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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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* Remove obsolete pointer to online documentation.wjv2001-07-111-4/+2
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* Update package's URL; my email address.wjv2001-07-112-3/+3
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* Update Tony Maher's email address.fenner2001-07-111-1/+1
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* ${PREFIX}/share/${PORTNAME} --> ${DATADIR}sobomax2001-07-101-2/+2
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* Update to version 1.00.a2wjv2001-07-096-8/+46
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* Add NOPORTDOCS support to pkg-plistijliao2001-07-0911-1381/+1380
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* Update to version 1.3.0wjv2001-07-062-3/+3
| | | | | PR: 28761 Submitted by: Patrick Li <pat@databits.net>
* - General clean-up of port.wjv2001-07-055-38/+252
| | | | | | | - Install PDF and HTML documentation. - Take over maintainership. Approved by: Silence from previous maintainer; no objections from -ports
* - Update to version 0.7.1wjv2001-07-044-3/+24
| | | | - Add a build-time message to inform the user of available options.
* - Add %%PORTDOCS%% support to pkg-plist.wjv2001-07-042-3/+3
| | | | | | | - $INSTALL_MAN -> $INSTALL_DATA in Makefile where appropriate. PR: 28668 Submitted by: Patrick Li <pat@databits.net>
* Add grappa 1.0.2, Genome Rearrangements Analysis and Phylogenywjv2001-07-047-0/+64
| | | | | | | Software. PR: 28541 Submitted by: dbader@eece.unm.edu
* Add %%PORTDOCS%% support to pkg-plist, and tweak Makefile slightly to supportwjv2001-07-042-107/+107
| | | | | | | it. PR: 28665 Submitted by: Patrick Li <pat@databits.net>
* Add %%PORTDOCS%% suppor to pkg-plist.wjv2001-07-032-12/+12
| | | | | | | Change $PREFIX to $MAN1PREFIX as appropriate in Makefile. PR: 28664 Submitted by: Patrick Li <pat@databits.net>
* Add support for %%PORTDOCS%%.wjv2001-07-031-42/+42
| | | | | PR: 28670 Submitted by: Patrick Li <pat@databits.net>
* Replace erroneous usage of INSTALL_MAN with INSTALL_DATA.wjv2001-07-032-2/+2
| | | | | PR: 28666 Submitted by: Patrick Li <pat@databits.net>
* Update to version 3.04wjv2001-07-033-5/+5
| | | | | PR: 28614 Submitted by: David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
* Update to version 1.82wjv2001-07-032-3/+2
| | | | | PR: 28609 Submitted by: David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
* Use $FILESDIR rather than hard-coded path.wjv2001-06-291-1/+1
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* Updating my email address in my remaining ports.wjv2001-06-273-3/+3
| | | | Prompted by: vanilla
* Embarrassingly long overdue update to 0.7.0, including optional support forwjv2001-06-263-66/+300
| | | | GUI (Tk) and CORBA extensions.
* Update to version 2001.04.03; add installation of some documentation.wjv2001-06-205-30/+86
| | | | Approved by: MAINTAINER
* Update to 1.00.a1; change MAINTAINER to my new address.wjv2001-06-156-124/+691
| | | | | | | | Many changes to port, including addition of CORBA functionality. PR: 27957 Submitted by: Johann Visagie <johann@egenetics.com> Reviewed by: nbm
* Update to 1.13.3; remove bogus file.wjv2001-06-154-71/+9
| | | | | PR: 28119 Reviewed by: nbm
* - Update to version 1.2.6akevlo2001-06-124-8/+9
| | | | | | | - Fix WWW: line PR: 28038 Submitted by: Ports Fury
* Distfile was moved and renamed.markp2001-06-112-3/+3
| | | | | PR: 28004 Submitted by: Jeff Palmer <scorpio@drkshdw.org>
* Use proper POSIX syntax for `chown'.obrien2001-06-011-1/+1
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* Update to version 1.13.1kevlo2001-05-305-42/+240
| | | | | PR: 27768 Submitted by: MAINTAINER
* math/numpy was renamed to math/py-numeric.sobomax2001-05-291-1/+1
| | | | | PR: 27594 Submitted by: Chang, Hye-Shik <perky@python.or.kr>
* upgrade to 4.3.2ijliao2001-05-2714-458/+389
| | | | | PR: 27273 Submitted by: maintainer
* Update the EMBOSS suite (biology/emboss) to version 1.12.0jeh2001-05-073-138/+25
| | | | | PR: 27179 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
* Updata biology/fasta3 to version 33.t08.d4jeh2001-05-073-8/+8
| | | | | PR: 27176 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
