aboutsummaryrefslogtreecommitdiffstats
path: root/biology
Commit message (Collapse)AuthorAgeFilesLines
* BROKEN: Unfetchablekris2006-05-221-0/+2
|
* - Update to 3.15sem2006-05-212-4/+4
| | | | | | PR: ports/96941 Submitted by: Paul Schmehl <pauls@utdallas.edu> Approved by: maintainer timeout
* - Updated from 0.07 to 0.12aaron2006-05-203-12/+25
| | | | | | | | | | | | | | | | | | | | | | Approved by: tobez (implicit) 0.08 20/Feb/2006 15:14 Improved referential integrity between nodes, taxa, and data. Implemented Fastnexus parser Node object silently implements Bio::Tree::NodeI interface if BioPerl is installed Tree object silently implements Bio::Tree::TreeI interface if BioPerl is installed Added convertor methods for XML and CIPRES Implemented more Matrix methods Implemented symbol tables in Bio::Phylo::Util::CONSTANT Implemented visit method for listable objects Implemented caching infrastructure for calculations Changed object-model to inside-out arrays Added Biodiversity measures code by Aki Mimoto Moved constants and exceptions to Bio::Phylo::Util::* Fixed memory leak due to circular references
* Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl.aaron2006-05-145-0/+110
| | | | Approved by: tobez (implicit)
* - Update to 34.t25.d6sem2006-05-084-38/+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>
* Update to 3.14bmnag2005-11-102-9/+11
| | | | | | | | | | Update MASTER_SITES Add SHA256 Remove extra TABS PR: 88007 Submitted by: Jean Milanez Melo <jmelo@freebsdbrasil.com.br> Approved by: maintainer timeout, 14 days
* Remove expired portskris2005-11-057-110/+0
|
* Bump PORTREVISION to chase the glib20 shared library update.marcus2005-11-054-3/+4
|
* Mark DEPRECATED since upstream is unmaintained and mastersite is gone.lawrance2005-10-291-0/+3
| | | | | | PR: ports/88004 Submitted by: Jean Milanez Melo <jmelo@freebsdbrasil.com.br> Approved by: Tony Maher <anthony.maher@uts.edu.au> (maintainer)
* BROKEN: Unfetchablekris2005-10-281-0/+2
|
* Add p5-Bio-ASN1-EntrezGene, a Regular expression-based Perl Parser forehaupt2005-10-165-0/+61
| | | | | | | | NCBI Entrez Gene. PR: 87423 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> Approved by: novel (mentor) (implicit)
* - Update to 20050605sem2005-10-125-20/+36
| | | | | PR: ports/87266 Submitted by: maintainer
* - Update to 3.13. It fixes fetching.sem2005-10-124-167/+61
| | | | | PR: ports/87264 Submitted by: maintainer
* Update to 0.9.8maho2005-10-103-318/+363
|
* Checking MACHINE_ARCH is deprecated.trevor2005-09-241-1/+1
|
* Update to version 7hq2005-09-203-47/+160
| | | | | | PR: 86196 Submitted by: Tony Maher <anthony.maher@uts.edu.au> Approved by: maintainer
* Don't strip static libraries on installation ;)vs2005-09-141-1/+2
| | | | (Unbreaks e.g. biology/nclever)
* Add p5-Bio-Das 1.02, client-side library for Distributed Genomegarga2005-09-015-0/+158
| | | | | | | Annotation System. PR: ports/76379 Submitted by: Razi Khaja <razi@genet.sickkids.on.ca>
* This port is scheduled for deletion on 2005-09-22 if it is still brokenkris2005-07-231-0/+2
| | | | at that time and no PRs have been submitted to fix it.
