diff options
Diffstat (limited to 'science')
33 files changed, 42 insertions, 151 deletions
diff --git a/science/ALPSCore/Makefile b/science/ALPSCore/Makefile index 336b1416a2dc..dbce96c38ca2 100644 --- a/science/ALPSCore/Makefile +++ b/science/ALPSCore/Makefile @@ -3,7 +3,7 @@ PORTNAME= ALPSCore DISTVERSIONPREFIX= v DISTVERSION= 2.2.0 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= science MAINTAINER= mike.d.ft402@gmail.com diff --git a/science/InsightToolkit/Makefile b/science/InsightToolkit/Makefile index e72b6585d679..ad5841b06bbe 100644 --- a/science/InsightToolkit/Makefile +++ b/science/InsightToolkit/Makefile @@ -3,7 +3,7 @@ PORTNAME= InsightToolkit PORTVERSION= 4.13.0 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= science biology MASTER_SITES= SF/itk/itk/${ITK_VER} diff --git a/science/MOOSE-neural-simulator/Makefile b/science/MOOSE-neural-simulator/Makefile index ff9d8ccca863..01c1c130cd1e 100644 --- a/science/MOOSE-neural-simulator/Makefile +++ b/science/MOOSE-neural-simulator/Makefile @@ -3,7 +3,7 @@ PORTNAME= MOOSE-neural-simulator DISTVERSION= 3.1.2 -PORTREVISION= 6 +PORTREVISION= 7 DISTVERSIONSUFFIX= -382-gc93d23a CATEGORIES= science biology diff --git a/science/avogadro2/Makefile b/science/avogadro2/Makefile index fab60b0537de..c4215833cb11 100644 --- a/science/avogadro2/Makefile +++ b/science/avogadro2/Makefile @@ -2,7 +2,7 @@ PORTNAME= avogadro2 DISTVERSION= 1.91.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/avogadrolibs/Makefile b/science/avogadrolibs/Makefile index 3d0e5f220759..8dc41a03ae1f 100644 --- a/science/avogadrolibs/Makefile +++ b/science/avogadrolibs/Makefile @@ -2,7 +2,7 @@ PORTNAME= avogadrolibs DISTVERSION= 1.92.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science PATCH_SITES= https://github.com/${GH_ACCOUNT}/${PORTNAME}/commit/ diff --git a/science/cdo/Makefile b/science/cdo/Makefile index 0dca2458628b..17ecbc0488cf 100644 --- a/science/cdo/Makefile +++ b/science/cdo/Makefile @@ -3,7 +3,7 @@ PORTNAME= cdo PORTVERSION= 1.9.5 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MASTER_SITES= https://code.mpimet.mpg.de/attachments/download/18264/ \ LOCAL/sunpoet diff --git a/science/cgnslib/Makefile b/science/cgnslib/Makefile index f33413a632f1..1cd39ffeb63a 100644 --- a/science/cgnslib/Makefile +++ b/science/cgnslib/Makefile @@ -4,7 +4,7 @@ PORTNAME= cgnslib DISTVERSIONPREFIX= v DISTVERSION= 3.3.1 -PORTREVISION= 1 +PORTREVISION= 2 PORTEPOCH= 1 CATEGORIES= science diff --git a/science/chemps2/Makefile b/science/chemps2/Makefile index 5dde503cd33a..7f124455a217 100644 --- a/science/chemps2/Makefile +++ b/science/chemps2/Makefile @@ -3,7 +3,7 @@ PORTNAME= CheMPS2 DISTVERSIONPREFIX= v DISTVERSION= 1.8.9 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/chrono/Makefile b/science/chrono/Makefile index 868617e0d37a..ef1f0c505077 100644 --- a/science/chrono/Makefile +++ b/science/chrono/Makefile @@ -3,7 +3,7 @@ PORTNAME= chrono DISTVERSION= 2.0.0-9070 DISTVERSIONSUFFIX= -g57a828dc0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science devel MAINTAINER= yuri@FreeBSD.org diff --git a/science/code_saturne/Makefile b/science/code_saturne/Makefile index c914d156e75f..8ce3411c2a7b 100644 --- a/science/code_saturne/Makefile +++ b/science/code_saturne/Makefile @@ -3,7 +3,7 @@ PORTNAME= code_saturne PORTVERSION= 5.3.1 -PORTREVISION= 1 +PORTREVISION= 2 DISTVERSIONPREFIX= v CATEGORIES= science parallel diff --git a/science/dft_tools/Makefile b/science/dft_tools/Makefile index 549385bfd242..8fab6a4be7c3 100644 --- a/science/dft_tools/Makefile +++ b/science/dft_tools/Makefile @@ -2,7 +2,7 @@ PORTNAME= dft_tools DISTVERSION= 1.5 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/erkale/Makefile b/science/erkale/Makefile index d30a2ab6f266..c0113817c830 100644 --- a/science/erkale/Makefile +++ b/science/erkale/Makefile @@ -2,7 +2,7 @@ PORTNAME= erkale DISTVERSION= g20181121 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/fleur/Makefile b/science/fleur/Makefile index 275080ff1702..85824d9968fd 100644 --- a/science/fleur/Makefile +++ b/science/fleur/Makefile @@ -2,7 +2,7 @@ PORTNAME= fleur DISTVERSION= 0.27-3 # Release 3 of Version 0.27 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science MASTER_SITES= http://www.flapw.de/pm/uploads/FLEUR/ DISTNAME= fleurMaXR${DISTVERSION:C/.*-//} diff --git a/science/gnudatalanguage/Makefile b/science/gnudatalanguage/Makefile index d2cd2c7e275f..19a41f5eb25a 100644 --- a/science/gnudatalanguage/Makefile +++ b/science/gnudatalanguage/Makefile @@ -3,7 +3,7 @@ PORTNAME= gnudatalanguage PORTVERSION= 0.9.9 -PORTREVISION= 2 +PORTREVISION= 3 DISTVERSIONPREFIX= v CATEGORIES= science lang .if defined(BUILD_PYTHON_MODULE) diff --git a/science/h5utils/Makefile b/science/h5utils/Makefile index 36707015d8d2..98e634c81088 100644 --- a/science/h5utils/Makefile +++ b/science/h5utils/Makefile @@ -3,7 +3,7 @@ PORTNAME= h5utils DISTVERSION= 1.13.1 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science MAINTAINER= aehlig@linta.de diff --git a/science/h5z-zfp/Makefile b/science/h5z-zfp/Makefile index 52eb5db61147..b198f40b2dad 100644 --- a/science/h5z-zfp/Makefile +++ b/science/h5z-zfp/Makefile @@ -3,6 +3,7 @@ PORTNAME= h5z-zfp DISTVERSIONPREFIX= v DISTVERSION= 0.9.0 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/hdf5/Makefile b/science/hdf5/Makefile index c9f32b30d839..5480eb0ed616 100644 --- a/science/hdf5/Makefile +++ b/science/hdf5/Makefile @@ -2,8 +2,7 @@ # $FreeBSD$ PORTNAME= hdf5 -PORTVERSION= 1.10.2 -PORTREVISION= 1 +PORTVERSION= 1.10.4 CATEGORIES= science archivers graphics MASTER_SITES= https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${PORTVERSION:R}/${DISTNAME}/src/ \ LOCAL/sunpoet diff --git a/science/hdf5/distinfo b/science/hdf5/distinfo index 83099508b371..c8d0e6ba5a67 100644 --- a/science/hdf5/distinfo +++ b/science/hdf5/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1523098063 -SHA256 (hdf5-1.10.2.tar.bz2) = 1cad5b7bfdf128dfc53cd16fba48f6e7ae4e93c75c371d9ec8dfc4df0c1fcb71 -SIZE (hdf5-1.10.2.tar.bz2) = 8609163 +TIMESTAMP = 1541673300 +SHA256 (hdf5-1.10.4.tar.bz2) = 1267ff06aaedc04ca25f7c6026687ea2884b837043431195f153401d942b28df +SIZE (hdf5-1.10.4.tar.bz2) = 8598986 diff --git a/science/hdf5/files/patch-src_H5detect.c b/science/hdf5/files/patch-src_H5detect.c deleted file mode 100644 index 76db6261fd7b..000000000000 --- a/science/hdf5/files/patch-src_H5detect.c +++ /dev/null @@ -1,112 +0,0 @@ ---- src/H5detect.c.orig 2018-12-12 22:50:50 UTC -+++ src/H5detect.c -@@ -1360,8 +1360,8 @@ bit.