Stephen Montgomery-Smith bd461d2230 - Take maintainership of devel/gdcm. ... - Update devel/gdcm to 2.8.8. - Bump portrevision of dependent ports.		2018-11-12 20:47:18 +00:00
..
2d-rewriter
abinit
afni	Add DOCS options to ports that should have one.	2018-09-10 13:14:50 +00:00
aircraft-datcom	Add DOCS options to ports that should have one.	2018-09-10 13:14:50 +00:00
ALPSCore	Remove compatibility code for FreeBSD < 11.2 from all ports.	2018-11-02 13:32:34 +00:00
antioch	Upgrade these ports to USES=compiler:c++11-lang to fix build on gcc-based	2018-09-18 09:28:34 +00:00
atom	science/libxc: Update 3.0.0 -> 4.2.3	2018-10-20 23:29:28 +00:00
atompaw	science/atompaw: Update 4.1.0.3 -> 4.1.0.4	2018-09-20 15:00:46 +00:00
avogadro	science/avogadro: Add CONFLICTS statement	2018-10-24 06:03:32 +00:00
avogadro2	science/avogadrolibs: Update 1.91.0 -> 1.91.0-107	2018-10-18 22:31:26 +00:00
avogadrolibs	science/avogadrolibs: Update 1.91.0-107 -> 1.92.0	2018-11-09 06:25:39 +00:00
bagel	Drop remaining BROKEN_FreeBSD_10 per EOL after r483807	2018-11-05 06:54:31 +00:00
bddsolve	Fix build on gcc-based archs by updating USES.	2018-09-22 05:30:31 +00:00
bodr
brian
buddy
cdcl	Add EXAMPLES options to ports that should have one.	2018-09-10 13:15:47 +00:00
cdf
cdo	Update science/hdf5 to 1.10.2	2018-09-05 22:05:23 +00:00
cgnslib	science/cgnslib: Update to 3.3.1 and modernize	2018-10-18 00:27:01 +00:00
cgribex
checkmol
chemical-mime-data
chemps2	science/chemps2: Update 1.8.8 -> 1.8.9	2018-10-30 06:00:05 +00:00
chemtool	science/chemtool: fix build with GCC-based architectures	2018-10-20 16:21:13 +00:00
chemtool-devel
chrono	Update science/hdf5 to 1.10.2	2018-09-05 22:05:23 +00:00
clhep	Remove compatibility code for FreeBSD < 11.2 from all ports.	2018-11-02 13:32:34 +00:00
clipper	science/clipper: Update 2.1.20180526 -> 2.1.20180802	2018-09-27 03:50:55 +00:00
code_saturne	On i386, OpenMP seems incompatible with libatomic.	2018-11-08 17:26:50 +00:00
colt
coordgenlibs	New port: science/coordgenlibs: Schrodinger-developed 2D coordinate generation	2018-10-25 07:36:58 +00:00
coot	Cleanup plists	2018-10-01 09:36:38 +00:00
cp2k	science/cp2k: Change from net/mpich2 -> net/mpich	2018-09-23 00:25:19 +00:00
crf++	science/crf++: Fix build with Clang 6	2018-09-01 10:29:11 +00:00
dalton	science/dalton: Fix build with GCC8	2018-11-04 18:15:36 +00:00
datawarrior	New port: science/datawarrior: Chemistry-aware multi-purpose data visualization and analysis program	2018-08-27 06:15:56 +00:00
dcl
devisor
dft_tools	Mark BROKEN: wrong LIB_DEPENDS	2018-09-27 05:26:32 +00:00
dftbplus	science/dftbplus science/mbdyn science/octopus: Change from math/arpack to math/arpack-ng	2018-10-04 21:10:42 +00:00
dkh
dlib-cpp
dlpoly-classic
eccodes	Update MASTER_SITES and WWW	2018-09-06 18:23:25 +00:00
elk	New port: science/elk: All-electron full-potential linearised augmented-planewave code	2018-09-23 08:43:32 +00:00
epte
erd
erkale	- Update math/armadillo to 9.200.4	2018-11-11 13:32:31 +00:00
esys-particle	New port: science/esys-particle: Particle-based numerical modelling software	2018-11-05 05:16:35 +00:00
