[120497] trunk/dports
mmoll at macports.org
mmoll at macports.org
Fri May 30 07:18:34 PDT 2014
Revision: 120497
https://trac.macports.org/changeset/120497
Author: mmoll at macports.org
Date: 2014-05-30 07:18:34 -0700 (Fri, 30 May 2014)
Log Message:
-----------
science/hdf5-18: update to 1.8.13; rev bump ports that depend on hdf5-18
Modified Paths:
--------------
trunk/dports/archivers/blosc/Portfile
trunk/dports/devel/lua-numlua/Portfile
trunk/dports/gis/gdal/Portfile
trunk/dports/graphics/field3d/Portfile
trunk/dports/graphics/vigra/Portfile
trunk/dports/math/dolfin/Portfile
trunk/dports/math/gnudatalanguage/Portfile
trunk/dports/math/octave/Portfile
trunk/dports/math/petsc/Portfile
trunk/dports/math/shogun/Portfile
trunk/dports/perl/p5-pdl/Portfile
trunk/dports/python/py-h5py/Portfile
trunk/dports/python/py-stfio/Portfile
trunk/dports/python/py-tables/Portfile
trunk/dports/science/H5Part/Portfile
trunk/dports/science/alps/Portfile
trunk/dports/science/armadillo/Portfile
trunk/dports/science/bob/Portfile
trunk/dports/science/cdo/Portfile
trunk/dports/science/flann/Portfile
trunk/dports/science/grads/Portfile
trunk/dports/science/h4h5tools/Portfile
trunk/dports/science/h5utils/Portfile
trunk/dports/science/hdf5-18/Portfile
trunk/dports/science/hdfeos5/Portfile
trunk/dports/science/nco/Portfile
trunk/dports/science/ncview/Portfile
trunk/dports/science/netcdf/Portfile
trunk/dports/science/silo/Portfile
trunk/dports/science/splash/Portfile
trunk/dports/science/stimfit/Portfile
trunk/dports/science/swarm/Portfile
trunk/dports/science/vapor/Portfile
trunk/dports/science/wgrib2/Portfile
trunk/dports/science/yorick-hdf5/Portfile
Added Paths:
-----------
trunk/dports/python/py-h5py/files/
trunk/dports/python/py-h5py/files/patch-h5py-h5fd.c.diff
Modified: trunk/dports/archivers/blosc/Portfile
===================================================================
--- trunk/dports/archivers/blosc/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/archivers/blosc/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -6,6 +6,7 @@
PortGroup github 1.0
github.setup Blosc c-blosc 1.3.5 v
+revision 1
name blosc
categories archivers devel
platforms darwin
Modified: trunk/dports/devel/lua-numlua/Portfile
===================================================================
--- trunk/dports/devel/lua-numlua/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/devel/lua-numlua/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -4,7 +4,7 @@
PortGroup github 1.0
github.setup carvalho numlua 0.3
-revision 3
+revision 4
name lua-numlua
license MIT
categories devel
Modified: trunk/dports/gis/gdal/Portfile
===================================================================
--- trunk/dports/gis/gdal/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/gis/gdal/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -5,7 +5,7 @@
name gdal
version 1.10.1
-revision 4
+revision 5
categories gis
license MIT BSD
platforms darwin
Modified: trunk/dports/graphics/field3d/Portfile
===================================================================
--- trunk/dports/graphics/field3d/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/graphics/field3d/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -6,7 +6,7 @@
github.setup imageworks Field3D 1.3.2 v
name field3d
-revision 3
+revision 4
categories graphics
maintainers blair
license BSD
Modified: trunk/dports/graphics/vigra/Portfile
===================================================================
--- trunk/dports/graphics/vigra/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/graphics/vigra/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -10,7 +10,7 @@
github.setup ukoethe vigra 1-10-0 Version-
version [strsed ${github.version} {g/-/./}]
-revision 2
+revision 3
categories graphics
platforms darwin
maintainers gmail.com:benjamin.seppke
Modified: trunk/dports/math/dolfin/Portfile
===================================================================
--- trunk/dports/math/dolfin/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/math/dolfin/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -9,7 +9,7 @@
mpi.setup require
bitbucket.setup fenics-project dolfin 1.3.0 dolfin-
-revision 2
+revision 3
categories math
platforms darwin
universal_variant no
Modified: trunk/dports/math/gnudatalanguage/Portfile
===================================================================
--- trunk/dports/math/gnudatalanguage/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/math/gnudatalanguage/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -12,7 +12,7 @@
name gnudatalanguage
version 0.9.4
-revision 4
+revision 5
epoch 1
categories math science
maintainers takeshi
Modified: trunk/dports/math/octave/Portfile
===================================================================
--- trunk/dports/math/octave/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/math/octave/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -8,7 +8,7 @@
name octave
version 3.6.4
-revision 12
+revision 13
#conflicts octave-devel
categories math science
maintainers michaelld openmaintainer
Modified: trunk/dports/math/petsc/Portfile
===================================================================
--- trunk/dports/math/petsc/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/math/petsc/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -8,6 +8,7 @@
mpi.setup
bitbucket.setup petsc petsc 3.4.4 v
+revision 1
categories math science
maintainers sean
description Portable, Extensible Toolkit for Scientific Computation
Modified: trunk/dports/math/shogun/Portfile
===================================================================
--- trunk/dports/math/shogun/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/math/shogun/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -6,7 +6,7 @@
name shogun
version 2.1.0
set branch [join [lrange [split ${version} .] 0 1] .]
