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* Remove biology/njplotJoseph Mingrone2018-12-114-110/+0
| | | | | | | | The author of both NJplot and SeaView says that NJplot can be considered deprecated and replaced by SeaView. Notes: svn path=/head/; revision=487239
* biology/njplot: Add site in MASTER_SITES because package builders areJoseph Mingrone2016-11-281-2/+4
| | | | | | | | | | timing out during fetch. Approved by: AMDmi3 (mentor) Differential Revision: https://reviews.freebsd.org/D8651 Notes: svn path=/head/; revision=427329
* biology/njplot: Revive and update to version 2.4Joseph Mingrone2016-11-164-0/+108
| | | | | | | | Approved by: AMDmi3 (mentor) Differential Revision: https://reviews.freebsd.org/D8518 Notes: svn path=/head/; revision=426241
* Remove expired ports:Rene Ladan2015-11-284-143/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 2015-11-26 audio/pecl-id3: Broken for more than 6 months 2015-11-26 dns/geta: Broken for more than 6 months 2015-11-26 finance/openerp-web: Broken for more than 6 months 2015-11-26 devel/py-async: Further using of this module is not encouraged by upstream 2015-11-26 chinese/kon2: Depends on expiring chinese/cce 2015-11-26 games/linux-skulltag: Depends on expiring audio/linux-fmodapi 2015-11-26 archivers/wzip: Broken for more than 6 months 2015-11-26 databases/sybtcl: Broken for more than 6 months 2015-11-26 biology/povchem: Broken for more than 6 months 2015-11-26 audio/btc: Broken for more than 6 months 2015-11-26 astro/wmglobe: Broken for more than 6 months 2015-11-26 graphics/pyro: Broken for more than 6 months 2015-11-26 graphics/jpeg2ps: Broken for more than 6 months 2015-11-26 chinese/gugod-clean: Broken for more than 6 months 2015-11-26 comms/bforce: Broken for more than 6 months 2015-11-26 cad/geda-docs: Broken for more than 6 months 2015-11-26 chinese/cwtexttf: Broken for more than 6 months 2015-11-26 comms/zmtx-zmrx: Broken for more than 6 months 2015-11-26 astro/sky2000: Broken for more than 6 months 2015-11-26 deskutils/libopensync-plugin-file: Broken for more than 6 months 2015-11-26 databases/sqlite-ext-mobigroup: Broken for more than 6 months 2015-11-26 chinese/bg5ps: Broken for more than 6 months 2015-11-26 deskutils/x-tile: Broken for more than 6 months 2015-11-26 graphics/pure-gl: Broken for more than 6 months 2015-11-26 audio/dvda-author: Broken for more than 6 months 2015-11-26 chinese/oxim: Broken for more than 6 months 2015-11-26 editors/spe: Broken for more than 6 months 2015-11-26 audio/mpdscribble: Broken for more than 6 months 2015-11-26 cad/geda-symcheck: Broken for more than 6 months 2015-11-26 audio/linux-fmodapi: Broken for more than 6 months 2015-11-26 audio/pure-audio: Broken for more than 6 months 2015-11-26 editors/bpatch: Broken for more than 6 months 2015-11-26 benchmarks/geekbench: Broken for more than 6 months 2015-11-26 graphics/icoconvert: Broken for more than 6 months 2015-11-26 cad/geda-utils: Broken for more than 6 months 2015-11-26 deskutils/tomboy-plugin-wordcount: Broken for more than 6 months 2015-11-26 graphics/sketch: Broken for more than 6 months 2015-11-26 ftp/spegla: Broken for more than 6 months 2015-11-26 graphics/clutter-box2d: Broken for more than 6 months 2015-11-26 audio/scmpc: Broken for more than 6 months 2015-11-26 ftp/gnusget: Broken for more than 6 months 2015-11-26 comms/gpsk31: Broken for more than 6 months 2015-11-26 cad/geda-gschem: Broken for more than 6 months 2015-11-26 audio/ampache: Broken for more than 6 months 2015-11-26 cad/slffea: Broken for more than 6 months 2015-11-26 audio/cripple: Broken for more than 6 months 2015-11-26 cad/geda-gattrib: Broken for more than 6 months 2015-11-26 cad/findhier: Broken for more than 6 months 2015-11-26 biology/njplot: Broken for more than 6 months 2015-11-26 audio/wmmp: Broken for more than 6 months 2015-11-26 x11/avant-window-navigator: Broken for more than 6 months 2015-11-26 cad/geda-netlist: Broken for more than 6 months 2015-11-26 deskutils/libopensync-plugin-sunbird: Broken for more than 6 months 2015-11-26 biology/ortep3: Broken for more than 6 months 2015-11-26 astro/aa: Broken for more than 6 months 2015-11-26 french/belote: Broken for more than 6 months 2015-11-26 converters/p5-String-SetUTF8: Broken for more than 6 months 2015-11-26 cad/geda-examples: Broken for more than 6 months 2015-11-26 editors/yasnippet: Broken for more than 6 months 2015-11-26 audio/musica: Broken for more than 6 months 2015-11-26 