06:08 yuri 

New port: science/dkh: Wolf, Reiher, and Hess's Douglas-Kroll-Hess relativistic
correction

Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13068

 

21:55 yuri 

New port: science/py-qspin: Learn quantum spin and entanglement

PR:		221401
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D12993

 

07:06 tota 

- Add new port: science/R-cran-kernlab

  Kernel-based machine learning methods for classification, regression,
  clustering, novelty detection, quantile regression and dimensionality
  reduction. Among other methods 'kernlab' includes Support Vector
  Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and
  a QP solver.

  WWW: https://cran.r-project.org/web/packages/kernlab/

 

12:08 lwhsu 

Ad TensorFlow 1.2.1

PR:		219609
Submitted by:	Jov <amutu@amutu.com>

 

03:36 tota 

- Add new port: science/R-cran-udunits2

  Provides simple bindings to Unidata's udunits library.

  WWW: https://cran.r-project.org/web/packages/udunits2/

 

03:22 jrm 

New port, science/hypre: Scalable Linear Solvers and Multigrid Methods

WWW: http://www.llnl.gov/casc/hypre/

PR:		219709
Submitted by:	pfg (maintainer)
Differential Revision:	https://reviews.freebsd.org/D11048

 

02:46 jmd 

science/iboview: new port. iboview is an advanced program for analyzing
molecular electronic structure.

Reviewed by:	swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D10553

 

23:37 lifanov 

add science/libgeodecomp - auto-parallelizing library for computer simulations

LibGeoDecomp (Library for Geometric Decomposition codes) is an
auto-parallelizing library for computer simulations. It is specifically targeted
computational science applications in the context of supercomputers and
heterogeneous systems. The library eases development of such tightly coupled
codes by essentially taking over the parallel programming: it handles both, the
parallelization itself and parameter tuning. This enables scientists to focus on
their simulation code, rather than the technical details of the parallel
computer.

PR:		213688
Submitted by:	Kurt Kanzenbach <kurt@kmk-computers.de>
Reviewed by:	matthew
Approved by:	matthew (mentor)
Differential Revision:	https://reviews.freebsd.org/D9390

 

01:47 sunpoet 

Add libaec 1.0.0

Libaec provides fast lossless compression of 1 up to 32 bit wide signed or
unsigned integers (samples). The library achieves best results for low entropy
data as often encountered in space imaging instrument data or numerical model
output from weather or climate simulations. While floating point representations
are not directly supported, they can also be efficiently coded by grouping
exponents and mantissa.

Libaec implements Golomb-Rice coding as defined in the Space Data System
Standard documents 121.0-B-2 and 120.0-G-2.

Libaec includes a free drop-in replacement for the SZIP library. Just replace
SZIP's shared library libsz.so* with libaec.so* and libsz.so* from libaec. Code
which is dynamically linked with SZIP such as HDF5 should continue to work with
libaec. No re-compilation required. HDF5 files which contain SZIP encoded data
can be decoded by HDF5 using libaec and vice versa.

WWW: https://gitlab.dkrz.de/k202009/libaec

 

12:32 thierry 

Resurrect hdf5-18, because it is required by french/med and french/aster.

Two releases of HDF5 are available for download. HDF5-1.10 should read files
created with earlier releases, but problem arise with MED and this version.

 

16:49 thierry 

`MFront` is a code generator which translates a set of closely related
domain specific languages into plain C++ on top of the `TFEL`
library. Those languages covers three kind of material knowledge:

- material properties (for instance the
  Young modulus, the thermal conductivity, etc.)
- mechanical behaviours. Numerical performances of
  generated mechanical behaviours was given a particular
  attention. Various benchmarks shows that `MFront`
  implementations are competitive with native implementations
  available in the `Cast3M`, `Code-Aster` and `Cyrano3` solvers.
- simple point-wise models, such as material swelling
  used in fuel performance codes.

`MFront` comes with an handy easy-to-use tool called `MTest` that can
test the local behaviour of a material, by imposing independent
constraints on each component of the strain or the stress. This tool
has been much faster (from ten to several hundred times depending on
the test case) than using a full-fledged finite element solver.

