray scene fileleeym2003-07-143-7/+168
| | | | | | | | | | | | | so that povchem works with povray-3.5. Maintainer prefer not to depend on ImageMagick since users can use their favorite picture viewer. display isn't the only one choice. Drop maintainership. PR: 54397 Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov> Reviewed by: Chen-hsiung Chan <frankch@waru.life.nthu.edu.tw>
* o Change library name from libgd to libgd1.nork2003-07-122-3/+4
| | | | | | | | | o Do not install everything except headers and libraries (to avoid conflicting with graphics/gd2) o Fix dependency on new libgd1(for many ports). PR: ports/54100 Submitted by: Ports Fury
* s/NOPORTSDOCS/NOPORTDOCS/ [1]osa2003-07-112-6/+6
| | | | | | | Use %%PORTDOCS%%%%DOCSDIR%% in pkg-plist. PR: 53911 [1] Approved by: maintainer
* update biology/nab: 4.4 -> 4.5.1daichi2003-07-0812-403/+393
| | | | | PR: 52786 Submitted by: M. L. Dodson <bdodson@scms.utmb.EDU> (maintainer)
* Update to 0.5.0.knu2003-06-263-5/+25
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* update ports/biology/act to latest release (v2)daichi2003-06-233-988/+1603
| | | | | PR: 49093 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
* - update to 1.83erwin2003-06-183-3/+4
| | | | | | | | | - give maintainership to submitter as the old maintainer's address bounces PR: 52054 Submitted by: Philip M. Gollucci <philip@p6m7g8.com> Approved by: maintainer bounces
* Move inclusion of bsd.port.pre.mk later in the file for conditional BROKENkris2003-06-051-5/+5
| | | | | | | tag. Early inclusion caused problems for some ports, so to be safe I'm updating all of them. Pointy hat to: kris
* Assign MAINTAINER to ports@FreeBSD.org.adamw2003-06-051-1/+1
| | | | | PR: ports/52534 Submitted by: Christian Brueffer <chris@unixpages.org>
* Upgrade to 2003.01.21. Appears to only add some more file export/printhoek2003-05-227-40/+49
| | | | | | options. Additional patches were necessary since the fltk port seems to have been upgraded and thus also broken this port (which would been already broken due to the checksum failure).
* Add back the WWW which was inexplicably deleted in a previoushoek2003-05-221-6/+11
| | | | | | revision. Make a few organisational improvements. However, be too lazy to move to pkg-message a note that really shouldn't be necessary for the end user at all.
* - fix build under gcc 3.3petef2003-05-191-1/+8
| | | | | | | - respect CC/CFLAGS PR: 52013 Submitted by: maintainer
* Back out previous commit, the port was fixed a few days ago.kris2003-05-191-7/+1
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* BROKEN on 5.1: bad C++kris2003-05-182-2/+14
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* - Update to latest release.mich2003-05-145-62/+3
| | | | | | | | | - Better autoconf/automake so patches no longer needed - Changed dependency. (now wxgtk-devel) PR: 51741 Submitted by: maintainer Approved by: roberto(mentor)
* BROKEN: Broken pkg-plistkris2003-05-071-0/+2
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* Update to 2003.04.21arved2003-05-058-79/+59
| | | | | PR: 51709 Submitted by: Tony Maher <tonymaher@optushome.com.au>
* - unbreak on 4.x: add dependency on gdkpixbuf, fix Makefiles to compile withpetef2003-05-043-44/+30
| | | | | | | | the correct libraries - add a WITH_OPTIMIZED_CFLAGS knob PR: 51614 Submitted by: maintainer
* Updated to 0.8.6.maho2003-05-035-362/+283
| | | | | Submitted by: M. L. Dodson <bdodson@scms.utmb.EDU> Pkg-plist by: maho
* Update to 20030425 snapshotlioux2003-04-263-6/+6
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* Remove USE_GNOMENG.marcus2003-04-183-3/+0
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* Update the biology/tinker Makefile so it builds on -currentedwin2003-03-301-1/+6
| | | | | PR: ports/50371 Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov>
* * Fix build with GCC3 (-CURRENT).naddy2003-03-255-24/+89
| | | | | | | * Honor CXX/CXXFLAGS. * Use predefined DOCSDIR and EXAMPLESDIR variables. Approved by: maintainer timeout
* Clear moonlight beckons.ade2003-03-0728-14/+14
| | | | | | | Requiem mors pacem pkg-comment, And be calm ports tree. E Nomini Patri, E Fili, E Spiritu Sancti.