fastcap
fasthenry
fisicalab	Update Objective-C LLVM version to 6.0.	2018-09-26 15:23:37 +00:00
fleur	Change 20 ports from net/mpich2 to net/mpich	2018-09-22 16:36:38 +00:00
fsom	science/fsom: Fix build on GCC-based architectures	2018-09-30 21:41:44 +00:00
fvcom
fvcom-mpi
gabedit	Change x11/xorgproto to become a build dep	2018-09-11 18:34:27 +00:00
gamess-us	science/gamess-us: Cosmetic change: internal version number change to 00 for convenence because it is a default	2018-10-15 06:12:03 +00:00
gchemutils
gdma
getdp	- Update to 3.0.3.	2018-10-24 14:36:09 +00:00
ghemical	science/libint: Update 1.1.6 -> 1.2.1	2018-08-27 22:56:43 +00:00
ghmm
gnudatalanguage	science/gnudatalanguage: Change from net/mpich2 to net/mpich	2018-10-02 21:54:14 +00:00
gpaw-setups	New port: science/gpaw-setups: Setups (data files) for py-gpaw, the DFT quantum chemistry software	2018-10-30 04:36:22 +00:00
gramps
grib_api	Update to 1.27.0	2018-09-06 18:23:31 +00:00
gromacs	Add compiler:c++11-lang to USES to fix build on gcc-based archs.	2018-11-05 23:51:03 +00:00
gsmc
gtamsanalyzer	Update Objective-C LLVM version to 6.0.	2018-09-26 15:23:37 +00:00
gwyddion	Update ilmbase and openexr to 2.3.0, rename OpenEXR to openexr.	2018-09-22 10:15:22 +00:00
h5utils	Update science/hdf5 to 1.10.2	2018-09-05 22:05:23 +00:00
harminv
hdf
hdf5	Update science/hdf5 to 1.10.2	2018-09-05 22:05:23 +00:00
hdf5-18	Upgrade science/hdf5-18 to 1.8.21.	2018-11-08 20:55:13 +00:00
hypre	science/hypre: Update 2.15.0 -> 2.15.1	2018-10-20 15:47:07 +00:00
iboview	Change x11/xorgproto to become a build dep	2018-09-11 18:34:27 +00:00
InsightToolkit	- Take maintainership of devel/gdcm.	2018-11-12 20:47:18 +00:00
isaac-cfd
jdftx	science/libxc: Update 3.0.0 -> 4.2.3	2018-10-20 23:29:28 +00:00
jstrack	Add DOCS options to ports that should have one.	2018-09-10 13:14:50 +00:00
kalzium	science/kalzium: switch to depend on science/avogadrolibs	2018-11-09 20:51:21 +00:00
kalzium-kde4	science/kalzium-kde4: Fix build	2018-10-28 02:37:33 +00:00
kst2	Fix build with Qt 5.11	2018-08-31 08:57:17 +00:00
lammps	science/lammps: BROKEN on i386	2018-11-12 08:41:11 +00:00
lamprop
latte	New port: science/latte: Quantum chemistry: Density functional tight binding molecular dynamics	2018-10-31 23:05:37 +00:00
libaec
libccp4
libcint
libctl
libefp
libgeodecomp
libghemical	science/libint: Update 1.1.6 -> 1.2.1	2018-08-27 22:56:43 +00:00
libgridxc	science/libxc: Update 3.0.0 -> 4.2.3	2018-10-20 23:29:28 +00:00
libint	science/libint: PORTSCOUT=limit	2018-08-30 17:24:44 +00:00
libint2	Remove compatibility code for FreeBSD < 11.2 from all ports.	2018-11-02 13:32:34 +00:00
libkml	devel/google{test,mock}: update to 1.8.1	2018-08-31 20:14:40 +00:00
liblinear
libmsym	New port: science/libmsym: Molecular point group symmetry library	2018-10-16 22:58:17 +00:00
liboglappth
libquantum
libssm
libsvm	- Update pkg-descr	2018-10-13 14:26:24 +00:00
libsvm-python
libxc	science/libxc: Update 3.0.0 -> 4.2.3	2018-10-20 23:29:28 +00:00
