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freebsd-ports/science
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Alexey Dokuchaev 3186e08e7c Update Guile to version 2.2.5, modern stable version, and fix dependent 
ports to build against it.  Most changes are rather minor and mechanical
except for the devel/gdb (obtained via their bugtracker [1], courtesy of
Doug Evans).  One port (science/meep) I had to mark BROKEN after fixing
it proved to be very tedious and actually unreliable.  It is very old,
there are newer versions available so it should be fixed by updating.

One port (devel/libruin) had revealed a bug in the new Guile code (an
auxiliary script, really) that had to be worked-round; reference to the
problematic upstream commit is provided in the patch.

PR:		229613
Exp-run by:	antoine

[1] https://sourceware.org/bugzilla/show_bug.cgi?id=21104#c8
2019-06-27 09:02:56 +00:00
..
2d-rewriter
abinit science/abinit: Fix libomp.so in LDFLAGS (this also might fix the breakage on 13) 2019-05-19 03:01:48 +00:00
afni science/afni: Upgrade to 19.1.20 2019-06-18 19:00:55 +00:00
agrum
aircraft-datcom
ALPSCore
antioch
apbs
atom
atompaw
avogadro2
avogadrolibs
bagel
bddsolve
berkeleygw
bodr
brian
buddy
cdcl
cdf
cdo - Update to 6.1.0 and fix some ports 2019-06-27 03:37:10 +00:00
cgnslib
cgribex
checkmol
chemical-mime-data
chemps2
chemtool
chemtool-devel
chrono science/chrono: Broken on i386 2019-05-18 22:28:29 +00:00
clhep
clipper science/clipper: add USES=compiler:c++11-lang 2019-05-11 20:30:19 +00:00
code_saturne Switch to Python 3.6 and upgrade to v5.3.3. 2019-05-19 19:22:45 +00:00
colt
coordgenlibs
coot Clean up LIB_DEPENDS 2019-06-16 16:05:28 +00:00
cp2k
cp2k-data
crf++
dalton
datawarrior
dcl
devisor
dftbplus science/dftbplus: Fix libomp.so in LDFLAGS (this also might fix the breakage on 13) 2019-05-19 02:47:01 +00:00
dkh
dlib-cpp
dlpoly-classic
drawxtl
dvc
eccodes Update to 2.12.5 2019-05-25 22:02:44 +00:00
elk
epte
erd
erkale
erkale-pseudopotentials
esys-particle science/esys-particle: Broken on 13-CURRENT 2019-05-18 22:58:19 +00:00
fastcap
fasthenry
fisicalab
fleur
fsom
fvcom
fvcom-mpi
gabedit Add compiler:c++11-lang to USES to fix the following on GCC-based systems: 2019-06-17 11:39:30 +00:00
gamess-us
gchemutils
gdma
getdp
ghemical
ghmm
gnudatalanguage - Update to 6.1.0 and fix some ports 2019-06-27 03:37:10 +00:00
gpaw-setups
gramps
grib_api
gromacs science/gromacs: Update 2019.2 -> 2019.3 2019-06-15 19:35:27 +00:00
gsmc
gtamsanalyzer
gwyddion
h5utils
h5z-zfp
harminv Update Guile to version 2.2.5, modern stable version, and fix dependent 2019-06-27 09:02:56 +00:00
hdf
hdf5
hdf5-18
healpix
hypre science/hypre: Update 2.15.1 -> 2.16.0 2019-05-13 07:57:57 +00:00
iboview
InsightToolkit - Update devel/gdcm to 3.0.0. 2019-06-01 21:59:13 +00:00
isaac-cfd
jdftx
jmol science/jmol: Update 14.29.42 -> 14.29.46 2019-06-07 05:59:51 +00:00
jstrack science/jstrack: remove meaningless 85+ from USES tk 2019-06-12 16:16:10 +00:00
kalzium Update KDE Applications to 19.04.2 2019-06-07 04:08:25 +00:00
kst2
lammps Clean up LIB_DEPENDS 2019-06-16 16:05:28 +00:00
lamprop
latte
libaec
libccp4
libcint
libctl Update Guile to version 2.2.5, modern stable version, and fix dependent 2019-06-27 09:02:56 +00:00
libefp
libgeodecomp
libghemical
libgridxc
libint
libint2
libkml
liblinear
libmsym
liboglappth
libquantum
libssm
libsvm
libsvm-python
libvdwxc New port: science/libvdwxc: Van der Waals density functional (DFT) library 2019-05-18 05:40:31 +00:00
libxc
liggghts Clean up LIB_DEPENDS 2019-06-16 16:05:28 +00:00
lm
luscus
madness
maeparser
massxpert
mbdyn
mcstas
mcstas-comps
mcxtrace
mcxtrace-comps
mdynamix
medit
meep Update Guile to version 2.2.5, modern stable version, and fix dependent 2019-06-27 09:02:56 +00:00
metaf2xml
metaphysicl
minc2
mmdb2
mmtf-cpp
mol2ps
molgif
molscript Clean up LIB_DEPENDS 2019-06-16 16:05:28 +00:00
