| Commit message (Collapse) | Author | Age | Files | Lines |
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Specifically, newer autoconf (> 2.13) has different semantic of the
configure target. In short, one should use --build=CONFIGURE_TARGET
instead of CONFIGURE_TARGET directly. Otherwise, you will get a warning
and the old semantic may be removed in later autoconf releases.
To workaround this issue, many ports hack the CONFIGURE_TARGET variable
so that it contains the ``--build='' prefix.
To solve this issue, under the fact that some ports still have
configure script generated by the old autoconf, we use runtime detection
in the do-configure target so that the proper argument can be used.
Changes to Mk/*:
- Add runtime detection magic in bsd.port.mk
- Remove CONFIGURE_TARGET hack in various bsd.*.mk
- USE_GNOME=gnometarget is now an no-op
Changes to individual ports, other than removing the CONFIGURE_TARGET hack:
= pkg-plist changed (due to the ugly CONFIGURE_TARGET prefix in * executables)
- comms/gnuradio
- science/abinit
- science/elmer-fem
- science/elmer-matc
- science/elmer-meshgen2d
- science/elmerfront
- science/elmerpost
= use x86_64 as ARCH
- devel/g-wrap
= other changes
- print/magicfilter
GNU_CONFIGURE -> HAS_CONFIGURE since it's not generated by autoconf
Total # of ports modified: 1,027
Total # of ports affected: ~7,000 (set GNU_CONFIGURE to yes)
PR: 126524 (obsoletes 52917)
Submitted by: rafan
Tested on: two pointyhat 7-amd64 exp runs (by pav)
Approved by: portmgr (pav)
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Submitted by: Steve Kargl <sgk at troutmask.apl.washington.edu> at ports@ ML
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PR: 125912
Submitted by: Wen heping <wenheping@gmail.com>
Approved by: maintainer timeout
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Approved by: gabor (mentor)
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FreeBSD versions: 5.3 and up, 6.x, 7.x, 8-CURRENT
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MAKE_ENV
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PR: ports/125891
Submitted by: M. L. Dodson <mldodson@comcast.net> (maintainer)
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Approved by: araujo (mentor)
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- bump PORTREVISION
Prompted by: QA Tindy run
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- Pass maintainership to submitter.
PR: ports/125497
Submitted by: Philip M. Gollucci <pgollucci@p6m7g8.com>
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PR: ports/124648
Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)
Reviewed by: lippe
Approved by: gabor (mentor, implicit)
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PR: ports/125134
Submitted by: Wen heping <wenheping@gmail.com>
Approved by: Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)
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- Bump PORTREVISION.
Reported by: QA Tindy
Approved by: gabor (mentor, implicit)
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sequences. It stands for Sequence Search and Alignment by Hashing
Algorithm. It achieves its fast search speed by converting sequence
information into a `hash table' data structure, which can then be
searched very rapidly for matches.
WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/
PR: ports/124525
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
Approved by: gabor (mentor, implicit)
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- Bump port revision
Reported by: pointyhat via pav
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The affected ports are the ones with gettext as a run-dependency
according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT
in Makefile (29 of them).
PR: ports/124340
Submitted by: edwin@
Approved by: portmgr (pav)
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- Sanitize Makefile a little bit
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assembly
Consed is a tool for viewing, editing, and finishing sequence
assemblies.
The port is constituted of 4 parts:
biology/phred: base caller with quality evaluation
biology/phrap: sequence assembler for shotgun sequencing
biology/consed: workbench
biology/phd2fasta: small utility
All these can be used separately; however, most function
of consed depends on the others.
Although these programs are licensed freely for academic
and nonprofit purposes, users have to contact the authors
to get the softwares.
Phred (including phd2fasta) and phrap are emailed,
and consed can be downloaded to a restricted IP address.
For commercial users, the licensing fee is ca. $10,000 at
the time of writing.
PR: ports/118548
Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
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assembly
Consed is a tool for viewing, editing, and finishing sequence
assemblies.