WWW: http://tfel.sourceforge.net/

PR:		212375
Submitted by:	Pedro F. Giffuni

 

20:48 rene 

Remove expired ports without open PRs:
2016-07-04 security/openpgpsdk: Broken for more than 6 months
2016-07-04 security/radiusniff: Broken for more than 6 months
2016-07-04 security/pear-Auth_OpenID: Broken for more than 6 months
2016-07-04 security/sshit: Broken for more than 6 months
2016-07-04 security/ifd-slb_rf60: Broken for more than 6 months
2016-07-04 security/rainbowcrack: Broken for more than 6 months
2016-07-04 security/vlog: Broken for more than 6 months
2016-07-04 security/cryptstring: Broken for more than 6 months
2016-07-04 x11/libdnd: Broken for more than 6 months
2016-07-04 x11/xlupe: Broken for more than 6 months
2016-07-04 x11/xco: Broken for more than 6 months
2016-07-04 x11/xclick: Broken for more than 6 months
2016-07-04 devel/ocfpcsc: Broken for more than 6 months
2016-07-04 devel/dits: Broken for more than 6 months
2016-07-04 devel/ruby-cache: Broken for more than 6 months
2016-07-04 devel/rapidsvn: Broken for more than 6 months
2016-07-04 devel/svnkit: Broken for more than 6 months
2016-07-04 devel/py-EnthoughtBase: Broken for more than 6 months
2016-07-04 devel/cl-uffi: Broken for more than 6 months
2016-07-04 devel/ruby-event-loop: Broken for more than 6 months
2016-07-04 devel/libqxt: Broken for more than 6 months
2016-07-04 devel/dasm: Broken for more than 6 months
2016-07-04 devel/libopendaap: Broken for more than 6 months
2016-07-04 devel/cl-uffi-sbcl: Depends on expiring devel/cl-uffi
2016-07-04 devel/cvs2p4: Broken for more than 6 months
2016-07-04 devel/bufferpool: Broken for more than 6 months
2016-07-04 devel/ifd-test: Broken for more than 6 months
2016-07-04 devel/eric4: Broken for more than 6 months
2016-07-04 devel/uclmmbase: Broken for more than 6 months
2016-07-04 devel/obfuscatejs: Broken for more than 6 months
2016-07-04 devel/oniguruma: Broken for more than 6 months
2016-07-04 devel/libbnr: Broken for more than 6 months
2016-07-04 devel/c4: Broken for more than 6 months
2016-07-04 devel/memcheck: Broken for more than 6 months
2016-07-04 devel/liblcfg: Broken for more than 6 months
2016-07-04 devel/omake: Broken for more than 6 months
2016-07-04 devel/svndelta: Broken for more than 6 months
2016-07-04 devel/papp: Broken for more than 6 months
2016-07-04 devel/mk: Broken for more than 6 months
2016-07-04 devel/avltree: Broken for more than 6 months
2016-07-04 devel/cbind: Broken for more than 6 months
2016-07-04 devel/tclgetopts: Broken for more than 6 months
2016-07-04 devel/antlrworks: Broken for more than 6 months
2016-07-04 devel/acme: Broken for more than 6 months
2016-07-04 devel/libopensync022: Broken for more than 6 months
2016-07-04 archivers/epkg: Broken for more than 6 months
2016-07-04 print/enscriptfonts: Broken for more than 6 months
2016-07-04 print/mup: Broken for more than 6 months
2016-07-04 lang/lua-mode.el: Broken for more than 6 months
2016-07-04 lang/s9fes: Broken for more than 6 months
2016-07-04 lang/alisp: Broken for more than 6 months
2016-07-04 lang/intel2gas: Broken for more than 6 months
2016-07-04 lang/stalin: Broken for more than 6 months
2016-07-04 french/eric4: Depends on expiring devel/eric4
2016-07-04 textproc/exslt: Broken for more than 6 months
2016-07-04 textproc/xt: Broken for more than 6 months
2016-07-04 textproc/ssddiff: Broken for more than 6 months
2016-07-04 textproc/xslint: Broken for more than 6 months
2016-07-04 textproc/cbedic: Broken for more than 6 months
2016-07-04 textproc/tralics: Broken for more than 6 months
2016-07-04 textproc/docbookide.el: Broken for more than 6 months
2016-07-04 textproc/glpi-plugins-AdditionalReports: Broken for more than 6
months
2016-07-04 textproc/tdhkit: Broken for more than 6 months
2016-07-04 textproc/p5-Groonga-API: Broken for more than 6 months
2016-07-04 textproc/glpi-plugins-DataInjection: Broken for more than 6 months
2016-07-04 dns/ldnsm: Broken for more than 6 months
2016-07-04 japanese/guesswork-classic: Broken for more than 6 months
2016-07-04 japanese/texinfo: Broken for more than 6 months
