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freebsd-ports/science
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Baptiste Daroussin c5fe34636c Update jasper to 2.0.16 
This is needed to be able to update gegl to latest version.
Bump revision of all consumer as the ABI is not 100% backward compatible.
Provide a patch for graphics/devil to properly build with latest jasper.
While here add a missing USES=xorg to graphics/devil
2019-12-27 13:43:00 +00:00
..
2d-rewriter Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
abinit Mark a few ports BROKEN (unfetchable) 2019-11-06 16:26:34 +00:00
afni math/gsl: update to 2.6 2019-10-25 23:41:34 +00:00
agrum science/agrum: fix build on powerpc64 elfv2 2019-12-22 18:08:07 +00:00
aircraft-datcom
ALPSCore devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
antioch math/gsl: update to 2.6 2019-10-25 23:41:34 +00:00
apbs
atom
atompaw
avogadro2
avogadrolibs
bagel devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
bddsolve devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
berkeleygw
bodr
brian
buddy
cdcl Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
cdf
cdo Update jasper to 2.0.16 2019-12-27 13:43:00 +00:00
cgnslib Add USES=xorg and USES=gl 2019-11-07 18:41:56 +00:00
cgribex Update jasper to 2.0.16 2019-12-27 13:43:00 +00:00
checkmol Mark a few ports BROKEN (unfetchable) 2019-11-06 16:26:34 +00:00
chemical-mime-data print, science: Add missing USES=gnome 2019-11-08 13:22:59 +00:00
chemps2
chemtool Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
chemtool-devel Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
chrono
clhep
clipper
code_saturne Unbreak bulk -a with non default version of python3 2019-11-20 14:47:05 +00:00
colt Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
coordgenlibs devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
coot Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
cp2k Mark a few ports BROKEN (unfetchable) 2019-11-06 16:26:34 +00:00
cp2k-data
crf++
dalton
datawarrior Mark a few ports BROKEN (unfetchable) 2019-11-06 16:26:34 +00:00
dcl Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
devisor Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
dftbplus
dkh
dlib-cpp Add USES=xorg and USES=gl 2019-11-07 18:41:56 +00:00
dlpoly-classic Mark a few ports BROKEN (unfetchable) 2019-11-06 16:26:34 +00:00
drawxtl Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
dvc
eccodes Update to 2.14.1 2019-11-04 15:58:47 +00:00
elk
epte
erd
erkale science/erkale: Update g20190812 -> g20191120 2019-11-23 16:27:52 +00:00
erkale-pseudopotentials
esys-particle devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
fastcap
fasthenry
fisicalab math/gsl: update to 2.6 2019-10-25 23:41:34 +00:00
fleur
fsom
fvcom
fvcom-mpi
gabedit Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
gamess-us
gchemutils Update to 0.10.46 and only keep one libgoffice version 2019-12-16 17:06:38 +00:00
gdma
getdp - Update to 3.3.0. 2019-12-22 02:28:57 +00:00
ghemical Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
ghmm print, science: Add missing USES=gnome 2019-11-08 13:22:59 +00:00
gnudatalanguage There is a bug with GraphicsMagick: see 2019-11-23 18:05:22 +00:00
gpaw-setups
gramps science/gramps: Update to 5.1.1 2019-12-10 13:54:03 +00:00
grib_api
gromacs science/gromacs: Update 2019.4 -> 2019.5 2019-12-24 07:45:13 +00:00
gsmc print, science: Add missing USES=gnome 2019-11-08 13:22:59 +00:00
gtamsanalyzer
gwyddion Deprecate a few ports 2019-12-26 07:54:28 +00:00
h5utils
h5z-zfp
harminv
hdf
hdf5
hdf5-18
healpix
highfive devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
