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freebsd-ports/science
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Brendan Fabeny aa89760550 - update math/R-cran-psych to 1.2.1 [1] 
- update math/R to 2.15.0, and adjust dependent ports
- minor changes to bsd.cran.mk [2]: rename MASTER_CRAN_SITES to
  MASTER_SITE_CRAN, as in bsd.sites.mk; make the install target more
  flexible and allow CRAN ports to override it; add a regression-test
  target; set USE_FORTRAN to match math/R; remove some of the
  redundant checks of USE_R_MOD; honor NOPORTDATA and NOPORTDOCS

Reviewed by:	thierry, tota, wen
Approved by:	D. Rue (maintainer) [1], wen [2]
2012-05-04 20:56:15 +00:00
..
2d-rewriter - remove MD5 2011-07-03 13:22:24 +00:00
2dhf adjust linking and comments in dependent ports after the math/atlas update; 2011-11-22 11:14:10 +00:00
abinit adjust linking and comments in dependent ports after the math/atlas update; 2011-11-22 11:14:10 +00:00
afni The vast majority of pkg-descr files had the following format when they 2011-10-24 09:11:38 +00:00
avogadro - Update to 1.0.3 2012-05-02 22:35:15 +00:00
bddsolve Mark as broken on powerpc. 2011-12-28 06:55:26 +00:00
bft - Remove WITH_FBSD10_FIX, is no longer needed 2011-11-09 15:26:04 +00:00
bodr - remove MD5 2011-07-03 13:22:24 +00:00
brian - Update to 1.3.1 2011-12-31 08:04:46 +00:00
buddy Remove more tags from pkg-descr files fo the form: 2011-10-24 04:17:37 +00:00
cdcl - remove MD5 2011-07-03 13:22:24 +00:00
cdf Mark broken on powerpc as well as sparc64. (In fact, on all the tier-2s.) 2011-11-10 05:38:32 +00:00
cdo - Update to 1.5.3 2011-11-01 15:08:47 +00:00
cgnslib - Bump PORTREVISION for science/hdf5-18 shlib change 2011-07-15 07:00:46 +00:00
checkmol - Bump PORTREVISION (freepascal ports were updated) 2012-04-19 06:51:44 +00:00
chemical-mime-data - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) 2011-09-23 22:26:39 +00:00
chemtool - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) 2011-09-23 22:26:39 +00:00
chemtool-devel - remove MD5 2011-07-03 13:22:24 +00:00
clhep Remove USE_GNOME=gnometarget from ports. It has been a empty keyword since 2011-08-11 19:20:17 +00:00
colt Now that the Java 1.3 and Java 1.4 ports are deprecated and will expire soon, 2011-07-21 05:03:02 +00:00
crf++ - remove MD5 2011-07-03 13:22:24 +00:00
dcl - Update to 5.4.4 2012-02-21 16:24:19 +00:00
devisor Now that the Java 1.3 and Java 1.4 ports are deprecated and will expire soon, 2011-07-21 05:03:02 +00:00
dlpoly-classic DL_POLY is a general purpose classical molecular dynamics (MD) simulation 2012-04-17 17:35:33 +00:00
dtiquery - remove MD5 2011-07-03 13:22:24 +00:00
ecs - Bump PORTREVISION for science/hdf5-18 shlib change 2011-07-15 07:00:46 +00:00
elmer-eio - remove MD5 2011-07-03 13:22:24 +00:00
elmer-hutiter adjust linking and comments in dependent ports after the math/atlas update; 2011-11-22 11:14:10 +00:00
elmer-matc - remove MD5 2011-07-03 13:22:24 +00:00
elmer-meshgen2d - remove MD5 2011-07-03 13:22:24 +00:00
elmergrid - remove MD5 2011-07-03 13:22:24 +00:00