* - Update to 1.0.0pat2005-06-133-368/+365
| | | | | | | | | - Make DATADIR/EXAMPLESDIR/DOCSDIR safe - Don't hardcode ${CPIO} PR: ports/82154 Submitted by: George Hartzell <hartzell@alerce.com> Approved by: maintainer
* change the libtool version to use from 1.3 to 1.5oliver2005-06-011-1/+1
|
* - Update to 2.10.0pav2005-05-305-42/+78
| | | | Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Update to 2.10.0pav2005-05-303-995/+1221
| | | | | | PR: ports/81579 Submitted by: "Choe, Cheng-Dae" <whitekid@gmail.com> Approved by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* Finish repo copy of wxgtk 2.4.2 ports to wxgtk24*fjoe2005-05-132-3/+3
|
* - Fix the packing list [1]jylefort2005-04-303-5/+6
| | | | | | | | | - Add a run dependency on ucpp - Correct the NABHOME used in pre-install PR: ports/80457 Submitted by: maintainer Reported by: pointyhat [1]
* - Update to 5.0jylefort2005-04-2915-782/+851
| | | | | | | - Cleanups PR: ports/80372 Submitted by: maintainer
* Bump PORTEPOCH. 3.6 < 3.62arved2005-04-221-0/+1
| | | | Pointyhat to: arved
* Upgrade to 3.62arved2005-04-212-3/+3
| | | | | PR: 79234 Submitted by: David A. Bader <dbader@ece.unm.edu>
* - update grappa to 2.0leeym2005-04-164-29/+13
| | | | | | | | | - utilize PLIST_FILES - unbreak it on 4.x - update maintainer's email PR: 79241 Submitted by: David A. Bader <dbader@ece.unm.edu>
* At Kris's request, back out the MACHINE_ARCH spelling correction untilobrien2005-04-129-9/+9
| | | | after 5.4-RELEASE.
* - Change maintainer's email address.flz2005-04-121-1/+1
|
* - ARCH is defined in bsd.port.pre.mkflz2005-04-111-1/+3
|
* Assist getting more ports working on AMD64 by obeying theobrien2005-04-119-9/+9
| | | | Ports Collection documentation and use 'ARCH' rather than 'MACHINE_ARCH'.
* Upgrade to 0.5 and take maintainership.thierry2005-04-094-9/+25
| | | | | | | | Remark: still broken on FreeBSD-5.x. PR: ports/79304 Submitted by: Fernan Aguero (new maintainer) Approved by: Tony Maher (previous maintainer)
* Try to unbreak on amd64 and ia64kris2005-03-271-1/+1
| | | | Approved by: portmgr (self)
* BROKEN: Unfetchablekris2005-03-271-0/+2
| | | | Approved by: portmgr (self)
* Fix build on amd64maho2005-03-241-2/+11
| | | | | Submitted by: kris via pointy hat Approved by: portmgr (marcus)
* - Add 'java' categoryhq2005-03-201-2/+1
| | | | | | | - Remove incorrect (and unneeded) JAVA_RUN statement PR: 78761 Submitted by: me
* - Fix man page damage I did last nightpav2005-03-201-7/+9
| | | | Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Update to 2.2.10 from 20041020pav2005-03-206-196/+161
| | | | | | | | | - Transfer maintainership PR: ports/67735 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Approved by: old maintainer indirectly in http://lists.freebsd.org/pipermail/freebsd-ports-bugs/2004-June/035351.html
* From the PR:danfe2005-03-182-4/+16
| | | | | | | | | | | | | | | | I've added PORTREVISION to the port and set it to the release date as in the lang/gcc* ports. Since the distinfo file is not used, this would help users know when they have to update their ports. Although newer release might be made, the idea is to bump PORTREVISION for important feature releases on when significant bugs are fixed. Other minor (cosmetic) changes also applied. PR: ports/78963 Sumbitted by: maintainer
* Bump PORTREVISION to chase the glib20 shared lib version change.marcus2005-03-124-3/+4
|
* - biology/act is redundant after biology/artemis updatesem2005-03-125-1648/+0
| | | | | | PR: ports/76217 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Approved by: maintainer timeout (2 monthes)
* - Update to version 6sem2005-03-124-1505/+1529
| | | | | | | | - Pass maintainership to submitter PR: ports/76219 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Approved by: maintainer timeout (2 monthes)
* Add finchtv 1.3.0, a chromatogram trace viewer.thierry2005-03-126-0/+209
| | | | | PR: 70271 Submitted by: Fernan Aguero <fernan (at) iib.unsam.edu.ar>
* Fix build on 4.xkrion2005-02-191-0/+4
| | | | | PR: ports/77697 Submitted by: Sam Lawrance <boris at brooknet.com.au>
* As previously announced, remove ports that have reached their expiry date,kris2005-02-197-455/+0
| | | | and the handful of ports that depended on them.