* Retire comment file.trevor2003-03-012-1/+1
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* Update to 20030227 snapshotlioux2003-02-282-2/+2
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* De-pkg-commentlioux2003-02-242-1/+1
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* De-pkg-comment.knu2003-02-2172-36/+36
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* De-pkg-comment.knu2003-02-218-4/+4
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* Fix install and packaging list.naddy2003-02-183-59/+67
| | | | Reported by: kris
* De-pkg-comment.knu2003-02-182-1/+1
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* Update to 1.83.naddy2003-02-1613-182/+179
| | | | | PR: 48264 Submitted by: David A. Bader <dbader@eece.unm.edu>
* * Update to 3.13.naddy2003-02-155-20/+7
| | | | | | | PR: 48255 Submitted by: David A. Bader <dbader@eece.unm.edu> * Also honor CC/CFLAGS.
* Add dependency on security/p5-Digest-MD5edwin2003-02-131-0/+3
| | | | Noticed on: bento
* Update to version 0.5.1.naddy2003-02-128-68/+4
| | | | | PR: 48047 Submitted by: Ports Fury
* Remove gaussian98kris2003-02-051-1/+0
| | | | Pointy hat to: maho
* Delete biology/gaussian98. Maintain is too hard andmaho2003-02-0111-820/+0
| | | | gray in license
* Update to 0.4.0.knu2003-01-293-14/+26
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* add '-f' argument to rm so that the script always work even if alioux2003-01-241-1/+1
| | | | | | file is not there Submitted by: Frerich Raabe <frerich.raabe@gmx.de>
* New Port: biology/actedwin2003-01-166-0/+1031
| | | | | PR: ports/35753 Submitted by: Camson Huynh <chuynh@biolateral.com.au>
* Add missing filekris2003-01-141-0/+1
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* Add some missing fileskris2003-01-141-0/+4
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* Update to 3.8arved2003-01-083-22/+6
| | | | Approved by: rmiya@cc.hirosaki-u.ac.jp (maintainer)
* update biology/babel to properly output mm3 files.edwin2003-01-032-1/+93
| | | | | PR: ports/42425 Submitted by: Glenn Johnson <glennpj@charter.net>
* upgrade to 3.7ijliao2003-01-025-193/+255
| | | | | PR: 44957 Submitted by: maintainer
* add missing includeijliao2002-12-291-0/+10
| | | | | PR: 46584 Submitted by: Ports Fury
* fix build on -currentijliao2002-12-225-0/+53
| | | | | PR: 46459 Submitted by: Ports Fury
* Fix typo: distribfold.org -> distributedfolding.orglioux2002-12-202-2/+2
| | | | Submitted by: Matt Mills <alpha@vanity.com>
* o Update to 20021105 snapshotlioux2002-12-192-4/+9
| | | | | | | | | | o Depend on compat4x on OSVERSION >= 500000 since these are 4.5-RELEASE binaries o House a copy under MASTER_SITE_LOCAL: the local copy will be versioned, developer has yet to be convinced of the advantages of distributing versioned files Approved by: portmgr (knu)
* Mark BROKEN due to "Unknown problem"lioux2002-11-251-0/+2
| | | | Submitted by: maintainer
* unbroke by upgrade to 20021018ijliao2002-11-208-30/+72
| | | | | | | drop maintainership PR: 45466 Submitted by: old maintainer
* add treepuzzle 5.1ijliao2002-11-206-0/+41
| | | | | | | Maximum likelihood phylogeny reconstruction using quartets PR: 45241 Submitted by: Jan Lentfer <lentferj@neslonek.bio.tu-darmstadt.de>
* 1. add a missing dependency on png and unbreak.maho2002-11-201-2/+3
| | | | 2. change e-mail address of maho.