elmerpost Mark as broken on recent i386-9: does not compile. 2011-08-29 04:10:04 +00:00
epte - remove MD5 2011-07-03 13:22:24 +00:00
euler Remove USE_GNOME=gnometarget from ports. It has been a empty keyword since 2011-08-11 19:20:17 +00:00
fastcap fix the clang build 2011-08-20 11:28:54 +00:00
fasthenry The vast majority of pkg-descr files had the following format when they 2011-10-24 09:11:38 +00:00
felt - remove MD5 2011-07-03 13:22:24 +00:00
flounder - Unbreak - fix build with latest x11-toolkits/fltk 2011-11-17 10:41:36 +00:00
fvm - Bump PORTREVISION for science/hdf5-18 shlib change 2011-07-15 07:00:46 +00:00
g3data adopt 2011-08-12 09:07:47 +00:00
gamess adjust linking and comments in dependent ports after the math/atlas update; 2011-11-22 11:14:10 +00:00
gchemutils Update to 0.12.10. 2011-11-22 14:49:25 +00:00
gdis - remove MD5 2011-07-03 13:22:24 +00:00
getdp - remove MD5 2011-07-03 13:22:24 +00:00
ghemical - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) 2011-09-23 22:26:39 +00:00
ghmm - remove MD5 2011-07-03 13:22:24 +00:00
gnudatalanguage Replace USE_GCC=4.5+ by USE_GCC=4.6+ which has been transparently 2012-03-17 11:39:09 +00:00
gramps - update to 3.3.0 2011-08-11 02:25:21 +00:00
gromacs - update fftw3* to 3.3 [1], and adjust dependent ports 2011-10-17 10:08:33 +00:00
gsmc Remove more tags from pkg-descr files fo the form: 2011-10-24 04:17:37 +00:00
gsystem Remove more tags from pkg-descr files fo the form: 2011-10-24 04:17:37 +00:00
gtamsanalyzer
gwyddion - Update to 2.27 2012-05-03 15:31:19 +00:00
h5utils
harminv - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) 2011-09-23 22:26:39 +00:00
hdf Add the three overlooked headers to the pkg-plist. 2012-04-23 21:09:10 +00:00
hdf5 - remove MD5 2011-07-03 13:22:24 +00:00
hdf5-18 Update to 1.8.8 2012-02-13 03:31:53 +00:00
hdf-java -Update to 2.8 2012-02-13 05:12:38 +00:00
hs-bio - Update to 0.5.1 2012-02-13 05:20:41 +00:00
ics - remove MD5 2011-07-03 13:22:24 +00:00
InsightToolkit - remove MD5 2011-07-03 13:22:24 +00:00
isaac-cfd - remove MD5 2011-07-03 13:22:24 +00:00
jmol - Update to 12.2.23 2012-04-26 01:15:18 +00:00
jstrack - Update to 3.3.3a 2012-03-18 04:47:23 +00:00
kalzium - Bump PORTREVISION to chase the update of multimedia/libvpx 2012-02-16 15:57:34 +00:00
kmovisto Fix master_site 2011-08-02 16:22:15 +00:00
kst Drop maintainership (I don't use Qt3 ports anymore) 2011-07-07 17:34:13 +00:00
kst2 Add patch from upstream to fix build on i386 2011-10-31 14:06:05 +00:00
lamprop - Update to 1.3.3 2011-06-23 10:17:37 +00:00
libctl Remove a special configuration for versions of FreeBSD before 7.0 2011-09-18 20:01:12 +00:00
libghemical Use libdata/pkgconfig instead of lib/pkgconfig, 2011-08-25 02:01:42 +00:00
libint - Remove WITH_FBSD10_FIX, is no longer needed 2011-11-09 15:26:04 +00:00
libkml - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) 2011-09-23 22:26:39 +00:00
liblinear - Update to 1.8 2011-05-02 12:19:32 +00:00
liboglappth - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) 2011-09-23 22:26:39 +00:00
