NetCDF (network Common Data Form) is an interface for array-oriented
data access and a library that provides an implementation of the
interface. The netCDF library also defines a machine-independent
format for representing scientific data. Together, the interface,
library, and format support the creation, access, and sharing of
scientific data. The netCDF software was developed at the Unidata
Program Center in Boulder, Colorado.
Git repository: https://github.com/Unidata/netcdf-fortran
WWW: http://www.unidata.ucar.edu/software/netcdf/
NetCDF (network Common Data Form) is an interface for array-oriented
data access and a library that provides an implementation of the
interface. The netCDF library also defines a machine-independent
format for representing scientific data. Together, the interface,
library, and format support the creation, access, and sharing of
scientific data. The netCDF software was developed at the Unidata
Program Center in Boulder, Colorado.
Git repository: https://github.com/Unidata/netcdf-cxx4
WWW: http://www.unidata.ucar.edu/software/netcdf/
GRIBEX is an interface for encoding and decoding WMO FM-92 GRIB edition 1
messages and some ancillary subroutines for controlling printing and debugging.
The GRIBEX software was developed at the European Centre for Medium-range
Weather Forecasts (ECMWF) and is part of the EMOS library. EMOS is mostly
written in Fortran. Therefore it has only a Fortran interface.
CGRIBEX is a lightweight version of GRIBEX written in ANSI C with a portable
Fortran interface. For best compatibility some of the C sources were converted
from the Fortran GRIBEX version.
WWW: https://code.zmaw.de/projects/cgribex
2014-04-16 ports-mgmt/pkgsearch: Upstream disappeared
2014-04-17 science/flounder: Unmaintained since 2002
2014-04-17 security/nbaudit: Unmaintained since 2002
2014-04-17 security/saint: Unmaintained since 2002
2014-04-17 graphics/gozer: Unmaintained since 2002
2014-04-17 misc/pdfmap: Unmaintained since 2002
2014-04-17 devel/showgrammar: Unmaintained since 2002
2014-04-17 biology/libgenome: Unmaintained since 2002
2014-04-17 deskutils/narval: Unmaintained since 2002
2014-04-17 devel/fampp: Unmaintained since 2002
2014-04-17 net-p2p/py-fngrab: Unmaintained since 2002
2014-04-17 misc/wmfirew: Unmaintained since 2002
2014-04-17 x11-wm/e16utils: Unmaintained since 2002
2014-04-17 misc/salias: Unmaintained since 2002
2014-04-17 print/latex2slides: Unmaintained since 2002
2014-04-17 lang/sxm: Unmaintained since 2002
2014-04-17 textproc/pybook: Unmaintained since 2002
2014-04-17 mail/mailcrypt: Unmaintained since 2002
2014-04-17 japanese/elvis: Unmaintained since 2002
2014-04-17 devel/prototype: Unmaintained since 2002
2014-04-17 print/wprint: Unmaintained since 2002
2014-04-17 science/euler: Unmaintained since 2002
2014-04-17 multimedia/gopchop: Unmaintained since 2002
2014-04-17 science/gdis: Unmaintained since 2002
2014-04-17 net/googolplex: Unmaintained since 2002
2014-04-17 lang/logo: Unmaintained since 2002
2014-04-17 textproc/roap: Unmaintained since 2002
2014-04-17 x11-wm/afterstep-i18n: Unmaintained since 2002
2014-04-17 games/yamsweeper: Unmaintained since 2002
2014-04-17 net-mgmt/echolot: Unmaintained since 2002
2014-04-17 security/pam_smb: Unmaintained since 2002
2014-04-18 devel/lua-redis-parser: Broken for more than 6 months
2014-04-18 biology/finchtv: Broken for more than 6 months
2014-04-18 net-im/ari-yahoo: Broken for more than 1 year (http://www.icculus.org/ari-yahoo/)
2014-04-12 net/pvm++: Unmaintained since 2001
2014-04-12 devel/ixlib: Unmaintained since 2001
2014-04-12 mail/althea: Unmaintained since 2001
2014-04-12 graphics/claraocr: Unmaintained since 2001
2014-04-12 graphics/qvplay: Unmaintained since 2001
2014-04-12 print/guitartex: Unmaintained since 2001
2014-04-12 print/pnm2ppa: Unmaintained since 2001
2014-04-12 graphics/opendis: Unmaintained since 2001
2014-04-12 net/gnome-mud: Unmaintained since 2001
2014-04-12 graphics/maverik: Unmaintained since 2001
2014-04-12 biology/rasmol: Unmaintained since 2001
2014-04-12 mail/mail2procmailrc: Unmaintained since 2001
2014-04-12 science/felt: Unmaintained since 2001
2014-04-12 textproc/pardiff: Unmaintained since 2001
2014-04-12 lang/klone: Unmaintained since 2001
2014-04-12 net/rmsg: Unmaintained since 2001
2014-04-12 net/sharity-light: Unmaintained since 2001
2014-04-12 biology/genpak: Unmaintained since 2001
2014-04-12 net/forg: Unmaintained since 2001
2014-04-12 misc/txt2regex: Unmaintained since 2001
2014-04-12 textproc/ipdf: Unmaintained since 2001
2014-04-12 graphics/plotmtv: Unmaintained since 2001
2014-04-12 devel/happydoc: Unmaintained since 2001
2014-04-12 print/cpp2latex: Unmaintained since 2001
2014-04-12 graphics/svg2swf: Unmaintained since 2001
2014-04-12 devel/flick: Unmaintained since 2001
2014-04-12 mail/smail: Unmaintained since 2001
2014-04-12 net/net-http: Unmaintained since 2001
2014-04-12 security/cfv: Unmaintained since 2001
2014-04-12 graphics/camediaplay: Unmaintained since 2001
2014-04-12 math/umatrix: Unmaintained since 2001
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
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.
WWW: http://sigrok.org/
PR: ports/179855
Submitted by: Uffe Jakobsen <uffe@uffe.org>
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.
WWW: https://github.com/gkassel/pyaixi
PR: ports/184572
Submitted by: Johannes Jost Meixner <xmj chaot.net>
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
application.
WWW: https://pypi.python.org/pypi/Pydap
PR: ports/181687
Submitted by: Johannes Meixner <xmj chaot.net>
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.
WWW: https://pypi.python.org/pypi/pupynere/
PR: ports/179744
Submitted by: Johannes Jost Meixner <xmj@chaot.net>
Unfortunately, this also affects some ports using QT3 as a GUI toolkit.
Changes to infrastructure files:
- bsd.kde.mk : obsolete, remove
- bsd.qt.mk : note that a CONFLICTS_BUILD line can probably go after a while
- CHANGES : document the removals from bsd.port.mk
- 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
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>
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
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
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>
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]
- 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/