\n"; - * - *------------------------------------------------------------------------- - */ --static void --detect_C89_integers(void) HDF_NO_UBSAN -+static void HDF_NO_UBSAN -+detect_C89_integers(void) - { - DETECT_BYTE(signed char, SCHAR, d_g[nd_g]); nd_g++; - DETECT_BYTE(unsigned char, UCHAR, d_g[nd_g]); nd_g++; -@@ -1388,8 +1388,8 @@ detect_C89_integers(void) HDF_NO_UBSAN - * - *------------------------------------------------------------------------- - */ --static void --detect_C89_floats(void) HDF_NO_UBSAN -+static void HDF_NO_UBSAN -+detect_C89_floats(void) - { - DETECT_F(float, FLOAT, d_g[nd_g]); nd_g++; - DETECT_F(double, DOUBLE, d_g[nd_g]); nd_g++; -@@ -1410,8 +1410,8 @@ detect_C89_floats(void) HDF_NO_UBSAN - * - *------------------------------------------------------------------------- - */ --static void --detect_C99_integers8(void) HDF_NO_UBSAN -+static void HDF_NO_UBSAN -+detect_C99_integers8(void) - { - #if H5_SIZEOF_INT8_T>0 - #if H5_SIZEOF_INT8_T==1 -@@ -1472,8 +1472,8 @@ detect_C99_integers8(void) HDF_NO_UBSAN - * - *------------------------------------------------------------------------- - */ --static void --detect_C99_integers16(void) HDF_NO_UBSAN -+static void HDF_NO_UBSAN -+detect_C99_integers16(void) - { - #if H5_SIZEOF_INT16_T>0 - DETECT_I(int16_t, INT16, d_g[nd_g]); nd_g++; -@@ -1510,8 +1510,8 @@ detect_C99_integers16(void) HDF_NO_UBSAN - * - *------------------------------------------------------------------------- - */ --static void --detect_C99_integers32(void) HDF_NO_UBSAN -+static void HDF_NO_UBSAN -+detect_C99_integers32(void) - { - #if H5_SIZEOF_INT32_T>0 - DETECT_I(int32_t, INT32, d_g[nd_g]); nd_g++; -@@ -1548,8 +1548,8 @@ detect_C99_integers32(void) HDF_NO_UBSAN - * - *------------------------------------------------------------------------- - */ --static void --detect_C99_integers64(void) HDF_NO_UBSAN -+static void HDF_NO_UBSAN -+detect_C99_integers64(void) - { - #if H5_SIZEOF_INT64_T>0 - DETECT_I(int64_t, INT64, d_g[nd_g]); nd_g++; -@@ -1599,8 +1599,8 @@ detect_C99_integers64(void) HDF_NO_UBSAN - * - *------------------------------------------------------------------------- - */ --static void --detect_C99_integers(void) HDF_NO_UBSAN -+static void HDF_NO_UBSAN -+detect_C99_integers(void) - { - /* break it down to more subroutines so that each module subroutine */ - /* is smaller and takes less time to compile with optimization on. */ -@@ -1625,8 +1625,8 @@ detect_C99_integers(void) HDF_NO_UBSAN - * - *------------------------------------------------------------------------- - */ --static void --detect_C99_floats(void) HDF_NO_UBSAN -+static void HDF_NO_UBSAN -+detect_C99_floats(void) - { - #if H5_SIZEOF_DOUBLE == H5_SIZEOF_LONG_DOUBLE - /* -@@ -1656,8 +1656,8 @@ detect_C99_floats(void) HDF_NO_UBSAN - * - *------------------------------------------------------------------------- - */ --static void --detect_alignments(void) HDF_NO_UBSAN -+static void HDF_NO_UBSAN -+detect_alignments(void) - { - /* Detect structure alignment for pointers, hvl_t, hobj_ref_t, hdset_reg_ref_t */ - DETECT_M(void *, POINTER, m_g[na_g]); na_g++; -@@ -1744,8 +1744,8 @@ static int verify_signal_handlers(int signum, void (*h - * - *------------------------------------------------------------------------- - */ --int --main(void) HDF_NO_UBSAN -+int HDF_NO_UBSAN -+main(void) - { - - #if defined(H5_HAVE_SETSYSINFO) && defined(SSI_NVPAIRS) diff --git a/science/hdf5/pkg-plist b/science/hdf5/pkg-plist index 06cba2a4dc28..19a804bc184f 100644 --- a/science/hdf5/pkg-plist +++ b/science/hdf5/pkg-plist @@ -34,6 +34,7 @@ include/H5CppDoc.h include/H5Cpublic.h include/H5DOpublic.h include/H5DSpublic.h +include/H5DaccProp.h include/H5DataSet.h include/H5DataSpace.h include/H5DataType.h @@ -136,25 +137,25 @@ include/hdf5_hl.h lib/libhdf5.a lib/libhdf5.settings lib/libhdf5.so -lib/libhdf5.so.101 -lib/libhdf5.so.101.1.0 +lib/libhdf5.so.103 +lib/libhdf5.so.103.0.0 lib/libhdf5_cpp.a lib/libhdf5_cpp.so -lib/libhdf5_cpp.so.102 -lib/libhdf5_cpp.so.102.0.0 +lib/libhdf5_cpp.so.103 +lib/libhdf5_cpp.so.103.0.0 %%FORTRAN%%lib/libhdf5_fortran.a %%FORTRAN%%lib/libhdf5_fortran.so %%FORTRAN%%lib/libhdf5_fortran.so.100 -%%FORTRAN%%lib/libhdf5_fortran.so.100.1.1 +%%FORTRAN%%lib/libhdf5_fortran.so.100.1.2 lib/libhdf5_hl.a lib/libhdf5_hl.so lib/libhdf5_hl.so.100 -lib/libhdf5_hl.so.100.1.0 +lib/libhdf5_hl.so.100.1.1 lib/libhdf5_hl_cpp.a lib/libhdf5_hl_cpp.so lib/libhdf5_hl_cpp.so.100 -lib/libhdf5_hl_cpp.so.100.1.1 +lib/libhdf5_hl_cpp.so.100.1.2 %%FORTRAN%%lib/libhdf5hl_fortran.a %%FORTRAN%%lib/libhdf5hl_fortran.so %%FORTRAN%%lib/libhdf5hl_fortran.so.100 -%%FORTRAN%%lib/libhdf5hl_fortran.so.100.0.2 +%%FORTRAN%%lib/libhdf5hl_fortran.so.100.0.3 diff --git a/science/jdftx/Makefile b/science/jdftx/Makefile index 2d6a8b6b075c..292f9e826677 100644 --- a/science/jdftx/Makefile +++ b/science/jdftx/Makefile @@ -3,7 +3,7 @@ PORTNAME= jdftx DISTVERSIONPREFIX= v DISTVERSION= 1.4.2-74 -PORTREVISION= 3 +PORTREVISION= 4 DISTVERSIONSUFFIX= -gba743849 CATEGORIES= science diff --git a/science/lm/Makefile b/science/lm/Makefile index 3b8fda3185e1..abb5f783427e 100644 --- a/science/lm/Makefile +++ b/science/lm/Makefile @@ -2,7 +2,7 @@ PORTNAME= lm DISTVERSION= 2.3.0 -PORTREVISION= 3 +PORTREVISION= 4 DISTVERSIONSUFFIX= -src CATEGORIES= science MASTER_SITES= http://scs.illinois.edu/schulten/${PORTNAME}/download/${PORTNAME}${DISTVERSION:R:S/.