hypre
iboview devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
InsightToolkit - Update devel/gdcm to 3.0.4. 2019-10-19 23:45:10 +00:00
isaac-cfd
jdftx math/gsl: update to 2.6 2019-10-25 23:41:34 +00:00
jmol science/jmol: Update 14.30.0 -> 14.30.1 2019-12-14 07:44:40 +00:00
jstrack
kalzium KDE's December 2019 Apps Update 2019-12-12 23:24:36 +00:00
kim-api
kst2 math/gsl: update to 2.6 2019-10-25 23:41:34 +00:00
lammps science/lammps: fix build on GCC architectures 2019-11-28 14:20:18 +00:00
lamprop
latte
libaec
libccp4
libcint
libctl
libefp
libgeodecomp devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
libghemical Pet portlint (trailing whitespace). 2019-11-08 03:23:25 +00:00
libgridxc
libint
libint2 devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
libkml devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
liblinear
libmsym
liboglappth Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
libquantum
libssm
libsvm
libsvm-python
libvdwxc
libxc
liggghts Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
lm
luscus Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
madness Update devel/tbb to 2020.0 and bump dependent ports' revisions [1] 2019-12-26 16:25:22 +00:00
maeparser devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
massxpert Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
mbdyn
mcstas
mcstas-comps
mcxtrace
mcxtrace-comps
mdynamix
medit Unbreak medit. 2019-11-20 20:40:53 +00:00
meep Deprecate ports broken for too long 2019-12-10 09:02:42 +00:00
metaphysicl science/metaphysicl: 0.5.2 -> 0.6.0 2019-10-13 21:17:17 +00:00
minc2
mmdb2
mmtf-cpp
mol2ps
molgif Bump PORTREVISION after r517743 to force relinking. 2019-11-16 12:52:39 +00:00
molscript Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
molsketch
mpb
mpqc Unmark these ports broken on aarch64. 2019-11-08 03:54:11 +00:00
msms
multiwfn
namd
ncnn science/ncnn: Update 20191113 -> 20191223 2019-12-24 07:25:08 +00:00
nest math/gsl: update to 2.6 2019-10-25 23:41:34 +00:00
netcdf Update to 4.7.3 2019-12-08 16:52:27 +00:00
netcdf-cxx
netcdf-fortran
nifticlib
nwchem science/nwchem: Update 6.8.1.20190820 -> 7.0.0-beta1 2019-11-23 17:44:06 +00:00
nwchem-data
octopus Mark a few ports BROKEN (unfetchable) 2019-11-06 16:26:34 +00:00
openbabel
openkim
openkim-models
openmx Mark a few ports BROKEN (unfetchable) 2019-11-06 16:26:34 +00:00
opensim-core Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
opensph
opsin
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 Mark a few ports BROKEN (unfetchable) 2019-11-06 16:26:34 +00:00
p5-Geo-WebService-Elevation-USGS Update to 0.116 2019-10-28 14:57:46 +00:00
p5-Mcstas-Tools
p5-PerlMol
p5-Physics-Unit
packmol
pagmo2 Update devel/tbb to 2020.0 and bump dependent ports' revisions [1] 2019-12-26 16:25:22 +00:00
paje
paraview Unbreak 2019-11-07 17:28:56 +00:00
pcmsolver science/pcmsolver: fix build on GCC architectures 2019-10-27 19:19:07 +00:00
PETSc Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
pnetcdf
psychopy Deprecate a few ports 2019-12-26 07:54:28 +00:00
pulseview devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
py-abipy
py-asdf
py-ase science/py-ase: Update 3.18.1 -> 3.19.0 2019-12-27 06:46:45 +00:00
py-avogadrolibs
py-cdo
py-chainer science/py-chainer: Update 6.5.0 -> 7.0.0 2019-12-06 05:52:06 +00:00
py-chainer-chemistry science/py-chainer-chemistry: Update 0.6.0 -> 0.7.0 2019-12-22 03:10:17 +00:00
py-chempy
py-coards
py-DendroPy
py-dlib devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
py-eccodes-python Update to 0.9.4 2019-12-08 17:03:53 +00:00
py-geometer
