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non port: head/science/Makefile

Number of commits found: 250 (showing only 100 on this page)

1 | 2 | 3  »  

Wed, 26 Mar 2014
[ 01:15 swills ] Original commit 
349203 science/Makefile
349203 science/rubygem-netcdf
349203 science/rubygem-netcdf/Makefile
349203 science/rubygem-netcdf/distinfo
349203 science/rubygem-netcdf/files
349203 science/rubygem-netcdf/files/patch-extconf.rb
349203 science/rubygem-netcdf/pkg-descr
This is a Ruby interface to the NetCDF scientific IO library.


PR:		ports/187932
Submitted by:	Shin-ya Murakami <>
Thu, 27 Feb 2014
[ 22:39 rene ] Original commit 
346397 MOVED
346397 graphics/Makefile
346397 graphics/kgraphviewer
346397 japanese/Makefile
346397 japanese/trac
346397 lang/Makefile
346397 lang/opa
346397 misc/Makefile
346397 misc/xbiso
346397 net-p2p/Makefile

(Only the first 10 of 27 ports in this commit are shown above. View all ports for this commit)
Remove expired ports:
2014-02-26 www/trac-hierwiki: Runtime is broken, doesn't support Trac>0.11
2014-02-27 net-p2p/microdc2: Broken for more than 6 month
2014-02-27 www/openvrml: Broken for more than 6 month
2014-02-27 science/peekabot: Broken for more than 6 month
2014-02-27 misc/xbiso: Broken for more than 6 month
2014-02-27 net/hornetq: Broken for more than 6 month
2014-02-27 sysutils/slmon: Broken for more than 6 month
2014-02-27 www/trac-revtree: Broken for more than 6 months
2014-02-27 security/crack: Broken for more than 6 month
2014-02-27 sysutils/graphicboot: Broken for more then 6 month
2014-02-27 graphics/kgraphviewer: Broken for more than 6 month
2014-02-27 sysutils/ckl: Broken for more than 6 month
2014-02-27 japanese/trac: Broken for more than 6 month
2014-02-27 lang/opa: Broken for more than 6 month
2014-02-27 sysutils/mmore: Broken for more than 6 month
2014-02-27 www/trac-announcer: Broken for more than 6 month
Fri, 21 Feb 2014
[ 15:39 thierry ] Original commit 
345491 science/Makefile
345491 science/openkim
345491 science/openkim/Makefile
345491 science/openkim/distinfo
345491 science/openkim/files
345491 science/openkim/files/
345491 science/openkim/pkg-descr
345491 science/openkim/pkg-plist
Adding OpenKIM, an application programming interface (API) for
coupling atomistic simulation codes and interatomic potential

PR:		ports/177692
Submitted by:	Jason Bacon <jwbacon (at)>
Fri, 3 Jan 2014
[ 00:13 jgh ] Original commit 
338510 science/Makefile
338510 science/sigrok-cli
338510 science/sigrok-cli/Makefile
338510 science/sigrok-cli/distinfo
338510 science/sigrok-cli/pkg-descr
The sigrok project aims at creating a portable, cross-platform,
Free/Libre/Open-Source signal analysis software suite that supports
various device types, such as logic analyzers, MSOs, oscilloscopes,
multimeters, LCR meters, sound level meters, thermometers,
hygrometers, anemometers, light meters, DAQs, dataloggers,
function generators, spectrum analyzers, power supplies,
GPIB interfaces, and more.

sigrok-cli is a command-line tool written in C, which uses both libsigrok
and libsigrokdecode to provide the basic sigrok functionality from the
command-line. Among other things, it's useful for scripting purposes.


PR:		ports/179855
Submitted by:	Uffe Jakobsen <>
Sun, 8 Dec 2013
[ 14:12 wg ] Original commit 
335895 science/Makefile
335895 science/py-pyaixi
335895 science/py-pyaixi/Makefile
335895 science/py-pyaixi/distinfo
335895 science/py-pyaixi/pkg-descr
science/py-pyaixi: Implementation of the MC-AIXI-CTW AI algorithm

pyaixi is a pure Python implementation of the Monte Carlo-AIXI-Context Tree
Weighting (MC-AIXI-CTW) artificial intelligence algorithm.

This is an approximation of the AIXI universal artificial intelligence
algorithm, which describes a model-based, reinforcement-learning agent capable
of general learning.


PR:		ports/184572
Submitted by:	Johannes Jost Meixner <xmj>
Thu, 5 Dec 2013
[ 12:14 rene ] Original commit 
335664 MOVED
335664 science/Makefile
335664 science/omnetpp
335664 x11-themes/Makefile
335664 x11-themes/lila-xfwm4
Remove expired ports:
2013-12-04 x11-themes/lila-xfwm4: Upstream development dead
2013-12-05 science/omnetpp: depends on expired textproc/libxml
Wed, 30 Oct 2013
[ 15:51 wg ] Original commit 
332132 science/Makefile
332132 science/py-pydap
332132 science/py-pydap/Makefile
332132 science/py-pydap/distinfo
332132 science/py-pydap/files
332132 science/py-pydap/files/
332132 science/py-pydap/pkg-descr
science/py-pydap: Implementation of the Opendap/DODS protocol

Pydap is an implementation of the Opendap/DODS protocol, written from scratch.
You can use Pydap to access scientific data on the internet without having to
download it; instead, you work with special array and iterable objects that
download data on-the-fly as necessary, saving bandwidth and time. The module
also comes with a robust-but-lightweight Opendap server, implemented as a WSGI


PR:		ports/181687
Submitted by:	Johannes Meixner <xmj>
Mon, 14 Oct 2013
[ 07:25 bapt ] Original commit 
330279 MOVED
330279 science/Makefile
330279 science/mayavi
Fix index by removing a hidden dependency on vtk4
[ 06:57 bapt ] Original commit 
330276 MOVED
330276 science/Makefile
330276 science/ovt
Remove ports depending on vtk4

Approved by: (maintainer)
Tue, 8 Oct 2013
[ 19:31 theraven ] Original commit 
329828 science/Makefile
329828 science/fisicalab
329828 science/fisicalab/Makefile
329828 science/fisicalab/distinfo
329828 science/fisicalab/pkg-descr
329828 science/fisicalab/pkg-plist
Added FisicaLab port.

Approved by:	bapt (mentor)
Mon, 2 Sep 2013
[ 11:27 koobs ] Original commit 
325976 science/Makefile
325976 science/py-pupynere
325976 science/py-pupynere/Makefile
325976 science/py-pupynere/distinfo
325976 science/py-pupynere/files
325976 science/py-pupynere/files/
325976 science/py-pupynere/pkg-descr
325976 science/py-pupynere/pkg-plist
science/py-pupynere: Module for reading and writing NetCDF files [NEW PORT]

Pupynere is a Python module for reading and writing NetCDF files, using the same
API as Scientific.IO.NetCDF and pynetcdf. It depends only on Numpy, so you don't
need to have the NetCDF library installed.


PR:		ports/179744
Submitted by:	Johannes Jost Meixner <>
Fri, 26 Jul 2013
[ 19:19 rene ] Original commit 
323748 CHANGES
323748 KNOBS
323748 MOVED
323748 Mk/
323748 Mk/
323748 accessibility/Makefile
323748 accessibility/kdeaccessibility
323748 arabic/Makefile
323748 arabic/kde3-i18n
323748 archivers/Makefile

(Only the first 10 of 435 ports in this commit are shown above. View all ports for this commit)
KDE3 and QT3 expired on 2013-07-01, remove these ports.
Unfortunately, this also affects some ports using QT3 as a GUI toolkit.