liggghts	science/liggghts: Set VTK_DIR to prevent conflicts with other vtk versions	2018-11-04 10:25:39 +00:00
linsmith	Deprecate some GNOME 2 applications	2018-10-07 20:25:16 +00:00
lm	Change 20 ports from net/mpich2 to net/mpich	2018-09-22 16:36:38 +00:00
luscus	Sscience/luscus: Update 0.8.5 -> 0.8.6	2018-10-18 07:30:25 +00:00
madness	science/libxc: Update 3.0.0 -> 4.2.3	2018-10-20 23:29:28 +00:00
maeparser	New port: science/maeparser: Parser for Schrodinger Maestro files	2018-10-25 07:24:36 +00:00
massxpert
mbdyn	science/dftbplus science/mbdyn science/octopus: Change from math/arpack to math/arpack-ng	2018-10-04 21:10:42 +00:00
mcstas
mcstas-comps
mcxtrace
mcxtrace-comps
mdynamix	Change 20 ports from net/mpich2 to net/mpich	2018-09-22 16:36:38 +00:00
medit
meep	Update science/hdf5 to 1.10.2	2018-09-05 22:05:23 +00:00
metaf2xml
metaphysicl	science/metaphysicl: Update 0.3.0.1 -> 0.3.1	2018-10-18 21:28:46 +00:00
minc2	Update science/hdf5 to 1.10.2	2018-09-05 22:05:23 +00:00
mmdb2
mmtf	New port: science/mmtf: C++ implementation of the MMTF API, decoder and encoder	2018-10-18 21:21:17 +00:00
mol2ps
molgif	New port: science/molgif: Tool to create GIF animations of molecules	2018-10-07 21:54:19 +00:00
molsketch	New port: science/molsketch: 2D molecule editor	2018-10-24 05:36:11 +00:00
MOOSE-neural-simulator	Update science/hdf5 to 1.10.2	2018-09-05 22:05:23 +00:00
mpb	Update science/hdf5 to 1.10.2	2018-09-05 22:05:23 +00:00
mpqc	science/mpqc: Add -lmpich to LDFLAGS: this fixes science/libghemical build	2018-09-07 02:23:54 +00:00
msms	science/msms: Add back NO_WRKSUBDIR	2018-09-10 07:09:49 +00:00
multiwfn	Fix typo in version.	2018-08-27 13:51:29 +00:00
namd	science/namd: Remove RESTRICTED because LICENSE_PERMS is restrictive	2018-09-10 06:59:36 +00:00
netcdf	Update science/hdf5 to 1.10.2	2018-09-05 22:05:23 +00:00
netcdf-cxx
netcdf-fortran
nifticlib
nwchem	science/nwchem: Fix build on 32-bit systems	2018-11-10 08:01:15 +00:00
octopus	science/libxc: Update 3.0.0 -> 4.2.3	2018-10-20 23:29:28 +00:00
openbabel
openkim
openmx	Change 20 ports from net/mpich2 to net/mpich	2018-09-22 16:36:38 +00:00
openstructure	Change x11/xorgproto to become a build dep	2018-09-11 18:34:27 +00:00
p5-Algorithm-SVMLight
p5-Chemistry-3DBuilder
p5-Chemistry-Bond-Find	- Add LICENSE	2018-10-09 09:08:39 +00:00
p5-Chemistry-Canonicalize	- Add LICENSE	2018-10-05 09:08:36 +00:00
p5-Chemistry-Elements
p5-Chemistry-File-MDLMol
p5-Chemistry-File-Mopac
p5-Chemistry-File-PDB	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-Chemistry-File-SLN
p5-Chemistry-File-SMARTS
p5-Chemistry-File-SMILES
p5-Chemistry-File-VRML
p5-Chemistry-File-XYZ
p5-Chemistry-FormulaPattern
p5-Chemistry-InternalCoords
p5-Chemistry-Isotope
p5-Chemistry-MacroMol	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-Chemistry-MidasPattern
p5-Chemistry-Mok
p5-Chemistry-Mol	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-Chemistry-Pattern
p5-Chemistry-Reaction
p5-Chemistry-Ring
p5-Geo-BUFR	Remove MASTER_SITE_SUBDIR	2018-09-10 20:27:04 +00:00
