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freebsd-ports/science
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Yuri Victorovich 2ef3ba3722 science/gromacs: Update 5.0.6 -> 2018.1 
Port changes:
* Take maintainership.
* Modernize the port, now using option helpers.
* Add the OPENCL option.
* Add the THREAD_MPI option that is now the default multiprocessing option.
* Add missing dependencies.
2018-04-19 08:04:10 +00:00
..
2d-rewriter
afni Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
aircraft-datcom Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
ALPSCore devel/boost-*: update to 1.67.0 2018-04-18 13:57:42 +00:00
antioch New port: science/antioch: C++ Chemical Kinetics, Thermodynaimics, and Transport Library 2018-04-18 06:51:47 +00:00
avogadro devel/boost-*: update to 1.67.0 2018-04-18 13:57:42 +00:00
bddsolve devel/boost-*: update to 1.67.0 2018-04-18 13:57:42 +00:00
bft - Fix LICENSE 2017-12-06 09:00:23 +00:00
bodr
brian Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
buddy
cdcl For ports that are marked BROKEN on armv6, and also fail to build on 2017-11-30 06:13:34 +00:00
cdf Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
cdo Update to 1.9.3 2018-02-04 10:12:35 +00:00
cgnslib - Add missing depend on libX11 2018-03-22 08:33:19 +00:00
cgribex
checkmol - Migrate Mk/bsd.fpc.mk to Mk/Uses/fpc.mk 2018-04-05 04:52:36 +00:00
chemical-mime-data
chemps2 science/chemps2: Update 1.8.6 -> 1.8.7 2018-03-26 09:47:56 +00:00
chemtool science/chemtool: Update 1.6.11 -> 1.6.14 2018-03-24 01:06:20 +00:00
chemtool-devel Return maho@'s ports to the pool after his commit bit expired. 2018-03-11 11:20:43 +00:00
clhep Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
colt
crf++
dcl Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
devisor
dkh Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
dlpoly-classic Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
ecs Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
epte
erd Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
fastcap
fasthenry
fisicalab Fix configure options for gnustep-make 2017-12-03 12:23:53 +00:00
fsom fsom: Tiny C library for managing SOM (Self-Organizing Maps) neural networks 2018-04-16 18:15:30 +00:00
fvcom Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
fvcom-mpi Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
fvm - Update WWW 2018-03-31 09:33:26 +00:00
gchemutils
gdma Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
getdp Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
ghemical Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
ghmm
gnudatalanguage Upgrade to 0.9.8. 2018-04-07 20:06:19 +00:00
gramps science/gramps: Tidy up the USE_PYTHON settings 2018-02-26 15:06:56 +00:00
grib_api Update to 1.26.0 2018-03-09 21:48:31 +00:00
gromacs science/gromacs: Update 5.0.6 -> 2018.1 2018-04-19 08:04:10 +00:00
gsmc
gtamsanalyzer Fix configure options for gnustep-make 2017-12-03 12:23:53 +00:00
gwyddion Security update OpenEXR and ilmbase to 2.2.1. 2017-12-01 01:58:23 +00:00
h5utils science/h5utils: Update to 1.13.1 2018-03-22 04:45:38 +00:00
harminv Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
hdf Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
hdf5 These two ports build and package without issues now on 10.4-STABLE 2018-01-15 05:40:13 +00:00
hdf5-18 These two ports build and package without issues now on 10.4-STABLE 2018-01-15 05:40:13 +00:00
hs-bio Switch C compiler used to compile GHC to base Clang. 2018-02-10 08:03:22 +00:00
hypre Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
iboview devel/boost-*: update to 1.67.0 2018-04-18 13:57:42 +00:00
InsightToolkit Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
isaac-cfd Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
jstrack
kalzium New port: science/step, science/kalzium 2018-04-09 18:32:24 +00:00
kalzium-kde4 Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
kst2 Add explicit dependence on Qt components 2018-04-07 18:49:01 +00:00
lamprop science/lamprop: Unbreak by fixing the python interpreter in the shebang 2018-03-13 08:27:23 +00:00
libaec Convert to USE_GITLAB 2018-03-14 18:11:33 +00:00
libcint science/libcint: Update 3.0.10 -> 3.0.11 2018-04-16 08:44:20 +00:00