The port is constituted of 4 parts:
biology/phred: base caller with quality evaluation
biology/phrap: sequence assembler for shotgun sequencing
biology/consed: workbench
biology/phd2fasta: small utility
All these can be used separately; however, most function
of consed depends on the others.
Although these programs are licensed freely for academic
and nonprofit purposes, users have to contact the authors
to get the softwares.
Phred (including phd2fasta) and phrap are emailed,
and consed can be downloaded to a restricted IP address.
For commercial users, the licensing fee is ca. $10,000 at
the time of writing.
PR: ports/118548
Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
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assembly
Consed is a tool for viewing, editing, and finishing sequence
assemblies.
The port is constituted of 4 parts:
biology/phred: base caller with quality evaluation
biology/phrap: sequence assembler for shotgun sequencing
biology/consed: workbench
biology/phd2fasta: small utility
All these can be used separately; however, most function
of consed depends on the others.
Although these programs are licensed freely for academic
and nonprofit purposes, users have to contact the authors
to get the softwares.
Phred (including phd2fasta) and phrap are emailed,
and consed can be downloaded to a restricted IP address.
For commercial users, the licensing fee is ca. $10,000 at
the time of writing.
PR: ports/118548
Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
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assembly
Consed is a tool for viewing, editing, and finishing sequence assemblies.
The port is constituted of 4 parts:
biology/phred: base caller with quality evaluation
biology/phrap: sequence assembler for shotgun sequencing
biology/consed: workbench
biology/phd2fasta: small utility
All these can be used separately; however, most function
of consed depends on the others.
Although these programs are licensed freely for academic
and nonprofit purposes, users have to contact the authors
to get the softwares.
Phred (including phd2fasta) and phrap are emailed,
and consed can be downloaded to a restricted IP address.
For commercial users, the licensing fee is ca. $10,000 at
the time of writing.
PR: ports/118548
Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
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- Support CC/CFLAGS properly
- Strip binary
PR: 123866
Submitted by: Ports Fury
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PR: ports/123530
Submitted by: Philip M. Gollucci <pgollucci@p6m7g8.com>
Reworked by: araujo (myself)
Approved by: flz (portmgr)
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Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
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Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
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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>
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The name stands for multiple sequence comparison by log-expectation.
A range of options is provided that give you the choice of optimizing
accuracy, speed, or some compromise between the two. Default parameters are
those that give the best average accuracy in the published tests. MUSCLE
can achieve both better average accuracy and better speed than CLUSTALW or
T-Coffee, depending on the chosen options.
Citation:
Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy
and high throughput. Nucleic Acids Research 32(5): 1792-1797.
Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with
reduced time and space complexity. BMC Bioinformatics 5(1): 113.
The NAR paper gives only a brief overview of the algorithm and
implementation details. For a full discussion of the method and many of
the non-default options that it offers, please see the BMC paper.
WWW: http://www.drive5.com/muscle/
PR: ports/118460
Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
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Remove BROKEN.
PR: 123218
Submitted by: maintainer
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- take maintainership
Approved by: maintainer
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- Pass maintainership to submitter
PR: 123193
Submitted by: Wen heping <wenheping@gmail.com>
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symbol
Reported by: pointyhat
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- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Remove X11BASE support in favor of LOCALBASE or PREFIX
- Use USE_LDCONFIG instead of INSTALLS_SHLIB
- Remove unneeded USE_GCC 3.4+
Thanks to all Helpers:
Dmitry Marakasov, Chess Griffin, beech@, dinoex, rafan, gahr,
ehaupt, nox, itetcu, flz, pav
PR: 116263
Tested on: pointyhat
Approved by: portmgr (pav)
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PR: ports/122130
Submitted by: Ganael Laplanche <ganael.laplanche@martymac.com>
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Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
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${MASTER_SITE_PERL_CPAN} to CPAN.
PR: ports/122674
Submitted by: Philip M. Gollucci <pgollucci@p6m7g8.com>
Reworked by: araujo (myself)
Approved by: portmgr (pav)
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the download site pointed by their webpage as first choice.
