19:08 mandree 

Add new port science/py-coards:
Coards is a parser for time values represented using the COADS convention.

WWW:		https://pypi.python.org/pypi/coards

PR:		ports/179576
Submitted by:	Johannes Meixner <xmj@chaot.net>

 

13:55 wen 

- Rename science/py-obspy-core to science/py-obspy

 

13:44 wen 

- Remove these obspy modules, because they are included in obspy upstream now.

 

22:46 jgh 

- 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.

WWW: http://math.lbl.gov/voro++/

PR:		177678
Submitted by:	jwbacon@tds.net

Feature safe:	yes

 

13:10 makc 

- Rename pyBioLCCC to pyteomics.biolccc (follow upstream)
- Update to 1.5.0
- Trim Makefile header

 

13:05 makc 

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

WWW: https://pypi.python.org/pypi/pyteomics

 

17:30 makc 

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.

WWW: http://fvcom.smast.umassd.edu/FVCOM/index.html

PR:		ports/166726
PR:		ports/166728
Submitted by:	Jason Bacon <jwbacon at tds.net>

 

07:46 bapt 

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math/gnuplot+||2013-02-06|Upstream says: This package is obsolete.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]

 

14:19 makc 

science/openbabel:
- 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

science/py-openbabel:
- Merge py-openbabel to openbabel

other:
- chase openbabel update

 

12:24 demon 

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.

WWW: http://scikit-learn.org/

Feature safe:	yes

 

01:57 linimon 

Complete the removal of ics to silence warnings on pointyhat.

Hat:            portmgr

15:15 thierry 

MEI stands for Mathematical Expression Interpreter.
It is intended to provide interpretation of mathematical formula in a string.

WWW: http://www.code-saturne.org/

12:43 tota 

- Add a new port: science/R-cran-som

  Self-Organizing Map (with application in gene clustering)

  WWW:  http://cran.r-project.org/web/packages/som/

17:35 pawel 

DL_POLY is a general purpose classical molecular dynamics (MD) simulation
software developed at Daresbury Laboratory by I.T. Todorov and W. Smith.

WWW: http://ccpforge.cse.rl.ac.uk/gf/project/dl_poly_classic/

PR:             ports/166725
Submitted by:   Jason Bacon <jwbacon@tds.net>

04:34 pgollucci 

- 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 <murashin@gfd-dennou.org>

02:26 tota 

- 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, ...

  WWW:  http://cran.r-project.org/web/packages/e1071/

12:04 tota 

- Remove science/R-cran-survival which has been already included in math/R

Reported by:    pointyhat (pav)

13:22 tota 

- 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.

  WWW:  http://cran.r-project.org/web/packages/survival/

13:14 tota 

- 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"
  computations.

  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.

  WWW:  http://cran.r-project.org/web/packages/snow/

06:55 wen 

The obspy.taup package contains Python wrappers for iaspei-tau - a travel
time library by Arthur Snoke (http://www.iris.edu/pub/programs/iaspei-tau/).
The library iaspei-tau is written in Fortran and interfaced via Python ctypes.

WWW: http://www.obspy.org/

01:20 wen 

R-cran-epicalc is functions making R easy for epidemiological calculation.

WWW: http://cran.r-project.org/web/packages/epicalc/

Feature safe:   yes

06:24 wen 

The obspy.iris package contains a client for the DMC Web services
provided by IRIS (http://www.iris.edu/ws/).

WWW: http://www.obspy.org/

Feature safe:   yes

08:59 wen 

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.