libctl Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
libefp science/libefp: Update to 1.5.0 2017-12-23 18:19:11 +00:00
libgeodecomp devel/boost-*: update to 1.67.0 2018-04-18 13:57:42 +00:00
libghemical Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
libint Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
libkml devel/boost-*: update to 1.67.0 2018-04-18 13:57:42 +00:00
liblinear
liboglappth Return maho@'s ports to the pool after his commit bit expired. 2018-03-11 11:20:43 +00:00
libquantum
libsvm
libsvm-python
libxc Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
linsmith Make libgnome and libgnomeui not implying esound dependency 2018-03-26 12:38:56 +00:00
massxpert Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
mbdyn Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
mcstas science/mcstas: switch back to PORTVERSION 2017-12-06 16:18:35 +00:00
mcstas-comps
mcxtrace New port: science/mcxtrace: Monte Carlo X-ray tracing package 2017-12-05 19:15:49 +00:00
medit
meep science/meep: Add license; Add missing dependencies; Order USExx section 2018-03-18 06:01:25 +00:00
mei Switch from swig1.3 to swig 3.0 2017-12-20 12:25:18 +00:00
metaf2xml
metaphysicl New port: science/metaphysicl: Metaprogramming, operator-overloaded classes for numerical simulations 2018-04-18 04:59:15 +00:00
minc2
mol2ps - Migrate Mk/bsd.fpc.mk to Mk/Uses/fpc.mk 2018-04-05 04:52:36 +00:00
MOOSE-neural-simulator Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
mpb Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
mpqc Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
mpqc-mpich Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
ncs science/ncs: Unbreak 2018-03-13 09:50:42 +00:00
netcdf Fix packaging when DAP option is disabled 2018-04-14 23:59:26 +00:00
netcdf-cxx Update WWW 2017-12-11 10:37:19 +00:00
netcdf-fortran Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
nifticlib Multiple ports: 2018-01-31 01:07:07 +00:00
openbabel New USES=eigen 2018-01-02 16:49:24 +00:00
openkim Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
orthanc devel/boost-*: update to 1.67.0 2018-04-18 13:57:42 +00:00
orthanc-dicomweb devel/boost-*: update to 1.67.0 2018-04-18 13:57:42 +00:00
orthanc-postgresql devel/boost-*: update to 1.67.0 2018-04-18 13:57:42 +00:00
orthanc-webviewer devel/boost-*: update to 1.67.0 2018-04-18 13:57:42 +00:00
p5-Algorithm-SVMLight
p5-Chemistry-3DBuilder
p5-Chemistry-Bond-Find
p5-Chemistry-Canonicalize
p5-Chemistry-Elements
p5-Chemistry-File-MDLMol
p5-Chemistry-File-Mopac
p5-Chemistry-File-PDB
p5-Chemistry-File-SLN
p5-Chemistry-File-SMARTS
p5-Chemistry-File-SMILES
p5-Chemistry-File-VRML
p5-Chemistry-File-XYZ
p5-Chemistry-FormulaPattern
p5-Chemistry-InternalCoords
p5-Chemistry-Isotope
p5-Chemistry-MacroMol
p5-Chemistry-MidasPattern
p5-Chemistry-Mok
p5-Chemistry-Mol
p5-Chemistry-Pattern
p5-Chemistry-Reaction
p5-Chemistry-Ring
p5-Geo-BUFR
p5-Geo-Coordinates-Converter
p5-Geo-Coordinates-Converter-iArea
p5-Geo-ReadGRIB
p5-Geo-WebService-Elevation-USGS Update to 0.108 2018-03-25 18:06:28 +00:00
p5-Mcstas-Tools Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
p5-PerlMol
p5-Physics-Unit
paje Fix configure options for gnustep-make 2017-12-03 12:23:53 +00:00
paraview Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
pcmsolver Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
PETSc science/PETSc: Update 3.8.3 -> 3.8.4 2018-03-26 10:11:16 +00:00
pnetcdf Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
psychopy science/psychopy: Update 1.90.0 -> 1.90.1 2018-04-06 08:14:03 +00:00
pulseview devel/boost-*: update to 1.67.0 2018-04-18 13:57:42 +00:00
py-cdo Update to 1.3.6 2018-04-04 18:53:03 +00:00
py-coards Relax USES=python 2018-02-25 05:34:03 +00:00
py-DendroPy %%PYTHON_PYOEXTENSION%% is harmful in python2 style plists 2018-01-28 22:26:46 +00:00
py-h5py Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-hcluster Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-mdp Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-mlpy Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-netCDF4 Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-obspy Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-OpenFermion science/py-OpenFermion: Update 0.4-29 -> 0.6 2018-03-30 23:18:19 +00:00
