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d>-38/+80 | | | | | PR: ports/96063 Submitted by: maintainer * Update to 21.u1.d1 (fixes fetch).lawrance2006-05-075-27/+18 | | | | Reported by: fenner's distfile survey * - Satisfy portlintsem2006-05-071-4/+3 | * Add protomol 2.0.3, OO, component based, framework for molecularehaupt2006-05-065-0/+201 | | | | | | | dynamics (MD) simulations. PR: 95123 Submitted by: Sangwoo Shim <sangwoos@gmail.com> * Remove USE_REINPLACE from all categories starting with Bedwin2006-05-0421-22/+0 | * - Update to 1.89leeym2006-05-036-16/+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 * Bioperl-run contain modules that provides a PERL interface to variousgarga2006-05-035-0/+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> * Bioperl-run contain modules that provides a PERL interface to variousgarga2006-05-035-0/+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> * - Update to 1.0.0pav2006-04-263-40/+174 | | | | | | | | - Provide OPTIONS - Take maintainership PR: ports/94123 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> * BROKEN: Does not compilekris2006-04-231-0/+2 | * Reset rmiya@cc.hirosaki-u.ac.jp who has not responded to email asking aboutlinimon2006-04-055-5/+5 | | | | | | maintainer timeouts. Hat: portmgr * Reset jeremy@external.org who has not responded to email asking aboutlinimon2006-04-051-1/+1 | | | | | | maintainer timeouts. Hat: portmgr * - Update to 2006.02.13mnag2006-04-053-8/+8 | | | | | PR: 95281 Submitted by: maintainer * Use SUB_FILES for pkg-messageedwin2006-04-014-1/+4 | * For EMBOSS:thierry2006-03-3122-1458/+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) * - Update to 34.t25.d5pav2006-03-212-4/+4 | | | | | PR: ports/94741 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) * - Update to 5.743garga2006-03-194-44/+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 * Add lagan 1.2, efficient tools for large-scale multiple alignments ofgarga2006-03-176-0/+136 | | | | | | | genomic DNA. PR: ports/93058 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> * Add mafft 5.734, multiple sequence alignments based on fast Fouriergarga2006-03-156-0/+119 | | | | | | | transform. PR: ports/93059 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> * Add dotter 20021204 # last modified date in FTP server, a viewer forgarga2006-03-154-0/+63 | | | | | | | multiple sequence alignments. PR: ports/93055 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> * Add blat 33, a fast tool for local sequence similarity searches.garga2006-03-156-0/+100 | | | | | PR: ports/93060 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> * Add belvu 2.29, a viewer for multiple sequence alignments.garga2006-03-154-0/+54 | | | | | PR: ports/93056 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> * Update to 1.5maho2006-03-154-211/+229 | | | | Submitted by: distfile survey by kris, fenner * Bump PORTREVISION on glib12/gtk12 consumer ports to ease the upgrade path.ade2006-03-071-1/+1 | | | | | Discussed with: kris Approved by: portmgr (implicit) * Conversion to a single libtool environment.ade2006-02-234-2/+8 | | | | Approved by: portmgr (kris) * BROKEN: Configure failskris2006-02-201-0/+2 | * Jalview is a multiple alignment editor written in Java. It is used widely in ahq2006-02-137-0/+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> * Reset maintainership to ports@ after ~4 months without any response to anynetchild2006-02-121-1/+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] * Update to 3.27.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) * Update to 34.t25.d4.lawrance2006-02-1011-167/+155 | | | | | PR: ports/93052 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) * Update to 2006.01.25.lawrance2006-02-092-10/+9 | | | | | PR: ports/93051 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) * Put PORTEPOCH back.lawrance2006-02-091-0/+1 | | | | Reported by: chkversion * Update to 3.65.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) * Remove CONFLICTS with nss.marcus2006-02-031-1/+1 | * Add missing USE_ICONVkris2006-01-261-0/+1 | * SHA256ify (manually done and checked)edwin2006-01-222-1/+5 | | | | Approved by: krion@ * SHA256ifyedwin2006-01-2230-0/+41 | | | | Approved by: krion@ * Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtryedwin2006-01-224-12/+12 | | | | | Approved by: krion@ PR: ports/88711 (related) * Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtryedwin2006-01-221-1/+1 | * Utilize EXAMPLESDIR.danfe2006-01-201-3/+3 | * - Resurrect, update to version 1.5 (literally 1.50 since I wanted to avoiddanfe2006-01-205-0/+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 * - Remove expired portspav2006-01-1517-462/+0 | * - Update to 2.0.20060101pav2006-01-152-2/+4 | | | | | PR: ports/91715 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) * - Update to 2005.12.06pav2006-01-154-44/+60 | | | | | PR: ports/91714 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) * - Chase openbabel updatepav2006-01-141-3/+2 | * BROKEN: Broken dependencykris2006-01-141-0/+2 | * - Update graphics/libglut to 6.4.1.sem2006-01-123-4/+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> * Fix maintainer addressedwin2006-01-096-6/+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> * Hash with SHA-256.trevor2006-01-081-0/+1 | * - Remove symlinks that belong to mtreepav2006-01-061-2/+0 | | | | Approved by: maintainers * possible fix to unbreak biology/L-Breederedwin2006-01-039-107/+60 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | L-Breeder is currently marked unfetchable: http://people.freebsd.org/~fenner/portsurvey/biology.html#L-Breeder So I tried to investigate the problem and I'm now submitting my homework so it doesn't get lost. This is what I noticed: i) L-Breeder upstream sources have "stagnated for some time, but now a new simplified version is available" (sic, from the web site) So, the fetch issue is resolved. And the pkg-descr is also updated to reflect the new home page. However: ii) L-Breeder is now called LBreeder. I have changed PORTNAME to reflect this, although I don't know if this is the right thing to do. Should the port be moved to biology/LBreeder? Or perhaps just leaving PORTNAME pointing to the old name and then work inside the Makefile to point the build/install to the correct name? iii) the sources have been reorganized so I have to update the port's Makefile to reflect this. The attached patch works for me under FreeBSD-4.11 (although it's possible that I may have missed a dependency if I already have a required library installed in my box. Sorry, I don't have a tinderbox-like setup to test builds) iv) the program does not have a version number, nor did I find one by looking inside the sources. To avoid changing too much the port I just left PORTVERSION at 1.0 and bumped PORTREVISION to 6 Finally, do note that I am not a user of LBreeder, so I cannot test the program myself. I just noticed that by calling the executable I get a black X screen, that I can quit by pressing 'q' as documented in Readme.txt, but I can't tell myself if this is the expected behaviour. Nor do I know how to use the example files. Caveat emptor. PR: ports/90073 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Approved by: maintainer timeout * - New upstream version; two patches incorporated.tdb2005-12-105-39/+9 | | | | | | PR: 90140 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Approved by: clement (mentor) * Update to 1.3.1ehaupt2005-12-072-3/+3 | | | | | PR: 90029 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) * - Update to 2005.13.07 to make fetchable againtdb2005-12-063-6/+31 | | | | | | PR: 89976 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Approved by: clement (mentor) * - Update to 3.18 to make fetchable againtdb2005-12-062-6/+11 | | | | | | | | - Mark broken on 6.x upwards PR: 89977 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Approved by: clement (mentor) * Update to 0.5.1mnag2005-12-063-23/+6 | | | | | | | | Unbroken >= 502126 Add SHA256 PR: 89980 Submitted by: maintainer * - Fix fetch problemstdb2005-12-062-3/+5 | | | | | | PR: 89971 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Approved by: clement (mentor) * Add conflicts:edwin2005-12-051-1/+1 | | | | | | CONFLICTS= p5-bioperl-1.[02468]* Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>, Mauricio Herrera Cuadra <arareko@yahoo.com> * Add conflicst:edwin2005-12-051-0/+2 | | | | | | CONFLICTS= p5-bioperl-1.[13579]* Submitted by: Mauricio Herrera Cuadra <arareko@yahoo.com>,Fernan Aguero <fernan@iib.unsam.edu.ar> * Fix port: biology/p5-bioperl-develedwin2005-12-041-0/+2 | | | | | | | | | This patch adds a LATEST_LINK line in the Makefile to avoid duplication with the 'p5-bioperl' port in the packages/Latest directory. PR: ports/89916 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> * - Re-add p5-bioperl-devel, development version of biology/p5-bioperlbarner2005-12-036-0/+2586 | | | | | | | (A collection of Perl modules for bioinformatics) PR: ports/89497 Submitted by: Mauricio Herrera Cuadra <arareko@yahoo.com> * - Unbreak by updating to 4.4barner2005-12-014-25/+22 | | | | | | | - Add dependecy to MESA PR: ports/89795 Submitted by: Johan van Selst <johans@stack.nl> * Add the right MASTER_SITE_SUBDIR, so that this port is fetchable fromfenner2005-11-261-0/+1 | | | | 20 sites instead of just 1. * - Add SHA256pav2005-11-2416-0/+16 | * - Drop old povchem.c checksumpav2005-11-241-1/+4 | | | | - Add SHA256, SIZE * - BROKEN: Size mismatchpav2005-11-241-0/+2 | * BROKEN: Size mismatchkris2005-11-161-0/+2 | * Mass-conversion to the USE_AUTOTOOLS New World Order. The code presentade2005-11-152-2/+2 | | | | | | | | | | | | | | | | | in bsd.autotools.mk essentially makes this a no-op given that all the old variables set a USE_AUTOTOOLS_COMPAT variable, which is parsed in exactly the same way as USE_AUTOTOOLS itself. Moreover, USE_AUTOTOOLS has already been extensively tested by the GNOME team -- all GNOME 2.12.x ports use it. Preliminary documentation can be found at: http://people.FreeBSD.org/~ade/autotools.txt which is in the process of being SGMLized before introduction into the Porters Handbook. Light blue touch-paper. Run. * - Mark it as DEPRECATED - master site disapearedgarga2005-11-111-0/+3 | | | | | | | | - Set EXPIRATION_DATE PR: ports/88003 Submitted by: Jean Milanez Melo <jmelo@freebsdbrasil.com.br> Approved by: maintainer timeout (17 days) * - Mark it as DEPRECATED - master site disapearedgarga2005-11-111-0/+3 | | | | | | | | - Set EXPIRATION_DATE PR: ports/88002 Submitted by: Jean Milanez Melo <jmelo@freebsdbrasil.com.br> Approved by: maintainer timeout (17 days) * - Mark it as DEPRECATED (mastersite disapeared)garga2005-11-111-0/+3 | | | | | | | | - Set EXPIRATION_DATE PR: ports/88000 Submitted by: Jean Milanez Melo <jmelo@freebsdbrasil.com.br> Approved by: maintainer timeout (16 days) * With portmgr hat on, reset maintainership of knu's ports since he haslinimon2005-11-111-1/+1 | | | | been inactive more than 6 months. We hope to see him back sometime. * Update to 1.41mnag2005-11-115-44/+87 | | | | | | | | Take MAINTAINER Add SHA256 PR: 88792 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net>