Changes to infrastructure files:
- : obsolete, remove
- : note that a CONFLICTS_BUILD line can probably go after a while
- CHANGES : document the removals from
- KNOBS : remove KDE and QT (KDE4 and QT4 should be used instead)
- MOVED : add the removed ports

PR:		ports/180745
Submitted by:	rene
Approved by:	portmgr (bapt)
Exp-run by:	bapt
Mon, 22 Jul 2013
[ 18:02 olivierd ] Original commit 
323488 science/Makefile
323488 science/xfce4-equake-plugin
323488 science/xfce4-equake-plugin/Makefile
323488 science/xfce4-equake-plugin/distinfo
323488 science/xfce4-equake-plugin/files
323488 science/xfce4-equake-plugin/files/patch-panel-plugin__equake_applet.c
323488 science/xfce4-equake-plugin/pkg-descr
323488 science/xfce4-equake-plugin/pkg-plist
Equake is a panel plugin which monitors and displays earthquakes each time
a new one occurs.

Sat, 15 Jun 2013
[ 19:08 mandree ] Original commit 
321012 science/Makefile
321012 science/py-coards
321012 science/py-coards/Makefile
321012 science/py-coards/distinfo
321012 science/py-coards/pkg-descr
321012 science/py-coards/pkg-plist
Add new port science/py-coards:
Coards is a parser for time values represented using the COADS convention.


PR:		ports/179576
Submitted by:	Johannes Meixner <>
Fri, 17 May 2013
[ 13:55 wen ] Original commit 
318385 science/Makefile
318385 science/py-obspy
318385 science/py-obspy-core
- Rename science/py-obspy-core to science/py-obspy
[ 13:44 wen ] Original commit 
318382 science/Makefile
318382 science/py-obspy.db
318382 science/py-obspy.gse2
318382 science/py-obspy.imaging
318382 science/py-obspy.iris
318382 science/py-obspy.mseed
318382 science/py-obspy.signal
318382 science/py-obspy.taup
318382 science/py-obspy.wav
318382 science/py-obspy.xseed
- Remove these obspy modules, because they are included in obspy upstream now.
Tue, 16 Apr 2013
[ 22:46 jgh ] Original commit 
315916 science/Makefile
315916 science/voro++
315916 science/voro++/Makefile
315916 science/voro++/distinfo
315916 science/voro++/pkg-descr
315916 science/voro++/pkg-plist
- add new port: science/voro++

Voro++ is a software library for carrying out three-dimensional computations
of the Voronoi tessellation. A distinguishing feature of the Voro++ library
is that it carries out cell-based calculations, computing the Voronoi cell
for each particle individually. It is particularly well-suited for
applications that rely on cell-based statistics, where features of Voronoi
cells (eg. volume, centroid, number of faces) can be used to analyze a
system of particles.


PR:		177678
Submitted by:

Feature safe:	yes
Thu, 28 Mar 2013
[ 13:10 makc ] Original commit 
315467 MOVED
315467 science/Makefile
315467 science/py-biolccc
315467 science/pyteomics.biolccc
315467 science/pyteomics.biolccc/Makefile
315467 science/pyteomics.biolccc/distinfo
315467 science/pyteomics.biolccc/pkg-descr
315467 science/pyteomics.biolccc/pkg-plist
- Rename pyBioLCCC to pyteomics.biolccc (follow upstream)
- Update to 1.5.0
- Trim Makefile header
[ 13:05 makc ] Original commit 
315466 science/Makefile
315466 science/pyteomics
315466 science/pyteomics/Makefile
315466 science/pyteomics/distinfo
315466 science/pyteomics/pkg-descr
315466 science/pyteomics/pkg-plist
Add new port science/pyteomics:

Pyteomics is a collection of lightweight and handy tools for Python
that help to handle various sorts of proteomics data.  Pyteomics
provides a growing set of modules to facilitate the most common
tasks in proteomics data analysis, such as:
 * calculation of basic physico-chemical properties of polypeptides:
   . mass and isotopic distribution
   . charge and pI
   . chromatographic retention time
 * access to common proteomics data:
   . MS or LC-MS data
   . FASTA databases
   . search engines output
 * easy manipulation of sequences of modified peptides and proteins

Wed, 20 Feb 2013
[ 17:30 makc ] Original commit 
312631 science/Makefile
312631 science/fvcom
312631 science/fvcom-mpi
312631 science/fvcom-mpi/Makefile
312631 science/fvcom/Makefile
312631 science/fvcom/distinfo
312631 science/fvcom/files
312631 science/fvcom/files/patch-METIS_source-makefile
312631 science/fvcom/files/patch-Makefile
312631 science/fvcom/files/patch-mod_lag.F

(Only the first 10 of 11 ports in this commit are shown above. View all ports for this commit)
Add new ports science/fvcom and science/fvcom-mpi:

FVCOM is a prognostic, unstructured-grid, finite-volume, free-surface,
3-D primitive equation coastal ocean circulation model developed
by UMASSD-WHOI joint efforts.


PR:		ports/166726
PR:		ports/166728
Submitted by:	Jason Bacon <jwbacon at>
Wed, 6 Feb 2013
[ 07:46 bapt ] Original commit 
311747 MOVED
311747 graphics/Makefile
311747 graphics/py-visual
311747 japanese/Makefile
311747 japanese/vflib
311747 math/Makefile
311747 math/gnuplot+
311747 science/Makefile
311747 science/vis5d+
japanese/vflib||2013-02-06|Has expired: No more public distfiles
graphics/py-visual||2013-02-06|Has expired: Depends on the expired
x11-toolkits/gtkglarea [1]
math/gnuplot+||2013-02-06|Upstream says: This package is obsolete. The author
does not recommend to use it
science/vis5d+||2013-02-06|No new release since 2001, depends on expired
x11-toolkits/gtkglarea [2]

Approved by:	stephen [1],
		nivit [2]
Tue, 11 Dec 2012
[ 14:19 makc ] Original commit 
308694 MOVED
308694 biology/xdrawchem/Makefile
308694 biology/xdrawchem/files
308694 biology/xdrawchem/files/patch-xdrawchem__application_ob.cpp
308694 science/Makefile
308694 science/avogadro/Makefile
308694 science/gchemutils/Makefile
308694 science/ghemical/Makefile
308694 science/kalzium/Makefile
308694 science/libghemical/Makefile

(Only the first 10 of 17 ports in this commit are shown above. View all ports for this commit)
- Update openbabel to 2.3.2
- Switch to CMake build system
- Add PYTHON and CAIRO options
- Don't rename babel binary, mark conflict with ancient biology/babel

- Merge py-openbabel to openbabel

- chase openbabel update
Fri, 19 Oct 2012
[ 12:24 demon ] Original commit 
306115 science/Makefile
306115 science/py-scikit-learn
306115 science/py-scikit-learn/Makefile
306115 science/py-scikit-learn/distinfo
306115 science/py-scikit-learn/pkg-descr
306115 science/py-scikit-learn/pkg-plist
scikit-learn is a Python module integrating classic machine learning
algorithms in the tightly-knit scientific Python world (numpy, scipy,
matplotlib).  It aims to provide simple and efficient solutions to
learning problems, accessible to everybody and reusable in various contexts:
machine-learning as a versatile tool for science and engineering.


Feature safe:	yes
Thu, 12 Jul 2012
[ 01:57 linimon ] Original commit 
1.239 science/Makefile
Complete the removal of ics to silence warnings on pointyhat.

Hat:            portmgr
Sat, 7 Jul 2012
[ 15:15 thierry ] Original commit 
1.238 science/Makefile
1.1 science/mei/Makefile
1.1 science/mei/distinfo
1.1 science/mei/files/
1.1 science/mei/pkg-descr
1.1 science/mei/pkg-plist
MEI stands for Mathematical Expression Interpreter.
It is intended to provide interpretation of mathematical formula in a string.