py-openpiv Add new port science/py-openpiv: 2018-04-02 08:43:54 +00:00
py-paida Convert Python ports to FLAVORS. 2017-11-30 15:50:30 +00:00
py-pupynere Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-pyaixi Relax USES=python 2018-02-25 05:34:18 +00:00
py-pydicom - Update to 1.0.2 2018-03-11 01:22:55 +00:00
py-pymol science/py-pymol: Add GUI options QT5 and TK; Add missing dependency NUMPY 2018-03-22 05:48:25 +00:00
py-pyosf Unbreak 2018-03-26 19:34:27 +00:00
py-pysal Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-pyteomics Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-pyteomics.biolccc Convert Python ports to FLAVORS. 2017-11-30 15:50:30 +00:00
py-qspin Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-quantities New port: science/py-quantities: Support for physical quantities with units, based on numpy 2018-03-29 20:37:39 +00:00
py-scikit-fuzzy Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-scikit-learn Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-scikit-sparse Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-scimath Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-scipy Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-scoria Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-tensorflow Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-veusz Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-ws2300 science/py-ws2300: Unbroke the port. 2018-02-26 04:16:14 +00:00
pybrain Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
pycdf Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
pynn Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
qcl
qtresistors Reset vg@'s ports after he resigned. 2018-02-23 21:09:47 +00:00
R-cran-AMORE Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
R-cran-bayesm Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
R-cran-cmprsk Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
R-cran-DCluster Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
R-cran-e1071 Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
R-cran-eco Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
R-cran-Epi - Update to 2.26 2018-04-02 09:54:34 +00:00
R-cran-epicalc Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
R-cran-etm Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
R-cran-fastICA Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
R-cran-kernlab Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
R-cran-snow Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
R-cran-som Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
R-cran-udunits2 Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
rdkit devel/boost-*: update to 1.67.0 2018-04-18 13:57:42 +00:00
rubygem-ai4r
rubygem-cdo Update to 1.3.6 2018-04-04 18:53:54 +00:00
rubygem-rgeo Add rubygem-rgeo 1.0.0 2018-04-07 16:32:18 +00:00
rubygem-rgeo-geojson Add rubygem-rgeo-geojson 2.0.0 2018-04-07 16:32:45 +00:00
rubygem-rgeo-proj4 Add rubygem-rgeo-proj4 1.0.0 2018-04-07 16:33:14 +00:00
rubygem-rgeo-shapefile Add rubygem-rgeo-shapefile 1.0.0 2018-04-07 16:33:40 +00:00
rubygem-ruby-dcl
rubygem-ruby-netcdf
sigrok-cli Switch pkg-pist WWW: label to apropriate HTTPS addresses. 2018-01-16 15:13:18 +00:00
sigrok-firmware
sigrok-firmware-fx2lafw science/sigrok-firmware-fx2lafw: Update to version 0.1.6. 2018-01-28 21:50:25 +00:00
sigrok-firmware-utils - Fix LICENSE 2018-02-06 15:17:45 +00:00
silo Fix order of variables 2018-03-17 14:43:34 +00:00
simlib For ports that are marked NOT_FOR/ONLY_FOR armv6, also mark them so 2017-11-30 05:55:17 +00:00
simsmith
step New port: science/step, science/kalzium 2018-04-09 18:32:24 +00:00
step-kde4 math/libqalculate: Update to 2.2.1 2018-02-26 11:22:36 +00:00
svmlight
szip
tfel devel/boost-*: update to 1.67.0 2018-04-18 13:57:42 +00:00
udunits Update to 2.2.26 2017-12-23 16:49:28 +00:00
v_sim Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
vmd Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
voro++ Multiple ports: 2018-01-31 01:07:07 +00:00
xfce4-equake-plugin
xmakemol
Makefile New port: science/antioch: C++ Chemical Kinetics, Thermodynaimics, and Transport Library 2018-04-18 06:51:47 +00:00