* o Rollback PORTCOMMENT modifications while this feature's implementationlioux2002-11-116-6/+3
| | | | | | | | is better studied o Turn PORTCOMMENT variable in Makefile back into pkg-comment files Approved by: kris (portmgr hat), portmgr, re (silence)
* Update WWWarved2002-11-081-1/+1
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* Updated to fix problems as stated in PR ports/42915edwin2002-11-073-2/+42
| | | | | PR: ports/42915 Submitted by: Tony Maher <tonym@biolateral.com.au>
* Fix PORTCOMMENTs that were killing INDEX builds.adamw2002-11-072-2/+1
| | | | | 105 pointy hats to: me Approved by: pat
* Use PORTCOMMENT in the Makefile, and whack the pkg-comment.adamw2002-11-078-4/+8
| | | | Approved by: pat
* Modify replace RE to match syntax of sed now ("\)" -> ")"edwin2002-11-051-8/+8
| | | | Noticed by: bento
* PERL -> REINPLACEedwin2002-11-044-10/+15
| | | | And some ports have USE_PERL5=yes now.
* PERL -> REINPLACEedwin2002-11-041-1/+2
| | | | Noticed on: bento
* PERL -> REINPLACEedwin2002-11-042-2/+4
| | | | Noticed on: bento
* Port needs perl to build.edwin2002-11-041-0/+2
| | | | Seen on: bento
* Make biology/avida building on -current againedwin2002-11-042-3/+2
| | | | | | PR: ports/44819 Submitted by: Oliver Lehmann <lehmann@ans-netz.de> Approved by: Jeremy Karlson <karlj000@unbc.ca>
* Add another entry for MASTER_SITES and unbreak with latest version of bisonpat2002-10-303-1/+25
| | | | | PR: ports/44711 Submitted by: maintainer
* Update CATEGORIES as per ports/44331.tom2002-10-211-2/+2
| | | | | | | While I'm here, remove unnecessary whitespace spotted by portlint. PR: ports/44331 Submitted by: Martin Klaffenboeck <martin.klaffenboeck@gmx.at>
* o Update to snapshot 20021015lioux2002-10-202-4/+17
| | | | o Fix an issue with the startup scripts
* Fix dependency on wxgtkkris2002-10-191-1/+1
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* CC, CXX, CFLAGS, PTHREAD_CFLAGS and PTHREAD_LIBS may contain `/' inknu2002-10-101-1/+1
| | | | | them when using a non-default compiler/linker, so do not use `/' as delimiter for s///. (I picked `|' instead)
* Connect distribfold to build after moving it from misc categorylioux2002-10-071-0/+1
| | | | | | | Prompted by: kris, Adam Weinberger <adam@vectors.cx>, Fernan Aguero <fernan@iib.unsam.edu.ar>, others
* o New port distribfold version 0.1: distribfold.org distributed proteinlioux2002-10-0711-0/+374
| | | | | | folding project o One can start multiple instances of this port. Just install it using WITH_NCPU
* Use RUBY_MOD*.knu2002-10-072-31/+31
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* - Unbreak fetching of distfiles. (Needs update as soon as freeze is over.)wjv2002-09-272-9/+7
| | | | | Submitted by: kris, bento Approved by: Implicitly by first rule of ports freeze, I hope!
* add forgotten "USE_REINPLACE=yes"ijliao2002-09-211-0/+1
| | | | Submitted by: maintainer
* upgrade to 20020426ijliao2002-09-216-22/+16
| | | | | PR: 39357 Submitted by: maintainer
* BROKEN: Does not fetchkris2002-09-211-0/+2
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* BROKEN: Does not buildkris2002-09-191-0/+2
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* add primer3 0.9ijliao2002-09-176-0/+437
| | | | | | | Primer3 helps to choose primers for PCR reactions PR: 35298 Submitted by: Tony Maher <tonym@biolateral.com.au>
* Flip is used to find/translate orfs.dinoex2002-09-106-0/+33
| | | | | | WWW: ftp://megasun.bch.umontreal.ca/pub/flip/ PR: 35332 Submitted by: tonym@biolateral.com.au
* "Wise2 is package that is focused on comparing DNA sequences atdinoex2002-09-107-0/+185
| | | | | the level of its conceptual translation, regardless of sequencing error and introns."