p5-Geo-Coordinates-Converter	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-Geo-Coordinates-Converter-iArea	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-Geo-ReadGRIB
p5-Geo-WebService-Elevation-USGS	- Update to 0.110	2018-10-10 01:38:11 +00:00
p5-Mcstas-Tools
p5-PerlMol
p5-Physics-Unit
paje	Update Objective-C LLVM version to 6.0.	2018-09-26 15:23:37 +00:00
paraview	Cleanup plist	2018-10-01 06:30:37 +00:00
pcmsolver
PETSc	science/PETSc: Update 3.10.1 -> 3.10.2	2018-10-20 16:08:58 +00:00
pnetcdf	Change from MPICH2 to MPICH option	2018-09-24 11:14:24 +00:00
psychopy
pulseview	science/pulseview: Update to version 0.4.1	2018-11-03 13:53:29 +00:00
py-abipy	science/py-abipy: Update 0.5.0 -> 0.6.0	2018-08-24 18:31:51 +00:00
py-ase	Never use ${FLAVOR} directly in dependencies, FLAVOR is not transitive.	2018-09-14 12:19:48 +00:00
py-avogadrolibs	New port: science/py-avogadrolibs: Python bindings for Avogadro2 chemistry libraries	2018-10-21 17:52:35 +00:00
py-cdo	Update to 1.4.0	2018-09-20 19:27:39 +00:00
py-chempy	science/py-chempy: Update 0.7.5 -> 0.7.6	2018-10-29 04:31:09 +00:00
py-coards
py-DendroPy	Fix packaging with python 3.x	2018-10-12 14:58:58 +00:00
py-dlib
py-gpaw	science/py-gpaw: Add pkg-message; Add LICENSE_FILE; Change /usr/local to LOCALBASE	2018-10-30 04:38:26 +00:00
py-gsd	science/py-gsd: Update 1.5.3 -> 1.5.4	2018-10-06 04:09:31 +00:00
py-h5py	Update science/hdf5 to 1.10.2	2018-09-05 22:05:23 +00:00
py-hcluster
py-kinematics
py-MDAnalysis	science/py-MDAnalysis: Update 0.19.0 -> 0.19.2	2018-11-11 22:33:50 +00:00
py-MDAnalysisTests	science/py-MDAnalysisTests/: Update 0.19.0 -> 0.19.2	2018-11-11 22:34:29 +00:00
py-mdp
py-mlpy
py-mmtf-python
py-molmod	New port: science/py-molmod: Collection of molecular modelling tools for python	2018-09-14 03:10:59 +00:00
py-netCDF4	Update science/hdf5 to 1.10.2	2018-09-05 22:05:23 +00:00
py-obspy
py-OpenFermion
py-openpiv
py-paida
py-phono3py	New port: science/py-phono3py: Software to calculate phonon-phonon interaction and related properties	2018-09-14 05:37:12 +00:00
py-phonopy	science/py-phonopy: Fix tests	2018-10-17 07:04:50 +00:00
py-pupynere
py-pyaixi
py-pydicom	- Update to 1.2.0	2018-10-08 12:03:51 +00:00
py-PyFR	science/py-PyFR: Update 1.7.6 -> 1.8.0	2018-10-17 07:27:27 +00:00
py-pymatgen	science/py-pymatgen: Update 2018.8.10 -> 2018.9.1	2018-09-17 20:29:11 +00:00
py-pymol	science/py-pymol: Update 2.1.0 -> 2.2.0	2018-09-17 20:48:45 +00:00
py-pyosf
py-PyQuante
py-pysal
py-pyteomics
py-pyteomics.biolccc
py-qspin
py-quantities
py-rmf	science/py-rmf: Correct version	2018-08-30 17:34:27 +00:00
py-ScientificPython
py-scikit-fuzzy	science/py-scikit-fuzzy: Update 0.3.1 -> 0.4.0	2018-10-19 04:43:52 +00:00
py-scikit-learn	- Add LICENSE	2018-10-30 09:00:15 +00:00
py-scikit-sparse	science/py-scikit-sparse: Update 0.4.3 -> 0.4.4	2018-11-11 22:39:13 +00:00
py-scimath
py-scipy	Update MASTER_SITES	2018-10-06 09:27:12 +00:00
py-scoria
py-SimpleSpectral
py-spglib	science/py-spglib: Update 1.10.4.1 -> 1.10.4.11	2018-09-19 18:35:55 +00:00
py-veusz
py-ws2300
pybrain
pycdf
pynn