Thu, 19 Apr 2012
[ 12:43 tota ] Original commit 
1.237 science/Makefile
1.1 science/R-cran-som/Makefile
1.1 science/R-cran-som/distinfo
1.1 science/R-cran-som/pkg-descr
- Add a new port: science/R-cran-som

  Self-Organizing Map (with application in gene clustering)

Tue, 17 Apr 2012
[ 17:35 pawel ] Original commit 
1.236 science/Makefile
1.1 science/dlpoly-classic/Makefile
1.1 science/dlpoly-classic/distinfo
1.1 science/dlpoly-classic/files/
1.1 science/dlpoly-classic/pkg-descr
1.1 science/dlpoly-classic/pkg-message
1.1 science/dlpoly-classic/pkg-plist
DL_POLY is a general purpose classical molecular dynamics (MD) simulation
software developed at Daresbury Laboratory by I.T. Todorov and W. Smith.


PR:             ports/166725
Submitted by:   Jason Bacon <>
Thu, 8 Mar 2012
[ 04:34 pgollucci ] Original commit 
1.769 math/Makefile
1.17 math/ruby-netcdf/Makefile
1.12 math/ruby-netcdf/distinfo
1.2 math/ruby-netcdf/files/patch-extconf.rb
1.3 math/ruby-netcdf/pkg-descr
1.5 math/ruby-netcdf/pkg-plist
1.235 science/Makefile
1.18 science/ruby-netcdf/Makefile
1.13 science/ruby-netcdf/distinfo
1.4 science/ruby-netcdf/pkg-descr

(Only the first 10 of 11 ports in this commit are shown above. View all ports for this commit)
- update to 0.6.6
- add and update URLs of MASTER_SITES
- update author's email address
- use @dirrmtry
- change port category from math to science.

- Completes repo copy from math/ruby-netcdf -> science/ruby-netcdf

PR:             ports/165314
Submitted by:   Shin-ya Murakami <>
Sat, 11 Feb 2012
[ 02:26 tota ] Original commit 
1.234 science/Makefile
1.1 science/R-cran-e1071/Makefile
1.1 science/R-cran-e1071/distinfo
1.1 science/R-cran-e1071/pkg-descr
- Add a new port: science/R-cran-e1071

  Functions for latent class analysis, short time Fourier transform,
  fuzzy clustering, support vector machines, shortest path computation,
  bagged clustering, naive Bayes classifier, ...

Fri, 3 Feb 2012
[ 12:04 tota ] Original commit 
1.2766 MOVED
1.233 science/Makefile
1.2 science/R-cran-survival/Makefile
1.2 science/R-cran-survival/distinfo
1.2 science/R-cran-survival/pkg-descr
- Remove science/R-cran-survival which has been already included in math/R

Reported by:    pointyhat (pav)
Tue, 31 Jan 2012
[ 13:22 tota ] Original commit 
1.232 science/Makefile
1.1 science/R-cran-survival/Makefile
1.1 science/R-cran-survival/distinfo
1.1 science/R-cran-survival/pkg-descr
- Add a new port: science/R-cran-survival

  survival analysis: descriptive statistics, two-sample tests,
  parametric accelerated failure models, Cox model. Delayed entry
  (truncation) allowed for all models; interval censoring for parametric
  models. Case-cohort designs.

[ 13:14 tota ] Original commit 
1.231 science/Makefile
1.1 science/R-cran-snow/Makefile
1.1 science/R-cran-snow/distinfo
1.1 science/R-cran-snow/pkg-descr
- Add a new port: science/R-cran-snow

  The snow package provides support for simple parallel computing on a
  network of workstations using R.  A master R process calls makeCluster
  to start a cluster of worker processes; the master process then uses
  functions such as clusterCall and clusterApply to execute R code on
  the worker processes and collect and return the results on the master.
  This framework supports many forms of "embarrassingly parallel"

  Snow can use one of four communications mechanisms: sockets, PVM, MPI,
  or NetWorkSpaces (NWS).  NWS support was provided by Steve Weston.
  PVM clusters use the rpvm package; MPI clusters use package Rmpi; NWS
  clusters use package nws.  If pvm is used, then pvm must be started,
  either using a pvm console (e.g the pvm text console or the graphical
  xpvm console, both available with pvm) or from R using functions
  provided by rpvm.  Similarly, LAM-MPI must be started, e.g.  using
  lamboot, for MPI clusters that use Rmpi and LAM-MPI.  If NWS is used,
  the NetWorkSpaces server must be running.  SOCK clusters are the
  easiest approach for using snow on a single multi-core computer as
  they require no additional software.

Mon, 16 Jan 2012
[ 06:55 wen ] Original commit 
1.230 science/Makefile
1.1 science/py-obspy.taup/Makefile
1.1 science/py-obspy.taup/distinfo
1.1 science/py-obspy.taup/files/
1.1 science/py-obspy.taup/pkg-descr
1.1 science/py-obspy.taup/pkg-plist
The obspy.taup package contains Python wrappers for iaspei-tau - a travel
time library by Arthur Snoke (
The library iaspei-tau is written in Fortran and interfaced via Python ctypes.

Thu, 15 Dec 2011
[ 01:20 wen ] Original commit 
1.229 science/Makefile
1.1 science/R-cran-epicalc/Makefile
1.1 science/R-cran-epicalc/distinfo
1.1 science/R-cran-epicalc/pkg-descr
R-cran-epicalc is functions making R easy for epidemiological calculation.


Feature safe:   yes
Tue, 13 Dec 2011
[ 06:24 wen ] Original commit 
1.228 science/Makefile
1.1 science/py-obspy.iris/Makefile
1.1 science/py-obspy.iris/distinfo
1.1 science/py-obspy.iris/pkg-descr
1.1 science/py-obspy.iris/pkg-plist
The obspy.iris package contains a client for the DMC Web services
provided by IRIS (


Feature safe:   yes
Fri, 9 Dec 2011
[ 08:59 wen ] Original commit 
1.227 science/Makefile
1.1 science/py-obspy.db/Makefile
1.1 science/py-obspy.db/distinfo
1.1 science/py-obspy.db/pkg-descr
1.1 science/py-obspy.db/pkg-plist
The obspy.db package contains a waveform indexer collecting metadata
from a file based waveform archive and storing in into a standard SQL
database. Supported waveform formats depend on installed ObsPy packages.


Feature safe:   yes
Wed, 2 Nov 2011
[ 01:35 dougb ] Original commit 
1.683 LEGAL
1.2661 MOVED
1.1195 audio/Makefile
1.12 audio/linux-shoutcast/Makefile
1.5 audio/linux-shoutcast/distinfo
1.2 audio/linux-shoutcast/files/
1.2 audio/linux-shoutcast/pkg-deinstall
1.2 audio/linux-shoutcast/pkg-descr
1.2 audio/linux-shoutcast/pkg-plist
1.19 audio/shoutcast/Makefile

(Only the first 10 of 399 ports in this commit are shown above. View all ports for this commit)
Remove ports@ ports that have been DEPRECATED for at least 1 month

audio/shoutcast         Unfetchable; website rearranged
audio/linux-shoutcast   Unfetchable; website rearranged
chinese/scim-chewing    Does not configure
converters/py-cjkcodecs Integrated into every python version in the tree
databases/kpogre        Does not compile
deskutils/mhc           Does not fetch
deskutils/org-mode.el6  Does not fetch
deskutils/gemcal        Does not fetch
devel/erlang-thrift     Does not build
dns/domtools            Does not fetch
editors/richtext        Does not compile
games/vultures-claw     Does not fetch
games/bomb              Does not fetch
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Mon, 17 Oct 2011
[ 00:03 avilla ] Original commit 
1.158 GIDs
1.2636 MOVED
1.122 Mk/
1.178 UIDs
1.33 accessibility/Makefile
1.10 accessibility/jovie/Makefile
1.5 accessibility/jovie/pkg-message
1.49 accessibility/kdeaccessibility4/Makefile
1.49 accessibility/kdeaccessibility4/distinfo

(Only the first 10 of 531 ports in this commit are shown above. View all ports for this commit)
The KDE/FreeBSD team is pleased to announce KDE Software Compilation
4.7.2. The official release notes can be found at:
This release ships with many improvements. Read more about them here:

We'd like to say thanks to all testers and contributors, especially to
lwhsu@ for his effort on hosting our test packages.