* Chase new name of wxgtk shared library.sobomax2002-09-091-1/+1
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* Remove USE_NEWGCC, which is no longer supported or required.kris2002-08-311-1/+0
| | | | | Submitted by: Tilman Linneweh <tilman@arved.de> PR: ports/40571
* Deploy USE_GNOMENG infrastructurelioux2002-08-302-2/+4
| | | | | PR: 42187 Submitted by: Edwin Groothuis <edwin@mavetju.org>
* o Fix examples directory path which is changed in last revision.perky2002-08-261-1/+5
| | | | Submitted by: Glenn Johnson <glennpj@charter.net>
* o Fix RUN_DEPENDS path (PMW -> Pmw)perky2002-08-252-4/+33
| | | | | | | | | o Fix DISTNAME which was broken by previous commit. o Install example files PR: 41977 Submitted by: Glenn Johnson <glennpj@charter.net> Approved by: maintainer
* Prefer <limits.h> over <values.h> as the latter has been removed fromkris2002-08-234-0/+44
| | | | | | -current. Noticed by: bento
* o Remove redundant dependency on py-tkinter.perky2002-08-221-1/+1
| | | | | | o Bump PORTREVISION that I've missed on last commit. Submitted by: Glenn Johnson <glennpj@charter.net>
* Add a dependecy to x11-toolkits/pmwperky2002-08-221-1/+2
| | | | | | PR: 41857 Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov> Approved by: maintainer
* New port L-Breeder version 1.0: Allows you to display and breedlioux2002-08-219-0/+96
| | | | | | | L-system forms PR: 38725 Submitted by: David Yeske <dyeske@yahoo.com>
* - Support CXXFLAGS properly.naddy2002-08-183-7/+22
| | | | | | | - Do not install .la file. PR: 41732 Submitted by: Ports Fury
* Update to version 3.6.a3.naddy2002-08-143-22/+7
| | | | | | | | | | | PR: 41412 Submitted by: David A. Bader <dbader@eece.unm.edu> Additional clean-up: * Respect CC, CFLAGS, X11BASE. * Use versioned DIST_SUBDIR. Approved by: maintainer
* Add pymol 0.82, Free and Open-Source molecular modeling system.perky2002-08-138-0/+715
| | | | | PR: 40694 Submitted by: Nakata Maho <chat95@mbox.kyoto-inet.or.jp>
* Update to 0.3.9.knu2002-08-033-2/+3
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* add libgenome 0.5.0ijliao2002-07-306-0/+381
| | | | Toolkit for developing bioinformatic related software in C++
* upgrade to 4.4ijliao2002-07-168-16/+97
| | | | | PR: 40612 Submitted by: maintainer
* Use $PYNUMERIC in the dependencies.tg2002-07-151-2/+2
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* - Add patch that will, for -CURRENT only, change: -pthread -> -lc_rwjv2002-07-112-0/+23
| | | | | | - Bump $PORTREVISION Prompted by: Various questions from Rune Linding <linding@EMBL-Heidelberg.DE>
* Update to 0.3.8.knu2002-07-083-6/+29
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* - Update to version 2.4.1wjv2002-07-054-111/+183
| | | | | | | | - Unmark BROKEN - Start adding support for Jemboss Java-based GUI (not active yet) PR: 40198 ; many private requests Submitted by: Tilman Linneweh <tilman@arved.de> (2.4.1 update)
* Bump XForms lib. version.mikeh2002-07-041-1/+1
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* Unbreak this port:glewis2002-06-162-586/+585
| | | | | | | | | | | . Fix dependencies to be in sync with the recent JDK ports renaming. . Replace MASTER_SITES with a location that actually contains the source. . Fix the packing list. Note that there is a much newer version of this application available, but that is beyond the scope of what I was trying to do (just fix the JDK dependency), as is the last two items.
