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freebsd-ports/science
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Raphael Kubo da Costa 68bc4af5c8 Update CMake to 3.0.1. 
The 3.0 series is an incremental improvement over the previous 2.8 series
despite the major version number change. A list of important changes is
available at http://www.cmake.org/cmake/help/v3.0/release/3.0.0.html

On the porting side
* The minimum FreeBSD release we have to support in the ports tree is now
  recent enough that ports/168671 can finally be committed: instead of
  building and using CMake's own copies of bzip2, curl, expat, libarchive,
  liblzma and zlib, we use the versions in ports and/or the base system.

* CMake's documentation system has been changed and vastly improved at the
  cost of now depending on Sphinx. We still generate only man pages, but can
  start generating the HTML documentation in the future if desired.

* devel/cmake-gui now uses Qt5 instead of Qt4 and does not needlessly build
  the ncurses UI that is installed by devel/cmake itself.

* CMake commit 3816cd2 fixes a longstanding issue in the detection of the
  Python interpreter and its libraries, but requires us to revert a
  workaround for that in Mk/Uses/python.mk itself, effectively reverting
  the patch introduced by ports/168159.

* Similarly, a few ports had to be fixed manually due to CMake being
  stricter when parsing some files or the ports detecting Python the wrong
  way. Fortunately, they all had been fixed upstream so I just grabbed the
  appropriate commits and pointed to them in the patches.
  science/gnudatalanguage had to have its PORTREVISION bumped because
  switching to USES=cmake:outsource removed a few files from the plist that
  were not supposed to have been installed in the first place.