graphics/rubyphoto: Broken for more than 6 months 2015-11-26 german/bsdpaste: Broken for more than 6 months 2015-11-26 audio/amrcoder: Broken for more than 6 months 2015-11-26 sysutils/bashburn: Broken for more than 6 months 2015-11-26 editors/e93: Broken for more than 6 months 2015-11-26 audio/tepsonic: Broken for more than 6 months 2015-11-26 astro/ephem: Broken for more than 6 months 2015-11-26 chinese/cce: Broken for more than 6 months 2015-11-26 graphics/qcread: Broken for more than 6 months 2015-11-26 databases/py-sqlkit: Broken for more than 6 months 2015-11-26 databases/usogres: Broken for more than 6 months 2015-11-26 cad/libgeda: Broken for more than 6 months 2015-11-26 chinese/p5-Lingua-ZH-BPMFConvert: Broken for more than 6 months 2015-11-26 french/alphabet_sounds_fr: Broken for more than 6 months 2015-11-26 deskutils/mrundlg: Broken for more than 6 months 2015-11-26 databases/erlang-mysql: Broken for more than 6 months 2015-11-26 graphics/linux-XnViewMP: Broken for more than 6 months 2015-11-26 deskutils/akamaru: Broken for more than 6 months 2015-11-26 dns/p5-Net-DNS-ZoneCheck: Broken for more than 6 months 2015-11-26 astro/dgpsip: Broken for more than 6 months 2015-11-26 databases/pecl-handlersocket: Broken for more than 6 months 2015-11-26 audio/cymbaline: Broken for more than 6 months 2015-11-26 french/dico: Broken for more than 6 months 2015-11-26 comms/qpage: Broken for more than 6 months 2015-11-26 audio/sonice: Broken for more than 6 months 2015-11-26 cad/geda-symbols: Broken for more than 6 months 2015-11-26 databases/java-mybatis: Broken for more than 6 months 2015-11-26 databases/openbase-jdbc: Broken for more than 6 months 2015-11-27 www/mediawiki119: Please upgrade to mediawiki-1.25 2015-11-28 www/R-cran-Rpad: Unmaintained upstream Notes: svn path=/head/; revision=402562
* Deprecate ports broken for more than 6 monthsAntoine Brodin2015-10-251-0/+2
| | | | Notes: svn path=/head/; revision=400160
* Mark as broken unfetchable portsBaptiste Daroussin2015-04-051-0/+2
| | | | Notes: svn path=/head/; revision=383309
* - add stage supportOlli Hauer2014-06-011-22/+16
| | | | | | | | - add OPTION for X11 - bump PORTREVISION Notes: svn path=/head/; revision=356098
* Remove trailing whitespaces from category biologyEmanuel Haupt2014-02-211-1/+1
| | | | Notes: svn path=/head/; revision=345397
* According to the Porter's Handbook (5.12.2.3.) default options must be added toEmanuel Haupt2014-02-101-0/+2
| | | | | | | | | | | | | | OPTIONS_DEFINE. This policy has been implemented only recently that's why we have many ports violating this policy. This patch adds the default options specified in the Porter's Handbook to OPTIONS_DEFINE where they are being used. Ports maintained by gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded. Approved by: portmgr (bapt) Notes: svn path=/head/; revision=343634
* Convert biology to MDOCS and MEXAMPLESAdam Weinberger2014-01-031-1/+3
| | | | Notes: svn path=/head/; revision=338550
* Fix NO_STAGE attributionBaptiste Daroussin2013-09-221-1/+1
| | | | Notes: svn path=/head/; revision=327888
* Add NO_STAGE all over the place in preparation for the staging support (cat: ↵Baptiste Daroussin2013-09-201-0/+1
| | | | | | | biology) Notes: svn path=/head/; revision=327709
* Convert from USE_MOTIF to USES=motifBaptiste Daroussin2013-07-101-6/+2
| | | | Notes: svn path=/head/; revision=322624
* s/X11BASE/LOCALBASE/, or equivalent.Doug Barton2012-06-241-1/+1
| | | | | | | The X11BASE variable is long gone, however these ports were not updated. Notes: svn path=/head/; revision=299908
* Bump PORTREVISION after open-mofit updateMax Brazhnikov2011-05-021-1/+1
| | | | Notes: svn path=/head/; revision=273475
* - Get Rid MD5 supportMartin Wilke2011-03-191-1/+0
| | | | Notes: svn path=/head/; revision=271305
* Convert most of remaining ports that depend on xorg-libraries toDmitry Marakasov2009-06-091-1/+2
| | | | | | | | | | | | | | | | 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) Notes: svn path=/head/; revision=235506
* - Update maintainer's email addressPav Lucistnik2008-05-171-1/+1
| | | | | | | Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer) Notes: svn path=/head/; revision=213206
* NJplot is a tree drawing program able to draw any phylogenetic tree expressedPav Lucistnik2008-05-144-0/+144
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> Notes: svn path=/head/; revision=213034
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