* Update distfile checksum (PORTREVISION bumped)olgeni2001-04-205-37/+14
| | | | | | | | | | also: * Change maintainer's email address. * Remove support for older FreeBSD versions. PR: 26710 Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov>
* activate IGNOREFILES.sf2001-04-141-0/+3
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* Ignore checksum. The distfile changes day by day.sf2001-04-131-1/+1
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* This port require X libraries to build/run.steve2001-04-111-0/+1
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* Overhaul QT/KDE support:will2001-04-031-2/+1
| | | | | | | | | | | | | | | | | | - bsd.port.mk update to use bsd.kde.mk for USE_{QT,KDE}* - Cleanup corresponding ports for bsd.kde.mk update. - Fix bsd.kde.mk: use correct kdelibs dependency, put qt at the bottom, introduce QT_NONSTANDARD variable for nonstandard configure setup. - Update KDE2 to 2.1.1. Two patches included in x11/kdelibs2 to fix the proxy authentication that was broken for 2.1.1. Remove old patches. - Potentially fix kdelibs build for alpha. - Fix qt-designer 2.3.0 build. - Ruby stuff left alone since it looks like black magic to me. Should still work w/ compat shims for older USE_QT[,2] style. Some others were also left alone for the same reason. Reviewed by: portmgr, ports (bsd.kde.mk+bsd.port.mk) Submitted by: David Faure <faure@kde.org> (proxy auth patches) Alex Zepeda <garbanzo@kde.org> (old patches removal)
* update to 3.03mharo2001-04-024-27/+5
| | | | | PR: 26094 Submitted by: maintainer
* updated port biology/phylip from vers 3.5 to 3.6mharo2001-04-025-94/+110
| | | | | PR: 26146 Submitted by: "David A. Bader" <dbader@eece.unm.edu>
* - Update MASTER_SITES and WWW: linekevlo2001-03-314-32/+21
| | | | | | | | | - Support CC/CFLAGS properly - Support install macros - Add PORTDOCS to pkg-plist PR: 26228 Submitted by: Ports Fury
* Update to 33.t08.d3.sobomax2001-03-223-4/+3
| | | | Submitted by: maintainer
* - Upgrade to version 1.70kevlo2001-03-135-18/+41
| | | | | | | - Update WWW PR: 25772 Submitted by: maintainer
* Upgrade to 0.4.kuriyama2001-03-134-12/+12
| | | | | Submitted by: Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp> (maintainer) PR: ports/25741
* o update to 2.7.2.sf2001-03-132-5/+5
| | | | | | | o pass maintainership to ports@. PR: 25685 Submitted by: maintainer
* pass maintainership to ports@.sf2001-03-131-1/+1
| | | | | PR: 25685 Submitted by: maintainer
* Update to lastest versionkevlo2001-03-122-2/+3
| | | | | PR: 25726 Submitted by: maintainer
* Update the EMBOSS suite to v1.11.0nbm2001-03-123-7/+12
| | | | | PR: 25728 Submitted by: johann@egenetics.com
* - A small bugfix lead to a rerelease without a version number change.nbm2001-03-122-1/+2
| | | | | | | - Bumped PORTREVISION. Submitted by: Johann Visagie <johann@egenetics.com> PR: 25725
* Update to 0.85.trevor2001-03-122-2/+2
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* Force -O0 on the Alpha.trevor2001-03-121-1/+7
| | | | Submitted by: steve
* fix WWW:sf2001-03-091-1/+1
| | | | | PR: 25625 Submitted by: maintainer
* update to 33.t08.d2.sf2001-03-082-2/+2
| | | | | PR: 25609 Submitted by: maintainer
* gd.2, not gd.1ijliao2001-03-051-1/+1
| | | | Submitted by: bento
* Change MASTER_SITE and FTP/WWW lines: caos.kun.nl is cmbi.kun.nl now.roam2001-03-052-3/+3
| | | | | PR: 25422 Submitted by: Marc van Woerkom <marc.vanwoerkom@science-factory.com>
* Remove do-configure section, use PERL_CONFIGURE now.vanilla2001-03-011-1/+0
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* Update to version 1.10.1kevlo2001-02-283-8/+7
| | | | | PR: 25449 Submitted by: maintainer
* reimport biology/genpakijliao2001-02-288-0/+164
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* module name conflict with print/gp, so remove it and I'll reimport it againijliao2001-02-288-163/+0
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* add gpijliao2001-02-288-0/+163
| | | | GP is a set of small utilities to manipulate DNA sequences
* Update to version 1.10.0kevlo2001-02-205-24/+51
| | | | | PR: 25228 Submitted by: MAINTAINER
* The author (at my request) has gone back to a more FreeBSD-friendlytrevor2001-02-202-2/+1
| | | | way of naming the distfile. Change the port accordingly.