* Update to version 2.0.3krion2005-02-183-10/+13
| | | | | PR: ports/77676 Submitted by: Sam Lawrance <boris at brooknet.com.au>
* Readd mistakenly removed patch to honour CC/CFLAGS.krion2005-02-181-0/+43
|
* Update to version 1.40krion2005-02-183-47/+6
| | | | | PR: ports/77675 Submitted by: Sam Lawrance <boris at brooknet.com.au>
* Fix unfetchable tarball, it was renamed and relocated on originalkrion2005-02-182-4/+4
| | | | | | | server. PR: ports/77674 Submitted by: Sam Lawrance <boris at brooknet.com.au>
* - Add (or fix) CONFLICTS line. The ports install bin/digest.sem2005-02-121-0/+2
| | | | Approved by: portmgr (krion)
* update to 0.97maho2005-02-074-338/+380
|
* With portmgr hat on, reset maintainership of this port. All of wjv'slinimon2005-01-221-1/+1
| | | | | other ports were reset a couple of months ago; this one appears to have been missed.
* o update to 4.3maho2005-01-202-7/+4
| | | | | o unbreak o due to no fix for long period, drop maintainership to ports.
* Update to 0.6.2.knu2004-12-263-7/+26
|
* This port is scheduled to be removed on 2005-02-18 if it is stillkris2004-12-192-0/+4
| | | | broken at that time, and a fix has not been submitted to GNATS.
* Update to version 2.0.8krion2004-12-193-10/+19
| | | | | PR: ports/75106 Submitted by: Ports Fury
* - Update to 2004.12.16sem2004-12-182-3/+3
| | | | | PR: ports/75205 Submitted by: maintainer
* Clean up wording of IGNORE output.linimon2004-12-171-1/+1
|
* Unquote the IGNORE string.linimon2004-12-171-1/+1
|
* With portmgr hat on, switch from BROKEN to ignore. It does indeed build.linimon2004-12-171-1/+1
|
* - Fix OPTIONS handlingpav2004-12-121-3/+1
| | | | Pointy hat to: sem
* Not a real update with the last patch.sem2004-12-112-4/+5
| | | | The real update here.
* - This update brings seaview to the latest release (dated 09.24.04sem2004-12-111-1/+1
| | | | | | | | | | | in the FTP site). - While here add a modeline for vi, and fix a tab (cosmetic) - Make portlint happy. PR: ports/74897 Submitted by: maintainer
* - Add some sites I found with Google, as old master site don't have thispav2004-12-091-1/+4
| | | | | | version anymore Reported by: pointyhat via krion
* BROKEN: Broken distinfo filekris2004-12-041-0/+2
|
* Fix build on Python 2.4perky2004-12-021-0/+14
| | | | Spotted by: kris
* Update MASTER_SITES and WWW: linekrion2004-11-272-2/+2
| | | | | PR: ports/74421 Submitted by: Ports Fury
* [new port] biology/embassysem2004-11-275-0/+271
| | | | | PR: ports/74330 Submitted by: Fernan Aguero <fernan(at)iib.unsam.edu.ar>
* - Update to 2.9.0sem2004-11-269-1812/+1632
| | | | | | | - Pass maintainership to submitter PR: ports/74333 Submitted by: Fernan Aguero <fernan(at)iib.unsam.edu.ar>
* Add missing fileskris2004-11-261-0/+11
|
* - Update to 2.03sem2004-11-267-384/+175
| | | | | | | - Pass maintainership to submitter PR: ports/74332 Submitted by: Fernan Aguero <fernan(at)iib.unsam.edu.ar>
* - Remove a junk white space.sem2004-11-261-1/+1
|
* - Update to 2.3.2sem2004-11-265-69/+38
| | | | | | | | - Add WITH_PVM knob - Pass maintainership to submitter PR: ports/74331 Submitted by: Fernan Aguero <fernan(at)iib.unsam.edu.ar>
* Minor cleanup.linimon2004-11-231-2/+2
| | | | | PR: ports/72094 Submitted by: M. L. Dodson <bdodson at scms dot utmb dot edu> (maintainer)
* - Update biology/biojava to 1.30vs2004-11-223-613/+255
| | | | | | | | | - Install javadoc and example files - Assign maintainership to submitter PR: ports/73391 Submitted by: Cheng-Dae Choe Add. reviewing: hq@
* With portmgr hat on, reset inactive maintainer. These ports are now uplinimon2004-11-208-8/+8
| | | | for adoption.