PR:             156293 [1]
                159219 [2]
                160164 [3]
Submitted by:   Oleg Sidorkin <> [1]
                Alvaro Castillo <> [2]
Tested by:      exp-run via pav
Sun, 9 Oct 2011
[ 02:47 dougb ] Original commit 
1.679 LEGAL
1.2622 MOVED
1.162 astro/Makefile
1.16 astro/gkrellsun/Makefile
1.5 astro/gkrellsun/distinfo
1.3 astro/gkrellsun/files/patch-CalcEphem.c
1.2 astro/gkrellsun/files/patch-Makefile
1.2 astro/gkrellsun/files/patch-gkrellsun.c
1.3 astro/gkrellsun/pkg-descr
1.2 astro/gkrellsun/pkg-plist

(Only the first 10 of 299 ports in this commit are shown above. View all ports for this commit)
Remove ports maintainted by ports@ which have passed their EXPIRATION_DATE

astro/gkrellsun         Abandonware
astro/xrmap             No more distfiles
audio/midimountain      Abandonware
audio/gkrellmss         Abandonware
audio/gnapster          Abandonware
databases/xbase         No more public distfiles
databases/xbsql         No more public distfiles
games/gtkabale          No more public distfiles
games/battleball        No more public distfiles, does not compile on ia64 or
games/race              No more public distfiles
games/stvef-paks        No more public distfiles
games/stvef-server      No more public distfiles
games/tome              No more public distfiles
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Wed, 28 Sep 2011
[ 07:33 wen ] Original commit 
1.223 science/Makefile
1.1 science/R-cran-eco/Makefile
1.1 science/R-cran-eco/distinfo
1.1 science/R-cran-eco/pkg-descr
eco is a publicly available R package that implements the Bayesian
and likelihood methods proposed in Imai, Lu, and Strauss (2008) for
ecological inference in $2 \times 2$ tables as well as the method
of bounds introduced by Duncan and Davis (1953).

Sun, 18 Sep 2011
[ 02:47 tota ] Original commit 
1.222 science/Makefile
1.1 science/R-cran-DCluster/Makefile
1.1 science/R-cran-DCluster/distinfo
1.1 science/R-cran-DCluster/pkg-descr
- Add a new port: science/R-cran-DCluster

  A set of functions for the detection of spatial clusters of disease
  using count data. Bootstrap is used to estimate sampling distributions
  of statistics.

Sat, 17 Sep 2011
[ 06:55 tota ] Original commit 
1.221 science/Makefile
1.1 science/R-cran-Epi/Makefile
1.1 science/R-cran-Epi/distinfo
1.1 science/R-cran-Epi/pkg-descr
- Add a new port: science/R-cran-Epi

  Functions for demographic and epidemiological analysis in the Lexis
  diagram, i.e. register and cohort follow-up data, including interval
  censored data and representation of multistate data. Also some
  useful functions for tabulation and plotting. Contains some
  epidemiological datasets.

Tue, 2 Aug 2011
[ 06:31 bapt ] Original commit 
1.2545 MOVED
1.1182 audio/Makefile
1.21 audio/rio/Makefile
1.7 audio/rio/distinfo
1.4 audio/rio/files/patch-ab
1.2 audio/rio/files/patch-ad
1.5 audio/rio/pkg-descr
1.13 audio/ruby-musicextras/Makefile
1.5 audio/ruby-musicextras/distinfo
1.3 audio/ruby-musicextras/pkg-descr

(Only the first 10 of 38 ports in this commit are shown above. View all ports for this commit)
Remove some expired ports

2011-08-01 audio/rio: Look like an abandonware, no more public distfile
2011-08-02 audio/ruby-musicextras: Upcoming ruby-gnome removes dependencies
2011-08-02 deskutils/sshmenu: Upcoming ruby-gnome removes dependencies
2011-08-02 japanese/gsuica: Upcoming ruby-gnome removes dependencies
2011-08-02 science/gave: Upcoming ruby-gnome removes dependencies
2011-08-02 x11-themes/gnome-art: Upcoming ruby-gnome removes dependencies
2011-08-02 x11-themes/gnome-splashscreen-manager: Upcoming ruby-gnome removes
Thu, 28 Jul 2011
[ 09:56 bf ] Original commit 
1.2531 MOVED
1.219 science/Makefile
1.16 science/bblimage/Makefile
1.5 science/bblimage/distinfo
1.2 science/bblimage/files/patch-src__parray.c
1.2 science/bblimage/files/patch-src__pyvox.c
1.2 science/bblimage/files/patch-src__tkphoto.c
1.3 science/bblimage/pkg-descr
1.5 science/bblimage/pkg-plist
remove science/bblimage; attach science/pyvox to build;
add an entry to MOVED

PR:             158562
Fri, 1 Jul 2011
[ 20:23 stephen ] Original commit 
1.218 science/Makefile
1.1 science/py-ws2300/Makefile
1.1 science/py-ws2300/distinfo
1.1 science/py-ws2300/files/ws2300
1.1 science/py-ws2300/pkg-descr
1.1 science/py-ws2300/pkg-plist
- New port science/py-ws2300

Ws2300 manipulates the LaCrosse WS-2300 weather station via its RS232
interface. It can read and write values, and can continuously log data
from WS-2300 to a file or SQL database.


PR:             ports/153452
Submitted by:   Stefan Bethke <>
Approved by:    gabor (mentor)
Wed, 29 Jun 2011
[ 08:18 wen ] Original commit 
1.217 science/Makefile
1.1 science/py-obspy.imaging/Makefile
1.1 science/py-obspy.imaging/distinfo
1.1 science/py-obspy.imaging/pkg-descr
1.1 science/py-obspy.imaging/pkg-plist
obspy.imaging provides tools for displaying features used in seismology.

[ 08:13 wen ] Original commit 
1.216 science/Makefile
1.1 science/py-obspy.xseed/Makefile
1.1 science/py-obspy.xseed/distinfo
1.1 science/py-obspy.xseed/pkg-descr
1.1 science/py-obspy.xseed/pkg-plist
The obspy.xseed package contains methods in order to read, write and
convert seismological meta data files in the Dataless SEED, RESP and
XML-SEED format.

Sun, 12 Jun 2011
[ 16:18 sunpoet ] Original commit 
1.215 science/Makefile
1.1 science/p5-Geo-Coordinates-Converter-iArea/Makefile
1.1 science/p5-Geo-Coordinates-Converter-iArea/distinfo
1.1 science/p5-Geo-Coordinates-Converter-iArea/pkg-descr
1.1 science/p5-Geo-Coordinates-Converter-iArea/pkg-plist
- Add p5-Geo-Coordinates-Converter-iArea 0.14

Geo::Coordinates::Converter::iArea is utilities for DoCoMo iArea.