* Update to 0.84.trevor2001-02-193-15/+14
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* Update to version 2001-02-06jeh2001-02-192-2/+2
| | | | | PR: 25200 Submitted by: Johann Visagie <johann@egenetics.com>
* Chase graphics/gd's shlib version bump.knu2001-02-121-1/+2
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* - New port: biology/fasta3, which comprises the FASTA3 suite of DNA andjeh2001-02-129-0/+204
| | | | | | | | | protein sequence search programs - FASTA3 updates only some of the elements of FASTA2, which is why I have submitted ports of both versions (as biology/fasta and biology/fasta3) PR: 24716 Submitted by: Johann Visagie <johann@egenetics.com>
* New port: biology/fasta, the FASTA2 suite of DNA and protein sequencejeh2001-02-128-0/+151
| | | | | | | search tools PR: 24715 Submitted by: Johann Visagie <johann@egenetics.com>
* add gaussian98, an ab-initio molecular orbital calculation program.sf2001-02-1112-0/+822
| | | | | PR: 23577 Submitted by: NAKATA, Maho <chat95@mbox.kyoto-inet.or.jp>
* Update to 0.84a. Generate the plist.trevor2001-02-093-8/+10
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* - Update EMBOSS (biology/emboss) from 1.9.0 to 1.9.1kevlo2001-01-2910-77/+118
| | | | | | | | - Update the EMBASSY package EMNU from 1.0.2 to 1.0.3 - Merged the four pkg-plist* files into one PR: 24717 Submitted by: MAINTAINER
* update from 3.7 to 3.8ijliao2001-01-2518-167/+706
| | | | | PR: 24371 Submitted by: MAINTAINER
* Upgrade to version 1.9.0kevlo2001-01-246-13/+47
| | | | | PR: 24597 Submitted by: MAINTAINER
* Massive style enforcement - use ^I instead of spaces for variables identation.sobomax2001-01-171-2/+2
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* Clean up inefficient perl invocations; use multiple REs in the same call.will2001-01-081-2/+2
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* Update to 1.2.6kevlo2000-12-234-7/+25
| | | | | PR: 23756 Submitted by: Ports Fury
* Remove trailing period and package name from the pkg-comment.demon2000-12-191-1/+1
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* Update to version 5.79.steve2000-12-113-26/+42
| | | | | PR: 23345 Submitted by: Jeremy Shaffner <jeremy@external.org>
* Update distfiles' checksums after the distfiles have been rerolled yetroam2000-12-042-4/+5
| | | | | | | again without changing names or versions. Also add a new MASTER_SITE. PR: 23262 Submitted by: Johann Visagie <johann@egenetics.com>
* Distfile tarballs were rerolled without notice due to a minor bug.roam2000-12-011-4/+4
| | | | | PR: 23193 Submitted by: Johann Visagie <johann@egenetics.com>
* - Update port biology/emboss from 1.7.0 to 1.8.0jeh2000-11-284-17/+124
| | | | | PR: 23130 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
* Make nolonger support :U. Fix to compensate for that.jeh2000-11-191-3/+6
| | | | | Submitted by: fenner Approved by: MAINTAINER
* They made changes to the "blast" program.jeh2000-11-152-2/+3
| | | | Submitted by: MAINTAINER
* - This is a fairly extensive rework of this port.jeh2000-11-133-0/+56
| | | | | | | | | | | - "EMBASSY" applications are third party tools which have been adapted to function as part of EMBOSS, but which are not included with the base EMBOSS distribution for licensing or other reasons. This new version of the EMBOSS port now contains the three current EMBASSY applications as well, and during installation the user is presented with a dialog(1) menu to PR: 22818 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
* - This is a fairly extensive rework of this port.jeh2000-11-134-5/+150
| | | | | | | | | | | | - "EMBASSY" applications are third party tools which have been adapted to function as part of EMBOSS, but which are not included with the base EMBOSS distribution for licensing or other reasons. This new version of the EMBOSS port now contains the three current EMBASSY applications as well, and during installation the user is presented with a dialog(1) menu to choose which of these should be isntalled. PR: 22818 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
* Change motif to a normal dependency. REQUIRES_MOTIF is now calledasami2000-11-081-1/+1
| | | | | | | | | | | | | | USE_MOTIF and generates a LIB_DEPENDS to x11-toolkits/open-motif. As before, it implies USE_XPM (and therefore USE_XLIB). Motif-dummy is removed from PKG_IGNORE_DEPENDS, whose sole resident is now XFree86-3. Most of the simple ".if defined(HAVE_MOTIF)"s are removed to always have USE_MOTIF. ftp/moxftp will define USE_MOTIF unless WANT_ATHENA_VERSION (new variable) is defined. I merged the X cases in cad/mars, so USE_MOTIF is used iff WITHOUT_X11 is not defined. I will remove x11-toolkits/Motif-dummy (which has been repo copied to open-motif) in a few days.