* With portmgr hat on, reset inactive maintainer.linimon2004-11-201-1/+1
|
* - Distfiles change every few days, so drop md5 checking on thempav2004-11-182-4/+5
| | | | Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* Add blast, a powerful software package for gene and protein identification,pav2004-11-126-0/+324
| | | | | | | | using sensitive, selective and rapid similarity searches of protein and nucleotide sequence databases. PR: ports/69636 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
* Bump PORTREVISIONS for all ports that depend on atk or pango to ease in themarcus2004-11-084-4/+4
| | | | big upgrade.
* - Fix build on amd64 (crude hack to pass -fPIC to c++ compiles)pav2004-11-071-0/+11
| | | | | Reported by: pointyhat via kris Tested on: arved's box
* Update to 3.14kevlo2004-11-063-5/+4
| | | | | PR: ports/72422 Submitted by: Choe, Cheng-Dae <whitekid@gmail.com>
* Correct a typo: s/linux-opera/linux-openmotif/g.mezz2004-11-021-1/+1
|
* - Update to 2004.06.16pav2004-11-024-167/+276
| | | | | Inspired by: ports/72726 Approved by: maintainer timeout (2 weeks)
* Chase the linux-openmotif shared library version and mark biology/spdbv asmezz2004-11-021-1/+4
| | | | | | | | broke, I get no respone from the maintainer since Oct 22, 2004. The www/linux-opera works fine with new linux-openmotif. Also, bump PORTREVISION. To fix or update for biology/spdbv is welcome, I shall commit them if I get patch(es) in my Inbox.
* Now installs on FreeBSD 5.x.kris2004-10-291-7/+1
|
* - Update to 1.30pav2004-10-283-128/+209
| | | | | | PR: ports/71400 Submitted by: Stefan Walter <sw@gegenunendlich.de> Approved by: maintainer timeout (2 months)
* Avoid the use of != statements in ports Makefilemaho2004-10-241-1/+5
| | | | | PR: 71095 Submitted by: eik
* - Update to 3.62pav2004-10-123-6/+16
| | | | | | | | - Install font files PR: ports/72212 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Approved by: David A. Bader <dbader@ece.unm.edu> (maintainer)
* BROKEN on 5.x: Does not compilekris2004-09-291-1/+7
| | | | Approved by: portmgr (self)
* Upgrade to latest revision to make fetchable again.thierry2004-09-252-3/+3
| | | | Approved by: portmgr (marcus)
* Update config.h and unbreak.thierry2004-09-241-2/+2
| | | | | | PR: ports/71505 Submitted by: maintainer Approved by: portmgr (marcus).
* The build should be fixed now, so remove BROKEN mark.danfe2004-09-231-7/+1
| | | | Approved by: portmgr (marcus), fjoe (mentor, implicit)
* BROKEN on 5.x: Does not compilekris2004-09-191-1/+7
| | | | Approved by: portmgr (self)
* BROKEN on 5.x: Does not installkris2004-09-191-0/+4
| | | | Approved by: portmgr (self)
* BROKEN on 5.x: Does not installkris2004-09-191-0/+4
| | | | Approved by: portmgr (self)
* Unbreak the build on 5.X and -CURRENT.danfe2004-09-181-0/+44
| | | | | Reported by: pointyhat.freebsd.org Approved by: portmgr (marcus), fjoe (mentor, implicit)
* BROKEN on 5.x: Does not compilekris2004-09-181-1/+7
| | | | Approved by: portmgr (self)
* - add missing MAN1 and MAN3leeym2004-09-042-357/+537
| | | | | | | | | - apply DATADIR, EXAMPLESDIR, and DOCSDIR in PLIST - update the usage of NOPORTDOCS PR: 71322 Submitted by: leeym Approved by: Fernan Aguero <fernan@iib.unsam.edu.ar>
* - Unbreak by upgrading to 4.2;thierry2004-08-204-444/+387
| | | | | | | | - Use DIST_SUBDIR because tarball is not versioned; - Add sysdate to PORTVERSION to handle minor revisions; - Do some cleaning.
