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296 Commits

Author SHA1 Message Date
Tim Vanderhoek
9dbc794cb4 Enforce random pkg/COMMENT rules, including the one that states Emacs 
should be spelled corrcetly, although I rather liked "Emasc".
 1999-09-18 04:56:11 +00:00
Tim Vanderhoek
a17666dc26 Grammar and WWW: fix. 1999-09-18 04:42:33 +00:00
Steve Price
ad9b8e4f9f Update to new version. 
PR:		13459
Submitted by:	maintainer
 1999-09-18 03:26:35 +00:00
Satoshi Taoka
73ec58caa5 Compile-error 
PR:		13513
Submitted by:	Glenn Johnson <gljohns@bellsouth.net>
 1999-09-10 07:39:26 +00:00
Satoshi Taoka
a1f39d4413 Compile error 
PR:		13613
Submitted by:	maintainer
 1999-09-08 16:32:18 +00:00
Satoshi Taoka
a6ade68cd4 Added gperiodic and xmolwt 1999-09-06 20:09:12 +00:00
Satoshi Taoka
e134a23a22 Displays a periodic table of the elements. 
PR:		12690
Submmitted by:	Andrey Zakhvatov <andy@icc.surw.chel.su>
Reviewed by:	Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
 1999-09-06 20:08:26 +00:00
Satoshi Taoka
2a1c4bb993 This program calculate formula weight and percent of each elements. 
PR:		ports/13467
Submitted by:	Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
 1999-09-06 20:04:15 +00:00
Chris Piazza
2174e47129 Distfile changed on the MASTER_SITE. I have no idea if this 
was functional or not, as there isn't a version number anywhere.
Support CC in patch-aa, too...
 1999-08-31 03:57:56 +00:00
Tim Vanderhoek
847ae8f2b6 Remove preceeding pkgname from some of the comments having one. 1999-08-29 19:19:43 +00:00
Tim Vanderhoek
325d03d1f8 grammar gnit 1999-08-29 18:13:56 +00:00
Michael Haro
af5f314286 ln -> ${LN} 1999-08-28 01:58:05 +00:00
Michael Haro
58942bab6d echo -> ${ECHO} or ${ECHO_MSG} and in some cases, move echo stuff 
to pkg/MESSAGE and use ${CAT} ${PKGMESSAGE}
 1999-08-27 21:14:04 +00:00
Satoshi Taoka
1300477e40 Updated to 2.7.1 
PR:		13327
Submitted by:	maintainer
 1999-08-25 05:17:58 +00:00
David E. O'Brien
fe1e09a6cc Change Id->FreeBSD. 1999-08-25 04:58:03 +00:00
Marcel Moolenaar
d7d791cfa6 Make port depend on linux_base instead of linux_lib. 1999-07-21 14:55:43 +00:00
Tim Vanderhoek
c51f88903c Fix typos and/or cleanup WWW:. 1999-07-17 14:50:53 +00:00
David E. O'Brien
4c3279b6a1 BROKEN='MD5 checksum error' 1999-07-14 18:43:06 +00:00
Chris Piazza
3ffd4caad5 Fix port after distfile change. 
PR:		12585
Submitted by:	maintainer
 1999-07-11 02:14:41 +00:00
Tim Vanderhoek
e32f86f31b Remove trailing spaces, and any periods that were hidden by them. 1999-06-28 00:45:20 +00:00
Tim Vanderhoek
748713c3f6 As threatened, enforce the "Capital, no period" rule. Ellipses are 
permitted.  Note that, given current numeric motif of PW, this is done
in four equally-sized commits of 393 files each.
 1999-06-26 17:19:19 +00:00
Chris Piazza
da58517f0a Install into ${PREFIX}, not /usr/local. 
PR:	12214
Submitted by:	n_hibma
 1999-06-25 19:23:45 +00:00
Chris Piazza
ea98b02b5a Clean up warnings for -current (g77) 
Submitted by:	maintainer
 1999-06-25 04:35:31 +00:00
Chris Piazza
365b79e792 Change ${INSTALL} to use -s and -c. 
Requested by:	maintainer
 1999-06-24 13:58:22 +00:00
Chris Piazza
d782b1db2a Update tinker from version 3.6 to version 3.7 
PR:	12301
Submitted by:	maintainer
 1999-06-23 00:26:02 +00:00
Chris Piazza
bea1cffae3 Make the psi88 port install into PREFIX instead of a hardcoded 
/usr/local.