libquantum - remove MD5 2011-07-03 13:22:24 +00:00
libsvm The vast majority of pkg-descr files had the following format when they 2011-10-24 09:11:38 +00:00
libsvm-python The vast majority of pkg-descr files had the following format when they 2011-10-24 09:11:38 +00:00
linsmith - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) 2011-09-23 22:26:39 +00:00
massxpert Remove CMAKE_USE_PTHREAD from the ports using it. 2011-11-14 03:26:46 +00:00
mayavi
mbdyn adjust linking and comments in dependent ports after the math/atlas update; 2011-11-22 11:14:10 +00:00
mcstas Change maintainer address to my FreeBSD address 2011-09-15 12:33:27 +00:00
medit
meep Replace USE_GCC=4.5+ by USE_GCC=4.6+ which has been transparently 2012-04-07 15:31:51 +00:00
minc - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) 2011-09-23 22:26:39 +00:00
minc2 - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) 2011-09-23 22:26:39 +00:00
mol2ps - Bump PORTREVISION (freepascal ports were updated) 2012-04-19 06:51:44 +00:00
mpb adjust linking and comments in dependent ports after the math/atlas update; 2011-11-22 11:14:10 +00:00
mpqc adjust linking and comments in dependent ports after the math/atlas update; 2011-11-22 11:14:10 +00:00
mpqc-mpich Fix the two affected ports 2012-02-10 09:33:05 +00:00
ncs adjust linking and comments in dependent ports after the math/atlas update; 2011-11-22 11:14:10 +00:00
netcdf - Remove WITH_FBSD10_FIX, is no longer needed 2011-11-09 15:26:04 +00:00
netcdf3-ftn
netcdf4 - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) 2011-09-23 22:26:39 +00:00
netcdf-ftn
nifticlib - remove MD5 2011-07-03 13:22:24 +00:00
omnetpp Remove optional dependency on graphics/giftrans, which is about to be removed 2011-10-09 01:39:20 +00:00
openbabel - Remove WITH_FBSD10_FIX, is no longer needed 2011-11-09 15:26:04 +00:00
ovt . Update to 2.3_4. 2012-02-07 04:00:04 +00:00
p5-Algorithm-SVMLight - Assign clsung's p5- ports to perl@ 2012-05-01 01:47:10 +00:00
p5-Chemistry-3DBuilder - Replace ../../authors in MASTER_SITE_SUBDIR with CPAN:CPANID macro. 2011-06-20 09:03:27 +00:00
p5-Chemistry-Bond-Find - Replace ../../authors in MASTER_SITE_SUBDIR with CPAN:CPANID macro. 2011-06-20 09:03:27 +00:00
p5-Chemistry-Canonicalize - Replace ../../authors in MASTER_SITE_SUBDIR with CPAN:CPANID macro. 2011-06-20 09:03:27 +00:00
p5-Chemistry-Elements - Cleaning MD5 in perl@'s ports 2011-05-17 11:14:02 +00:00
p5-Chemistry-File-MDLMol - Replace ../../authors in MASTER_SITE_SUBDIR with CPAN:CPANID macro. 2011-06-20 09:03:27 +00:00
p5-Chemistry-File-Mopac - Replace ../../authors in MASTER_SITE_SUBDIR with CPAN:CPANID macro. 2011-06-20 09:03:27 +00:00
p5-Chemistry-File-PDB - remove MD5 2011-07-03 13:22:24 +00:00
p5-Chemistry-File-SLN - Replace ../../authors in MASTER_SITE_SUBDIR with CPAN:CPANID macro. 2011-06-20 09:03:27 +00:00
p5-Chemistry-File-SMARTS - Replace ../../authors in MASTER_SITE_SUBDIR with CPAN:CPANID macro. 2011-06-20 09:03:27 +00:00
p5-Chemistry-File-SMILES - Replace ../../authors in MASTER_SITE_SUBDIR with CPAN:CPANID macro. 2011-06-20 09:03:27 +00:00