Noticed by: pointyhat via pav
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PR: ports/122437
Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
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PR: ports/122437
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
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Requested over: IRC
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PR: ports/122607
Submitted by: maintainer (Fernan Aguero)
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Approved by: thierry (mentor)
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- Mark as deprecated
PR: ports/122474
Submitted by: M. L. Dodson <mldodson at comcast.net> (maintainer with another email)
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linkage maps of markers segregating in experimental crosses. MAPMAKER/EXP
performs full multipoint linkage analysis (simultaneous estimation of all
recombination fractions from the primary data) for dominant, recessive, and co-
dominant (e.g. RFLP-like) markers. MAPMAKER/EXP is an experimental-cross-only
successor to the original MAPMAKER program.
MAPMAKER/QTL is a companion program to MAPMAKER/EXP which allows one to map
genes controlling polygenic quantitative traits in F2 intercrosses and BC1
backcrosses relative to a genetic linkage map. More information on MAPMAKER/QTL
can be found in the technical report (included with MAPMAKER/QTL).
WWW: http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/
PR: ports/122452
Submitted by: Tassilo Philipp <tphilipp at potion-studios.com>
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- Remove gcc version restriction
PR: ports/122435
Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
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PR: ports/122374
Submitted by: Wen heping <wenheping@gmail.com>
Patch revised: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
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Reported by: pointyhat
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- Switch to .tar.gz distfile so that we don't define our do-extract
- While I'm here, using substitution for version numbers in pkg-plist
for easier upgrade
PR: ports/121690
Submitted by: Wen heping <wenheping at gmail.com>
Approved by: maintainer timeout (2 weeks)
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Approved by: miwi (mentor)
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- Bump PORTREVISION
Submitted by: pointyhat via pav
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- Bump PORTREVISION
Approved by: portmgr (xorg cleanup)
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- Bump PORTREVISION
Approved by: portmgr (xorg cleanup)
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- Bump PORTREVISION
Approved by: portmgr (xorg cleanup)
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- Bump PORTREVISION
Approved by: portmgr (xorg cleanup)
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- Bump portrevision
Approved by: David Yeske <dyeske@gmail.com> (maintainer, implicit)
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- Add RESTRICTED due to non-commercial use licence.
PR: ports/121794
Submitted by: KATO Tsuguru <tkato432@yahoo.com>
Approved by: thierry and tabthorpe (mentors)
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- Add RESTRICTED due to a non-commercial use licence.
PR: ports/121794
Submitted by: KATO Tsuguru <tkato432@yahoo.com>
Approved by: thierry and tabthorpe (mentors)
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Submitted by: pav
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Submitted by: pointyhat via pav/erwin
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Reported by: pointyhat
Pointy hat to: pav
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Submitted by: Ports Fury
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Submitted by: pointyhat via pav
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PR: 119719
Submitted by: KATO Tsuguru <tkato432@yahoo.com>
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PR: 118922
Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
Approved by: Fernan Aguero <fernan@iib.unsam.edu.ar>
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PR: ports/117713
Submitted by: Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
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Bayesian inference of phylogeny is based upon a quantity called the
posterior probability distribution of trees, which is the probability of a
tree conditioned on the observations. The conditioning is accomplished
using Bayes's theorem. The posterior probability distribution of trees is
impossible to calculate analytically; instead, MrBayes uses a simulation
technique called Markov chain Monte Carlo (or MCMC) to approximate the
posterior probabilities of trees.
WWW: http://mrbayes.csit.fsu.edu/
PR: ports/118542
Submitted by: mzaki at biol.s.u-tokyo.ac.jp
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or draft sequence. This package provides an efficient suffix tree library,
seed-and-extend alignment, SNP detection, repeat detection, and
visualization tools.