* Correct MASTER_SITES.petef2002-06-081-1/+1
| | | | | PR: 39016 Submitted by: maintainer
* Note distribution term.sada2002-05-271-8/+6
| | | | Requested by: maintainer
* Back my last commit out.sada2002-05-232-2/+2
| | | | | | We couldn't update distinfo without inspecting distfile's changes. PR: ports/37476 Suggested by: kris
* distfile has silently changed,sada2002-05-182-1/+2
| | | | | | so md5 has to be rewritten. PR: ports/37476 Submitted by: maintainer
* BROKEN: Checksum is incorrectkris2002-05-181-0/+2
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* BROKEN: incorrect checksumskris2002-05-171-0/+2
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* Update to sim4-2002.03.03 to unbreak build.kris2002-05-052-3/+3
| | | | Noticed by: bento
* upgrade to V110-1ijliao2002-04-212-4/+3
| | | | | | | | build with newer bison remove BROKEN PR: 37313 Submitted by: maintainer
* add avida 1.6.0ijliao2002-04-2011-0/+146
| | | | | | | Avida is an auto-adaptive genetic system designed for ALife research PR: 37268 Submitted by: Jeremy Karlson <karlj000@unbc.ca>
* Update to 0.3.6.knu2002-04-112-4/+3
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* Swiss-PdbViewer is an application that provides a user friendly interfacedinoex2002-04-038-0/+388
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. Moreover, Swiss-PdbViewer is tightly linked to Swiss-Model, an automated homology modelling server developped at Glaxo Welcome Experimental Research in Geneva. Working with these two programs greatly reduces the amount of work necessary to generate models, as it is possible to thread a protein primary sequence onto a 3D template and get an immediate feedback of how well the threaded protein will be accepted by the reference structure before submitting a request to build missing loops and refine sidechain packing. Swiss-PdbViewer can also read electron density maps, and provides various tools to build into the density. In addition, various modelling tools are integrated and command files for popular energy minimisation packages can be generated. Finally, as a special bonus, POV-Ray scenes can be generated from the current view in order to make stunning ray-traced quality images. WWW: http://www.expasy.ch/spdbv/ PR: 33902 Submitted by: chuynh@biolateral.com.au
* Remove #include <malloc.h>kris2002-03-311-0/+4
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* change master siteijliao2002-03-293-10/+32
| | | | | | | add mpich support PR: 36468 Submitted by: maintainer
* Respect CFLAGS/CC.petef2002-03-291-0/+21
| | | | | | PR: 36395 Submitted by: maintainer Reported by: bento
* Add crimap 2.4, a tool for the creation of multilocus linkage maps.wjv2002-03-276-0/+59
| | | | | PR: 35198 Submitted by: Tony Maher <tonym@biolateral.com.au>
* Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection.wjv2002-03-277-0/+102
| | | | | PR: 33853 Submitted by: chuynh@biolateral.com.au
* - Add a new patchwjv2002-03-272-1/+11
| | | | | | | - Bump $PORTREVISION PR: 36206 Submitted by: David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
* Add USE_SUBMAKE, where it might be necessary.sobomax2002-03-251-0/+1
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* BROKEN: Does not buildkris2002-03-251-0/+2
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* - Fix certain mistakes in FreeBSD patcheswjv2002-03-228-70/+320
| | | | | | | | | - Bump PORTREVISION - Poroblem originally reported by Fernan Aguero <fernan@iib.unsam.edu.ar> on FreeBSD-bio list PR: 36169 Submitted by: David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
* Update to 0.3.5.knu2002-03-133-3/+13
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* Fix WWW.dannyboy2002-03-091-1/+1
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* Update to 2001.12.20pat2002-02-226-18/+88
| | | | | PR: 35203 Submitted by: maintainer
* Pass maintainership to submitter and add a backup master site.petef2002-02-201-2/+3
| | | | | PR: 35043 Submitted by: Christian Brueffer <chris@unixpages.org>
* - Install documentationpat2002-02-134-6/+19
| | | | | | | - Update WWW: PR: 34889 Submitted by: maintainer
* Use ${ECHO_CMD} instead of ${ECHO} where you mean the echo command;knu2002-01-291-4/+4
| | | | | | | | the ECHO macro is set to "echo" by default, but it is set to "true" if make(1) is invoked with the -s option while ECHO_CMD is always set to the echo command. Use command macros where appropriate.
