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* - Update to 34.t25.d6Sergey Matveychuk2006-05-074-38/+80
| | | | | | | | PR: ports/96063 Submitted by: maintainer Notes: svn path=/head/; revision=161621
* Update to 21.u1.d1 (fixes fetch).Sam Lawrance2006-05-075-27/+18
| | | | | | | Reported by: fenner's distfile survey Notes: svn path=/head/; revision=161589
* - Satisfy portlintSergey Matveychuk2006-05-061-4/+3
| | | | Notes: svn path=/head/; revision=161516
* Add protomol 2.0.3, OO, component based, framework for molecularEmanuel Haupt2006-05-055-0/+201
| | | | | | | | | | dynamics (MD) simulations. PR: 95123 Submitted by: Sangwoo Shim <sangwoos@gmail.com> Notes: svn path=/head/; revision=161442
* Remove USE_REINPLACE from all categories starting with BEdwin Groothuis2006-05-0321-22/+0
| | | | Notes: svn path=/head/; revision=161307
* - Update to 1.89Yen-Ming Lee2006-05-026-16/+60
| | | | | | | | | | | | | - refine BROKEN to make portlint happier - patch to use on Scalar::Util instead of WeakRef - mark IGNORE under old perl which don't support weak reference PR: 96656 Submitted by: leeym Approved by: maintainer Notes: svn path=/head/; revision=161224
* Bioperl-run contain modules that provides a PERL interface to variousRenato Botelho2006-05-025-0/+784
| | | | | | | | | | | | | bioinformatics applications. This allows various applications to be used with common Bioperl objects. WWW: http://bioperl.org/ PR: ports/93675 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> Notes: svn path=/head/; revision=161215
* Bioperl-run contain modules that provides a PERL interface to variousRenato Botelho2006-05-025-0/+752
| | | | | | | | | | | | | bioinformatics applications. This allows various applications to be used with common Bioperl objects. WWW: http://bioperl.org/ PR: ports/93674 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> Notes: svn path=/head/; revision=161213
* - Update to 1.0.0Pav Lucistnik2006-04-253-40/+174
| | | | | | | | | | | - Provide OPTIONS - Take maintainership PR: ports/94123 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> Notes: svn path=/head/; revision=160479
* BROKEN: Does not compileKris Kennaway2006-04-221-0/+2
| | | | Notes: svn path=/head/; revision=160169
* Reset rmiya@cc.hirosaki-u.ac.jp who has not responded to email asking aboutMark Linimon2006-04-055-5/+5
| | | | | | | | | maintainer timeouts. Hat: portmgr Notes: svn path=/head/; revision=158838
* Reset jeremy@external.org who has not responded to email asking aboutMark Linimon2006-04-051-1/+1
| | | | | | | | | maintainer timeouts. Hat: portmgr Notes: svn path=/head/; revision=158835
* - Update to 2006.02.13Marcus Alves Grando2006-04-053-8/+8
| | | | | | | | PR: 95281 Submitted by: maintainer Notes: svn path=/head/; revision=158815
* Use SUB_FILES for pkg-messageEdwin Groothuis2006-04-014-1/+4
| | | | Notes: svn path=/head/; revision=158546
* For EMBOSS:Thierry Thomas2006-03-3122-1458/+7820
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This patch brings EMBOSS up to date with the current version. i. The patches included in files/ are bugfixes for files in EMBOSS-3.0.0 that appeared after the release. They are documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README This is just 'for the record' so that we remember to remove these patches in the next update. ii. EMBOSS is now installed by default in LOCALBASE/emboss This is to avoid CONFLICTS with other ports that install files with the same names. Installing EMBOSS to another PREFIX is also possible. iii. now EMBASSY and EMBOSS both store their distfiles in the same DIST_SUBDIR iv. use built-in PKGMESSAGE and SUB_FILES instead of doing it the old (manual) way For EMBASSY: This update brings embassy in sync with the update of EMBOSS to 3.0.0. Things that changed from previous version of the port: i. embassy now installs by default in $LOCALBASE/emboss (the new default PREFIX for emboss as well). ii. changed DIST_SUBDIR so that all the distfiles are put together with emboss. This makes sense(TM) iii. incorporated new EMBASSY apps (this accounts for the changes in OPTIONS and pkg-plist) iv. removed obsoleted patches Finally, I included a sample text that could go in UPDATING. PR: 93053 Submitted by: Fernan Aguero <fernan (at) iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=158468