2016-07-04 japanese/jyuroku: Broken for more than 6 months
2016-07-04 japanese/mtools: Broken for more than 6 months
2016-07-04 palm/pdbar: Broken for more than 6 months
2016-07-04 graphics/gplot: Broken for more than 6 months
2016-07-04 graphics/white_dune: Broken for more than 6 months
2016-07-04 graphics/whirlgif: Broken for more than 6 months
2016-07-04 graphics/libaux: Broken for more than 6 months
2016-07-04 graphics/import-pictures: Broken for more than 6 months
2016-07-04 math/xgobi: Broken for more than 6 months
2016-07-04 math/fricas: Broken for more than 6 months
2016-07-04 math/dcdflib: Broken for more than 6 months
2016-07-04 math/libneural: Broken for more than 6 months
2016-07-04 math/open-axiom: Broken for more than 6 months
2016-07-04 irc/nefarious: Broken for more than 6 months
2016-07-04 irc/slirc: Broken for more than 6 months
2016-07-04 irc/ratbox-respond: Broken for more than 6 months
2016-07-04 irc/qwebirc: Broken for more than 6 months
2016-07-04 biology/platon: Broken for more than 6 months
2016-07-04 news/slnr: Broken for more than 6 months
2016-07-04 science/jmol: Broken for more than 6 months
2016-07-04 net/nstxd: Broken for more than 6 months
2016-07-04 net/sprinkle: Broken for more than 6 months
2016-07-04 editors/ssam: Broken for more than 6 months
2016-07-04 editors/fb: Broken for more than 6 months
2016-07-04 misc/quotes: Broken for more than 6 months
2016-07-04 misc/boxquote.el: Broken for more than 6 months
2016-07-04 misc/pypanda: Broken for more than 6 months
2016-07-04 misc/cuecat: Broken for more than 6 months
2016-07-04 deskutils/displaycalibrator: Broken for more than 6 months
2016-07-04 german/eric4: Depends on expiring devel/eric4
2016-07-04 multimedia/vic: Depends on expiring devel/uclmmbase
2016-07-04 multimedia/ggrab: Broken for more than 6 months
2016-07-04 emulators/dynamips: Broken for more than 6 months
2016-07-04 emulators/dynamips-devel: Broken for more than 6 months
2016-07-04 emulators/sim6811: Broken for more than 6 months
2016-07-04 emulators/minivmac: Broken for more than 6 months
2016-07-04 cad/qcad-partslib: Broken for more than 6 months
2016-07-04 comms/dump1090_mr: Broken for more than 6 months
2016-07-04 x11-fm/asfiles: Depends on expiring x11/libdnd
2016-07-04 x11-fonts/fonts-te: Broken for more than 6 months
2016-07-04 sysutils/rsyncmanager: Broken for more than 6 months
2016-07-04 sysutils/jfbterm: Broken for more than 6 months
2016-07-04 sysutils/daedalus: Broken for more than 6 months
2016-07-04 sysutils/pcfclock: Broken for more than 6 months
2016-07-04 sysutils/vlogger: Broken for more than 6 months
2016-07-04 sysutils/bontmia: Broken for more than 6 months
2016-07-04 mail/pop3gwd: Broken for more than 6 months
2016-07-04 mail/mailtray: Broken for more than 6 months
2016-07-04 mail/pflogstats: Broken for more than 6 months
2016-07-04 mail/exact: Broken for more than 6 months
2016-07-04 mail/wmpop3: Broken for more than 6 months
2016-07-04 mail/qmail-conf: Broken for more than 6 months
2016-07-04 mail/gld: Broken for more than 6 months
2016-07-04 mail/dsbl-testers: Broken for more than 6 months
2016-07-04 mail/vqregister: Broken for more than 6 months
2016-07-04 mail/atmail: Broken for more than 6 months
2016-07-04 mail/ml: Broken for more than 6 months
2016-07-04 net-im/icb: Broken for more than 6 months
2016-07-04 net-im/cicquin: Broken for more than 6 months
2016-07-04 net-im/pidgin-manualsize: Broken for more than 6 months
2016-07-04 net-im/pidgin-rhythmbox: Broken for more than 6 months
2016-07-04 russian/eric4: Depends on expiring devel/eric4
2016-07-04 russian/fortune-bashorgru: Broken for more than 6 months
2016-07-04 www/xpi-clearfields: Broken for more than 6 months
2016-07-04 www/pecl-varnish: Broken for more than 6 months
2016-07-04 www/py-requests-oauth-hook: Broken for more than 6 months
2016-07-04 www/hudson: Broken for more than 6 months
2016-07-04 www/xpi-mldonkey: Broken for more than 6 months
2016-07-04 www/xpi-cookiesafe: Broken for more than 6 months
2016-07-04 www/trac-mastertickets: Broken for more than 6 months
2016-07-04 www/dotclear: Broken for more than 6 months