Tue, 3 May 2011
[ 13:05 bapt ] Original commit 
1.2444 MOVED
1.1166 audio/Makefile
1.7 audio/albumart/Makefile
1.3 audio/albumart/distinfo
1.2 audio/albumart/files/
1.2 audio/albumart/pkg-descr
1.2 audio/albumart/pkg-plist
1.14 audio/aylet/Makefile
1.6 audio/aylet/distinfo
1.3 audio/aylet/pkg-descr

(Only the first 10 of 42 ports in this commit are shown above. View all ports for this commit)
Another bunch of expired ports removal

2011-05-01 audio/albumart: Upstream disapear and distfile is no more available
2011-05-01 audio/aylet: Upstream disapear and distfile is no more available
2011-05-01 audio/cantus: Upstream disapear and distfile is no more available
2011-05-01 audio/xaylet: Upstream disapear and distfile is no more available
2011-05-01 science/oases: Upstream disapear and distfile is no more available
2011-05-01 shells/pash: Upstream disapear and distfile is no more available
Mon, 18 Apr 2011
[ 22:25 rene ] Original commit 
1.645 LEGAL
1.2396 MOVED
1.132 cad/Makefile
1.17 cad/tclspice/Makefile
1.3 cad/tclspice/distinfo
1.2 cad/tclspice/files/
1.2 cad/tclspice/files/patch-src_frontend_aspice.c
1.2 cad/tclspice/files/patch-src_frontend_parser_complete.c
1.2 cad/tclspice/files/patch-src_frontend_resource.c
1.2 cad/tclspice/files/patch-src_frontend_subckt.c

(Only the first 10 of 499 ports in this commit are shown above. View all ports for this commit)
Remove most expired ports:
2011-04-17 cad/tclspice: has been broken for more than a year
2011-04-17 comms/hcfmdm: does not compile on 7.X or higher
2011-04-17 databases/mysqlcc: has been broken for almost a year
2011-04-17 devel/ruby-rjudy: does not compile on FreeBSD 7.x or newer
2011-04-17 devel/xfc: does not compile on FreeBSD 7.x or newer
2011-04-17 devel/lamson: has been broken for a half year
2011-04-17 devel/cocktail: does not build on FreeBSD 7.x or newer
2011-04-17 devel/djgpp-gcc: has been broken for half a year
2011-04-17 devel/gauche-sdl: has been broken for a year
2011-04-17 devel/gdb53-act: does not compile on FreeBSD 7.x and up
2011-04-17 editors/zed: does not compile on FreeBSD 7.x or newer
2011-04-17 games/aqbubble: does not compile on FreeBSD 7.x or newer
2011-04-17 graphics/libvisual-plugins: has been broken for 3 years
2011-04-17 japanese/roundcube: has been broken for almost a year
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Fri, 25 Mar 2011
[ 12:08 miwi ] Original commit 
1.212 science/Makefile
1.1 science/rubygem-ai4r/Makefile
1.1 science/rubygem-ai4r/distinfo
1.1 science/rubygem-ai4r/pkg-descr
AI4R is a collection of ruby algorithms implementations,
covering several Artificial intelligence fields.  It implements:

 * Genetic algorithms
 * Self-organized maps (SOM)
 * Neural Networks
    - Multilayer perceptron with Backpropagation learning
    - Hopfield net
 * Automatic classifiers (Machine Learning)
    - ID3 (Decision Trees)
    - PRISM (J. Cendrowska, 1987)
    - Multilayer Perceptron
    - OneR (AKA One Attribute Rule, 1R)
    - ZeroR
    - Hyperpipes
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Mon, 21 Mar 2011
[ 06:28 wen ] Original commit 
1.211 science/Makefile
1.1 science/py-obspy.wav/Makefile
1.1 science/py-obspy.wav/distinfo
1.1 science/py-obspy.wav/pkg-descr
1.1 science/py-obspy.wav/pkg-plist
The obspy.wav package contains methods in order to read and write
seismogram files in the WAV(audio) format. The data are squeezed to
audible frequencies.

ObsPy is an open-source project dedicated to provide a Python framework
for processing seismological data. It provides parsers for common
file formats and seismological signal processing routines which allow
the manipulation of seismological time series (see Beyreuther et. al.
2010). The goal of the ObsPy project is to facilitate rapid application
development for seismology.

Fri, 18 Mar 2011
[ 19:42 swills ] Original commit 
1.210 science/Makefile
1.1 science/h5utils/Makefile
1.1 science/h5utils/distinfo
1.1 science/h5utils/pkg-descr
1.1 science/h5utils/pkg-plist
h5utils is a set of utilities for visualization and conversion of
scientific data in the free, portable HDF5 format.

Besides providing a simple tool for batch visualization as PNG images,
h5utils also includes programs to convert HDF5 datasets into the formats
required by other free visualization software (e.g. plain text, Vis5d,
and VTK).


PR:             ports/155482
Submitted by:   Klaus Aehlig <aehlig at>
Wed, 16 Mar 2011
[ 09:56 wen ] Original commit 
1.209 science/Makefile
1.2 science/py-obspy.core/Makefile
1.2 science/py-obspy.core/distinfo
1.2 science/py-obspy.core/pkg-descr
1.2 science/py-obspy.core/pkg-plist
- Remove py-obspy.core because the default cvsupd configuration (cvsignore to be
exact) prevents the download of files named *.core, use py-obspy-core instead

Thanks to:      dougb@, cperciva@,
[ 08:46 wen ] Original commit 
1.208 science/Makefile
1.1 science/py-obspy-core/Makefile
1.1 science/py-obspy-core/distinfo
1.1 science/py-obspy-core/pkg-descr
1.1 science/py-obspy-core/pkg-plist
The obspy.core package contains common methods and classes
for ObsPy. It includes UTCDateTime, Stats, Stream and Trace
classes and methods for reading seismograms.

ObsPy is an open-source project dedicated to provide a Python
framework for processing seismological data. It provides
parsers for common file formats and seismological signal
processing routines which allow the manipulation of
seismological time series (see Beyreuther et. al. 2010).
The goal of the ObsPy project is to facilitate rapid application
development for seismology.

Mon, 14 Mar 2011
[ 14:09 wen ] Original commit 
1.207 science/Makefile
1.1 science/py-obspy.signal/Makefile
1.1 science/py-obspy.signal/distinfo
1.1 science/py-obspy.signal/pkg-descr
1.1 science/py-obspy.signal/pkg-plist
The obspy.signal package contains signal processing routines
for seismology. Capabilities include filtering, triggering,
rotation, instrument correction and coordinate transformations.

ObsPy is an open-source project dedicated to provide a Python
framework for processing seismological data. It provides parsers
for common file formats and seismological signal processing
routines which allow the manipulation of seismological time
series (see Beyreuther et. al. 2010). The goal of the ObsPy
project is to facilitate rapid application development for seismology.

[ 14:05 wen ] Original commit 
1.206 science/Makefile
1.1 science/py-obspy.gse2/Makefile
1.1 science/py-obspy.gse2/distinfo
1.1 science/py-obspy.gse2/pkg-descr
1.1 science/py-obspy.gse2/pkg-plist
This module contains Python wrappers for gse_functions - The GSE2 library
of Stefan Stange (
Currently CM6 compressed GSE2 files are supported, this should be sufficient
for most cases. Gse_functions are written in C and interfaced via Python

[ 13:08 wen ] Original commit 
1.205 science/Makefile
1.1 science/py-obspy.mseed/Makefile
1.1 science/py-obspy.mseed/distinfo
1.1 science/py-obspy.mseed/pkg-descr
1.1 science/py-obspy.mseed/pkg-plist
This module contains Python wrappers for libmseed - The MiniSeed
library of Chad Trabant. Libmseed is written in C and interfaced
via Python ctypes.