* biology/lsysexp is not brokenedwin2004-08-181-3/+5
| | | | | | | fix gtk build error PR: ports/70598 Submitted by: David Yeske <dyeske@yahoo.com>
* This is now buildable on 5.x, remove BROKEN.kris2004-08-171-7/+1
|
* After devel/p5-File-Temp has gained an IGNORE for PERL_LEVEL > 500800, allmat2004-08-121-1/+3
| | | | | these ports were broken because they always depended on it. I've rearranged all the dependencies to fit the new scheme.
* - Update to 5.2pav2004-07-312-3/+13
| | | | | PR: ports/69799 Submitted by: Jan Lentfer <Jan.Lentfer@web.de> (maintainer)
* Use X_IMAKE_PORT instead of dist-specific imake dependencies. While here,anholt2004-07-241-6/+3
| | | | make the BROKEN message a little more informative.
* Update to version 2.7.2.1.1krion2004-07-105-42/+35
| | | | | PR: ports/68861 Submitted by: Ports Fury
* Apply a big libtool patch to allow porters to use the libtool installed bymarcus2004-07-101-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | the libtoolX ports instead of the one included with each port. Ports that set USE_LIBTOOL_VER=X will now use the ports version of libtool instead of the included version. To restore previous behavior, use the new macro, USE_INC_LIBTOOL_VER. Both macros accept the same argument: a libtool version. For example, to use the ports version of libtool-1.5, add the following to your Makefile: USE_LIBTOOL_VER= 15 To use the included version of libtool with extra hacks provided by libtool-1.5, add the following to your Makefile: USE_INC_LIBTOOL_VER= 15 With this change, ports that had to add additional libtool hacks to prevent .la files from being installed or to fix certain threading issues can now delete those hacks (after appropriate testing, of course). PR: 63944 Based on work by:eik and marcus Approved by: ade (autotools maintainer) Tested by: kris on pointyhat Bound to be hidden problems: You bet
* Fix distsitevs2004-07-061-2/+1
| | | | | | PR: ports/67473 Submitted by: Roman Neuhauser Approved by: maintainer timeout
* BROKEN: Checksum mismatchkris2004-07-031-0/+2
|
* Update to 4.6vs2004-07-027-51/+58
| | | | | PR: ports/68561 Submitted by: maintainer
* BROKEN: Does not buildkris2004-07-021-0/+2
|
* Update to fix fetch. Rework PORTVERSION to be more like biology/fasta3linimon2004-07-014-9/+11
| | | | | | | | and pacify portlint. PR: ports/67428 Submitted by: Roman Neuhauser <neuhauser at chello dot cz> Approved by: maintainer timeout (one month)
* Chase mastersite and fix checksum to unbreak. (Changes are inclusion of alinimon2004-07-012-8/+4
| | | | | | | | | logfile, one Linux-only change, and one change in a test script). Assign submitter as new maintainer as current one has not responded to PRs for some time. PR: ports/68199 Submitted by: Fernan Aguero <fernan at iib dot unsam dot edu dot ar>
* Update to 1.7.6.1.linimon2004-06-304-11/+43
| | | | | | PR: ports/67429 Submitted by: Roman Neuhauser <neuhauser at chello dot cz> Approved by: maintainer timeout (4 weeks)
* Drop maintainershiplioux2004-06-241-1/+1
|
* Fix MASTER_SITES:vs2004-06-231-2/+2
| | | | | | | | | - add trailing slash - ftp.ebi.ac.uk only has 2.8.0 PR: ports/67427 Submitted by: Roman Neuhauser Approved by: maintainer timeout
* Add ariadne 1.3, programs to compare protein sequences andkrion2004-06-225-0/+60
| | | | | | | profiles, using the Smith-Waterman algorithm. PR: ports/67811 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
* Set an expiry date of 2004-08-20 for these BROKEN/IGNORE/FORBIDDENkris2004-06-222-1/+5
| | | | | ports. They will be removed on or after that date if they are still broken and no fix has been submitted to GNATS.