PR:	12215
Submitted by:	Nick Hibma <nick.hibma@jrc.it>
 1999-06-19 10:23:07 +00:00
Steve Price
593990a1e7 The xforms ports is no longer an i386-only port. 1999-06-08 22:15:15 +00:00
Marc G. Fournier
be1c40c148 Fill in a couple of missing WWW references... 1999-06-05 05:47:43 +00:00
Steve Price
b285b7b5d8 Fix build for -current boxes with egcs' f77 compiler. 1999-05-24 02:20:21 +00:00
Steve Price
2a4ca60b6e Allow this port to be built on -current i386 boxes that have egcs' f77 
compiler.  Mark it broken for -current Alpha boxes.
 1999-05-24 02:12:36 +00:00
Steve Price
8229278306 This port doesn't build with egcs' f77 compiler. 1999-05-24 02:08:22 +00:00
Steve Price
0398acd76c Build this port on an Alpha box instead of trying to use i386 binaries. 1999-05-24 02:06:46 +00:00
Steve Price
e932801d57 Fix build for Alpha. 1999-05-24 02:04:22 +00:00
Steve Price
e13591e2ec Fix build on -current (Alpha) machines. 1999-05-24 02:01:41 +00:00
Satoshi Taoka
c8897de12f Added WWW: for www-site target in DESCR 1999-05-19 14:20:07 +00:00
Satoshi Taoka
a7634e3e23 Added deft and ortep3 1999-05-19 13:38:46 +00:00
Satoshi Taoka
7c4ecfacd5 The Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure 
PR:		11649
Submitted by:	Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
 1999-05-19 13:37:59 +00:00
Satoshi Taoka
e8bdb86580 Density functional molecular orbital calculation. 
PR:		11647
Submitted by:	Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
 1999-05-19 13:37:08 +00:00
Seiichirou Hiraoka
d460029ab2 Fix checksum 1999-05-08 18:16:57 +00:00
Satoshi Taoka
5edd697aeb Changed MASTER_SITES 
PR:		11572
Submitted by:	maintainer
 1999-05-08 08:09:55 +00:00
Satoshi Taoka
6c62e99d9b Changed MASTER_SITES 
PR:		11571
Submitted by:	maintainer
 1999-05-08 08:06:43 +00:00
Satoshi Taoka
7e4a643ed1 Add platon and molden 1999-05-07 06:59:25 +00:00
Satoshi Taoka
eb0c4e1552 display molecular orbitals and electron densities in 2D and 3D 
Submitted by:	rmiya@cc.hirosaki-u.ac.jp (Ryo MIYAMOTO)
 1999-05-07 06:57:52 +00:00
Satoshi Taoka
5a653f9998 the one of crystallographic tools 
Submitted by:		rmiya@cc.hirosaki-u.ac.jp (Ryo MIYAMOTO)
 1999-05-07 06:56:52 +00:00
Satoshi Taoka
54c21509a1 Be able to use ${PREFIX} 
Submitted by:	maintainer
 1999-05-07 05:12:20 +00:00
Satoshi Taoka
70f1f62811 Fixed ${CATEGORIES} (removed misc from it) 1999-05-06 08:27:29 +00:00
Satoshi Taoka
f9974dbc46 Semi-empirical (MNDO, etc.) molecular orbital calculation 
PR:             ports/8863
Submitted by:   Ryo MIYAMOTO rmiya@cc.hirosaki-u.ac.jp
 1999-05-06 08:23:21 +00:00
Satoshi Taoka
d05574972e Plotting wavefunctions (molecular orbitals) in 3D 
PR:             ports/8696
Submitted by:   Ryo MIYAMOTO rmiya@cc.hirosaki-u.ac.jp
 1999-05-06 08:22:15 +00:00
Satoshi Taoka
9674eb1cb0 Add mopac and psi88 (Move mopac and psi88 from misc to biology) 1999-05-06 08:18:35 +00:00
Tim Vanderhoek
c8bd4fdcd3 Weasal and Wabbits and BIG FOOT. 1999-05-02 21:38:01 +00:00
Bill Fenner
b0f9653aea Upgrade to 2.1.1 
PR:		ports/10228
Submitted by:	Michael Haro mharo@area51.fremont.ca.us
 1999-03-08 20:23:47 +00:00
Satoshi Asami
5114e2637e Adjust port Makefiles to new EXTRACT_* variable defaults. See log of 
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.