2016-07-04 www/ruby-wgettsv: Broken for more than 6 months
2016-07-04 www/wwwstat: Broken for more than 6 months
2016-07-04 www/xpi-prism: Broken for more than 6 months
2016-07-04 www/xpi-fasterfox: Broken for more than 6 months
2016-07-04 www/siteframe: Broken for more than 6 months
2016-07-04 www/py-urljr: Broken for more than 6 months
2016-07-04 www/reviewboard: Broken for more than 6 months
2016-07-04 www/xpi-tabletools: Broken for more than 6 months
2016-07-04 www/wikindx: Broken for more than 6 months
2016-07-04 www/typolight: Broken for more than 6 months
2016-07-04 www/varnish-libvmod-header: Broken for more than 6 months
2016-07-04 www/xpi-gbrain: Broken for more than 6 months
2016-07-04 www/trac-robotstxt: Broken for more than 6 months
2016-07-04 www/simplog: Broken for more than 6 months
2016-07-04 www/chtml: Broken for more than 6 months
2016-07-04 databases/postgresql_autodoc: Broken for more than 6 months
2016-07-04 databases/oracle_odbc_driver: Broken for more than 6 months
2016-07-04 databases/mysql-xql: Broken for more than 6 months
2016-07-04 databases/mysql-udf-sys: Broken for more than 6 months
2016-07-04 games/lucidlife: Broken for more than 6 months
2016-07-04 games/gma: Broken for more than 6 months
2016-07-04 games/smiley: Broken for more than 6 months
2016-07-04 games/noegnud-littlehack: Broken for more than 6 months
2016-07-04 games/sdlquake2: Broken for more than 6 months
2016-07-04 games/daimonin: Depends on expiring games/daimonin-music
2016-07-04 games/noegnud-nethack: Broken for more than 6 months
2016-07-04 games/xbomber: Broken for more than 6 months
2016-07-04 games/xwelltris: Broken for more than 6 months
2016-07-04 games/ftjava: Broken for more than 6 months
2016-07-04 games/daimonin-music: Broken for more than 6 months
2016-07-04 games/gno3dtet: Broken for more than 6 months
2016-07-04 games/qtv: Broken for more than 6 months
2016-07-04 games/xwordpy: Broken for more than 6 months
2016-07-04 games/netris: Broken for more than 6 months
2016-07-04 games/rt2-demo: Broken for more than 6 months
2016-07-04 games/noegnud-addons: Broken for more than 6 months
2016-07-04 games/noegnud-nethack-deet: Broken for more than 6 months
2016-07-04 games/live-f1: Broken for more than 6 months
2016-07-04 games/xonix: Broken for more than 6 months
2016-07-04 games/fgkicker: Broken for more than 6 months
2016-07-04 games/tank: Depends on expiring graphics/libaux
2016-07-04 games/linux-nwserver: Broken for more than 6 months
2016-07-04 games/quake2-zaero: Broken for more than 6 months
2016-07-04 games/pyching: Broken for more than 6 months
2016-07-04 games/thevalley: Broken for more than 6 months
2016-07-04 games/xroads: Broken for more than 6 months
2016-07-04 games/fxsudoku: Broken for more than 6 months
2016-07-04 games/sudoku: Broken for more than 6 months
2016-07-04 games/kmancala: Broken for more than 6 months
2016-07-04 games/plonx: Broken for more than 6 months
2016-07-04 games/wmminichess: Broken for more than 6 months
2016-07-04 games/noegnud-slashem: Broken for more than 6 months
2016-07-04 games/latrine: Broken for more than 6 months
2016-07-04 games/pysycache-themes: Broken for more than 6 months
2016-07-04 games/nibbles: Broken for more than 6 months
2016-07-04 games/hlstatsx: Broken for more than 6 months
2016-07-04 audio/streamtuner: Broken for more than 6 months
2016-07-04 audio/mangler: Broken for more than 6 months
2016-07-04 audio/hawkvoice: Broken for more than 6 months
2016-07-04 audio/alac: Broken for more than 6 months
2016-07-04 x11-wm/e-module-mpdule: Broken for more than 6 months
2016-07-04 x11-wm/e-module-tclock: Broken for more than 6 months
2016-07-04 x11-wm/musca: Broken for more than 6 months
2016-07-04 x11-wm/e-module-places: Broken for more than 6 months
2016-07-04 x11-wm/e-module-forecasts: Broken for more than 6 months
2016-07-04 x11-wm/e-module-net: Broken for more than 6 months
2016-07-04 x11-wm/e-module-penguins: Broken for more than 6 months
2016-07-04 ftp/fget: Broken for more than 6 months
2016-07-04 net-mgmt/netmond: Broken for more than 6 months
2016-07-04 net-mgmt/ipfm: Broken for more than 6 months