* Yes. They did re-roll this version, it is legit.jeh2000-11-032-2/+2
| | | | | | | | They donot version the dist, but store them in versioned dir. Update Makefile to handle that. Update CHECKSUM Submitted by: bento
* Updated to new version. That is the pits, the day after it becomesjeh2000-11-024-4/+3
| | | | | | | a port they release a new version. This is a new version, w/o a number. PR: 22522 Submitted by: Tony Maher <tonym@dt.home> MAINTAINER
* Make portlint happy, remove a spacejeh2000-11-011-1/+1
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* Update to version 1.7.0jeh2000-11-013-2/+11
| | | | | PR: 22474 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
* File missing in pkg-plistjeh2000-10-301-0/+1
| | | | Submitted by: bento
* New Port: biology/ncbi-toolkitjeh2000-10-2911-0/+376
| | | | | | | National Center for Biotechnology Information (NCBI) Development Toolkit. PR: 22388 Submitted by: Tony Maher <tony.maher@ebioinformatics.com>
* Update biology/sim4 to 2000.10.19jeh2000-10-263-5/+7
| | | | | | | Maintainership over to FreeBSD bio-porters mailing list PR: 22306 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
* gmake is neededjeh2000-10-241-0/+1
| | | | Submitted by: bento
* Update to version 0.6.2jeh2000-10-133-174/+132
| | | | | PR: 21954 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
* A file was added to distfile and then repackaged with the same name.jeh2000-10-133-2/+5
| | | | | | | No response from MAINTAINER PR: 21345 Submitted by: Johann Visagie <wjv@cityip.co.za> (actual patch)
* Initial import of fastDNAml Version 1.2.2jeh2000-10-126-0/+93
| | | | | | | The faster variant of DNAML, makes phylogenetic trees using maximum likelihood PR: 21931 Submitted by: Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
* Missing " in post-patch targetjeh2000-10-111-1/+1
| | | | Submitted by: bento
* PR 21608 was not processed as intented.jeh2000-10-112-21/+22
| | | | | | | Bumped PORTREVISION and removed duplicate from pkg-plist. PR: 21894 Submitted by: KATO Tsuguru <tkato@prontomail.ne.jp>
* Initial import of biology/biojavajeh2000-10-106-0/+661
| | | | | PR: 21678 Submitted by: Brad Chapman <chapmanb@arches.uga.edu>
* - Update to 1.6.0kevlo2000-10-103-363/+372
| | | | | | | - Reorder packing list PR: 21857 Submitted by: MAINTAINER
* - Update biology/p5-AcePerl from 1.62 to 1.67kevlo2000-10-106-61/+88
| | | | | | | | | | | - Alphabetise ${PLIST} to ease future maintenance - Port now compiles in XS optimisations and RPC server interface - Port now honours ${CC} properly, also for compiled extensions - Port now uses PERL_CONFIGURE - Hand over port MAINTAINERship to FreeBSD bio-porters mailing list PR: 21865 Submitted by: MAINTAINER
* Initiail version of nab (4.2)jeh2000-10-1017-0/+666
| | | | | PR: 21585 Submitted by: M. L. Dodson <bdodson@scms.utmb.EDU>
* This is nab (nucleic acid builder), a language for macromoleculesjeh2000-10-101-0/+1
| | | | | PR: 21585 Submitted by: M. L. Dodson <bdodson@scms.utmb.EDU>
* - Fix MASTER_SITES/DISTNAMEjeh2000-10-103-20/+19
| | | | | | | | | | | | - USEPGPLOT -> WITH_PGPLOT - Support FFLAGS/X11BASE properly Remove file: files/patch-ab PR: 21608 Submitted by: KATO Tsuguru <tkato@prontomail.ne.jp> Approved by: rmiya@cc.hirosaki-u.ac.jp (Ryo MIYAMOTO) MAINTAINER
* The last commit changes the ports and therefore need a PORTREVISION bumpjeh2000-10-102-0/+2
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* Support PREFIX properlyjeh2000-10-102-1/+5
| | | | | | PR: 21607 Submitted by: KATO Tsuguru <tkato@prontomail.ne.jp> Approved by: rmiya@cc.hirosaki-u.ac.jp (Ryo MIYAMOTO) MAINTAINER
* - Fix MASTER_SITESjeh2000-10-104-18/+36
| | | | | | | | | | | | | - Support CC/LOCALBASE/X11BASE/PREFIX properly Remove file: patches/patch-aa Approval from MAINTAINER after sending EMail PR: 21609 Submitted by: KATO Tsuguru <tkato@prontomail.ne.jp> Approved by: Chen Hsiung Chan <frankch@waru.life.nthu.edu.tw> MAINTAINER
* Add do-install target to port's Makefile. Remove patch sectiontrevor2000-10-092-10/+5
| | | | | | | adding install target to ${WRKSRC}/Makefile. PR: 21792 Submitted by: Kato Tsuguru <tkato@prontomail.ne.jp>
* Change PKGDIR from pkg/ to . Also fix places where ${PKGDIR} isasami2000-10-081-1/+1
| | | | | | spelled out (many of which are ${PKGDIR}/MESSAGE -> ${PKGMESSAGE} type fixes that shouldn't have been necessary) and the string "/pkg/" appear.