WWW: http://www.obspy.org/

Feature safe:   yes

01:35 dougb 

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
games/lgeneral-data     Bad plist
games/linux-enemyterritory-jaymod       Does not fetch
games/xphotohunter      Does not fetch
graphics/gimpshop       Fails to patch
graphics/lightspark-devel       Does not compile
graphics/xmms-plazma    Does not fetch
graphics/py-cgkit       Does not fetch, does not compile on ia64, powerpc, or
sparc64
japanese/rxvt           Does not fetch, fails to build with new utmpx
japanese/epic4          Some distfiles do not fetch
java/jde                Does not fetch
java/kaffe              Does not fetch
korean/gdick    HTMLs from the Yahoo! Korea Dictionary cannot be parsed, other
runtime problems
korean/hanterm-xf86     Does not compile
korean/stardict2-dict-kr Does not fetch
lang/p5-JavaScript      Does not fetch
lang/TenDRA     Website disappeared; last release 2006, Does not compile on
recent FreeBSD-9
mail/freepops           Does not build
mail/itraxp             Does not build
misc/tellico            Leaves file behind on deinstall
net/gsambad             Does not fetch
net/nocatauth-gateway   Uses a UID registered to another port
net/nocatauth-server    Uses a UID registered to another port
net/libosip2            Does not fetch
net/kmuddy              Does not fetch
net/netboot             Does not build
net-mgmt/jffnms         Does not fetch
net-p2p/frostwire       Does not fetch
net-p2p/azureus         Does not fetch
news/cleanscore         Does not fetch
news/nntpswitch         Does not fetch
news/p5-NewsLib         Does not fetch
russian/cyrproxy        Does not fetch
science/gerris          Does not fetch
security/opensaml       Does not fetch
sysutils/wmbattery      Does not fetch
sysutils/cpuburn        No more public distfiles
textproc/tei-guidelines-p4      Does not fetch
textproc/tei-p4         Does not fetch
textproc/py-hyperestraier       Does not fetch
textproc/tdtd.el        Does not fetch
textproc/tei-lite       Does not fetch
www/phpwiki13           Does not fetch
www/p5-Apache-Scoreboard        Depends on mod_perl
www/p5-B-LexInfo        Broken due the new mod_perl2 API
www/phpwiki             Does not fetch
www/smb2www             Apache13 is deprecated, migrate to 2.2.x+ now
www/spip                Checksum is changing daily
www/monkey              Does not fetch
x11-toolkits/jdic       Does not fetch
x11-toolkits/py-kde     Does not compile

00:03 avilla 

The KDE/FreeBSD team is pleased to announce KDE Software Compilation
4.7.2. The official release notes can be found at:
http://kde.org/announcements/announce-4.7.2.php
This release ships with many improvements. Read more about them here:
http://FreeBSD.kde.org/news.php#itemKDESC472availableinports

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 <osidorkin@gmail.com> [1]
                Alvaro Castillo <gobledb@gmail.com> [2]
                dkeav04@gmail.com [3]
Tested by:      exp-run via pav

02:47 dougb 

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
sparc64
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
games/qkmj              No more public distfiles
games/oilwar            No more public distfiles
games/xbaby             No more public distfiles
games/xword             Abandonware
games/kslide            No more public distfiles
graphics/xmrm           No more public distfiles, does not compile on amd64 or
sparc64
graphics/giftrans       Upstream disappeared and distfile is not available
graphics/wildmagic      BROKEN for more than 6 months, does not fetch
irc/ircd-rusnet         No more public distfiles
irc/tkirc               No more public distfiles
korean/mizifont         No more public distfiles
lang/freetxl            No more public distfiles
math/nsc2ke             No more public distfiles
misc/mgp-mode.el        No more public distfiles
multimedia/p5-RIFF-Info No more public distfiles
net/p5-Net-OpenDHT      No more public distfiles
net/mudix               No more public distfiles
net-im/newsbot          No more public distfiles
net-im/libicq2000       Abandonware
net-im/gossip           No longer maintain by upstream, use net-im/empathy
instead
net-im/ickle            Abandonware
net-mgmt/nipper         BROKEN for more than 6 month, does not fetch
net-p2p/mldonkey-serverspy      No more public distfiles
news/p5-Gateway         No more public distfiles
print/epsmerge          No more public distfiles
science/at              No more public distfiles
science/pyvox           No more public distfiles
security/p5-Email-Obfuscate     No more public distfiles
security/libparanoia    No more public distfiles
security/execwrap       No more public distfiles

07:33 wen 

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).

WWW: http://imai.princeton.edu/software/eco.html

02:47 tota 

- 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.

  WWW:  http://cran.r-project.org/web/packages/DCluster/

06:55 tota 

- 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.

  WWW:  http://www.pubhealth.ku.dk/~bxc/Epi/

06:31 bapt 

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
dependencies

09:56 bf 

remove science/bblimage; attach science/pyvox to build;
add an entry to MOVED

PR:             158562

20:23 stephen 

- 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.