* BROKEN: Checksum mismatchkris2004-06-201-0/+2
|
* Replace explicit imake dependency with USE_IMAKE=yesanholt2004-06-181-5/+1
|
* Update to 20040613 releaselioux2004-06-132-3/+3
|
* - Remove obsolete MASTER_SITESkrion2004-06-081-2/+1
| | | | | PR: ports/67690 Submitted by: Roman Neuhauser <neuhauser@chello.cz>
* - Update MASTER_SITESpav2004-06-021-3/+3
| | | | | PR: ports/67472 Submitted by: Roman Neuhauser <neuhauser@chello.cz>
* [PATCH] biology/mopac patchsite fixedwin2004-06-011-1/+1
| | | | | | | | | | | | this is a followup to ports/67432 I completely overlooked the fact that the port was setting PATCH_SITES, here's a fix for that maintainer cc'd PR: ports/67441 Submitted by: Roman Neuhauser <neuhauser@chello.cz>
* [PATCH] biology/mopac distsite fixedwin2004-06-011-1/+1
| | | | | | | connection refused (portsurvey reports timeouts) PR: ports/67432 Submitted by: Roman Neuhauser <neuhauser@chello.cz>
* [PATCH] biology/gff2ps distsite fixedwin2004-06-011-3/+3
| | | | | | | couple distfiles with their respective urls to reduce time and traffic PR: ports/67430 Submitted by: Roman Neuhauser <neuhauser@chello.cz>
* - Update WWWpav2004-05-301-1/+1
|
* - Fix MASTER_SITESkrion2004-05-231-4/+1
| | | | | PR: ports/67045 Submitted by: Stefan Walter <sw@gegenunendlich.de>
* - Remove long time unresponsive MASTER_SITEpav2004-05-221-1/+0
| | | | | PR: ports/67016 Submitted by: Roman Neuhauser <neuhauser@chello.cz>
* - Update MASTER_SITES and WWW: linekrion2004-05-222-2/+2
| | | | | PR: ports/67015 Submitted by: Roman Neuhauser <neuhauser@chello.cz>
* Add forgotten patches...thierry2004-05-214-2/+62
|
* BROKEN: Broken pkg-plistkris2004-05-211-0/+2
|
* unbreak, only minor changes in the distfiles (see PR)eik2004-05-182-8/+7
| | | | | | | | Since the distfile has no version number, put it in DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} PR: 66817 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (new maintainer)
* Add a missing BUILD_DEPENDS.thierry2004-05-111-0/+1
| | | | Reported by: Kris.
* Upgrade to 2.0b7 and unbreak.thierry2004-05-117-113/+128
|
* Fix MASTER_SITESmarkus2004-05-091-1/+1
|
* Make portlint happy by replacing space to tabmaho2004-05-072-4/+4
| | | | | PR: 65409 Submitted by: trevor
* - update to 4.5.3petef2004-05-026-17/+235
| | | | | | | - remove version from pkg-descr PR: 65972 Submitted by: maintainer
* - Honor CFLAGSkrion2004-04-161-1/+1
| | | | | PR: ports/65599 Submitted by: michael johnson <ahze at ahze dot net>
* BROKEN: Checksum mismatchkris2004-04-121-0/+2
|
* Mark this port BROKEN with gtk+-2.4.marcus2004-04-111-0/+2
| | | | Reported by: bento via kris
* Tidy up whitespace.trevor2004-04-112-6/+6
|
* Trim whitespace.trevor2004-04-112-66/+66
|
* Add openbabel dependency (bento log forwarded by kris).trevor2004-04-091-0/+2
|
* Update to 1.7.8.trevor2004-04-083-16/+16
|
* After patching, remove the carriage-return characters from povchem.ctrevor2004-04-071-0/+2
| | | | | | because they because they choke GCC 2.95.4. noticed by: kris
* Chase home page.trevor2004-04-071-1/+1
|
* Fix build with gtk 2.4.adamw2004-04-051-1/+6
|
* Chase the glib20 update, and bump all affected ports' PORTREVISIONs.marcus2004-04-054-3/+4
|
* Remove category pkg/COMMENT files in favour of a COMMENT variable in thekris2004-04-022-1/+2
| | | | | | | category makefile. Submitted by: Matthew Seaman <m.seaman@infracaninophile.co.uk> PR: 59651
* SIZEify (maintainer timeout)trevor2004-03-3134-0/+38
|
* Add SIZE data.knu2004-03-221-0/+1
| | | | Submitted by: trevor
* Do not hardcord PICFLAGmaho2004-03-201-7/+1
| | | | Submitted by: ru