qbox	Change 20 ports from net/mpich2 to net/mpich	2018-09-22 16:36:38 +00:00
qcl
qmcpack	Remove compatibility code for FreeBSD < 11.2 from all ports.	2018-11-02 13:32:34 +00:00
qtresistors
quantum-espresso	Change 20 ports from net/mpich2 to net/mpich	2018-09-22 16:36:38 +00:00
qwalk	science/qwalk: Add PORTSCOUT=limit	2018-08-30 17:50:38 +00:00
R-cran-AMORE
R-cran-bayesm
R-cran-cmprsk
R-cran-DCluster
R-cran-e1071
R-cran-eco
R-cran-Epi	- Update to 2.32	2018-08-27 02:22:54 +00:00
R-cran-epicalc
R-cran-etm	- Update to 1.0.4	2018-08-20 09:30:52 +00:00
R-cran-fastICA
R-cran-kernlab
R-cran-snow	- Update to 0.4-3	2018-09-18 06:51:54 +00:00
R-cran-som
R-cran-udunits2
rdkit	science/rdkit: Update 2018_03_4 -> 2018_09_1	2018-10-25 07:00:51 +00:00
rmf	Update science/hdf5 to 1.10.2	2018-09-05 22:05:23 +00:00
rubygem-ai4r
rubygem-cdo	Update to 1.4.0	2018-09-20 19:28:05 +00:00
rubygem-rgeo	Update to 1.1.2	2018-10-11 23:45:49 +00:00
rubygem-rgeo-geojson
rubygem-rgeo-proj4
rubygem-rgeo-shapefile
rubygem-ruby-dcl
rubygem-ruby-netcdf
siesta	New port: science/siesta: Program to perform efficient electronic structure calculations	2018-09-03 17:51:32 +00:00
sigrok-cli	science/sigrok-cli: Update to version 0.7.1	2018-11-03 12:53:26 +00:00
sigrok-firmware
sigrok-firmware-fx2lafw	Add DOCS options to ports that should have one.	2018-09-10 13:14:50 +00:00
sigrok-firmware-utils	Add DOCS options to ports that should have one.	2018-09-10 13:14:50 +00:00
silo	Update science/hdf5 to 1.10.2	2018-09-05 22:05:23 +00:00
simint	science/simint: Update 0.7 -> 0.8	2018-10-11 03:21:01 +00:00
simlib	Remove compatibility code for FreeBSD < 11.2 from all ports.	2018-11-02 13:32:34 +00:00
simsmith
sparta	New port: science/sparta: Gas simulator: SPARTA DSMC software package	2018-11-12 03:02:28 +00:00
spglib
step	Update KDE Applications to 18.09.3	2018-11-09 20:09:13 +00:00
step-kde4	Deprecate KDE4 software in categories graphics-textproc.	2018-08-30 18:23:24 +00:00
svmlight
szip
teem	New port: science/teem: Libraries for representing, processing and visualizing scientific data	2018-09-02 06:43:29 +00:00
tfel
tinker	biology/tinker: Update 7.1.3 -> 8.4.4; Move to science/	2018-10-07 00:19:22 +00:00
triqs	Remove compatibility code for FreeBSD < 11.2 from all ports.	2018-11-02 13:32:34 +00:00
udunits	Install texinfo files (GNU info) into ${PREFIX}/share/info	2018-11-10 18:12:57 +00:00
v_sim
vmd	science/vmd: Remove RESTRICTED: not required	2018-09-10 07:06:17 +00:00
voro++	science/voro++: Add shared library	2018-11-04 15:52:42 +00:00
wannier90	New port: science/wannier90: Maximally-localized Wannier functions (MLWFs) and Wannier90	2018-09-03 04:09:00 +00:00
wxmacmolplt	New port: science/wxmacmolplt: Graphical user interface principally for the GAMESS program	2018-10-14 23:15:09 +00:00
xcrysden	Update ImageMagick to 6.9.10.14 [1]	2018-11-10 19:57:07 +00:00
xdrawchem	Change x11/xorgproto to become a build dep	2018-09-11 18:34:27 +00:00
xfce4-equake-plugin
xmakemol
Makefile	New port: science/sparta: Gas simulator: SPARTA DSMC software package	2018-11-12 03:02:28 +00:00