* Add t_coffee 1.37, a multiple DNA or protein sequence alignment package.wjv2002-01-259-0/+438
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* - Update to version of 2001-12-30wjv2002-01-252-2/+2
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* - Update to version 1.82wjv2002-01-254-13/+28
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* - Update to version 0.7.2, somewhat overdue. :-)wjv2002-01-252-27/+53
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* o update to 3.7.sf2002-01-242-34/+7
| | | | | | | | | differences from the PR: - this port requires Xlib so add USE_XLIB. - remove unnecessary PORTREVISION. PR: 34196 Submitted by: maintainer
* o update to 0.7.sf2002-01-242-2/+2
| | | | | PR: 34197 Submitted by: maintainer
* update to 1.3.3.sf2002-01-232-2/+2
| | | | | PR: 34180 Submitted by: KATO Tsuguru <tkato@prontomail.com>
* - Update to version 1.00a4wjv2002-01-223-10/+261
| | | | | PR: 33719 Submitted by: Hye-Shik Chang <perky@fallin.lv>
* Update to 0.99.7. Use new DATADIR macro. Install documentation,trevor2002-01-204-24/+55
| | | | including examples. Add warning.
* Upgrade tinker to the latest revisionijliao2002-01-195-64/+101
| | | | | PR: 33425 Submitted by: maintainer
* - Update to version 2.2.0wjv2002-01-183-15/+335
| | | | | | | | | - Update included EMBASSY package EMNU - Fix a long-standing bug in Makefile that would preclude PKGMESSAGE from being generated properly - Consider this an interim update merely to track the latest version - more work is required to activate the newly included "Jemboss" Java GUI interface
* Update to 0.2.petef2001-12-294-19/+8
| | | | | PR: 33218 Submitted by: maintainer
* Initial import of artemis 4.0kevlo2001-12-226-0/+1529
| | | | | | | Artemis is a DNA sequence viewer and annotation tool. PR: 32914 Submitted by: Camson <chuynh@biolateral.com.au>
* Update to 0.3.3.knu2001-12-223-2/+3
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* Add gff2ps 0.97b, converts gff-formated genomic data-sets topetef2001-12-196-0/+42
| | | | | | | PostScript. PR: 32920 Submitted by: Camson Huynh <chuynh@biolateral.com.au>
* Add dna-qc 1993.07.26, a quality control algorithm for DNApetef2001-12-197-0/+94
| | | | | | | sequencing projects. PR: 32998 Submitted by: Tony Maher <tonym@biolateral.com.au>
* Update to version 2001.10.12.steve2001-12-172-2/+2
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* fix pkg-plistijliao2001-12-091-0/+1
| | | | | PR: 32609 Submitted by: Ports Fury
* * Replace pkg-message about setting BABEL_DIR with a wrapper scriptnaddy2001-12-028-26/+55
| | | | | | | | that does. * Remove misleading full path name from usage message. * Improve fgets() usage. * Add converters category. * Improve pkg-comment and pkg-descr.
* - update to 1.3.2petef2001-11-292-7/+4
| | | | | | | - use DOCSDIR PR: 32305 Submitted by: KATO Tsuguru <tkato@prontomail.com>
* Update to 0.3.2.knu2001-11-283-4/+21
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* Style police: WWW tags should either end in a file/script or TRAILING /; Fix ↵lioux2001-11-211-1/+1
| | | | the later case
* Style police: WWW tags should either end in a file/script or TRAILING /; Fix ↵lioux2001-11-212-2/+2
| | | | the later case
* chase checksum for repacked distfile almost an year ago.sf2001-11-063-2/+3
| | | | | | | | | Maintainer does not have previous distfile. As the distfile for this port is not distributable, it is OK to me to change distinfo now. PR: 31010 Submitted by: maintainer
* Add ruby-bio (BioRuby), an integrated environment for Bioinformaticsknu2001-10-246-0/+91
| | | | written in Ruby.