 

15:15 rene 

Remove expired ports:
2016-04-11 deskutils/qlabels: Does not fetch, unmaintained
2016-04-14 french/tvdownloader: Many channels have modified their protocols and
cannot be DL anymore
2016-04-14 comms/cdr_read: unfetchable
2016-04-14 russian/rubygem-rutils: Deprecated by upstream
2016-04-14 devel/rubygem-dotenv-deployment: Deprecated by upstream in latest
version (0.3.0)
2016-04-15 www/p5-LWP-ConsoleLogger: Depends on expiring
www/p5-HTTP-CookieMonster
2016-04-15 www/p5-WWW-Mechanize-Cached: Depends on expiring
www/p5-HTTP-CookieMonster
2016-04-15 www/p5-HTTP-CookieMonster: Broken for more than 6 months
2016-04-15 misc/diary-hercules: Broken for more than 6 months
2016-04-15 graphics/ffff: Broken for more than 6 months
2016-04-15 net-im/sigram: Broken for more than 6 months
2016-04-15 games/annelid: Broken for more than 6 months
2016-04-15 science/py-pydap: Broken for more than 6 months
2016-04-15 sysutils/su2: Broken for more than 6 months
2016-04-15 www/download-gemist: Broken for more than 6 months
2016-04-15 databases/p5-qdbm: Broken for more than 6 months
2016-04-15 comms/libfec: Broken for more than 6 months
2016-04-15 deskutils/ladon: Broken for more than 6 months

Sponsored by:	Essen Linuxhotel Hackathon 2016

 

13:41 miwi 

Fuzzy logic toolkit for SciPy.

The goals of scikit-fuzzy are:

* To provide the community with a robust toolkit of independently developed
  and implemented fuzzy logic algorithms
* To increase the attractiveness of scientific Python as a valid alternative
  to closed-source options.

WWW: https://github.com/scikit-fuzzy/scikit-fuzzy/

PR:		205621
Submitted by:	Yuri Victorovich <yuri@rawbw.com>

 

23:20 rene 

Remove expired ports:
2015-12-30 www/ocsigen: Broken for more than 6 months
2015-12-30 devel/monodevelop-database: Broken for more than 6 months
2015-12-30 lang/cduce: Broken for more than 6 months
2015-12-30 science/hdf-java: Broken for more than 6 months
2015-12-30 math/p5-Math-Geometry-Planar-GPC-Polygon: Broken for more than 6
months
2015-12-30 www/eliom: Depends on broken and expiring www/ocsigen
2015-12-30 audio/py-fastaudio: Broken for more than 6 months
2015-12-30 devel/jgoodies-common: Broken for more than 6 months
2015-12-30 graphics/pinta: Broken for more than 6 months
2015-12-30 games/kanatest: Broken for more than 6 months
2015-12-30 editors/bless: Broken for more than 6 months
2015-12-30 security/burpsuite: Broken for more than 6 months

 

23:34 rodrigo 

Add new port p5-Mcstas-Tools, a general tool for simulating neutron scattering
instruments and experiments

PR:		194849
Submitted by:	Erik B Knudsen <erkn@fysik.dtu.dk>

 

06:15 tota 

- Add new port: science/R-cran-etm

  Matrix of transition probabilities for any time-inhomogeneous
  multistate model with finite state space

  WWW: https://cran.r-project.org/web/packages/etm/

 

05:46 tota 

- Add new port: science/R-cran-cmprsk

  Estimation, testing and regression modeling of subdistribution
  functions in competing risks, as described in Gray (1988), A class
  of K-sample tests for comparing the cumulative incidence of a
  competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ
  (1999), A proportional hazards model for the subdistribution of a
  competing risk, JASA, 94:496-509.

  WWW: https://cran.r-project.org/web/packages/cmprsk/

 

09:24 makc 

Rename my ports to comply with Python ports policy

Requested by:	koobs

 

10:10 danfe 

Add a port of Libxc, a library of exchange-correlation functionals for
density-functional theory.