[ 13:04 wen ] Original commit 
1.204 science/Makefile
1.1 science/py-obspy.core/Makefile
1.1 science/py-obspy.core/distinfo
1.1 science/py-obspy.core/pkg-descr
1.1 science/py-obspy.core/pkg-plist
The obspy.core package contains common methods and classes
for ObsPy. It includes UTCDateTime, Stats, Stream and Trace
classes and methods for reading seismograms.

ObsPy is an open-source project dedicated to provide a Python
framework for processing seismological data. It provides
parsers for common file formats and seismological signal
processing routines which allow the manipulation of
seismological time series (see Beyreuther et. al. 2010).
The goal of the ObsPy project is to facilitate rapid application
development for seismology.

Thu, 10 Mar 2011
[ 06:15 wen ] Original commit 
1.203 science/Makefile
1.1 science/p5-Geo-BUFR/Makefile
1.1 science/p5-Geo-BUFR/distinfo
1.1 science/p5-Geo-BUFR/pkg-descr
1.1 science/p5-Geo-BUFR/pkg-plist
BUFR = Binary Universal Form for the Representation of meteorological data.
BUFR is approved by WMO (World Meteorological Organization) as the standard
universal exchange format for meteorological observations, gradually
replacing a lot of older alphanumeric data formats.

This module provides methods for decoding and encoding BUFR messages, and
for displaying information in BUFR B and D tables and in BUFR flag and code

Installing this module also installs some programs:,,, and See for examples of use. For the majority of
potential users of Geo::BUFR I would expect these programs to be all that
you will need Geo::BUFR for.

Mon, 7 Mar 2011
[ 12:04 wen ] Original commit 
1.202 science/Makefile
1.1 science/R-cran-bayesm/Makefile
1.1 science/R-cran-bayesm/distinfo
1.1 science/R-cran-bayesm/pkg-descr
bayesm covers many important models used in marketing and micro-econometrics
applications. The package includes: Bayes Regression (univariate or
multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
Mixtures of Normals (including clustering), Dirichlet Process Prior Density
Estimation with normal base, Hierarchical Linear Models with normal prior and
covariates, Hierarchical Linear Models with a mixture of normals prior and
covariates, Hierarchical Multinomial Logits with a mixture of normals prior
and covariates, Hierarchical Multinomial Logits with a Dirichlet Process
prior and covariates, Hierarchical Negative Binomial Regression Models,
Bayesian analysis of choice-based conjoint data, Bayesian treatment of linear
instrumental variables models, and Analysis of Multivariate Ordinal survey
data with scale usage heterogeneity (as in Rossi et al, JASA (01)).

[ 10:57 wen ] Original commit 
1.201 science/Makefile
1.1 science/R-cran-AMORE/Makefile
1.1 science/R-cran-AMORE/distinfo
1.1 science/R-cran-AMORE/pkg-descr
R-cran-AMORE was born to release the TAO robust neural network algorithm
to the R users. It has grown and I think it can be of interest for
the users wanting to implement their own training algorithms as well as
for those others whose needs lye only in the "user space".

Sun, 20 Feb 2011
[ 03:54 wen ] Original commit 
1.200 science/Makefile
1.1 science/py-scimath/Makefile
1.1 science/py-scimath/distinfo
1.1 science/py-scimath/pkg-descr
1.1 science/py-scimath/pkg-plist
The SciMath project includes packages to support scientific and
mathematical calculations, beyond the capabilities offered by SciPy.
    * enthought.interpolate
    * enthought.mathematics
    * enthought.units


PR:             ports/154351
Submitted by:   Wen Heping (myself)
Thu, 6 Jan 2011
[ 02:39 wen ] Original commit 
1.199 science/Makefile
1.1 science/veusz/Makefile
1.1 science/veusz/distinfo
1.1 science/veusz/pkg-descr
1.1 science/veusz/pkg-plist
Veusz is a GUI scientific plotting and graphing package. It
is designed to produce publication-ready Postscript or PDF
output. SVG, EMF and bitmap formats export are also supported.
The program runs under Unix/Linux, Windows or Mac OS X, and
binaries are provided. Data can be read from text, CSV or FITS
files, and data can be manipulated or examined from within the


PR:             ports/153686
Submitted by:   Stas Timokhin <>
Wed, 29 Dec 2010
[ 08:50 wen ] Original commit 
1.198 science/Makefile
1.1 science/p5-Geo-Coordinates-Converter/Makefile
1.1 science/p5-Geo-Coordinates-Converter/distinfo
1.1 science/p5-Geo-Coordinates-Converter/pkg-descr
1.1 science/p5-Geo-Coordinates-Converter/pkg-plist
Geo::Coordinates::Converter is a simple converter of geo coordinates, the
format and datum of geo coordinates are simply converted. when it is
insufficient in the coordinate system and the format of the standard, it
is possible to add it easily.

Sat, 13 Nov 2010
[ 21:41 makc ] Original commit 
1.197 science/Makefile
Connect py-biolccc
Thu, 9 Sep 2010
[ 00:26 sahil ] Original commit 
1.196 science/Makefile
1.1 science/p5-Physics-Unit/Makefile
1.1 science/p5-Physics-Unit/distinfo
1.1 science/p5-Physics-Unit/pkg-descr
1.1 science/p5-Physics-Unit/pkg-plist
Objects of class Physics::Unit define units of measurement that correspond
to physical quantities.  This module allows you to manipulate these units,
generate new derived units from other units, and convert from one unit
to another.


PR:             ports/150245
Submitted by:   Frederic Culot <>
Wed, 8 Sep 2010
[ 03:09 sahil ] Original commit 
1.195 science/Makefile
1.1 science/epte/Makefile
1.1 science/epte/distinfo
1.1 science/epte/files/patch-definitions.h
1.1 science/epte/files/patch-do_element.c
1.1 science/epte/files/patch-do_radii.c
1.1 science/epte/files/patch-epte.1
1.1 science/epte/files/patch-fill_information.c
1.1 science/epte/files/patch-makefile
1.1 science/epte/files/patch-periodic.h

(Only the first 10 of 12 ports in this commit are shown above. View all ports for this commit)
epte is a curses-based periodic table of the elements. It provides a
set of examples of the basic sets of constants and procedures needed
to understand the behavior of matter.


PR:             ports/150183
Submitted by:   Frederic Culot <>
Mon, 23 Aug 2010
[ 18:15 makc ] Original commit 
1.194 science/Makefile
Connect kst2
Wed, 21 Jul 2010
[ 09:53 ashish ] Original commit 
1.193 science/Makefile
1.2 science/qelectrotech/Makefile
1.2 science/qelectrotech/distinfo
1.2 science/qelectrotech/pkg-descr
1.2 science/qelectrotech/pkg-plist
- Remove the port from 'science' category.

PR:             ports/146513
Approved by:    pgj (mentor)
[ 03:27 ashish ] Original commit 
1.192 science/Makefile
1.1 science/qelectrotech/Makefile
1.1 science/qelectrotech/distinfo
1.1 science/qelectrotech/pkg-descr
1.1 science/qelectrotech/pkg-plist
QElectroTech is a Qt4 application to design electric diagrams. It uses XML
files for elements and diagrams, and includes both a diagram editor and an
element editor.


PR:             ports/146513
Submitted by:   Gvozdikov Veniamin <g.veniamin at>
Approved by:    tabthorpe (mentor)
Tue, 29 Jun 2010
[ 01:22 wen ] Original commit 
1.191 science/Makefile
1.1 science/jstrack/Makefile
1.1 science/jstrack/distinfo
1.1 science/jstrack/files/
1.1 science/jstrack/pkg-descr
1.1 science/jstrack/pkg-plist
JStrack is written by and for people who are in areas that are
prone to hits from tropical systems (currently only in the Tropical
Atlantic). It's intended to display the NHC/TPC data and give you
what you need to make decisions, etc.. It does NOT, nor will it ever,
attempt to do any forecasting on its own---I leave that to the gurus
at the NHC/TPC.