* update WWW and master siteijliao2001-10-222-2/+10
| | | | | PR: 31011 Submitted by: maintainer
* Remove a redundant trailing space.knu2001-10-211-1/+1
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* - Update the included (optional) Biopython-CORBA pacakge to version 0.3.0wjv2001-10-025-263/+210
| | | | | | - If CORBA support is included, the default ORB has changed from omniORB to ORBit - PORTREVISION bump
* Add nclever 4.0, a character-based version of NCBI's Entrez program.wjv2001-09-268-0/+105
| | | | | PR: 30783 Submitted by: Tony Maher <tonym@biolateral.com.au>
* - Add NO_LATEST_LINK, which should've been there in the first place. :-(wjv2001-09-201-0/+1
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* - Add installation of include fileswjv2001-09-194-134/+445
| | | | | | | - Bump PORTREVISION PR: 30660 Submitted by: Tony Maher <tonym@biolateral.com.au> (MAINTAINER)
* style fix: un"echo" commandslioux2001-09-131-40/+40
| | | | Approved by: MAINTAINER
* Update to 3.9lioux2001-09-1312-116/+161
| | | | | PR: 30398 Submitted by: MAINTAINER
* Bump png majorache2001-09-111-1/+1
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* Fix a buglet with the use of XFREE86_VERSION without includingtobez2001-09-071-1/+3
| | | | | | bsd.port.pre.mk first. Spotted by: Dan Langille <dan@langille.org>
* Make biology/rasmol work at all color depths.tobez2001-09-074-8/+91
| | | | | PR: 30406 Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov>
* - Update to version 1.00.a3wjv2001-09-064-105/+167
| | | | - Use pkg-req to check the installed version of Python
* - Update to version 3.1wjv2001-08-294-6/+18
| | | | | PR: 30176 Submitted by: David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
* - Update to version 1.0.3wjv2001-08-292-3/+3
| | | | | PR: 30175 Submitted by: David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
* - Update to version 1.2.4wjv2001-08-222-2/+2
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* - Update port to version 2.2gwjv2001-08-224-223/+34
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* Add seqio 1.2.2, a set of C functions which can read/writewjv2001-08-2210-0/+400
| | | | | | | biological sequence files. PR: 29922 Submitted by: Tony Maher <tonym@biolateral.com.au>
* - Update to version 3.6.a2.1 - since the distribution tarball hadn't beenwjv2001-08-225-43/+30
| | | | | | | | | renamed between versions, this port failed checksum. - Apply some whitespace edits and cut pkg-descr down to size to placate portlint. Reported by: Jason Stajich <jason@chg.mc.duke.edu> Approved by: No response from MAINTAINER
* - Move the (very) long list of manpages from the port Makefile to a separatewjv2001-08-202-123/+240
| | | | | | file. Inspired by: nectar's treatment of security/heimdal
* Update to 0.95.trevor2001-08-204-27/+30
| | | | | | | Compile molecule_tools.cpp with -O0 on all architectures, not just the Alpha, to avoid g++ pessimization. Submitted by: Matthew Emmerton <matt@gsicomp.on.ca>
* Remove a patch turd from the pkg-plistkris2001-08-201-1/+0
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* Add treeviewx 0.1.1, a phylogenetic tree viewer.wjv2001-08-179-0/+82
| | | | | PR: 29770 Submitted by: Tony Maher <tonym@biolateral.com.au>
* Add p5-bioperl-devel 0.9.0,wjv2001-08-148-0/+566
| | | | | a collection of Perl modules for bioinformatics (developer's release).
* Update to version 1.75wjv2001-08-134-14/+27
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* - Properly list run-time dependencies in RUN_DEPENDS in Makefile.wjv2001-08-133-40/+46
| | | | | | | - Deploy %%PERL_VER%% and %%PERL_ARCH%% pragmas consistently throughout pkg-plist. (Ouch, that was embarrassing.) - Bump PORTREVISION due to the above. - Update my email address and the project's URL in pkg-descr.
* upgrade to 0.26ijliao2001-08-105-32/+30
| | | | drop maintainership
* Add lamarc 2001.08.06,wjv2001-08-075-0/+42
| | | | | a package of programs for computing population parameters.
* Add recombine 1.40, a program to fit population models across sites.wjv2001-08-067-0/+166
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* Add fluctuate 1.30, a program to fit population models.wjv2001-08-067-0/+89
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* Add coalesce 1.50, a program to fit population models.wjv2001-08-067-0/+73
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* Correct my email address.wjv2001-08-061-1/+1
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* Add migrate 1.2,wjv2001-08-066-0/+63
| | | | | a program to estimate population sizes and migration rates.
* Update maintainer's email address.wjv2001-08-061-1/+1
| | | | Approved by: MAINTAINER
* - Update port to version 2.0.1wjv2001-08-035-24/+110
| | | | - Add two new EMBASSY applications, MEME and HMMER.
* add USE_XLIBlioux2001-07-311-0/+2
| | | | | PR: 29330 Submitted by: bento, Patrick Li <pat@databits.net>
* This port require bison to build so add USE_BISON.steve2001-07-261-0/+1
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