PR:		201266 (modified)
Submitted by:	Johannes Dieterich

 

15:54 amdmi3 

This plugin extends the RESTful API of Orthanc with WADO and DICOMweb
support.

WWW: http://www.orthanc-server.com/

PR:		202816
Submitted by:	mp39590@gmail.com

 

14:48 amdmi3 

- Add science/orthanc-postgresql

The plugin replaces the default SQLite engine of Orthanc with a
PostgreSQL back-end.

WWW: http://www.orthanc-server.com/

PR:		201673
Submitted by:	mp39590@gmail.com

 

14:45 amdmi3 

- Add science/orthanc-webviewer

Web viewer plugin allows easy serial view of medical images stored in
Orthanc server in a browser, using HTML5 technology.
Demo: http://youtu.be/ub5IxlVqoOE

The plugin can't be used for diagnostic purposes.

WWW: http://www.orthanc-server.com/

PR:		201049
Submitted by:	mp39590@gmail.com

 

12:39 wen 

scikits-sparse is a Python module for sparse matrix calculations.

WWW: https://scikits.appspot.com/sparse/

PR:		200678
Submitted by:	yuri@rawbw.com

 

14:07 amdmi3 

- Add science/orthanc

Orthanc aims at providing a simple, yet powerful standalone DICOM
server. It is designed to improve the DICOM flows in hospitals and to
support research about the automated analysis of medical images.

Orthanc can turn any computer running Windows, Linux, FreeBSD or OS X
into a DICOM store (in other words, a mini-PACS system). Its
architecture is lightweight and standalone, meaning that no complex
database administration is required, nor the installation of third-party
dependencies.

What makes Orthanc unique is the fact that it provides a RESTful API.
Thanks to this major feature, it is possible to drive Orthanc from any
computer language. The DICOM tags of the stored medical images can be
downloaded in the JSON file format. Furthermore, standard PNG images can
be generated on-the-fly from the DICOM instances by Orthanc.

Orthanc lets its users focus on the content of the DICOM files, hiding
the complexity of the DICOM format and of the DICOM protocol.

WWW: http://www.orthanc-server.com/

PR:		199146
Submitted by:	mp39590@gmail.com

 

15:35 sunpoet 

- Move science/rubygem-netcdf to science/rubygem-ruby-netcdf
- Update to 0.7.1.1
- Remove BUILD_DEPENDS
- Remove USE_RAKE
- Update WWW

Changes:	http://www.gfd-dennou.org/arch/ruby/products/ruby-netcdf/ChangeLog

 

16:58 xmj 

science/rubygem-ruby-dcl: Add port

This is a Ruby interface to the scientific graphic library DCL.

WWW: http://ruby.gfd-dennou.org/products/ruby-dcl/

PR:		197018
Differential Revision:	https://reviews.freebsd.org/D2036
Submitted by:	Shin-ya MURAKAMI <murashin@gfd-dennou.org>
Approved by:	mentors (implicit)

 

09:38 pi 

New port: science/mcstas-comps

McStas component library for McStas, a tool for simulating neutron
instrumentation and experiments using a ray-tracing formalism.
Currently the main use of McStas is in the field of instrument
design.

WWW: http://www.mcstas.org

PR:		194847
Submitted by:	Erik B. Knudsen <erkn@fysik.dtu.dk>

 

09:15 pi 

New port: science/mcstas

Monte Carlo ray tracing simulations of neutron experiments.

McStas is a tool for simulating neutron instrumentation and experiments
using a ray-tracing formalism. Currently the main use of McStas is
in the field of instrument design.

WWW: http://www.mcstas.org

PR:		194846
Submitted by:	Erik B. Knudsen <erkn@fysik.dtu.dk>

 

13:55 rene 

Resurrect science/mpb, pass maintainership to PR submitter.
- update to 1.5
- change to lang/guile2
- fix up USES and post-patch
- add optional dependency on math/nlopt
- install header files

PR:		196179
Submitted by:	Rainer Hurling

 

00:24 rene 

Remove expired ports:
2014-12-27 games/secretmaryochronicles-music: Depends on expiring
games/secretmaryochronicles
2014-12-27 science/mpb: Broken for more than 6 months
2014-12-27 x11-fm/pbi-thumbnailer: Broken for more than 6 months

 

14:58 rene 

Remove expired ports:
2014-11-07 math/elmer-umfpack: Obsoleted by cad/elmerfem
2014-11-07 science/elmer-eio: Obsoleted by cad/elmerfem
2014-11-07 science/elmer-matc: Obsoleted by cad/elmerfem
2014-11-07 science/elmer-meshgen2d: Obsoleted by cad/elmerfem
2014-11-07 science/elmergrid: Obsoleted by cad/elmerfem