* Rename ${FILESDIR}/patch-* to ${PATCHDIR}/extra-patch-*.asami2000-10-081-2/+2
| | | | | (This should probably be rewritten to use EXTRA_PATCHES but I don't have time to test it now.)
* Implement USE_GTK, part 1.reg2000-10-053-38/+26
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* - Support CC/CFLAGS/PREFIX properlyjeh2000-10-036-8/+127
| | | | | | | | | | | | - gets() -> fgets() - Add WWW: line into pkg/DESCR Also bumped PORTREVISION to 1 PR: 21572 Submitted by: tkato@prontomail.ne.jp <KATO@FreeBSD.ORG, Tsuguru@FreeBSD.ORG> Reviewed by: will Approved by: MAINTAINER (dbader@eece.unm.edu)
* Correct and sort PLISTs.reg2000-10-032-6/+6
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* Change MAINTAINER for my ports.trevor2000-10-021-1/+1
| | | | Approved by: will
* Add USE_XLIBkris2000-09-221-0/+1
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* respect CXX and CXXFLAGS (Kato Tsuguru)ade2000-09-194-20/+39
| | | | | | | | | | install data files (Kato Tsuguru) bump version (myself) use USE_NEWGCC (Will Andrews) make whitespace changes to Makefile PR: 21359 Submitted by: maintainer
* Update to 0.90.d03nbm2000-09-113-132/+152
| | | | | PR: 21202 Submitted by: Johann Visagie <johann@egenetics.com>
* Fix checksumkevlo2000-09-091-18/+1
| | | | | PR: 21115 Submitted by: Andreas Schulz <ats@first.gmd.de>
* Don't break package building on Satoshi's cluster. Explicitly dependtg2000-09-081-1/+1
| | | | on python1.5:lang/python15.
* Upgrade to 1.5.0nbm2000-09-084-66/+113
| | | | | PR: 21108 Submitted by: Johann Visagie <johann@egenetics.com>
* Update to emboss 1.4.0.nbm2000-09-074-52/+83
| | | | | PR: ports/20898 Submitted by: Johann Visagie <johann@egenetics.com>
* Update to version 2000.08.24kevlo2000-09-044-7/+23
| | | | | PR: 20897 Submitted by: MAINTAINER
* USE_LIBTOOL implies GNU_CONFIGURE, so remove redundant GNU_CONFIGURE lines.sobomax2000-08-211-1/+0
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* Update to emboss 1.1.0, fixing some style bugs too.nbm2000-08-135-6/+321
| | | | | PR: ports/20519 Submitted by: Johann Visagie <johann@egenetics.com> (maintainer)
* Upgrade to 0.90.d02.will2000-08-062-3/+3
| | | | | PR: 20383 Submitted by: maintainer
* Fix MASTER_SITESjedgar2000-08-021-1/+1
| | | | | PR: 20120 Submitted by: Maintainer
* Add emboss, the European Molecular Biology Open Software Suitenbm2000-08-016-0/+700
| | | | | PR: ports/20317 Submitted by: Johann Visagie <johann@egenetics.com>
* Add py-biopython, is a collection of Python packages and modules creatednbm2000-07-316-0/+166
| | | | | | | | by the Biopython Project, intended to provide the basis for building bioinformatics applications in the Python language. PR: ports/20260 Submitted by: Johann Visagie <johann@egenetics.com>
* Add BioPerl, a collection of Perl5 mods for bioinformatics/genomicsnbm2000-07-287-0/+259
| | | | | PR: ports/20252 Submitted by: Johann Visagie <johann@egenetics.com>
* Add p5-AcePerl, a perl interface to the ACEDB genome database systemnbm2000-07-289-0/+177
| | | | | PR: ports/20223 Submitted by: Johann Visagie <johann@egenetics.com>
* Add sim4, an implementation of the sim4 algorithm for aligning expressednbm2000-07-277-0/+48
| | | | | | | DNA with genomic sequences PR: ports/20219 Submitted by: Johann Visagie <johann@egenetics.com>
* Add xdrawchem 0.82 - a program for drawing moleculesalex2000-07-197-0/+65
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* Activating the chemeq, clustalw, paml, and phylip ports.steve2000-07-101-0/+4
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* Adding phylip version 3.5.steve2000-07-105-0/+161
| | | | | | | | | This is a FREE package of programs for inferring phylogenies and carrying out certain related tasks. At present it contains 30 programs, which carry out different algorithms on different kinds of data. PR: 19705 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu>
* Add paml version 3.01.steve2000-07-107-0/+89
| | | | | | | | A set of utilities for performing Phylogenetic Analysis by Maximum Likelihood (PAML). PR: 19753 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu>
* Adding clustalw version 1.81.steve2000-07-106-0/+66
| | | | | | | A CLUSTAL W Multiple Sequence Alignment Program. PR: 19746 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu>
* Adding chemeq version 1.10.steve2000-07-105-0/+62
| | | | | | | Outputs LaTeX code for chemical reactions. PR: 19374 Submitted by: Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
* - Use GTK_CONFIG/GLIB_CONFIG instead of hardcoded gtk12-config/glib12-configsteve2000-07-082-19/+27