* - Update to 34.t25.d5Pav Lucistnik2006-03-202-4/+4
| | | | | | | | PR: ports/94741 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=157817
* - Update to 5.743Renato Botelho2006-03-194-44/+13
| | | | | | | | | | | - Add a MASTER_SITE backup since oficial one just have last version and make it fetchable again Submitted by: maintainer by email Reported by: krismail Notes: svn path=/head/; revision=157664
* Add lagan 1.2, efficient tools for large-scale multiple alignments ofRenato Botelho2006-03-166-0/+136
| | | | | | | | | | genomic DNA. PR: ports/93058 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=157464
* Add mafft 5.734, multiple sequence alignments based on fast FourierRenato Botelho2006-03-156-0/+119
| | | | | | | | | | transform. PR: ports/93059 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=157209
* Add dotter 20021204 # last modified date in FTP server, a viewer forRenato Botelho2006-03-154-0/+63
| | | | | | | | | | multiple sequence alignments. PR: ports/93055 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=157195
* Add blat 33, a fast tool for local sequence similarity searches.Renato Botelho2006-03-156-0/+100
| | | | | | | | PR: ports/93060 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=157190
* Add belvu 2.29, a viewer for multiple sequence alignments.Renato Botelho2006-03-154-0/+54
| | | | | | | | PR: ports/93056 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=157188
* Update to 1.5Maho Nakata2006-03-154-211/+229
| | | | | | | Submitted by: distfile survey by kris, fenner Notes: svn path=/head/; revision=157146
* Bump PORTREVISION on glib12/gtk12 consumer ports to ease the upgrade path.Ade Lovett2006-03-071-1/+1
| | | | | | | | Discussed with: kris Approved by: portmgr (implicit) Notes: svn path=/head/; revision=157004
* Conversion to a single libtool environment.Ade Lovett2006-02-234-2/+8
| | | | | | | Approved by: portmgr (kris) Notes: svn path=/head/; revision=156749
* BROKEN: Configure failsKris Kennaway2006-02-201-0/+2
| | | | Notes: svn path=/head/; revision=156450
* Jalview is a multiple alignment editor written in Java. It is used widely in aHerve Quiroz2006-02-137-0/+137
| | | | | | | | | | | | | variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) and is also available as a general purpose alignment editor. WWW: http://www.jalview.org PR: 93054 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=155905
* Reset maintainership to ports@ after ~4 months without any response to anyAlexander Leidinger2006-02-111-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | PR. Thanks for contributing. Since the acroread7 port is a somewhat important port for our users, I will hand it over to emulation@ if no _active_ *committer* takes it before the ports freeze. While I'm here: - fix a little nit in the csound port (I think the intention was to create no backup file instead of creating one with a "-e" extension) - set ARCH to i386 in the amd64 case for the acroread7 port. This is a work-around to be able to install everything when a dependency is not already installed (ARCH is read-only in sub-makes, so the dependencies can't change it). This should be removed when the dependencies are fixed or converted to use bsd.linux-rpm.mk. [1] Not objected to by: portmgr (explicit: krion; silence: rest) Maintainer timeout: ~4 months Submitted by: Sangwoo Shim <sangwoos@gmail.com> [1] PR: 87985 [1] Notes: svn path=/head/; revision=155784
* Update to 3.27.Sam Lawrance2006-02-103-10/+18
| | | | | | | | | | Use GCC 3.3 on systems with 3.4, due to an internal compiler error. PR: ports/93050 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=155634