 

09:45 rene 

Remove expired ports
Keep some which are optional dependencies of non-expired ports
2014-09-18 sysutils/moreutils-parallel: Use moreutils-parallel in
sysutils/moreutils instead
2014-09-20 science/ruby-netcdf: Depends on deprecated math/ruby-narray
2014-09-20 x11-toolkits/ruby-fox16: RubyForge shutdown May 15 2014
2014-09-20 math/ruby-gnuplot: Depends on deprecated math/ruby-narray
2014-09-20 science/ruby-gphys: Depends on deprecated math/ruby-narray
2014-09-20 math/ruby-fftw3: Depends on deprecated math/ruby-narray
2014-09-20 science/ruby-dcl: Depends on deprecated math/ruby-narray
2014-09-20 math/ruby-numru_misc: Depends on deprecated math/ruby-narray
2014-09-20 math/ruby-narray: RubyForge shutdown May 15 2014
2014-09-20 textproc/ruby-liquid: RubyForge shutdown May 15 2014
2014-09-20 comms/callsign: RubyForge shutdown May 15 2014
2014-09-20 misc/ruby-vpim: RubyForge shutdown May 15 2014
2014-09-20 net/ruby-ldap: RubyForge shutdown May 15 2014
2014-09-20 devel/rubygem-echoe: Depends on deprecated rubyforge
2014-09-20 www/ruby-borges: RubyForge shutdown May 15 2014
2014-09-20 www/ruby-fcgiwrap: RubyForge shutdown May 15 2014
2014-09-20 www/rubygem-scrubyt: RubyForge shutdown May 15 2014
2014-09-20 devel/ruby-multi: RubyForge shutdown May 15 2014
2014-09-20 databases/ruby-dbd_sqlite3: RubyForge shutdown May 15 2014
2014-09-20 math/ruby-gsl: RubyForge shutdown May 15 2014
2014-09-20 security/ruby-gpgme: RubyForge shutdown May 15 2014
2014-09-20 multimedia/vodcatcher: RubyForge shutdown May 15 2014
2014-09-20 japanese/ruby-ming: RubyForge shutdown May 15 2014
2014-09-20 devel/ruby-statgrab: RubyForge shutdown May 15 2014
2014-09-20 security/ruby-crypt: RubyForge shutdown May 15 2014
2014-09-20 sysutils/philesight: Depends on deprecated devel/ruby-locale2
2014-09-20 multimedia/podcatcher: RubyForge shutdown May 15 2014
2014-09-20 audio/ruby-mp3info: RubyForge shutdown May 15 2014
2014-09-20 multimedia/ruby-flvtool2: RubyForge shutdown May 15 2014
2014-09-20 audio/ruby-freedb: RubyForge shutdown May 15 2014
2014-09-20 graphics/ruby-ming: RubyForge shutdown May 15 2014
2014-09-20 devel/ruby-locale2: RubyForge shutdown May 15 2014
2014-09-20 devel/rubygem-rubyforge: RubyForge shutdown May 15 2014
2014-09-20 databases/ruby-dbd_odbc: RubyForge shutdown May 15 2014
2014-09-20 devel/ruby-fastri: RubyForge shutdown May 15 2014
2014-09-20 devel/ri-emacs: RubyForge shutdown May 15 2014
2014-09-20 security/p5-openxpki-client-html-mason: security/p5-openxpki-0.15+
abandoned Mason UI technology in favor of FastCGI

 

15:18 sunpoet 

- Add rubygem-cdo 1.2.3

Ruby binding to CDO (Climate Data Operators)

GitHub repository at https://github.com/Try2Code/cdo-bindings

WWW: https://code.zmaw.de/projects/cdo/wiki/Cdo%7Brbpy%7D
RG:  https://rubygems.org/gems/cdo

 

15:18 sunpoet 

- Add py-cdo 1.2.3

Python binding to CDO (Climate Data Operators)

GitHub repository at https://github.com/Try2Code/cdo-bindings

WWW: https://code.zmaw.de/projects/cdo/wiki/Cdo%7Brbpy%7D

 

16:24 sunpoet 

- Add py-pysal 1.8.0

PySAL is a cross-platform library of spatial analysis functions written in
Python. It is intended to support the development of high level applications for
spatial analysis.