| | | | | | | - Support CC/CFLAGS/PREIFX/LOCALBASE/X11BASE/MAKE/etc. properly PR: 19623 Submitted by: KATO Tsuguru <tkato@prontomail.ne.jp>
* Unbreak by extracting the correct distfilekris2000-07-031-8/+2
| | | | Noticed by: bento
* ...local-distfiles... -> MASTER_SITE_LOCALalex2000-06-201-1/+2
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* fc is ftn77 now, adjust accordingly.alex2000-06-123-5/+6
| | | | | | PR: 19160, 19161 Submitted by: Glenn Johnson <gjohnson@nola.srrc.usda.gov> Reviewed by: will
* Update to version 1.0.3alex2000-06-114-24/+23
| | | | | | | | | | | | PR: 19094 Submitted by: maintainer While I'm hear, clean up the port, e.g.: * Don't create/delete PATCHDIR while building this port * put the distfile, which is unversioned, to my local-distfiles space. * remove/reorder some actions, such as stripping twice. Reviewed by: will
* Clean up this port so that it installs stuff in a more proper locationwill2000-06-093-138/+138
| | | | | | | as per hier(7) and Porter's Handbook. PR: 18929 Submitted by: MAINTAINER
* Update to the latest version as of 5 June.knu2000-06-084-15/+26
| | | | | PR: ports/19113, ports/19115 Submitted by: Maintainer
* Fix build for 4.0 and later. Make DESCR shorter.will2000-06-085-165/+181
| | | | | PR: 19092 Submitted by: MAINTAINER
* Update to 3.6.will2000-06-086-114/+145
| | | | | PR: 19091 Submitted by: MAINTAINER
* Convert to usable F77 binary, especially on 4.0 and newer.will2000-06-084-82/+73
| | | | | PR: 19090 Submitted by: MAINTAINER
* Fix MD5 checksum. Since I was unable to find an older version of thewill2000-06-051-1/+1
| | | | | | | distfile, I can't say what changes were made. PR: 18986 Submitted by: Andreas Schulz <ats@first.gmd.de>
* Fix this port after the recent PORT{NAME,VERSION} changes. portlint(1)steve2000-05-281-2/+4
| | | | while I'm here.
* Update to version 2000.04.26.steve2000-05-283-5/+3
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* Chase the checksum (lots of code changes)kris2000-04-241-1/+1
| | | | Noticed by: bento
* WRKSRC-related fixes.asami2000-04-161-0/+1
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* update with the new PORTNAME/PORTVERSION variablesmharo2000-04-0915-53/+51
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* Remove andy@icc.surw.chel.su as maintainer from his ports..he doesn'tkris2000-03-291-1/+1
| | | | | | have time to maintain them. Approved by: andy
* Add virtual category "linux" to Linux apps and support libs/utils.asami2000-02-281-1/+1
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* Chase the checksum (minor source changes)kris2000-02-271-1/+1
| | | | Noticed by: bento
* update URLsmharo2000-02-241-2/+2
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* update WWWmharo2000-02-241-1/+1
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* Forgot to remove this linecpiazza2000-02-071-1/+0
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* Don't strip things we don't know how to stripcpiazza2000-01-311-1/+1
| | | | | PR: 16445 Submitted by: Alexander Langer <alex@cichlids.com>
* fix some pkg/MESSAGE stuffmharo2000-01-302-2/+2
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* Update to ver 1.2.2cpiazza2000-01-152-3/+3
| | | | | PR: 15955 Submitted by: Alexander Langer <alex@cichlids.com>
* Bump glib12 's share library version to 3,vanilla1999-10-102-10/+2
| | | | and portlint.
* f77(1) on the Alpha doesn't grok '-malign-double' so only use it on thesteve1999-09-271-0/+4
| | | | i386 port.
* Enforce random pkg/COMMENT rules, including the one that states Emacshoek1999-09-182-2/+2
| | | | should be spelled corrcetly, although I rather liked "Emasc".
* Grammar and WWW: fix.hoek1999-09-181-7/+6
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* Update to new version.steve1999-09-183-8/+5
| | | | | PR: 13459 Submitted by: maintainer
* Compile-errortaoka1999-09-102-3/+9
| | | | | PR: 13513 Submitted by: Glenn Johnson <gljohns@bellsouth.net>
* Compile errortaoka1999-09-091-1/+1
| | | | | PR: 13613 Submitted by: maintainer
* Added gperiodic and xmolwttaoka1999-09-071-0/+2
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* Displays a periodic table of the elements.taoka1999-09-075-0/+58
| | | | | | PR: 12690 Submmitted by: Andrey Zakhvatov <andy@icc.surw.chel.su> Reviewed by: Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
* This program calculate formula weight and percent of each elements.taoka1999-09-076-0/+82
| | | | | PR: ports/13467 Submitted by: Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
* Distfile changed on the MASTER_SITE. I have no idea if thiscpiazza1999-08-312-6/+6
| | | | | was functional or not, as there isn't a version number anywhere. Support CC in patch-aa, too...