WWW: http://ace-host.stuart.id.au/russell/files/ws2300/

PR:             ports/153452
Submitted by:   Stefan Bethke <stb@lassitu.de>
Approved by:    gabor (mentor)

08:18 wen 

obspy.imaging provides tools for displaying features used in seismology.

WWW: http://www.obspy.org/

08:13 wen 

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.

WWW: http://www.obspy.org/

16:18 sunpoet 

- Add p5-Geo-Coordinates-Converter-iArea 0.14

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

WWW: http://search.cpan.org/dist/Geo-Coordinates-Converter-iArea/

13:05 bapt 

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

22:25 rene 

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
2011-04-17 japanese/tkstep80: does not compile on FreeBSD 7.x or newer
2011-04-17 lang/u++: has been broken for over a half year
2011-04-17 lang/pugs: has been broken for over a year
2011-04-17 lang/mozart: does not compile on FreeBSD 7.x or newer
2011-04-17 math/linalg: does not build on FreeBSD 7.x or newer
2011-04-17 math/R-cran-igraph: has been broken for over a half year
2011-04-17 misc/ftree: has been broken for over a half year
2011-04-17 multimedia/katchtv: has been broken for a half year
2011-04-17 multimedia/libomxil-bellagio: has been broken for almost a year
2011-04-17 multimedia/banshee-mirage: has been broken for over a half year
2011-04-17 net-p2p/trackerbt: has been broken for a half year
2011-04-17 net/cap: does not compile on FreeBSD 7.x or newer
2011-04-17 net/ggsd: does not compile on FreeBSD 7.x or newer
2011-04-17 net/b2bua: does not compile on FreeBSD 7.x or newer
2011-04-17 net/penguintv: has been broken for a half year
2011-04-17 news/openftd: has been broken for almost a year
2011-04-17 palm/romeo: does not compile on FreeBSD 7.x or newer
2011-04-17 science/pcp: does not compile on FreeBSD 7.x or newer
2011-04-17 science/elmer-fem: has been broken for over a year
2011-04-17 security/newpki-lib: does not compile on FreeBSD 7.x or newer
2011-04-17 security/newpki-server: does not compile on FreeBSD 7.x or newer
2011-04-17 security/xmlsec: does not compile on FreeBSD 7.x or newer
2011-04-17 security/f-protd: has been broken for over a year
2011-04-17 sysutils/xwlans: does not compile on FreeBSD 7.x or newer
2011-04-17 www/bk_edit: does not compile on FreeBSD 7.x and newer
2011-04-17 www/bricolage: has been broken for a half year
2011-04-17 x11-toolkits/gauche-gtk: has been broken for a year
2011-04-17 x11-toolkits/gambas2-gb-qt: has been broken for over a year
2011-04-17 x11-toolkits/php-gtk2: has been broken for over a half year
2011-04-17 x11-toolkits/p5-Tcl-Tk: has been broken for 2 year
2011-04-17 x11/metisse: has been broken for over a half year

12:08 miwi 

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
    - Naive Bayes
    - IB1 (D. Aha, D. Kibler - 1991)
 * Data clustering
    - K-means
    - Bisecting k-means
    - Single linkage
    - Complete linkage
    - Average linkage
    - Weighted Average linkage
    - Centroid linkage
    - Median linkage
    - Ward's method linkage
    - Diana (Divisive Analysis)

WWW: http://ai4r.rubyforge.org/

PR:             ports/155699
Submitted by:   Eric Freeman <freebsdports at chillibear.com>

06:28 wen 

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.

WWW: http://www.obspy.org/

19:42 swills 

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).

WWW: http://ab-initio.mit.edu/wiki/index.php/H5utils

PR:             ports/155482
Submitted by:   Klaus Aehlig <aehlig at linta.de>

09:56 wen 

- 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@, demelier.david@gmail.com

08:46 wen 

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.

WWW: http://www.obspy.org/

14:09 wen 

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.

WWW: http://www.obspy.org/

14:05 wen 

This module contains Python wrappers for gse_functions - The GSE2 library
of Stefan Stange (http://www.orfeus-eu.org/Software/softwarelib.html#gse).
Currently CM6 compressed GSE2 files are supported, this should be sufficient
for most cases. Gse_functions are written in C and interfaced via Python
ctypes.

WWW: http://www.obspy.org/

13:08 wen 

This module contains Python wrappers for libmseed - The MiniSeed
library of Chad Trabant. Libmseed is written in C and interfaced
via Python ctypes.