p5-Chemistry-File-VRML - Replace ../../authors in MASTER_SITE_SUBDIR with CPAN:CPANID macro. 2011-06-20 09:03:27 +00:00
p5-Chemistry-File-XYZ - Replace ../../authors in MASTER_SITE_SUBDIR with CPAN:CPANID macro. 2011-06-20 09:03:27 +00:00
p5-Chemistry-FormulaPattern - Replace ../../authors in MASTER_SITE_SUBDIR with CPAN:CPANID macro. 2011-06-20 09:03:27 +00:00
p5-Chemistry-InternalCoords - Replace ../../authors in MASTER_SITE_SUBDIR with CPAN:CPANID macro. 2011-06-20 09:03:27 +00:00
p5-Chemistry-Isotope - Replace ../../authors in MASTER_SITE_SUBDIR with CPAN:CPANID macro. 2011-06-20 09:03:27 +00:00
p5-Chemistry-MacroMol At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450 2012-01-21 17:40:15 +00:00
p5-Chemistry-MidasPattern - Replace ../../authors in MASTER_SITE_SUBDIR with CPAN:CPANID macro. 2011-06-20 09:03:27 +00:00
p5-Chemistry-Mok - Replace ../../authors in MASTER_SITE_SUBDIR with CPAN:CPANID macro. 2011-06-20 09:03:27 +00:00
p5-Chemistry-Mol - remove MD5 2011-07-03 13:22:24 +00:00
p5-Chemistry-Pattern - Replace ../../authors in MASTER_SITE_SUBDIR with CPAN:CPANID macro. 2011-06-20 09:03:27 +00:00
p5-Chemistry-Reaction - Replace ../../authors in MASTER_SITE_SUBDIR with CPAN:CPANID macro. 2011-06-20 09:03:27 +00:00
p5-Chemistry-Ring - Replace ../../authors in MASTER_SITE_SUBDIR with CPAN:CPANID macro. 2011-06-20 09:03:27 +00:00
p5-Geo-BUFR - Update to 1.21 2012-02-08 07:25:19 +00:00
p5-Geo-Coordinates-Converter At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450 2012-01-21 17:40:15 +00:00
p5-Geo-Coordinates-Converter-iArea - Add p5-Geo-Coordinates-Converter-iArea 0.14 2011-06-12 16:18:59 +00:00
p5-Geo-ReadGRIB - remove MD5 2011-07-03 13:22:24 +00:00
p5-Geo-WebService-Elevation-USGS - Update to 0.010 2012-01-07 17:37:32 +00:00
p5-PerlMol - Replace ../../authors in MASTER_SITE_SUBDIR with CPAN:CPANID macro. 2011-06-20 09:03:27 +00:00
p5-Physics-Unit - remove MD5 2011-07-03 13:22:24 +00:00
paje - fix build with gcc46 2012-01-14 09:14:53 +00:00
paraview Update to 3.10.1 2011-08-16 21:55:45 +00:00
peekabot - Remove unnecessary LIB_DEPENDS for x11-toolkits/fltk 2012-04-08 10:31:29 +00:00
pnetcdf
psi3 adjust linking and comments in dependent ports after the math/atlas update; 2011-11-22 11:14:10 +00:00
psychopy At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450 2012-01-21 17:40:15 +00:00
py-biolccc
py-DendroPy Update to 3.11.0 2012-04-14 18:41:27 +00:00
py-h5py - remove MD5 2011-07-03 13:22:24 +00:00
py-hcluster At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450 2012-01-21 17:40:15 +00:00
py-mdp
py-mlpy At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450 2012-01-21 17:40:15 +00:00
py-netCDF4 - Update to 0.9.9 2012-03-06 06:32:28 +00:00
py-obspy-core - Update to 0.6.2 2012-02-09 00:12:41 +00:00
py-obspy.db - update to 0.5.1 2012-01-11 05:41:26 +00:00
py-obspy.gse2 - update to 0.5.1 2012-01-11 05:41:26 +00:00
py-obspy.imaging - update to 0.5.1 2012-01-11 05:41:26 +00:00
py-obspy.iris - update to 0.5.1 2012-01-11 05:52:18 +00:00
py-obspy.mseed - Update to 0.6.1 2012-05-03 11:59:31 +00:00