WWW: http://mummer.sourceforge.net/
PR: ports/118142
Submitted by: Tony Maher
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Reported by: pointyhat
Approved by: portmgr (hat)
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- Fix pkg-plist
- Bump PORTREVISION
PR: 117435
Submitted by: "M. L. Dodson" <mldodson@comcast.net> (maintainer)
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PR: ports/117369
Submitted by: Motomichi Matsuzaki <mzaki_AT_e-mail dot ne dot jp>
Approved by: maintainer (Mauricio Herrera Cuadra)
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PR: 117336
Submitted by: KATO Tsuguru <tkato432@yahoo.com>
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PR: 117086
Tested by: -exp runs
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PR: 116017
Submitted by: KATO Tsuguru <tkato432@yahoo.com>
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Inspired by: Jason Harris <jharris@widomaker.com>
Howto: http://twiki.cenkes.org/Cenkes/SortingCategoryMakefiles
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(also: update to 5.0.4)
Upon installing FoldingAtHome I ran the software from a
user account only to find that I was stuck in a loop of
trying to enter configuration options. Shortly thereafter
I realized that it was trying to write to
/usr/local/share/foldingathome, and therefore requires being
run as root to write there unless one changes permissions
there. Seing as this isn't installed with a startup script
for daemonization, and running as root seems a little
excessive for this application, should this be adapted to
run from a user account or set up to be able to start at
boot?
And from maintainer:
This diff updates the port to version 5.04, and adds
support to running as normal user using ~/.fah
directory.
PR: ports/113335
Submitted by: James Snyder <jbsnyder@fanplastic.org>
Approved by: maintainer
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Drop support for antique perl.
Work done by: gabor
Sponsored by: Google Summer of Code 2007
Hat: portmgr
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- Remove 4.X cruft
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PR: ports/116019
Submitted by: KATO Tsuguru
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PR: 115302
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Submitted by: maintainer
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Spotted by: pav
Approved by: miwi (mentor)
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PR: 114738
Submitted by: KATO Tsuguru <tkato432 (AT) yahoo.com>
Approved by: miwi (mentor)
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Approved by: maintainer (implicit)
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Reported by: Rene Ladan <r.c.ladan@gmail.com>
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- Don't install CVS directories which are going to be removed
in next release
PR: ports/113831
Submitted by: Thomas Abthorpe <thomas at goodking.ca>
Approved by: maintainer timeout (20 days)
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PR: 111719
Submitted by: araujo@bsdmail.org
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- Remove BROKEN tag
Reported by: pointyhat (logs)
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Reported by: stas@
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PR: 111817
Submitted by: "P.BandieraPaiva" <paiva@unifesp.br>
Approved by: maintainer
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Approved by: gurkan (maintainer)
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dasher.wustl.edu
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- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
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PR: ports/111728
Submitted by: Edwin Groothuis <edwin@mavetju.org>
Approved by: maintainer timeout
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PR: ports/111726
Submitted by: Edwin Groothuis <edwin@mavetju.org>
Approved by: maintainer timeout
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PR: ports/111725
Submitted by: Edwin Groothuis <edwin@mavetju.org>
Approved by: maintainer timeout
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PR: ports/111724
Submitted by: Edwin Groothuis <edwin@mavetju.org>
Approved by: maintainer timeout
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Approved by: delphij (mentor)
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- Add backup MASTER_SITES
PR: 111963
Submitted by: Jason Harris <jharris@widomaker.com>
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PR: ports/111727
Submitted by: Edwin Groothuis <edwin@mavetju.org>
Approved by: Bob Zimmermann <rpz@cse.wustl.edu>
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- Make portlint happier
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Reported by: pointyhat
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- Pass maintainership to submitter
PR: 110621
Submitted by: Nemo Liu<nemoliu@gmail.com>
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PR: ports/109954
Submitted by: Tsurutani Naoki <turutani@scphys.kyoto-u.ac.jp>
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email.
Hat: portmgr
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Hat: portmgr
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Hat: portmgr
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PR: 110080
Submitted by: Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
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PR: 110079
Submitted by: Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
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PR: 110078
Submitted by: Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
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Approved by: maintainer
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broken at that time and no fix has been submitted.
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PR: 108940
Submitted by: CHAO Shin
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PR: 103931
Approved by: pav
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Submitted by: kris via pointyhat and pav.