WWW: http://www.obspy.org/

13:04 wen 

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.

WWW: http://www.obspy.org/

06:15 wen 

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
tables.

Installing this module also installs some programs: bufrread.pl,
bufrresolve.pl, bufrencode.pl, bufr_reencode.pl and bufralter.pl. See
https://wiki.met.no/bufr.pm/start 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.

WWW: http://search.cpan.org/dist/Geo-BUFR/

12:04 wen 

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)).

WWW: http://www.perossi.org/home/bsm-1

10:57 wen 

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".

WWW: http://rwiki.sciviews.org/doku.php?id=packages:cran:amore

03:54 wen 

The SciMath project includes packages to support scientific and
mathematical calculations, beyond the capabilities offered by SciPy.
    * enthought.interpolate
    * enthought.mathematics
    * enthought.units

WWW: http://pypi.python.org/pypi/SciMath/

PR:             ports/154351
Submitted by:   Wen Heping (myself)

02:39 wen 

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
application.

WWW: http://home.gna.org/veusz/

PR:             ports/153686
Submitted by:   Stas Timokhin <devel@stasyan.com>

08:50 wen 

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.

WWW:    http://search.cpan.org/dist/Geo-Coordinates-Converter/

21:41 makc 

Connect py-biolccc

00:26 sahil 

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.

WWW: http://search.cpan.org/dist/Physics-Unit/

PR:             ports/150245
Submitted by:   Frederic Culot <frederic@culot.org>

03:09 sahil 

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.

WWW: http://www.toddmiller.com/epte/

PR:             ports/150183
Submitted by:   Frederic Culot <frederic@culot.org>

18:15 makc 

Connect kst2

09:53 ashish 

- Remove the port from 'science' category.

PR:             ports/146513
Approved by:    pgj (mentor)

03:27 ashish 

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.

WWW:    http://qelectrotech.org/

PR:             ports/146513
Submitted by:   Gvozdikov Veniamin <g.veniamin at googlemail.com>
Approved by:    tabthorpe (mentor)

01:22 wen 

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.

WWW: http://www.jstrack.org/jstrack/

PR:             ports/148208
Submitted by:   Chris Rees <utisoft@gmail.com>
Feature safe:   yes

14:21 lwhsu 

Add netcdf3-ftn , netCDF (network Common Data Form), with Fortran
support.

Submitted by:   Sunpoet Po-Chuan Hsieh <sunpoet AT sunpoet.net>

09:43 wen 

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 <g.veniamin@googlemail.com>

05:31 wen 

PyNN(pronounced 'pine') is a simulator-independent language for
building neuronal network models.

WWW: http://neuralensemble.org/trac/PyNN

00:14 wen 

- Remove pyNN and re-add as pynn

Reviewed by:    danfe@

08:14 wen 

PyNN(pronounced 'pine') is a simulator-independent language for
building neuronal network models.

WWW: http://neuralensemble.org/trac/PyNN

PR:             ports/146664
Submitted by:   Ju Pengfei <jupengfei@gmail.com>

13:25 beat 

Bddsolve is a BDD-based tool for solving satisfiability and reachability
problems.  It uses the BDD package Buddy as a backend.

WWW: http://www.win.tue.nl/~wieger/bddsolve/

Submitted by:   ed@

15:36 miwi 

Perl modules for molecular chemistry

WWW:    http://search.cpan.org/dist/PerlMol/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:35 miwi 

Perl module which parses a SMILES (Simplified Molecular Input Line Entry
Specification) string.

WWW:    http://search.cpan.org/dist/Chemistry-File-SMILES/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:35 miwi 

Perl module implements an object class for representing internal
coordinates and provides methods for converting them to Cartesian
coordinates.

WWW:    http://search.cpan.org/dist/Chemistry-InternalCoords/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:34 miwi 

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.

WWW:    http://search.cpan.org/dist/Chemistry-File-SMARTS/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:33 miwi 

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.

WWW:    http://search.cpan.org/dist/Chemistry-3DBuilder/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net

15:33 miwi 

SLN linear notation parser/writer

WWW:    http://search.cpan.org/dist/Chemistry-File-SLN/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:32 miwi 

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.