py-obspy.signal - Update to 0.6.1 2012-05-04 07:12:12 +00:00
py-obspy.taup The obspy.taup package contains Python wrappers for iaspei-tau - a travel 2012-01-16 06:55:05 +00:00
py-obspy.wav - Update to 0.5.1 2012-05-04 07:14:16 +00:00
py-obspy.xseed - Update to 0.5.2 2012-05-04 07:24:07 +00:00
py-openbabel - remove MD5 2011-07-03 13:22:24 +00:00
py-paida - remove MD5 2011-07-03 13:22:24 +00:00
py-pydicom - remove MD5 2011-07-03 13:22:24 +00:00
py-scimath At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450 2012-01-21 17:40:15 +00:00
py-scipy - Update to 0.10.0 2011-12-09 08:05:48 +00:00
py-ws2300 - New port science/py-ws2300 2011-07-01 20:23:41 +00:00
pybrain - remove MD5 2011-07-03 13:22:24 +00:00
pycdf At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450 2012-01-21 17:40:15 +00:00
pynn - Update to 0.7.3 2012-04-11 07:17:21 +00:00
qcl Remove more tags from pkg-descr files fo the form: 2011-10-24 04:17:37 +00:00
qtresistors - remove MD5 2011-07-03 13:22:24 +00:00
R-cran-AMORE - update math/R-cran-psych to 1.2.1 [1] 2012-05-04 20:56:15 +00:00
R-cran-bayesm - update math/R-cran-psych to 1.2.1 [1] 2012-05-04 20:56:15 +00:00
R-cran-DCluster - update math/R-cran-psych to 1.2.1 [1] 2012-05-04 20:56:15 +00:00
R-cran-e1071 - update math/R-cran-psych to 1.2.1 [1] 2012-05-04 20:56:15 +00:00
R-cran-eco - update math/R-cran-psych to 1.2.1 [1] 2012-05-04 20:56:15 +00:00
R-cran-Epi - update math/R-cran-psych to 1.2.1 [1] 2012-05-04 20:56:15 +00:00
R-cran-epicalc - update math/R-cran-psych to 1.2.1 [1] 2012-05-04 20:56:15 +00:00
R-cran-snow - update math/R-cran-psych to 1.2.1 [1] 2012-05-04 20:56:15 +00:00
R-cran-som - update math/R-cran-psych to 1.2.1 [1] 2012-05-04 20:56:15 +00:00
ruby-dcl - Update to 1.6.3 2012-02-17 22:22:43 +00:00
ruby-gphys - Chase math/ruby-netcdf -> science/ruby-netcdf rename 2012-03-08 04:50:36 +00:00
ruby-netcdf - update to 0.6.6 2012-03-08 04:34:40 +00:00
rubygem-ai4r - Cannoicalize the WWW: [again], 2011-06-23 17:51:43 +00:00
silo - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) 2011-09-23 22:26:39 +00:00
simlib - remove MD5 2011-07-03 13:22:24 +00:00
step - Bump PORTREVISION to chase the update of multimedia/libvpx 2012-02-16 15:57:34 +00:00
svmlight Fix fetch. 2011-07-08 04:07:55 +00:00
szip - Update distinfo because distfile was rerolled upstream [1] 2012-02-04 07:44:50 +00:00
udunits - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) 2011-09-23 22:26:39 +00:00
v_sim - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) 2011-09-23 22:26:39 +00:00
veusz Update to 1.12 2011-07-21 11:11:03 +00:00
vis5d+ - Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) 2011-09-23 22:26:39 +00:00
vmd Update to 1.9.1. 2012-04-23 04:48:03 +00:00
x11iraf - remove MD5 2011-07-03 13:22:24 +00:00
xmakemol Remove USE_GNOME=gnometarget from ports. It has been a empty keyword since 2011-08-11 19:20:17 +00:00
xmds The vast majority of pkg-descr files had the following format when they 2011-10-24 09:11:38 +00:00
Makefile - Add a new port: science/R-cran-som 2012-04-19 12:43:14 +00:00