PR:             ports/148208
Submitted by:   Chris Rees <>
Feature safe:   yes
Thu, 20 May 2010
[ 14:21 lwhsu ] Original commit 
1.190 science/Makefile
1.1 science/netcdf3-ftn/Makefile
Add netcdf3-ftn , netCDF (network Common Data Form), with Fortran

Submitted by:   Sunpoet Po-Chuan Hsieh <sunpoet AT>
[ 09:43 wen ] Original commit 
1.189 science/Makefile
1.1 science/massxpert/Makefile
1.1 science/massxpert/distinfo
1.1 science/massxpert/pkg-descr
1.1 science/massxpert/pkg-plist
The massXpert project aims at providing (bio)chemists with a software
package allowing the following:

* User-specific atom definitions and polymer chemistry definitions;
* Powerful sequence editing with user-defined glyphs for each monomer
and monomer chemical modification. Multi-region selections;
* Polymer sequence chemical/enzymatic cleavage;
* Intramolecular cross-linking, like disulfide bonds with total resolution
of the peptides generated upon enzymatic cleavage;
* Gas-phase fragmentation of oligomers;
* Mass-to-charge ratio calculations with inline change of ionization agent;
* Calculation of net electrical charge and of isoelectric point (even by
taking into account monomer modifications if polymer is a protein);
* Simulation of isotopic patterns for any chemical formula and z charge;
* A number of plugins allow 1) translation of the sequence from one format
to another (using a dictionary, like between the 1-letter code and the 3-letter
code of proteins) 2) conversion of number format according to any localized
number format 3) sort mass lists.

PR:             ports/146564
Submitted by:   Gvozdikov Veniamin <>
Wed, 19 May 2010
[ 05:31 wen ] Original commit 
1.188 science/Makefile
1.1 science/pynn/Makefile
1.1 science/pynn/distinfo
1.1 science/pynn/pkg-descr
1.1 science/pynn/pkg-plist
PyNN(pronounced 'pine') is a simulator-independent language for
building neuronal network models.

[ 00:14 wen ] Original commit 
1.187 science/Makefile
1.2 science/pyNN/Makefile
1.2 science/pyNN/distinfo
1.2 science/pyNN/pkg-descr
1.2 science/pyNN/pkg-plist
- Remove pyNN and re-add as pynn

Reviewed by:    danfe@
Tue, 18 May 2010
[ 08:14 wen ] Original commit 
1.186 science/Makefile
1.1 science/pyNN/Makefile
1.1 science/pyNN/distinfo
1.1 science/pyNN/pkg-descr
1.1 science/pyNN/pkg-plist
PyNN(pronounced 'pine') is a simulator-independent language for
building neuronal network models.


PR:             ports/146664
Submitted by:   Ju Pengfei <>
Wed, 12 May 2010
[ 13:25 beat ] Original commit 
1.185 science/Makefile
1.1 science/bddsolve/Makefile
1.1 science/bddsolve/distinfo
1.1 science/bddsolve/pkg-descr
1.1 science/bddsolve/pkg-plist
Bddsolve is a BDD-based tool for solving satisfiability and reachability
problems.  It uses the BDD package Buddy as a backend.


Submitted by:   ed@
Fri, 2 Apr 2010
[ 15:36 miwi ] Original commit 
1.184 science/Makefile
1.1 science/p5-PerlMol/Makefile
1.1 science/p5-PerlMol/distinfo
1.1 science/p5-PerlMol/files/patch-Makefile.PL
1.1 science/p5-PerlMol/pkg-descr
1.1 science/p5-PerlMol/pkg-plist
Perl modules for molecular chemistry


PR:             ports/145143
Submitted by:   Steve Wills <steve at>
[ 15:35 miwi ] Original commit 
1.183 science/Makefile
1.1 science/p5-Chemistry-File-SMILES/Makefile
1.1 science/p5-Chemistry-File-SMILES/distinfo
1.1 science/p5-Chemistry-File-SMILES/pkg-descr
1.1 science/p5-Chemistry-File-SMILES/pkg-plist
Perl module which parses a SMILES (Simplified Molecular Input Line Entry
Specification) string.


PR:             ports/145143
Submitted by:   Steve Wills <steve at>
[ 15:35 miwi ] Original commit 
1.182 science/Makefile
1.1 science/p5-Chemistry-InternalCoords/Makefile
1.1 science/p5-Chemistry-InternalCoords/distinfo
1.1 science/p5-Chemistry-InternalCoords/pkg-descr
1.1 science/p5-Chemistry-InternalCoords/pkg-plist
Perl module implements an object class for representing internal
coordinates and provides methods for converting them to Cartesian


PR:             ports/145143
Submitted by:   Steve Wills <steve at>
[ 15:34 miwi ] Original commit 
1.181 science/Makefile
1.1 science/p5-Chemistry-File-SMARTS/Makefile
1.1 science/p5-Chemistry-File-SMARTS/distinfo
1.1 science/p5-Chemistry-File-SMARTS/pkg-descr
1.1 science/p5-Chemistry-File-SMARTS/pkg-plist
Perl module which will parse a SMARTS (SMiles ARbitrary Target Specification)
string, generating a Chemistry::Pattern object. It is a file I/O driver for
the PerlMol toolkit.


PR:             ports/145143
Submitted by:   Steve Wills <steve at>
[ 15:33 miwi ] Original commit 
1.180 science/Makefile
1.1 science/p5-Chemistry-3DBuilder/Makefile
1.1 science/p5-Chemistry-3DBuilder/distinfo
1.1 science/p5-Chemistry-3DBuilder/pkg-descr
1.1 science/p5-Chemistry-3DBuilder/pkg-plist
Perl module which generates a three-dimensional molecular structure from a
connection table, such as that obtained by a 2D representation of the
molecule or from a SMILES string.


PR:             ports/145143
Submitted by:   Steve Wills <steve at
[ 15:33 miwi ] Original commit 
1.179 science/Makefile
1.1 science/p5-Chemistry-File-SLN/Makefile
1.1 science/p5-Chemistry-File-SLN/distinfo
1.1 science/p5-Chemistry-File-SLN/pkg-descr
1.1 science/p5-Chemistry-File-SLN/pkg-plist
SLN linear notation parser/writer


PR:             ports/145143
Submitted by:   Steve Wills <steve at>
[ 15:32 miwi ] Original commit 
1.178 science/Makefile
1.1 science/p5-Chemistry-File-MDLMol/Makefile
1.1 science/p5-Chemistry-File-MDLMol/distinfo
1.1 science/p5-Chemistry-File-MDLMol/pkg-descr
1.1 science/p5-Chemistry-File-MDLMol/pkg-plist
Perl module which will parse a SMARTS (SMiles ARbitrary Target Specification)
string, generating a Chemistry::Pattern object. It is a file I/O driver for
the PerlMol toolkit.