* Update to 34.t25.d4.Sam Lawrance2006-02-1011-167/+155
| | | | | | | | PR: ports/93052 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=155633
* Update to 2006.01.25.Sam Lawrance2006-02-092-10/+9
| | | | | | | | PR: ports/93051 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=155580
* Put PORTEPOCH back.Sam Lawrance2006-02-091-0/+1
| | | | | | | Reported by: chkversion Notes: svn path=/head/; revision=155550
* Update to 3.65.Sam Lawrance2006-02-083-73/+17
| | | | | | | | | PR: ports/92182 Submitted by: "Choe, Cheng-Dae" <whitekid@gmail.com> Approved by: dbader@ece.unm.edu (maintainer, timeout 14 days) Notes: svn path=/head/; revision=155521
* Remove CONFLICTS with nss.Joe Marcus Clarke2006-02-021-1/+1
| | | | Notes: svn path=/head/; revision=155108
* Add missing USE_ICONVKris Kennaway2006-01-261-0/+1
| | | | Notes: svn path=/head/; revision=154471
* SHA256ify (manually done and checked)Edwin Groothuis2006-01-222-1/+5
| | | | | | | Approved by: krion@ Notes: svn path=/head/; revision=154147
* SHA256ifyEdwin Groothuis2006-01-2230-0/+41
| | | | | | | Approved by: krion@ Notes: svn path=/head/; revision=154141
* Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtryEdwin Groothuis2006-01-224-12/+12
| | | | | | | | Approved by: krion@ PR: ports/88711 (related) Notes: svn path=/head/; revision=154109
* Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtryEdwin Groothuis2006-01-221-1/+1
| | | | Notes: svn path=/head/; revision=154104
* Utilize EXAMPLESDIR.Alexey Dokuchaev2006-01-201-3/+3
| | | | Notes: svn path=/head/; revision=153969
* - Resurrect, update to version 1.5 (literally 1.50 since I wanted to avoidAlexey Dokuchaev2006-01-195-0/+57
| | | | | | | | | | | | | | unnecessary PORTEPOCH bump) - Update MASTER_SITES and WWW line, provide backup download site - Come up with better port description - Reset maintainer to ports@ - Uphold CXX and CXXFLAGS - Clean up Makefile slightly - Don't install yet another copy of GPL and texts in French - Add SHA256 hash to distinfo Notes: svn path=/head/; revision=153895
* - Remove expired portsPav Lucistnik2006-01-1417-462/+0
| | | | Notes: svn path=/head/; revision=153501
* - Update to 2.0.20060101Pav Lucistnik2006-01-142-2/+4
| | | | | | | | PR: ports/91715 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=153495
* - Update to 2005.12.06Pav Lucistnik2006-01-144-44/+60
| | | | | | | | PR: ports/91714 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=153494
* - Chase openbabel updatePav Lucistnik2006-01-141-3/+2
| | | | Notes: svn path=/head/; revision=153451
* BROKEN: Broken dependencyKris Kennaway2006-01-141-0/+2
| | | | Notes: svn path=/head/; revision=153439
* - Update graphics/libglut to 6.4.1.Sergey Matveychuk2006-01-123-4/+7
| | | | | | | | | | | | | | - Shared lib version and PORTREVISION bumb for all affected ports. While I'm here: - Remove USE_MESA knob where it was (35 ports). It marked as depricated for 2 years. PR: ports/90247 Submitted by: Ermal Lu?i <eri--@albabsd.org> Notes: svn path=/head/; revision=153347
* Fix maintainer addressEdwin Groothuis2006-01-096-6/+6
| | | | | | | | | | | | | | | | | | | | | | | | From: Tony Maher <anthony.maher@uts.edu.au> To: Edwin Groothuis <edwin@FreeBSD.org> Subject: Re: ports/91537: maths/xgobi - download site moved/maintainer addressupdate Actually I need modify all my ports to use OptusNet rather than Biolateral. Is there an easy way to do this or should I submit a separate 1-line patch and PR for each port? biology/crimap biology/dna-qc biology/flip biology/primer3 biology/seqio biology/wise math/xgobi net/generic-nqs Submitted by: Tony Maher <anthony.maher@uts.edu.au> Notes: svn path=/head/; revision=153111
* Hash with SHA-256.Trevor Johnson2006-01-071-0/+1
| | | | Notes: svn path=/head/; revision=153010
* - Remove symlinks that belong to mtreePav Lucistnik2006-01-051-2/+0
| | | | | | | Approved by: maintainers Notes: svn path=/head/; revision=152842
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