WWW: https://pypi.python.org/pypi/PySAL
WWW: http://pysal.org/

 

10:07 bapt 

Remove non staged ports without pending PR from s*

 

17:31 sunpoet 

- Add grib_api 1.12.3

The ECMWF GRIB API is an application program interface accessible from C,
FORTRAN and Python programs developed for encoding and decoding WMO FM-92 GRIB
edition 1 and edition 2 messages. A useful set of command line tools is also
provided to give quick access to GRIB messages.

WWW: https://software.ecmwf.int/wiki/display/GRIB/Home

 

22:37 marino 

Add new port: science/sigrok-firmware

PR:		188810
Submitted by:	uffe

      ===============================================================

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.

 

22:24 marino 

Add new port: science/sigrok-firmware-fx2lafw

PR:		188809
Submitted by:	uffer

      ===============================================================

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.

 

22:09 marino 

Add new port: science/sigrok-firmware-utils

PR:		188808
Submitted by:	uffer

      ===============================================================

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.

 

23:22 marino 

Add new port: science/pulseview

PR:		179854
Submitted by:	uffe (uffe.org)
Major QA:	marino

    ==================================================================

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.

WWW: http://sigrok.org/

 

21:02 shurd 

Java based Smith chart program. Performs single-frequency and sweep charting
with both Smitch charts and SWR/PWR curves. Does drag-and-drop schematic entry
with direct entry of component values as well as "drag tuning". Can import
load parameters directly from the following:

- EZNEC (and EZNEC GAM files)
- miniVNA and miniVNApro
- AIM4170
- CocoaNEC
- Rig Expert ".aaplot" files
- Touchstone S1P ".s1p" files (shunt and series)

Reviewed by:	db, skreuzer
Approved by:	db, skreuzer (mentors)
Differential Revision: https://phabric.freebsd.org/D311

 

05:44 xmj 

textproc/metaf2xml: Upgrade to 1.55

- Upgrade to 1.55
- Move from textproc to science
- Introduce conditional run dependency on Apache
- Introduce perl install dependency
- Improve comment and pkg-descr
- Stagify
- Pet portlint

PR: 180441
Submitted by: Thomas <metaf2xml@users.sourceforge.net>
Approved by: maintainer timeout (clsung, 50 weeks)
Approved by: swills (mentor)

 

03:32 sunpoet 

- Remove science/netcdf-ftn, science/netcdf3-ftn and science/netcdf4

 

03:25 sunpoet 

- Remove science/hdf5-18

 

03:20 sunpoet 

- Add netcdf-fortran 4.2

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/

 

03:18 sunpoet 

- Add netcdf-cxx 4.2.1

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/

 

13:28 sunpoet 

- Add cgribex 1.6.3

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

 

11:17 rene 

Remove expired ports:
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/)

 

10:55 rene 

Remove expired ports:
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

 

01:15 swills 

This is a Ruby interface to the NetCDF scientific IO library.

WWW: http://ruby.gfd-dennou.org/products/ruby-netcdf

PR:		ports/187932
Submitted by:	Shin-ya Murakami <murashin@gfd-dennou.org>

 

22:39 rene 

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

 

15:39 thierry 

Adding OpenKIM, an application programming interface (API) for
coupling atomistic simulation codes and interatomic potential
subroutines.

PR:		ports/177692
Submitted by:	Jason Bacon <jwbacon (at) tds.net>

 

00:13 jgh 

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.

WWW: http://sigrok.org/

PR:		ports/179855
Submitted by:	Uffe Jakobsen <uffe@uffe.org>

 

14:12 wg 

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.

WWW: https://github.com/gkassel/pyaixi

PR:		ports/184572
Submitted by:	Johannes Jost Meixner <xmj chaot.net>

 

12:14 rene 

Remove expired ports:
2013-12-04 x11-themes/lila-xfwm4: Upstream development dead
2013-12-05 science/omnetpp: depends on expired textproc/libxml

 

15:51 wg 

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
application.

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

PR:		ports/181687
Submitted by:	Johannes Meixner <xmj chaot.net>

 

07:25 bapt 

Fix index by removing a hidden dependency on vtk4

 

06:57 bapt 

Remove ports depending on vtk4

Approved by:	yuri@irfu.se (maintainer)

 

19:31 theraven 

Added FisicaLab port.

Approved by:	bapt (mentor)

 

11:27 koobs 

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.

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

PR:		ports/179744
Submitted by:	Johannes Jost Meixner <xmj@chaot.net>

 

19:19 rene 

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:
- 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

 

18:02 olivierd 

Equake is a panel plugin which monitors and displays earthquakes each time
a new one occurs.

WWW: http://freecode.com/projects/equake-xfce

 

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