py-gpaw
py-GPy science/py-GPy: Update 1.9.8 -> 1.9.9 2019-10-20 00:41:22 +00:00
py-GPyOpt
py-gsd science/py-gsd: Update 1.8.1 -> 1.9.3 2019-10-12 16:47:23 +00:00
py-h5py
py-hcluster Deprecate a few ports 2019-12-26 07:54:28 +00:00
py-kinematics
py-lifelines
py-MDAnalysis
py-MDAnalysisTests
py-mdp
py-mlpy math/gsl: update to 2.6 2019-10-25 23:41:34 +00:00
py-mmtf-python
py-molmod
py-netCDF4
py-obspy
py-oddt science/py-oddt: Update 0.6 -> 0.7 2019-12-27 05:12:21 +00:00
py-OpenFermion
py-openpiv
py-paida
py-paramz
py-phono3py
py-phonopy
py-pupynere
py-pyaixi
py-pydicom
py-PyFR
py-pygeodesy
py-pymatgen
py-pymol
py-pyosf
py-PyQuante Unmark these ports broken on aarch64. 2019-11-08 03:54:11 +00:00
py-pysal
py-pyteomics
py-pyteomics.biolccc Deprecate a few ports 2019-12-26 07:54:28 +00:00
py-qcelemental science/py-qcelemental: Update 0.9.0 -> 0.11.0 2019-10-29 03:42:56 +00:00
py-qcengine
py-qspin
py-quantities
py-rmf
py-rmsd
py-ruffus
py-ScientificPython Mark a few ports BROKEN (unfetchable) 2019-11-06 16:26:34 +00:00
py-scikit-fuzzy science/py-scikit-fuzzy: Update 0.4.1 -> 0.4.2 2019-11-16 09:42:27 +00:00
py-scikit-learn - Update to 0.22 2019-12-17 13:09:33 +00:00
py-scikit-sparse
py-scimath
py-scipy
py-scoria
py-SimpleSpectral
py-spglib
py-tensorflow Unbreak bulk -a with non default versions of python3 2019-11-20 14:42:36 +00:00
py-tensorflow-estimator Mark BROKEN: fails to build 2019-11-20 14:00:42 +00:00
py-veusz science/py-veusz: Update 3.0.1 -> 3.1 2019-10-29 03:36:12 +00:00
py-ws2300
pybrain
pycdf Deprecate a few ports 2019-12-26 07:54:28 +00:00
pynn
qbox
qcl
qmcpack devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
quantum-espresso
quantum-espresso-pseudopotentials
qwalk
R-cran-AMORE
R-cran-bayesm - Update to 3.1.4 2019-11-29 23:26:04 +00:00
R-cran-cmprsk
R-cran-DCluster
R-cran-e1071 - Update to 1.7-3 2019-11-28 14:43:13 +00:00
R-cran-eco
R-cran-Epi - Update to 2.40 2019-11-28 00:12:45 +00:00
R-cran-epicalc
R-cran-etm
R-cran-fastICA
R-cran-kernlab - Update to 0.9-29 2019-11-14 22:29:41 +00:00
R-cran-snow
R-cran-som
R-cran-udunits2
rdkit devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
rmf devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
rubygem-ai4r
rubygem-cdo
rubygem-rgeo
rubygem-rgeo-geojson Cosmetic change 2019-11-03 17:23:27 +00:00
rubygem-rgeo-proj4
rubygem-rgeo-shapefile
rubygem-ruby-dcl Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
rubygem-ruby-netcdf
scidavis math/gsl: update to 2.6 2019-10-25 23:41:34 +00:00
siesta
sigrok-cli
sigrok-firmware
sigrok-firmware-fx2lafw science/sigrok-firmware-fx2lafw: Update to version 0.1.7 2019-11-15 20:39:58 +00:00
sigrok-firmware-utils
silo
simbody science/simbody: Update 3.6.1 -> 3.7 2019-12-09 16:20:00 +00:00
simgrid devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
simint
simlib
simsmith Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
smoldyn Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
sparta
spglib
step KDE's December 2019 Apps Update 2019-12-12 23:24:36 +00:00
svmlight
szip
teem
tfel science/tfel: update to version 3.3 2019-12-21 19:53:14 +00:00
tinker science/tinker: Update 8.7.1 -> 8.7.2 2019-11-29 07:44:51 +00:00
udunits
v_sim Make fetchable again. 2019-11-19 21:38:47 +00:00
vipster Mark a few ports BROKEN (unfetchable) 2019-11-06 16:26:34 +00:00
vmd Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
voro++
wannier90
wwplot
wxmacmolplt
xcrysden Add USES=xorg USES=gl, ports categories s 2019-11-07 17:17:53 +00:00
xdrawchem
xfce4-equake-plugin
yoda
Makefile New port: science/highfive: Header-only C++ HDF5 interface 2019-11-03 01:27:45 +00:00