 1999-02-03 11:12:01 +00:00
Vanilla I. Shu
95789c639b Correct the MD5 checksum. 
Submitted by:	maintainer
 1999-01-30 17:14:25 +00:00
Hidetoshi Shimokawa
ec8a4e66c1 Added 'ONLY_FOR_ARCHS=i386' to XForms dependent ports. 
XForms has not been available for FreeBSD/alpha yet.
 1999-01-07 08:19:57 +00:00
Hidetoshi Shimokawa
4b86d315ca Add 'ONLY_FOR_ARCHS=i386' to linux_lib dependent ports. 1999-01-07 02:31:51 +00:00
Satoshi Asami
4b07f0329b Change *_DEPENDS on lang/perl5 to USE_PERL5 so we won't have any 
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.
 1999-01-02 00:12:21 +00:00
Bill Fumerola
4f183f626d Update MASTER_SITES. 
Thanks To:	Fenner's portsurvey and ftpsearch.lycos.com
 1998-12-09 22:35:05 +00:00
Joseph Koshy
be1c648551 Add a comment about setting env var 'FC' to 'g77' if EGCS is to be 
used for building.
 1998-11-18 02:10:54 +00:00
Joseph Koshy
3b87bc1ac4 Activate tinker. 1998-11-17 04:54:28 +00:00
Joseph Koshy
b7793771c4 New port of the Tinker Molecular modelling program. 
PR:		8690
Reviewed by:	jkoshy
Submitted by:	Glenn Johnson <gljohns@bellsouth.net>
 1998-11-17 04:53:17 +00:00
Satoshi Asami
96bc8048c3 Use bsd.port.{pre,post}.mk to move PORTOBJFORMAT to front, or change 
shell loops to make loops.  Use EXTRA_PKG_FLAGS to add install scripts
instead of adding it to PKG_FLAGS after bsd.port.mk.
 1998-11-14 09:43:39 +00:00
Bill Fumerola
66cc6ff6b2 Update of MASTER_SITES. 
PR:		ports/8600
Submitted by:	frankch@waru.life.nthu.edu.tw
 1998-11-13 15:27:42 +00:00
Justin M. Seger
b6840acf52 Unbreak for ELF 1998-11-03 00:51:24 +00:00
Joseph Koshy
634cbdbc27 Master site changed, update MD5. 
PR:		8200
Submitted by:	frankch@waru.life.nthu.edu.tw (maintainer)
 1998-10-08 10:08:33 +00:00
Satoshi Asami
a519f639f6 Checksum changed again.... 1998-09-28 09:20:49 +00:00
Steve Price
e7efc40d5f Remove empty doc dir on deinstall. 1998-09-27 01:38:24 +00:00
Steve Price
00d3f5c321 Don't strip the binary when building ELF. 1998-09-27 01:36:52 +00:00
Steve Price
037daaf39e Checksum of seaview.tar changed. 1998-09-27 01:34:55 +00:00
Steve Price
5d04b9652f Mark broken for ELF because of xforms port. 1998-09-26 23:18:10 +00:00
Steve Price
53cb0c2f6a Take the manpages out of pkg/PLIST and put them in MAN1. 1998-09-16 02:25:06 +00:00
Justin M. Seger
395755e27a Unbreak by making a new checksum and fixing the makefile to find a new source 
file.
 1998-08-21 03:09:08 +00:00
Justin M. Seger
4a3440955e BROKEN: 
# make checksum
>> Checksum mismatch for seaview.tar.
 1998-08-20 17:41:16 +00:00
David E. O'Brien
09b64b0d35 Remove manpages from pkg/PLIST 1998-08-13 21:16:00 +00:00
Satoshi Asami
5264cbceb5 Fix up dependencies for ports that moved into the x11-toolkits category. 1998-08-07 23:56:56 +00:00
Satoshi Asami
ceba211283 Rename all USE_X11 to USE_X_PREFIX. Requires 1.279 (3.0-current) or 
1.227.2.41 (2.2-stable) of bsd.port.mk for this to be interpreted
correctly.