//}/ diff --git a/science/meep/Makefile b/science/meep/Makefile index 0927ba0942ff..203385276a9c 100644 --- a/science/meep/Makefile +++ b/science/meep/Makefile @@ -3,7 +3,7 @@ PORTNAME= meep PORTVERSION= 1.2.1 -PORTREVISION= 16 +PORTREVISION= 17 CATEGORIES= science MASTER_SITES= http://ab-initio.mit.edu/meep/ diff --git a/science/minc2/Makefile b/science/minc2/Makefile index cff8fcb03ede..d7e233bf1aa4 100644 --- a/science/minc2/Makefile +++ b/science/minc2/Makefile @@ -4,7 +4,7 @@ PORTNAME= minc PORTVERSION= 2.2.00 DISTVERSIONPREFIX= release- -PORTREVISION= 7 +PORTREVISION= 8 PORTEPOCH= 1 CATEGORIES= science biology PKGNAMESUFFIX= 2 diff --git a/science/mpb/Makefile b/science/mpb/Makefile index a942eef74908..7a92f614644d 100644 --- a/science/mpb/Makefile +++ b/science/mpb/Makefile @@ -3,7 +3,7 @@ PORTNAME= mpb PORTVERSION= 1.5 -PORTREVISION= 11 +PORTREVISION= 12 CATEGORIES= science MASTER_SITES= http://ab-initio.mit.edu/mpb/ diff --git a/science/netcdf/Makefile b/science/netcdf/Makefile index 89027ac419c7..61394aa52250 100644 --- a/science/netcdf/Makefile +++ b/science/netcdf/Makefile @@ -3,7 +3,7 @@ PORTNAME= netcdf PORTVERSION= 4.6.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MASTER_SITES= https://www.unidata.ucar.edu/downloads/netcdf/ftp/ \ ftp://ftp.unidata.ucar.edu/pub/netcdf/ \ diff --git a/science/paraview/Makefile b/science/paraview/Makefile index efb08e3ce0c3..1ef7e8c4542c 100644 --- a/science/paraview/Makefile +++ b/science/paraview/Makefile @@ -3,7 +3,7 @@ PORTNAME= paraview DISTVERSION= 5.5.1 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= science graphics MASTER_SITES= http://www.paraview.org/files/v${VERMAJORMINOR}/ DISTNAME= ParaView-v${PORTVERSION} diff --git a/science/py-h5py/Makefile b/science/py-h5py/Makefile index cbed3afee0da..f72a5f14edaf 100644 --- a/science/py-h5py/Makefile +++ b/science/py-h5py/Makefile @@ -3,6 +3,7 @@ PORTNAME= h5py PORTVERSION= 2.9.0 +PORTREVISION= 1 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-netCDF4/Makefile b/science/py-netCDF4/Makefile index 640d4adefcda..ba2a1a80ad87 100644 --- a/science/py-netCDF4/Makefile +++ b/science/py-netCDF4/Makefile @@ -3,7 +3,7 @@ PORTNAME= netCDF4 PORTVERSION= 1.3.1 -PORTREVISION= 3 +PORTREVISION= 4 DISTVERSIONPREFIX= v DISTVERSIONSUFFIX= rel CATEGORIES= science python diff --git a/science/qmcpack/Makefile b/science/qmcpack/Makefile index 07afcd854e7b..06005d013140 100644 --- a/science/qmcpack/Makefile +++ b/science/qmcpack/Makefile @@ -3,6 +3,7 @@ PORTNAME= qmcpack DISTVERSIONPREFIX= v DISTVERSION= 3.6.0 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/rmf/Makefile b/science/rmf/Makefile index 6aaa60b9baed..692992d4ddcc 100644 --- a/science/rmf/Makefile +++ b/science/rmf/Makefile @@ -2,7 +2,7 @@ PORTNAME= rmf DISTVERSION= 1.1 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science graphics MAINTAINER= yuri@FreeBSD.org diff --git a/science/silo/Makefile b/science/silo/Makefile index 502ba3a2273e..f0b80c763b17 100644 --- a/science/silo/Makefile +++ b/science/silo/Makefile @@ -4,7 +4,7 @@ PORTNAME= silo PORTVERSION= 4.10.2 DISTVERSIONSUFFIX= -bsd -PORTREVISION= 9 +PORTREVISION= 10 CATEGORIES= science MASTER_SITES= http://wci.llnl.gov/content/assets/docs/simulation/computer-codes/${PORTNAME}/silo-${PORTVERSION}/ diff --git a/science/triqs/Makefile b/science/triqs/Makefile index 406f91cec1bf..e3ed4422e6f2 100644 --- a/science/triqs/Makefile +++ b/science/triqs/Makefile @@ -2,7 +2,7 @@ PORTNAME= triqs DISTVERSION= 2.0 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org |