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PR: ports/108434
Submitted by: Marcelo Araujo
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2007-01-07 biology/coalesce: distfile disappeared from homepage
Actually the software is still available at:
http://evolution.gs.washington.edu/lamarc/coalesce.html, but it is
not supported by the authors. Last version is from 1995 and
biology/fluctuate can be used instead.
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shortly.
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PR: ports/108214
Submitted by: Thomas Abthorpe <thomas at goodking.ca>
Approved by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
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Submitted by: kris via pointyhat.
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Submitted by: kris via pointyhat.
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* Bump port revision.
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. bump PORTREVISION (RUN_DEPENDS changes);
. for converters/konwert:
- introduce PATCHLEVEL to be used instead of PORTREVISION at filenames;
- update to new PATCHLEVEL=11.
PR: 107000 [1], 107046 [2], 107106 [3], 107114 [4]
Submitted by: bsam (me)
Approved by: all maintainers timeout three and a half week:
mij at bitchx.it [1]
j.koopmann at seceidos.de [2]
chuynh at biolateral.com.au [3]
alexs at snark.rinet.ru [4]
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* Bump port revision.
* fix build [1].
Submitted by: kris [1]
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Approved by: gurkan@linuks.mine.nu
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* Bump port revision.
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Bump portrevision.
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Bump portrevision.
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migration. currently it is not buildable with gfrotran42.
* Honor FC and FFLAGS.
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support for reading and writing BEAST, Clustal, EMBL, Fasta, GCG-MSF, GDE,
Hennig86, NCBI, NEXUS, NONA, PDB, Phylip, PIR, Plain/Raw, Swiss-Prot and
TNT files by writing only three lines of code.
The framework is written in Cocoa (Objective-C).
WWW: http://bioinformatics.org/biococoa/
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- Update MASTER_SITES
- Pass maintainership to submitter
PR: ports/107246
Submitted by: Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
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to email.
Hat: portmgr
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- Update maintainer mail adresse
PR: ports/107118
Submitted by: M. L. Dodson <bdodson@houston.rr.com> (maintainer)
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PR: ports/106300
Submitted by: chinsan
Approved by: maintainer timeout (15 days)
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Hat: portmgr
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Hat: portmgr
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- Fix fetching
- Remove old patch and use MAKE_ARGS instead
- portlint(1) and whitespace
Approved by: erwin (mentor)
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- Set EXPIRATION_DATE
Approved by: erwin (mentor)
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Approved by: portmgr (linimon)
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Submitted by: Jin-Shan Tseng <tjs@cdpa.nsysu.edu.tw>
Approved by: maintainer timeout (3 months)
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cc -O -pipe -fPIC -g -Wall -DACEDB4 -I. -I./wh -DFREEBSD -c -O -pipe -fPIC -g -Wall -DACEDB4 -c arraysub.c
arraysub.c: In function `stackused':
arraysub.c:54: error: unrecognizable insn:
(insn 44 22 24 2 arraysub.c:53 (set (reg:SI 1 dx [66])
(subreg:SI (plus:DI (subreg:DI (reg:SI 7 sp) 0)
(const_int -1 [0xffffffffffffffff])) 0)) -1 (nil)
(nil))
arraysub.c:54: internal compiler error: in extract_insn, at recog.c:2083
Reported by: pointyhat via kris
Approved by: Philip M. Gollucci (maintainer)
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Approved by: maintainer (implicit)
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PR: ports/101613
Submitted by: alepulver
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PR: ports/105891
Submitted by: trasz
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- Unbreak on amd64
PR: ports/105414
Submitted by: rafan
Approved by: maintainer timeout (15 days)
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- Add a regression-test target;
- Fix plist for WITHOUT_SAMPLES.
PR: ports/104685
Approved by: maintainer's time-out (1 month)
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Submitted by: Gürkan Sengün
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includes data management and analysis capabilities.