WWW:    http://search.cpan.org/dist/Chemistry-File-SMARTS/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:32 miwi 

MOPAC 6 input file reader/writer

WWW:    http://search.cpan.org/dist/Chemistry-File-Mopac/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:32 miwi 

Explicit chemical reactions

WWW:    http://search.cpan.org/dist/Chemistry-Raction/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:31 miwi 

Match molecule by formula

WWW:    http://search.cpan.org/dist/Chemistry-ForumulaPattern/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:29 miwi 

Select atoms in macromolecule

WWW:    http://search.cpan.org/dist/Chemistry-MidasPattern/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:29 miwi 

Perl molecular awk interpreter

WWW:    http://search.cpan.org/dist/Chemistry-Mok/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:28 miwi 

XYZ molecule format reader/writer

WWW:    http://search.cpan.org/dist/Chemistry-File-XYZ/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:28 miwi 

Generate VRML models for molecules

WWW:    http://search.cpan.org/dist/Chemistry-File-VRML/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:27 miwi 

Perl module which provides some basic methods for representing a ring.

WWW:    http://search.cpan.org/dist/Chemistry-Ring/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:26 miwi 

Perl module which contains the exact mass data from the table of the isotopes.

WWW:    http://search.cpan.org/dist/Chemistry-Isotope/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:25 miwi 

Perl module which implements basic pattern matching for molecules.

WWW:    http://search.cpan.org/dist/Chemistry-Pattern/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:25 miwi 

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.

WWW:    http://search.cpan.org/dist/Chemistry-Canonicalize/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

15:24 miwi 

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
orders.

WWW:    http://search.cpan.org/dist/Chemistry-Bond-Find/

PR:             ports/145143
Submitted by:   Steve Wills <steve at mouf.net>

11:21 miwi 

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.

WWW: http://www.hdfgroup.org/hdf-java-html/index.html

PR:             ports/143859
Submitted by:   rfarmer at predatorlabs.net

00:27 wen 

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.

WWW: http://ab-initio.mit.edu/wiki/index.php/Meep

PR:             ports/142158
Submitted by:   Stas Timokhin <devel@stasyan.com>

06:46 pgollucci 

- 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
graphics/irit||2010-01-18|Has expired: has been broken for 3 months
graphics/pixieplus||2010-01-18|Has expired: has been broken for 6 months
japanese/expect||2010-01-18|Has expired: has been broken for 3 months
lang/pnetc||2010-01-18|Has expired: has been broken for 5 months
mail/libnewmail||2010-01-18|Has expired: has been broken for 3 months
net-mgmt/flowscan||2010-01-18|Has expired: has been broken for 5 months
net/astmanproxy||2010-01-18|Has expired: has been broken for 3 months
palm/prc-tools||2010-01-18|Has expired: has been broken for 4 months
print/latex-msc||2010-01-18|Has expired: has been broken for 3 months
science/xloops-ginac||2010-01-18|Has expired: has been broken for 3 months
shells/bush||2010-01-18|Has expired: has been broken for 3 months
textproc/iiimf-gnome-im-switcher||2010-01-18|Has expired: has been broken for 4
months
textproc/iiimf-gtk||2010-01-18|Has expired: has been broken for 3 months
x11-toolkits/gtkada-devel||2010-01-18|Has expired: has been broken for 3 months
x11-toolkits/gtkada||2010-01-18|Has expired: has been broken for 3 months
x11-wm/ion-2||2010-01-18|Has expired: has been broken for 4 months

07:20 wen 

Geo::WebService::Elevation::USGS executes elevation queries against the
United States Geological Survey's web server. You provide the latitude
and longitude in degrees, with south latitude and west longitude being
negative. The return is typically a hash containing the data you want.
Query errors are exceptions by default, though the object can be configured
to signal an error by an undef response, with the error retrievable from
the 'error' attribute.

WWW: http://search.cpan.org/dist/Geo-WebService-Elevation-USGS/

19:26 amdmi3 

qtResistors - calculate resistance of resistor by the colors on the resistor

WWW:    http://qt-apps.org/content/show.php/qtResistors?content=118297

PR:             142554
Submitted by:   zloidemon <g.veniamin@googlemail.com>

12:19 wen 

py-DendroPy is a python library for phylogenetic scripting,
simulation, data processing and manipulation.