* Remove preceeding pkgname from some of the comments having one.hoek1999-08-301-1/+1
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* grammar gnithoek1999-08-301-1/+1
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* ln -> ${LN}mharo1999-08-282-2/+2
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* echo -> ${ECHO} or ${ECHO_MSG} and in some cases, move echo stuffmharo1999-08-281-8/+8
| | | | to pkg/MESSAGE and use ${CAT} ${PKGMESSAGE}
* Updated to 2.7.1taoka1999-08-253-11/+24
| | | | | PR: 13327 Submitted by: maintainer
* Change Id->FreeBSD.obrien1999-08-2514-14/+14
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* Make port depend on linux_base instead of linux_lib.marcel1999-07-211-3/+3
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* Fix typos and/or cleanup WWW:.hoek1999-07-174-18/+13
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* BROKEN='MD5 checksum error'obrien1999-07-151-1/+3
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* Fix port after distfile change.cpiazza1999-07-112-3/+2
| | | | | PR: 12585 Submitted by: maintainer
* Remove trailing spaces, and any periods that were hidden by them.hoek1999-06-282-2/+2
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* As threatened, enforce the "Capital, no period" rule. Ellipses arehoek1999-06-279-9/+9
| | | | | permitted. Note that, given current numeric motif of PW, this is done in four equally-sized commits of 393 files each.
* Install into ${PREFIX}, not /usr/local.cpiazza1999-06-263-7/+7
| | | | | PR: 12214 Submitted by: n_hibma
* Clean up warnings for -current (g77)cpiazza1999-06-251-7/+9
| | | | Submitted by: maintainer
* Change ${INSTALL} to use -s and -c.cpiazza1999-06-241-45/+45
| | | | Requested by: maintainer
* Update tinker from version 3.6 to version 3.7cpiazza1999-06-237-310/+289
| | | | | PR: 12301 Submitted by: maintainer
* Make the psi88 port install into PREFIX instead of a hardcodedcpiazza1999-06-191-4/+14
| | | | | | | /usr/local. PR: 12215 Submitted by: Nick Hibma <nick.hibma@jrc.it>
* The xforms ports is no longer an i386-only port.steve1999-06-091-4/+1
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* Fill in a couple of missing WWW references...scrappy1999-06-052-0/+4
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* Fix build for -current boxes with egcs' f77 compiler.steve1999-05-242-11/+29
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* Allow this port to be built on -current i386 boxes that have egcs' f77steve1999-05-241-2/+11
| | | | compiler. Mark it broken for -current Alpha boxes.
* This port doesn't build with egcs' f77 compiler.steve1999-05-241-2/+7
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* Build this port on an Alpha box instead of trying to use i386 binaries.steve1999-05-241-1/+5
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* Fix build for Alpha.steve1999-05-241-1/+1
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* Fix build on -current (Alpha) machines.steve1999-05-242-18/+29
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* Added WWW: for www-site target in DESCRtaoka1999-05-192-2/+2
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* Added deft and ortep3taoka1999-05-191-1/+3
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* The Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structuretaoka1999-05-197-0/+594
| | | | | PR: 11649 Submitted by: Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
* Density functional molecular orbital calculation.taoka1999-05-197-0/+226
| | | | | PR: 11647 Submitted by: Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
* Fix checksumflathill1999-05-091-1/+1
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* Changed MASTER_SITEStaoka1999-05-081-2/+2
| | | | | PR: 11572 Submitted by: maintainer
* Changed MASTER_SITEStaoka1999-05-081-3/+3
| | | | | PR: 11571 Submitted by: maintainer
* Add platon and moldentaoka1999-05-071-1/+3
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* display molecular orbitals and electron densities in 2D and 3Dtaoka1999-05-077-0/+201
| | | | Submitted by: rmiya@cc.hirosaki-u.ac.jp (Ryo MIYAMOTO)
* the one of crystallographic toolstaoka1999-05-076-0/+175
| | | | Submitted by: rmiya@cc.hirosaki-u.ac.jp (Ryo MIYAMOTO)
* Be able to use ${PREFIX}taoka1999-05-075-13/+67
| | | | Submitted by: maintainer
* Fixed ${CATEGORIES} (removed misc from it)taoka1999-05-061-2/+2
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* Semi-empirical (MNDO, etc.) molecular orbital calculationtaoka1999-05-0611-0/+213
| | | | | PR: ports/8863 Submitted by: Ryo MIYAMOTO rmiya@cc.hirosaki-u.ac.jp
* Plotting wavefunctions (molecular orbitals) in 3Dtaoka1999-05-069-0/+365
| | | | | PR: ports/8696 Submitted by: Ryo MIYAMOTO rmiya@cc.hirosaki-u.ac.jp
* Add mopac and psi88 (Move mopac and psi88 from misc to biology)taoka1999-05-061-1/+3
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* Weasal and Wabbits and BIG FOOT.hoek1999-05-036-17/+12
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* Upgrade to 2.1.1fenner1999-03-093-8/+16
| | | | | PR: ports/10228 Submitted by: Michael Haro mharo@area51.fremont.ca.us
* Adjust port Makefiles to new EXTRACT_* variable defaults. See log ofasami1999-02-031-1/+3
| | | | | | | | | | | | | | | | | | | bsd.port.mk rev. 1.304 for details on the change. The fix here is one of the following. (1) Define USE_BZIP2 instead of BUILD_DEPENDS on bzip2 and redefining EXTRACT_* commands. (2) Change ${EXTRACT_CMD} to ${TAR} when the command is obviously calling the "tar" command (i.e., arguments like "-xzf" are spelled out). (3) If ${EXTRACT_CMD} is called directly with ${EXTRACT_BEFORE_ARGS}, add ${EXTRACT_AFTER_ARGS} to the command line as well. (4) If any of EXTRACT_CMD, EXTRACT_BEFORE_ARGS or EXTRACT_AFTER_ARGS is set, define the other two too.
