| Commit message (Collapse) | Author | Age | Files | Lines |
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Reported by: rene
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- Update my mail address to FreeBSD
PR: ports/137652
Submitted by: wenheping@gmail.com(myself)
Approved by: miwi(mentor)
Feature safe: yes
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Feature safe: yes
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Feature safe: yes
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PR: 138813
Submitted by: Ports Fury
Feature safe: yes
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implies lang/gcc44 up from lang/gcc43.
Approved by: portmgr
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Notes:
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PR: 138038
Submitted by: Wen Heping <wenheping@gmail.com>
Approved by: maintainer
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PR: 138264
Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
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way) SCF chromatographic sequence files. It is an interface to
Roger Staden's io-lib. See the installation directions for further
instructions.
WWW: http://search.cpan.org/dist/Bio-SCF/
PR: ports/138263
Submitted by: Wen Heping <wenheping at gmail.com>
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general purpose trace file (and Experiment File) reading interface.
The programmer simply calls the (eg) read_reading to create a "Read"
C structure with the data loaded into memory. It has been compiled
and tested on a variety of unix systems, MacOS X and MS Windows.
WWW: http://staden.sourceforge.net/
PR: ports/138254
Submitted by: Wen Heping <wenheping at gmail.com>
Notes:
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- Reset maintainer to submitter.
PR: ports/138192
Submitted by: Sylvio Cesar <scjamorim@bsd.com.br>
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PR: 138230
Submitted by: Wen Heping <wenheping@gmail.com>
Notes:
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PR: ports/137991
Submitted by: Fernan Aguero (maintainer)
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applications programming interface (API) to the NEXUS file
format of Maddison, et al., 1997 (Syst. Biol. 46:590-621).
NEXUS is a powerful and extensible format designed for use
in evolutionary analysis, including the analysis of molecular
sequence data as well as classical morphological and life-history
data. NEXUS is the input or output format for software such as
PAUP*, MacClade, Mesquite, SIMMAP, MrBayes, Nexplorer, and
so on. This package also contains the demonstration applications
nexplot.pl (plot character data with a tree) and nextool.pl
(allowing programmatic editing, e.g., selecting particular
clades or subsets of data).
WWW: http://search.cpan.org/dist/Bio-NEXUS/
PR: ports/137983
Submitted by: Wen Heping <wenheping at gmail.com>
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Notes:
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starting with B,C
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PR: 137840
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
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PR: 137750
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
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PR: 137625
Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
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Submitted by: pointyhat
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when updating bioperl port
Reported by: pointyhat
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Submitted by: maintainer
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-Update libtool and libltdl to 2.2.6a.
-Remove devel/libtool15 and devel/libltdl15.
-Fix ports build with libtool22/libltdl22.
-Bump ports that depend on libltdl22 due to shared library version change.
-Explain what to do update in the UPDATING.
It has been tested with GNOME2, XFCE4, KDE3, KDE4 and other many wm/desktop
and applications in the runtime.
With help: marcus and kwm
Pointyhat-exp: a few times by pav
Tested by: pgollucci, "Romain Tartière" <romain@blogreen.org>, and
a few MarcusCom CVS users. Also, I might have missed a few.
Repocopy by: marcus
Approved by: portmgr
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bumped or updated
Requested by: edwin
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PR: ports/136771
Exp Run by: pav
Approved by: portmgr (pav)
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PR: ports/135398
Tested by: 2 -exp runs by pav
Approved by: portmgr (pav)
Notes:
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alignments of nucleotide or amino acid sequences. It provides a wide range of
options that were designed to facilitate standard phylogenetic analyses. The
main strengths of PhyML lies in the large number of substitution models coupled
to various options to search the space of phylogenetic tree topologies, going
from very fast and efficient methods to slower but generally more accurate
approaches. It also implements two methods to evaluate branch supports in a
sound statistical framework (the non-parametric bootstrap and the approximate
likelihood ratio test). PhyML was designed to process moderate to large data
sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long
can analyzed. In practice however, the amount of memory required to process a
data set is proportional of the product of the number of sequences by their
length. Hence, a large number of sequences can only be processed provided that
they are short. Also, PhyML can handle long sequences provided that they are
not numerous. With most standard personal computers, the "comfort zone" for
PhyML generally lies around 3 to 500 sequences less than 2,000 character long.
WWW: http://code.google.com/p/phyml/
PR: 136877
Submitted by: Ben Allen <ben@sysadminschronicles.com>
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Tested by: pav on pointyhat
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Reported by: pointyhat
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Notes:
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PR: 136310
Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
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Notes:
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is a beta release. All functions have now been implemented and most
have test suites; the exceptions include the modules involved in
export of MAGE-TAB documents, which are still a little experimental in
nature. The API is mostly finalised (and fully documented), but some
details may yet change where necessary to improve usability.
WWW: http://search.cpan.org/dist/Bio-MAGETAB/
PR: ports/136021
Submitted by: Wen Heping <wenheping at gmail.com>
Notes:
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and thoroughly tested framework for: controlling third-party applications;
devising workflows; querying databases; conducting novel probabilistic
analyses of biological sequence evolution; and generating publication quality
graphics. It is distinguished by many unique built-in capabilities (such as
true codon alignment) and the frequent addition of entirely new methods for
the analysis of genomic data.
WWW: http://pycogent.sourceforge.net/
PR: ports/135863
Submitted by: Wen Heping <wenheping at gmail.com>
Notes:
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Fix the ATLAS/LAPACK build option.
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- Unbreak
PR: 135376
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
Notes:
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Add missing pkg-plist entry for Parsing.so. [2]
Change RUN_DEPENDS --> LIB_DEPENDS for optional math/atlas dependency.
Submitted by: [1] erwin
Reported by: [2] QAT
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modular xorg.
- supply corresponding USE_XORG for all imake-using ports that need it
- USE_IMAKE no longer implies USE_XLIB in absence of USE_XORG
- retire USE_X_PREFIX which is not really used anywhere after the
above change
- a few minor nits like whitespace and SF macro
Tested by: 2 tinderbox runs by pav
Approved by: portmgr (pav)
Notes:
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- Obey PREFIX [2]
Submitted by: maintainer [1] [2]
Reported by: QATty [2]
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Notes:
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Tested by: 3 pointyhat runs
Thanks to: pav, gahr, lwhsu, mva, amdmi3
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Notes:
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2009-05-31 biology/p5-bioperl-run-devel: no longer under development
2009-06-01 net-p2p/deluge05: use net-p2p/deluge instead
2009-06-03 textproc/gmat: failed to build for a long time, no maintainer and apparently no users either
Notes:
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PR: 135141
Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
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Reported by: QAT
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Reported by: QAT
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manipulate, translate, and validate SBML files and data streams. It is
not an application itself (though it does come with example programs),
but rather a library you can embed in your own applications.
LibSBML understands all Levels and Versions of SBML, as well as the
SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in
ISO C and C++ but can be used from all the languages listed in the
right-hand box.
WWW: http://www.sbml.org/
PR: ports/135022
Submitted by: Wen Heping <wenheping at gmail.com>
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Notes:
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Tested by: several builds in P6 TB
Notes:
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