PR:		168671
PR:		192644
2014-09-02 12:59:54 +00:00
..
2d-rewriter
afni math/gsl: 2014-08-17 13:09:56 +00:00
avogadro Convert a bunch of USE_BZIP2 to USES=tar:bzip2 2014-07-29 18:41:15 +00:00
bddsolve
bft Add USES=libtool and INSTALL_TARGET=install-strip 2014-07-08 15:24:14 +00:00
bodr Convert a bunch of USE_BZIP2 to USES=tar:bzip2 2014-07-29 18:41:15 +00:00
brian
buddy Add DOCS option where PORTDOCS is in plist. 2014-07-16 03:18:26 +00:00
cdcl
cdf Remove NOPORTDOCS and NOPORTEXAMPLES. 2014-07-04 22:08:14 +00:00
cdo - Update to 1.6.4 2014-07-04 02:49:34 +00:00
cgnslib
cgribex
checkmol
chemical-mime-data Remove indefinite articles and trailing periods from COMMENT, plus 2014-07-17 08:57:51 +00:00
chemtool - Fix missing library problems when the linker enforces explicit linking 2014-08-26 14:06:08 +00:00
chemtool-devel - Fix missing library problems when the linker enforces explicit linking 2014-08-26 14:06:08 +00:00
clhep science/clhep: Upgrade version 2.2.0.1 => 2.2.0.3 2014-08-24 09:07:33 +00:00
colt Remove NOPORTDOCS and NOPORTEXAMPLES. 2014-07-04 22:08:14 +00:00
crf++ - Convert to USES=libtool 2014-07-08 15:18:44 +00:00
dcl Remove NOPORTDOCS and NOPORTEXAMPLES. 2014-07-04 22:08:14 +00:00
devisor
dlpoly-classic - Update net/openmpi from 1.8.1 to 1.8.2 2014-08-26 11:25:13 +00:00
ecs Fix build with texlive 2014-07-21 21:57:18 +00:00
elmer-eio
elmer-matc
elmer-meshgen2d Remove indefinite articles and trailing periods from COMMENT, plus 2014-07-17 08:57:51 +00:00
elmergrid Remove indefinite articles and trailing periods from COMMENT, plus 2014-07-17 08:57:51 +00:00
epte
fastcap Repair instances, almost all courtesy of bf ;-), of spaces 2014-07-29 20:55:27 +00:00
fasthenry Support stage 2014-08-29 18:33:30 +00:00
fisicalab math/gsl: 2014-08-17 13:09:56 +00:00
fvcom - Update to 4.4.0 2014-08-15 21:08:21 +00:00
fvcom-mpi - Update net/openmpi from 1.8.1 to 1.8.2 2014-08-26 11:25:13 +00:00
fvm - Upgrade to 1.5; 2014-09-01 21:50:14 +00:00
gchemutils
getdp math/gsl: 2014-08-17 13:09:56 +00:00
ghemical - Stagify 2014-08-06 16:05:23 +00:00
ghmm - Convert to USES=libtool 2014-07-08 14:50:22 +00:00
gnudatalanguage Update CMake to 3.0.1. 2014-09-02 12:59:54 +00:00
gramps Berkeley DB cleanup, remove versions 4.0 ... 4.7. 2014-08-21 22:50:29 +00:00
grib_api - Add grib_api 1.12.3 2014-08-29 17:31:42 +00:00
gromacs - Upgrade to 1.5; 2014-09-01 21:50:14 +00:00
gsmc - Fix missing library problems when the linker enforces explicit linking 2014-08-26 14:06:08 +00:00
gtamsanalyzer Bump PORTREVISION on more ports that depend on libgcrypt after the update 2014-08-05 22:13:29 +00:00
gwyddion math/fftw3: 2014-08-31 16:36:22 +00:00
h5utils Remove indefinite articles and trailing periods from COMMENT, plus 2014-07-17 08:57:51 +00:00
harminv lang/guile: 2014-08-31 15:17:49 +00:00
hdf - USES=libtool tar:bzip2 2014-07-08 14:49:02 +00:00
hdf5
hdf-java
hs-bio - Update The Glorious Glasgow Haskell Compiler to version 7.8.3 2014-08-10 22:34:50 +00:00
InsightToolkit
isaac-cfd
jmol
jstrack Mark BROKEN: Checksum and size mismatch 2014-08-01 17:26:45 +00:00
kalzium Upgrade OpenEXR and ilmbase to 2.2.0. 2014-08-15 20:37:31 +00:00
kst2 math/gsl: 2014-08-17 13:09:56 +00:00
lamprop science/lamprop: switch to USES=python 2014-08-16 11:42:41 +00:00
libctl lang/guile: 2014-08-31 15:17:49 +00:00
libghemical - Switch to USES=libtool, drop .la files 2014-08-06 16:06:22 +00:00
libint - Stagify 2014-08-06 16:06:55 +00:00
libkml
liblinear Remove indefinite articles and trailing periods from COMMENT, plus 2014-07-17 08:57:51 +00:00
liboglappth - Add USES=libtool and INSTALL_TARGET=install-strip 2014-07-08 13:54:24 +00:00
libquantum Convert to USES=libtool 2014-07-08 13:34:32 +00:00
libsvm Remove indefinite articles and trailing periods from COMMENT, plus 2014-07-17 08:57:51 +00:00
libsvm-python
linsmith
massxpert - Support staging. 2014-06-30 20:38:59 +00:00
mbdyn Update to 1.4.3 2014-08-29 18:43:03 +00:00
medit - Fix missing library problems when the linker enforces explicit linking 2014-08-26 14:06:08 +00:00
meep lang/guile: 2014-08-31 15:17:49 +00:00
mei - Add USES=libtool 2014-07-07 21:57:42 +00:00
metaf2xml Add DOCS option where PORTDOCS is in plist. 2014-07-16 03:18:26 +00:00
minc2 science/minc2: Unbreak, Upgrade version 2.0.18 => 2.2.00 and stage 2014-07-29 21:33:51 +00:00
mol2ps
mpb lang/guile: 2014-08-31 15:17:49 +00:00
mpqc Chase the upgrade of net/mpich2. 2014-08-26 19:55:00 +00:00
mpqc-mpich
ncs - Upgrade to 1.5; 2014-09-01 21:50:14 +00:00
netcdf
netcdf-cxx - Use USE_GITHUB 2014-08-15 17:27:48 +00:00
netcdf-fortran - Cleanup Makefile 2014-08-17 09:56:47 +00:00
nifticlib
openbabel
openkim Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
p5-Algorithm-SVMLight Modernize LIB_DEPENDS 2014-07-14 18:42:04 +00:00
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
p5-PerlMol
p5-Physics-Unit
paje Bump PORTREVISION on more ports that depend on libgcrypt after the update 2014-08-05 22:13:29 +00:00
paraview science/paraview: alternative fix with USES+= execinfo instead 2014-09-01 19:53:11 +00:00
pnetcdf - Upgrade to 1.5; 2014-09-01 21:50:14 +00:00
psychopy
pulseview science/pulseview: Remove unnecessary RUN_DEPENDS 2014-08-03 16:16:21 +00:00
py-coards
py-DendroPy
py-h5py
py-hcluster
py-mdp
py-mlpy math/gsl: 2014-08-17 13:09:56 +00:00
py-netCDF4
py-obspy
py-paida science/py-paida: support stage 2014-08-05 13:22:35 +00:00
py-pupynere
py-pyaixi
py-pydap
py-pydicom
py-scikit-learn Update to versiob 0.15.0 2014-07-16 11:53:12 +00:00
py-scimath
py-scipy math/fftw3: 2014-08-31 16:36:22 +00:00
py-ws2300
pybrain
pycdf science/pycdf: support stage and use auto plist 2014-08-05 13:27:44 +00:00
pynn
pyteomics
pyteomics.biolccc
qcl
qtresistors
R-cran-AMORE
R-cran-bayesm
R-cran-DCluster
R-cran-e1071
R-cran-eco
R-cran-Epi
R-cran-epicalc
R-cran-snow
R-cran-som
ruby-dcl science/ruby-dcl: fixed broken; use gcc 2014-08-21 20:29:20 +00:00
ruby-gphys many ruby/rubygem ports: death of rubyforge.org 2014-08-19 15:35:35 +00:00
ruby-netcdf many ruby/rubygem ports: death of rubyforge.org 2014-08-19 15:35:35 +00:00
rubygem-ai4r science/rubygem-ai4r: update to 1.13 2014-08-23 21:52:50 +00:00
rubygem-netcdf
sigrok-cli science/sigrok-cli: update to 0.5.0 2014-07-28 23:06:29 +00:00
sigrok-firmware Add new port: science/sigrok-firmware 2014-08-03 22:37:51 +00:00
sigrok-firmware-fx2lafw Add new port: science/sigrok-firmware-fx2lafw 2014-08-03 22:24:50 +00:00
sigrok-firmware-utils Add new port: science/sigrok-firmware-utils 2014-08-03 22:09:07 +00:00
silo - Add USES=libtool 2014-07-07 21:56:17 +00:00
simlib
simsmith Java based Smith chart program. Performs single-frequency and sweep charting 2014-07-03 21:02:10 +00:00
step math/gsl: 2014-08-17 13:09:56 +00:00
svmlight In some straightforward cases, protect documentation behind 2014-08-04 03:40:14 +00:00
szip
udunits - Revert r362761 2014-07-25 07:35:24 +00:00
v_sim - Add USES=libtool 2014-07-07 21:35:34 +00:00
veusz
vmd Stage science/vmd 2014-08-30 14:17:53 +00:00
voro++
xfce4-equake-plugin
xmakemol
Makefile Remove non staged ports without pending PR from s* 2014-09-02 10:07:49 +00:00