* Correct the MD5 checksum.vanilla1999-01-311-1/+1
| | | | Submitted by: maintainer
* Added 'ONLY_FOR_ARCHS=i386' to XForms dependent ports.simokawa1999-01-071-1/+4
| | | | XForms has not been available for FreeBSD/alpha yet.
* Add 'ONLY_FOR_ARCHS=i386' to linux_lib dependent ports.simokawa1999-01-071-1/+3
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* Change *_DEPENDS on lang/perl5 to USE_PERL5 so we won't have anyasami1999-01-021-3/+2
| | | | | | | dependencies to perl5 in -current. This might cause some unwanted perl5 installations on -stable (if it was originally RUN_DEPENDS, perl5 will now be installed during build too, etc.), but its lifetime is limited anyway.
* Update MASTER_SITES.billf1998-12-102-4/+6
| | | | Thanks To: Fenner's portsurvey and ftpsearch.lycos.com
* Add a comment about setting env var 'FC' to 'g77' if EGCS is to bejkoshy1998-11-181-3/+4
| | | | used for building.
* Activate tinker.jkoshy1998-11-171-1/+2
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* New port of the Tinker Molecular modelling program.jkoshy1998-11-1711-0/+725
| | | | | | PR: 8690 Reviewed by: jkoshy Submitted by: Glenn Johnson <gljohns@bellsouth.net>
* Use bsd.port.{pre,post}.mk to move PORTOBJFORMAT to front, or changeasami1998-11-141-6/+8
| | | | | shell loops to make loops. Use EXTRA_PKG_FLAGS to add install scripts instead of adding it to PKG_FLAGS after bsd.port.mk.
* Update of MASTER_SITES.billf1998-11-131-2/+2
| | | | | PR: ports/8600 Submitted by: frankch@waru.life.nthu.edu.tw
* Unbreak for ELFjseger1998-11-031-3/+1
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* Master site changed, update MD5.jkoshy1998-10-082-3/+3
| | | | | PR: 8200 Submitted by: frankch@waru.life.nthu.edu.tw (maintainer)
* Checksum changed again....asami1998-09-281-1/+1
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* Remove empty doc dir on deinstall.steve1998-09-271-0/+1
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* Don't strip the binary when building ELF.steve1998-09-271-1/+5
|
* Checksum of seaview.tar changed.steve1998-09-271-1/+1
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* Mark broken for ELF because of xforms port.steve1998-09-271-2/+4
|
* Take the manpages out of pkg/PLIST and put them in MAN1.steve1998-09-162-2/+3
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* Unbreak by making a new checksum and fixing the makefile to find a new sourcejseger1998-08-213-6/+4
| | | | file.
* BROKEN:jseger1998-08-211-1/+3
| | | | | # make checksum >> Checksum mismatch for seaview.tar.
* Remove manpages from pkg/PLISTobrien1998-08-141-8/+0
|
* Fix up dependencies for ports that moved into the x11-toolkits category.asami1998-08-081-2/+2
|
* Rename all USE_X11 to USE_X_PREFIX. Requires 1.279 (3.0-current) orasami1998-08-051-2/+2
| | | | | 1.227.2.41 (2.2-stable) of bsd.port.mk for this to be interpreted correctly.
* Making x11 category more useful project part 1: take out "x11" ofasami1998-07-282-4/+4
| | | | | | ports that are mere users of X. Partial list submitted by: Josh Gilliam <josh@quick.net>
generated by cgit (git 2.34.1) at 2024-12-29 18:09:33 +0800