PR:             ports/145143
Submitted by:   Steve Wills <steve at>
[ 15:32 miwi ] Original commit 
1.177 science/Makefile
1.1 science/p5-Chemistry-File-Mopac/Makefile
1.1 science/p5-Chemistry-File-Mopac/distinfo
1.1 science/p5-Chemistry-File-Mopac/pkg-descr
1.1 science/p5-Chemistry-File-Mopac/pkg-plist
MOPAC 6 input file reader/writer


PR:             ports/145143
Submitted by:   Steve Wills <steve at>
[ 15:32 miwi ] Original commit 
1.176 science/Makefile
1.1 science/p5-Chemistry-Reaction/Makefile
1.1 science/p5-Chemistry-Reaction/distinfo
1.1 science/p5-Chemistry-Reaction/pkg-descr
1.1 science/p5-Chemistry-Reaction/pkg-plist
Explicit chemical reactions


PR:             ports/145143
Submitted by:   Steve Wills <steve at>
[ 15:31 miwi ] Original commit 
1.175 science/Makefile
1.1 science/p5-Chemistry-FormulaPattern/Makefile
1.1 science/p5-Chemistry-FormulaPattern/distinfo
1.1 science/p5-Chemistry-FormulaPattern/pkg-descr
1.1 science/p5-Chemistry-FormulaPattern/pkg-plist
Match molecule by formula


PR:             ports/145143
Submitted by:   Steve Wills <steve at>
[ 15:29 miwi ] Original commit 
1.174 science/Makefile
1.1 science/p5-Chemistry-MidasPattern/Makefile
1.1 science/p5-Chemistry-MidasPattern/distinfo
1.1 science/p5-Chemistry-MidasPattern/pkg-descr
1.1 science/p5-Chemistry-MidasPattern/pkg-plist
Select atoms in macromolecule


PR:             ports/145143
Submitted by:   Steve Wills <steve at>
[ 15:29 miwi ] Original commit 
1.173 science/Makefile
1.1 science/p5-Chemistry-Mok/Makefile
1.1 science/p5-Chemistry-Mok/distinfo
1.1 science/p5-Chemistry-Mok/pkg-descr
1.1 science/p5-Chemistry-Mok/pkg-plist
Perl molecular awk interpreter


PR:             ports/145143
Submitted by:   Steve Wills <steve at>
[ 15:28 miwi ] Original commit 
1.172 science/Makefile
1.1 science/p5-Chemistry-File-XYZ/Makefile
1.1 science/p5-Chemistry-File-XYZ/distinfo
1.1 science/p5-Chemistry-File-XYZ/pkg-descr
1.1 science/p5-Chemistry-File-XYZ/pkg-plist
XYZ molecule format reader/writer


PR:             ports/145143
Submitted by:   Steve Wills <steve at>
[ 15:28 miwi ] Original commit 
1.171 science/Makefile
1.1 science/p5-Chemistry-File-VRML/Makefile
1.1 science/p5-Chemistry-File-VRML/distinfo
1.1 science/p5-Chemistry-File-VRML/pkg-descr
1.1 science/p5-Chemistry-File-VRML/pkg-plist
Generate VRML models for molecules


PR:             ports/145143
Submitted by:   Steve Wills <steve at>
[ 15:27 miwi ] Original commit 
1.170 science/Makefile
1.1 science/p5-Chemistry-Ring/Makefile
1.1 science/p5-Chemistry-Ring/distinfo
1.1 science/p5-Chemistry-Ring/pkg-descr
1.1 science/p5-Chemistry-Ring/pkg-plist
Perl module which provides some basic methods for representing a ring.


PR:             ports/145143
Submitted by:   Steve Wills <steve at>
[ 15:26 miwi ] Original commit 
1.169 science/Makefile
1.1 science/p5-Chemistry-Isotope/Makefile
1.1 science/p5-Chemistry-Isotope/distinfo
1.1 science/p5-Chemistry-Isotope/pkg-descr
1.1 science/p5-Chemistry-Isotope/pkg-plist
Perl module which contains the exact mass data from the table of the isotopes.


PR:             ports/145143
Submitted by:   Steve Wills <steve at>
[ 15:25 miwi ] Original commit 
1.168 science/Makefile
1.1 science/p5-Chemistry-Pattern/Makefile
1.1 science/p5-Chemistry-Pattern/distinfo
1.1 science/p5-Chemistry-Pattern/pkg-descr
1.1 science/p5-Chemistry-Pattern/pkg-plist
Perl module which implements basic pattern matching for molecules.


PR:             ports/145143
Submitted by:   Steve Wills <steve at>
[ 15:25 miwi ] Original commit 
1.167 science/Makefile
1.1 science/p5-Chemistry-Canonicalize/Makefile
1.1 science/p5-Chemistry-Canonicalize/distinfo
1.1 science/p5-Chemistry-Canonicalize/pkg-descr
1.1 science/p5-Chemistry-Canonicalize/pkg-plist
Perl module which provides functions for "canonicalizing" a molecular
structure; that is, to number the atoms in a unique way regardless of the
input order.


PR:             ports/145143
Submitted by:   Steve Wills <steve at>
[ 15:24 miwi ] Original commit 
1.166 science/Makefile
1.1 science/p5-Chemistry-Bond-Find/Makefile
1.1 science/p5-Chemistry-Bond-Find/distinfo
1.1 science/p5-Chemistry-Bond-Find/pkg-descr
1.1 science/p5-Chemistry-Bond-Find/pkg-plist
Perl module which provides functions for detecting the bonds in a molecule from
its 3D coordinates by using simple cutoffs, and for guessing the formal bond


PR:             ports/145143
Submitted by:   Steve Wills <steve at>
Sat, 13 Feb 2010
[ 11:21 miwi ] Original commit 
1.165 science/Makefile
1.1 science/hdf-java/Makefile
1.1 science/hdf-java/distinfo
1.1 science/hdf-java/pkg-descr
1.1 science/hdf-java/pkg-plist
The HDF Java Products include a visual tool for browsing and editing HDF
files, a Java package providing an object-oriented interface to HDF data
objects, and Java Native Interfaces to the standard HDF libraries.


PR:             ports/143859
Submitted by:   rfarmer at
Mon, 25 Jan 2010
[ 00:27 wen ] Original commit 
1.164 science/Makefile
1.1 science/meep/Makefile
1.1 science/meep/distinfo
1.1 science/meep/files/patch-configure
1.1 science/meep/files/patch-src_mympi.hpp
1.1 science/meep/pkg-descr
1.1 science/meep/pkg-plist
Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation
software package developed at MIT to model electromagnetic systems,
along with our MPB eigenmode package.


PR:             ports/142158
Submitted by:   Stas Timokhin <>
Mon, 18 Jan 2010
[ 06:46 pgollucci ] Original commit 
1.2076 MOVED
1.1087 audio/Makefile
1.28 audio/ccaudio/Makefile
1.13 audio/ccaudio/distinfo
1.2 audio/ccaudio/files/patch-src-audio.h
1.2 audio/ccaudio/files/patch-src-audiofile.cpp
1.4 audio/ccaudio/pkg-descr
1.8 audio/ccaudio/pkg-plist
1.8 audio/py-libmpdclient/Makefile
1.5 audio/py-libmpdclient/distinfo

(Only the first 10 of 211 ports in this commit are shown above. View all ports for this commit)
- remove broken/expired ports@ ports

Approved by: portmgr (miwi)

audio/ccaudio||2010-01-18|Has expired: has been broken for 4 months
audio/py-libmpdclient||2010-01-18|Has expired: has been broken for 3 months
chinese/gbk2uni||2010-01-18|Has expired: has been broken for 6 months
chinese/iiimf-le-xcin||2010-01-18|Has expired: has been broken for 3 months
devel/adabindx||2010-01-18|Has expired: has been broken for 3 months
devel/agide||2010-01-18|Has expired: has been broken for 6 months
devel/asis||2010-01-18|Has expired: has been broken for 3 months
devel/callgrind||2010-01-18|Has expired: Included in devel/valgrind
devel/florist||2010-01-18|Has expired: has been broken for 3 months
editors/xml2rfc-xxe||2010-01-18|Has expired: has been broken for 4 months
graphics/gephex||2010-01-18|Has expired: has been broken for 3 months
(Only the first 15 lines of the commit message are shown above View all of this commit message)

Number of commits found: 250 (showing only 100 on this page)

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