molsketch
mpb Update Guile to version 2.2.5, modern stable version, and fix dependent 2019-06-27 09:02:56 +00:00
mpqc
msms
multiwfn
namd
nest science/nest: Broken on i386 2019-05-18 22:12:49 +00:00
netcdf
netcdf-cxx
netcdf-fortran
nifticlib science/nifticlib: fix build 2019-06-08 19:24:18 +00:00
nwchem science/nwchem: Update 6.8.1.20190509 -> 6.8.1.20190606 2019-06-08 07:54:52 +00:00
nwchem-data
octopus Clean up LIB_DEPENDS 2019-06-16 16:05:28 +00:00
openbabel
openkim
openmx Chase devel/openmp expiration 2019-05-27 20:55:56 +00:00
opensim-core
opensph New port: science/opensph: Library and graphical tools for running SPH and N-body simulations 2019-05-26 04:08:09 +00:00
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
p5-Geo-WebService-Elevation-USGS Update to 0.113 2019-06-22 21:50:07 +00:00
p5-Mcstas-Tools
p5-PerlMol
p5-Physics-Unit
pagmo2
paje
paraview
pcmsolver
PETSc
pnetcdf
psychopy
pulseview
py-abipy
py-asdf
py-ase
py-avogadrolibs
py-cdo Update to 1.5.3 2019-06-25 20:52:05 +00:00
py-chempy
py-coards
py-DendroPy
py-dlib
py-eccodes-python Update to 0.9.1 2019-06-07 23:04:38 +00:00
py-geometer
py-gpaw
py-GPy science/py-GPy: Fix build by explicitly setting the path to libomp.so in xx_DEPENDS lines 2019-05-23 21:21:49 +00:00
py-GPyOpt
py-gsd
py-h5py
py-hcluster
py-kinematics
py-lifelines
py-MDAnalysis
py-MDAnalysisTests
py-mdp
py-mlpy
py-mmtf-python
py-molmod
py-netCDF4 Cleanup cython dependency. 2019-05-11 21:10:31 +00:00
py-obspy
py-oddt
py-OpenFermion
py-openpiv
py-paida
py-paramz science/py-paramz: Update 0.9.4 -> 0.9.5 2019-05-18 15:56:47 +00:00
py-phono3py Chase devel/openmp expiration 2019-05-27 20:55:56 +00:00
py-phonopy
py-pupynere
py-pyaixi
py-pydicom
py-PyFR Chase devel/openmp expiration 2019-05-27 20:55:56 +00:00
py-pygeodesy
py-pymatgen
py-pymol
py-pyosf
py-PyQuante
py-pysal
py-pyteomics Update to 4.1.2 2019-06-09 16:52:36 +00:00
py-pyteomics.biolccc
py-qcelemental science/py-qcelemental: Update 0.4.1 -> 0.4.2 2019-06-19 08:14:24 +00:00
py-qcengine science/py-qcengine: Update 0.6.4 -> 0.7.1 2019-06-19 08:15:53 +00:00
py-qspin
py-quantities
py-rmf
py-rmsd science/py-rmsd: Fix license 2019-05-26 18:17:15 +00:00
py-ScientificPython
py-scikit-fuzzy
py-scikit-learn - Update to 0.20.3 2019-05-14 02:17:08 +00:00
py-scikit-sparse
py-scimath
py-scipy
py-scoria
py-SimpleSpectral
py-spglib
py-veusz
py-ws2300
pybrain
pycdf
pynn
qbox science/qbox: Update 1.67.2 -> 1.67.4 2019-06-20 22:06:56 +00:00
qcl
qmcpack
quantum-espresso
quantum-espresso-pseudopotentials
qwalk
R-cran-AMORE
R-cran-bayesm
R-cran-cmprsk
R-cran-DCluster
R-cran-e1071 - Update to 1.7-1 2019-06-02 07:44:51 +00:00
R-cran-eco
R-cran-Epi
R-cran-epicalc
R-cran-etm
R-cran-fastICA
R-cran-kernlab
R-cran-snow
R-cran-som
R-cran-udunits2
rdkit
rmf
rubygem-ai4r
rubygem-cdo
rubygem-rgeo
rubygem-rgeo-geojson
rubygem-rgeo-proj4
rubygem-rgeo-shapefile
rubygem-ruby-dcl
rubygem-ruby-netcdf
scidavis
siesta
sigrok-cli
sigrok-firmware
sigrok-firmware-fx2lafw
sigrok-firmware-utils
silo
simbody
simgrid New port: science/simgrid: Simulator of the behavior of large-scale distributed systems 2019-05-16 16:00:15 +00:00
simint
simlib
simsmith
smoldyn New port: science/smoldyn: Biochemical simulator for molecular diffusion, surface interactions 2019-06-09 03:26:15 +00:00
sparta
spglib
step KDE Applications: complete dependency lists 2019-06-23 15:39:32 +00:00
svmlight
szip
teem Clean up LIB_DEPENDS 2019-06-16 16:05:28 +00:00
tfel
tinker
udunits
v_sim
vipster
vmd
voro++
wannier90
wxmacmolplt science/wxmacmolplt: fix build with GCC-based architectures 2019-05-20 20:09:32 +00:00
xcrysden
xdrawchem
xfce4-equake-plugin - Simplify XFCE MASTER_SITES usage 2019-06-19 16:14:27 +00:00
xmakemol
yoda
Makefile New port: science/smoldyn: Biochemical simulator for molecular diffusion, surface interactions 2019-06-09 03:26:15 +00:00