- 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
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
- 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>
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/
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/
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
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
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
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
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
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/
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/
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)
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
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
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/
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>
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/
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/
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/
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/
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
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
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>
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/
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>
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>
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)