* Backout previous change of PICFLAG, sincemaho2004-03-191-0/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | behaviour of -fPIC and -fpic are different. Here is the comment form obrien: -- "-fpic" is a [minor?] optimization for machines that can handle it: -fpic Generate position-independent code (PIC) suitable for use in a shared library, if supported for the target machine. Such code accesses all constant addresses through a global offset table (GOT). The dynamic loader resolves the GOT entries when the program starts (the dynamic loader is not part of GCC; it is part of the operating system). If the GOT size for the linked executable exceeds a machine-specific maximum size, you get an error message from the linker indicating that -fpic does not work; in that case, recompile with -fPIC instead. (These maximums are 16k on the m88k, 8k on the SPARC, and 32k on the m68k and RS/6000. The 386 has no such limit.) -fPIC If supported for the target machine, emit position-independent code, suitable for dynamic linking and avoiding any limit on the size of the global offset table. This option makes a difference on the m68k, m88k, and the SPARC. Thanks to: obrien
* -fPIC is appropreate on all architectures.maho2004-03-191-6/+0
| | | | Submitted by: kris
* Add size data, approved by maintainers.trevor2004-03-191-0/+1
|
* 1) Silent version up without changing the version numbermaho2004-03-183-6/+6
| | | | | | | | very minor change in README 2) change WWW: section at pkg-descr 3) SIZEify Submitted by: kris via bento
* Add size data.trevor2004-03-181-0/+1
| | | | Approved by: maintainers
* SIZEify.trevor2004-03-182-0/+2
|
* 1) update to 0.9.3maho2004-03-175-11/+44
| | | | | | 2) honor PREFIX & LOCALBASE 3) SIZEify 4) possible fix for amd64 and ia64
* Whoa there, boy, that's a mighty big commit y'all have there...ade2004-03-141-1/+1
| | | | | | | | | | | | | | | Begin autotools sanitization sequence by requiring ports to explicitly specify which version of {libtool,autoconf,automake} they need, erasing the concept of a "system default". For ports-in-waiting: USE_LIBTOOL=YES -> USE_LIBTOOL_VER=13 USE_AUTOCONF=YES -> USE_AUTOCONF_VER=213 USE_AUTOMAKE=YES -> USE_AUTOMAKE_VER=14 Ports attempting to use the old style system after June 1st 2004 will be sorely disappointed.
* - Update to version 2003.09.21krion2004-03-124-15/+9
| | | | | PR: ports/64160 Submitted by: Liam J. Foy <liamfoy@sepulcrum.org>
* Insert "-l" into PATCH_ARGS, to cause the "patch" command to ignoretrevor2004-03-091-0/+1
| | | | | carriage-return characters in povchem.c which otherwise cause patch-ab to fail to apply.
* Add MD5 of 2004-01-06 version of povchem.c. Its contents aretrevor2004-03-091-1/+1
| | | | | identical to the 1999-08-22 version, except that the new file has a carriage return character added at the end of each line, DOS-style.
* Unmark as broken for 4.x; instead, mark as ignore for perl < 5.6.linimon2004-03-081-2/+2
|
* BROKEN on amd64 and ia64: Does not compile (missing -fPIC)kris2004-03-071-1/+7
|
* Maintainer reports being unable to look after this port any longer.linimon2004-03-071-1/+1
| | | | Thanks for your efforts in the past.
* - Update to version 0.4krion2004-02-282-3/+3
| | | | | PR: ports/63478 Submitted by: maintainer
* - Fix MASTER_SITESkrion2004-02-281-1/+1
| | | | | PR: ports/63469 Submitted by: maintainer
* Update to 20040226 releaselioux2004-02-273-3/+10
|
* BROKEN on alpha: Does not compilekris2004-02-231-1/+7
|
* BROKEN on alpha 5.x: does not compilekris2004-02-231-1/+7
|
* BROKEN: Checksum mismatchkris2004-02-221-0/+2
|
* BROKEN on 4.x: Configure failskris2004-02-221-1/+7
|
* BROKEN: Does not fetchkris2004-02-221-0/+2
|
* BROKEN: Checksum mismatchkris2004-02-221-0/+2
|
generated by cgit (git 2.34.1) at 2024-11-17 20:27:35 +0800