WWW: http://diana.imim.es/Adun
Submitted by: Gürkan Sengün
Reviewed by: dinoex
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PR: ports/104635
Submitted by: Thomas Abthorpe <thomas@goodking.ca>
Approved by: maintainer
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PR: ports/104508
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
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PR: ports/104341
Submitted by: Frank J. Laszlo <laszlof@vonostingroup.com>
Approved by: portmgr (marcus)
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new freetype2 where needed.
Submitted by: mezz, ahze, pav, and many others
Approved by: portmgr (implicit, kris)
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PR: ports/102168
Approved by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
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PR: ports/103408
Submitted by: chinsan
Approved by: maintainer (timeout)
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and EST Sequences.
PR: ports/103651
Submitted by: Bob Zimmermann <rpz at cse.wustl.edu>
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Changelog at <http://www.cmbi.ru.nl/molden/HISTORY>.
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Submitted by: kris
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for termination on 2006-12-01
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world download and run software to band together to make one of the largest
supercomputers in the world. Every computer makes the project closer to our
goals.
Folding@Home uses novel computational methods coupled to distributed computing,
to simulate problems thousands to millions of times more challenging than
previously achieved.
WWW: http://folding.standford.edu
PR: ports/101235
Submitted by: Yonatan <onatan@gmail.com>
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- these include astro/ audio/ biology/ chinese/ maintained by ports@
PR: ports/101916
Submitted by: Gea-Suan Lin <gslin_AT_gslin dot org>
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PR: ports/101789
Submitted by: Scott Flatman <sf@slappy.org>
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- pet portlint(1)
Noticed by: pointyhat via linimon [1]
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- Pass maintainersip to submitter
PR: 99901
Submitted by: Scott Flatman <sf slappy.org>
Approved by: delphij (mentor, implicit)
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PR: 99757
Submitted by: Jin-Shan Tseng <tjs@cdpa.nsysu.edu.tw>
Approved by: delphij (mentor, implicit)
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o add data dir to have working port[1]
PR: 95121[1]
Submitted by: Sangwoo Shim <sangwoos at gmail.com>[1]
This commit is a result of hacks at the CodeFest Akihabara 2006 hosted by FSIJ.
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protein similarities that plays a key role in many bioinformatics methods. It
contains about all currently published protein sequences and is continuously
updated.
The computational effort for keeping SIMAP up-to-date is constantly increasing.
Please help to update SIMAP by calculating protein similarities on your
computer.
WWW: http://boinc.bio.wzw.tum.de/boincsimap/
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PR: ports/99072 (fu2)
Submitted by: Josh Tolbert <hemi (at) puresimplicity.net> (maintainer)
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- Take maintainership.
PR: ports/99072
Submitted by: Josh Tolbert <hemi (at) puresimplicity.net>
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2 years ago. Clean out the last traces of it.
With hat: portmgr
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- Update the port to add other architectures (amd64)
PR: ports/98764
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
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PR: ports/98761
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
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Quoting from www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml
Major changes include:
blastall now uses the new engine by default, resulting
in significant performance improvements and enabling
query concatenation for all program types.
PR: ports/98570
Submitted by: maintainer
Approved by: lawrance (mentor, implict)
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- Use DATADIR
PR: 97603
Submitted by: miwi
Approved by: maintainer timeout
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- While I'm here, pet portlint [2]
PR: 98398 [1]
Submitted by: miwi [1], self [2]
Approved by: maintainer [1]
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- add MASTER_SITE_LOCAL as a second master site
PR: ports/97310
Submitted by: maintainer
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PR: ports/96941
Submitted by: Paul Schmehl <pauls@utdallas.edu>
Approved by: maintainer timeout
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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
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Approved by: tobez (implicit)
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PR: ports/96063
Submitted by: maintainer
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Reported by: fenner's distfile survey
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dynamics (MD) simulations.
PR: 95123
Submitted by: Sangwoo Shim <sangwoos@gmail.com>
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- 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
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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>
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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>
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- Provide OPTIONS
- Take maintainership
PR: ports/94123
Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net>
|