WWW:    http://packages.python.org/DendroPy/

05:02 pgj 

This is a collection of Haskell data structures and algorithms useful for
building bioinformatics-related tools and utilities.
Current list of features includes: a Sequence data type supporting
protein and nucleotide sequences and conversion between them.

WWW: http://blog.malde.org/index.php/the-haskell-bioinformatics-library/

PR:             ports/142187
Submitted by:   Jacula Modyun <jacula(at)gmail.com>

02:54 wen 

Harminv is a free program (and accompanying library) to solve the problem
of harmonic inversion - given a discrete-time, finite-length signal
that consists of a sum of finitely-many sinusoids (possibly exponentially
decaying) in a given bandwidth, it determines the frequencies, decay
constants, amplitudes, and phases of those sinusoids.

WWW: http://ab-initio.mit.edu/wiki/index.php/Harminv

PR:             ports/142154
Submitted by:   Stas Timokhin <devel@stasyan.com>

13:44 wen 

PyBrain is a modular Machine Learning Library for Python.
It's goal is to offer flexible, easy-to-use yet still powerful
algorithms for Machine Learning Tasks and a variety of
predefined environments to test and compare your algorithms.

PyBrain is short for Python-Based Reinforcement Learning,
Artificial Intelligence and Neural Network Library. In fact,
we came up with the name first and later reverse-engineerer
this quite descriptive "Backronym".

WWW:    http://pybrain.org/

11:10 wen 

libkml is a library for use with applications that want to
parse, generate and operate on KML. It is an implementation
of the OGC KML 2.2 standard.

WWW: http://code.google.com/p/libkml/

Approved by:    miwi(mentor)

11:02 miwi 

mol2ps is a freely available command-line utility program which reads
molecular structure files in different formats and generates
Postscript output for 2D display. The Postscript file can then be used
e.g. for creating a bitmap file, using a Postscript interpreter like
Ghostscript.

WWW: http://merian.pch.univie.ac.at/~nhaider/cheminf/mol2ps.html

PR:             ports/138673
Feature safe:   yes
Submitted by:   Fernan Aguero <fernan at iib.unsam.edu.ar>

09:53 miwi 

Checkmol is a command-line utility program which reads molecular
structure files in different formats and analyzes the input
molecule for the presence of various functional groups and structural
elements. At present, approx. 200 different functional groups are
recognized. This output can be easily placed into a database table,
permitting the creation of chemical databases with a functional group
search option. Checkmol also outputs a set of statistical values derived
from a given molecule, which can also be used for quick retrieval from a
database. These values include: the number of atoms, bonds, and rings,
the number of differently hybridized carbon, oxgen, and nitrogen atoms,
the number of C=O double bonds, the number of rings of different sizes,
the number of rings containing nitrogen, oxygen, sulfur, the number of
aromatic rings, the number of heterocyclic rings, etc. The combination
of all of these values for a given molecule represents some kind of
"fingerprint" which is useful for rapid pre-selection in a database
structure/substructure search prior to a full atom-by-atom match.

WWW: http://merian.pch.univie.ac.at/~nhaider/cheminf/cmmm.html

PR:             ports/138670
Feature safe:yes
Submitted by:   Fernan Aguero <fernan at iib.unsam.edu.ar>

20:02 miwi 

libquantum is a C library for the simulation of quantum
mechanics, with a special focus laid to quantum computing.
It started as a pure quantum computer simulator, but
support for general quantum simulation has been recently
added.

WWW:    http://www.libquantum.de/

PR:             ports/137468
Submitted by:   Wen Heping <wenheping at gmail.com>

05:14 maho 

Remove science/dft++. Not actively maintained the original site. Old
style coding with lots of warnings, and build error with gcc44.

Also suggested by: gerald@

14:07 lwhsu 

Add py-h5py 1.2.0, a general-purpose Python interface to the HDF5
library.

PR:             ports/136096
Submitted by:   TAOKA Fumiyoshi

15:55 amdmi3 

peekabot is a distributed real-time 3D visualization tool for robotics
researchers and developers, written in C++.

Its purpose is to simplify the visualization needs faced by a roboticist
daily - using visualization as a debugging aid or making fancy slides for
a presentation, for example.

Chris Petrik (chris@officialunix.com)
WWW: http://www.peekabot.org

PR:             135892
Submitted by:   Chris Petrik <c.petrik.sosa@gmail.com>