 1998-08-05 09:31:52 +00:00
Satoshi Asami
c23cc4074c Making x11 category more useful project part 1: take out "x11" of 
ports that are mere users of X.

Partial list submitted by: Josh Gilliam <josh@quick.net>
 1998-07-27 23:25:33 +00:00
Tim Vanderhoek
4bdfc29501 Another batch of "Add homepage." for benchmarks through converters. 1998-07-25 07:31:29 +00:00
Steve Price
1a8f3a68f5 Turn on hmmer. 1998-07-12 23:30:50 +00:00
Steve Price
91f5c278fe Initial import of hmmer version 2.0. 
Profile hidden Markov models for biological sequence analysis.

PR:		7120
Submitted by:	Matthew Jason Euclid Barnhart <barnhart@sequencer.wustl.edu>
 1998-07-12 23:30:04 +00:00
Steve Price
4b25e777f4 Update to 2.6b2.1. 
PR:		6673
Submitted by:	maintainer
 1998-05-24 04:04:31 +00:00
Satoshi Asami
e9ef36a1c4 mkdir -> ${MKDIR}. This also has the side-effect of making this 
port reinstall-friendly.
 1998-03-30 23:44:07 +00:00
Satoshi Asami
1be4245844 Add DIST_SUBDIR, the name "periodic.tab" is kinda generic. Speaking of which, 
its checksum was different so fix it too.
 1998-03-17 05:27:24 +00:00
Justin M. Seger
ab0598a359 Add linux_lib DEPEND lines. 
PR:             5816
Submitted by:   frankch@waru.life.nthu.edu.tw
 1998-03-16 22:15:32 +00:00
Vanilla I. Shu
e1870a74df Activate povchem. 1998-03-16 07:01:32 +00:00
Vanilla I. Shu
f53fc71c73 Povchem is a tool to generate POV file from a PDB(Protein 
DataBank) entry. One can adjust many parameters for a high
quality molecular graphic.
PR:		 ports/6008
Submitted by:	Frank Chen Hsiung Chan <frankch@waru.life.nthu.edu.tw>
 1998-03-16 06:57:14 +00:00
Justin M. Seger
587c07e3f0 Activate kinemage 1998-01-29 17:25:59 +00:00
Justin M. Seger
7e196bac6f Import of ports/biology/kinemage 4.2 
Kinemage is a molecular visualization program. It is very suitable for
educational usage.

PR:		ports/5217
Submitted by:	frankch@waru.life.nthu.edu.tw
 1998-01-29 17:24:27 +00:00
Satoshi Asami
4c088732da Typo (LIB_DEPEND -> LIB_DEPENDS). 1997-12-26 11:49:39 +00:00
Vanilla I. Shu
742d411eed Move pkg/INSTALL to pkg/MESSAGE, add another patch from maintainer. 
PR:		ports/5361
Reviewed by:	asami
Submitted by:	maintainer
 1997-12-24 07:24:22 +00:00
Vanilla I. Shu
94da48e798 Activate seaview. 1997-12-21 22:05:43 +00:00
Vanilla I. Shu
9e9c823ade Seaview is a multiple DNA sequence alignment editor. 
It is capable of align DNA sequences from various organisms
and assign their position in the phylogenic tree.
PR:		ports/5229
Submitted by:	Frank Chen Hsiung Chan <frankch@waru.life.nthu.edu.tw>
 1997-12-21 22:04:39 +00:00
Vanilla I. Shu
862cbba9c7 Activate babel. 1997-12-21 21:58:57 +00:00
Vanilla I. Shu
77daf87099 This is a port of a molecular file format converter, babel. 
Babel is developed by Dolata Group, Department of Chemistry,
University of Arizona and Ohio State University.
PR:		ports/5215
Submitted by:	Frank Chen Hsiung Chan <frankch@waru.life.nthu.edu.tw>
 1997-12-21 21:57:37 +00:00
Vanilla I. Shu
c5d1290f89 Activate rasmol. 1997-12-15 17:47:41 +00:00
Vanilla I. Shu
072b6ce7dc rasmol is a biological molecule visualization program. 
PR:		ports/5214
Submitted by:	frankch@waru.life.nthu.edu.tw
 1997-12-15 17:45:33 +00:00
Satoshi Asami
07eba866f1 The new ports category "biology" starts here today. No Darwin 
jokes please!
 1997-12-13 05:54:24 +00:00