-revision 3
+revision 4
categories math science
platforms darwin
license GPL-3
Modified: trunk/dports/perl/p5-pdl/Portfile
===================================================================
--- trunk/dports/perl/p5-pdl/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/perl/p5-pdl/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -6,6 +6,7 @@
perl5.branches 5.8 5.10 5.12 5.14 5.16
perl5.setup PDL 2.007
+revision 1
maintainers saao.ac.za:tim
license Artistic GPL-2
description Perl Data Language - scientific computing capability for perl
Modified: trunk/dports/python/py-h5py/Portfile
===================================================================
--- trunk/dports/python/py-h5py/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/python/py-h5py/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -7,8 +7,10 @@
name py-h5py
version 2.2.1
# h5py needs to be re-built after hdf5-18 upgrades
-revision 1
+revision 2
+# MPIPOSIX driver is removed in hdf5-18 version 1.8.13
+patchfiles patch-h5py-h5fd.c.diff
checksums \
rmd160 9e5ee73fa28e07e21439cef289b8e1945eccfd4e \
sha256 b4510cb74aef332847dc88e3df6910d7af68c709b3556fc960a687c56ba6a4cb \
Added: trunk/dports/python/py-h5py/files/patch-h5py-h5fd.c.diff
===================================================================
--- trunk/dports/python/py-h5py/files/patch-h5py-h5fd.c.diff (rev 0)
+++ trunk/dports/python/py-h5py/files/patch-h5py-h5fd.c.diff 2014-05-30 14:18:34 UTC (rev 120497)
@@ -0,0 +1,27 @@
+--- h5py/h5fd.c.orig 2014-05-30 09:05:20.000000000 -0500
++++ h5py/h5fd.c 2014-05-30 09:06:39.000000000 -0500
+@@ -854,11 +854,12 @@
+ * MULTI = H5FD_MULTI
+ * SEC2 = H5FD_SEC2
+ */
++ /*
+ __pyx_t_1 = __Pyx_PyInt_to_py_hid_t(H5FD_MPIPOSIX); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__MPIPOSIX, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+-
++ */
+ /* "h5py/h5fd.pyx":35
+ * MPIO = H5FD_MPIO
+ * MPIPOSIX = H5FD_MPIPOSIX
+--- h5py/h5fd.pyx.orig 2014-05-30 09:10:49.000000000 -0500
++++ h5py/h5fd.pyx 2014-05-30 09:11:07.000000000 -0500
+@@ -31,7 +31,7 @@
+ FAMILY = H5FD_FAMILY
+ LOG = H5FD_LOG
+ MPIO = H5FD_MPIO
+-MPIPOSIX = H5FD_MPIPOSIX
++#MPIPOSIX = H5FD_MPIPOSIX
+ MULTI = H5FD_MULTI
+ SEC2 = H5FD_SEC2
+ STDIO = H5FD_STDIO
Modified: trunk/dports/python/py-stfio/Portfile
===================================================================
--- trunk/dports/python/py-stfio/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/python/py-stfio/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -6,6 +6,7 @@
name py-stfio
version 0.13.15
+revision 1
categories python science
platforms darwin
license GPL-2
Modified: trunk/dports/python/py-tables/Portfile
===================================================================
--- trunk/dports/python/py-tables/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/python/py-tables/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -10,6 +10,7 @@
set realname tables
name py-${realname}
version 3.1.1
+revision 1
categories-append science
platforms darwin
license BSD
Modified: trunk/dports/science/H5Part/Portfile
===================================================================
--- trunk/dports/science/H5Part/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/H5Part/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -5,7 +5,7 @@
name H5Part
version 1.6.6
-revision 3
+revision 4
categories science
maintainers lbl.gov:ghweber
license BSD
Modified: trunk/dports/science/alps/Portfile
===================================================================
--- trunk/dports/science/alps/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/alps/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -7,7 +7,7 @@
name alps
version 2.1.1
-revision 4
+revision 5
categories science
platforms darwin
maintainers gmail.com:gamperl
Modified: trunk/dports/science/armadillo/Portfile
===================================================================
--- trunk/dports/science/armadillo/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/armadillo/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -6,6 +6,7 @@
name armadillo
version 4.100.2
+revision 1
categories science
platforms darwin
maintainers gmail.com:christian.frisson openmaintainer
Modified: trunk/dports/science/bob/Portfile
===================================================================
--- trunk/dports/science/bob/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/bob/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -8,7 +8,7 @@
PortGroup compiler_blacklist_versions 1.0
github.setup idiap bob 1.2.2 v
-revision 2
+revision 3
set soversion 1.2
categories science math devel
platforms darwin
Modified: trunk/dports/science/cdo/Portfile
===================================================================
--- trunk/dports/science/cdo/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/cdo/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -5,7 +5,7 @@
name cdo
version 1.6.2
-revision 1
+revision 2
platforms darwin
maintainers takeshi
license GPL-2
Modified: trunk/dports/science/flann/Portfile
===================================================================
--- trunk/dports/science/flann/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/flann/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -6,7 +6,7 @@
name flann
version 1.8.4
-revision 5
+revision 6
categories science devel
maintainers mmoll
description Fast Library for Approximate Nearest Neighbors
Modified: trunk/dports/science/grads/Portfile
===================================================================
--- trunk/dports/science/grads/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/grads/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -5,7 +5,7 @@
name grads
version 2.0.2
-revision 3
+revision 4
set branch [join [lrange [split ${version} .] 0 1] .]
platforms darwin
maintainers takeshi
Modified: trunk/dports/science/h4h5tools/Portfile
===================================================================
--- trunk/dports/science/h4h5tools/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/h4h5tools/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -4,7 +4,7 @@
name h4h5tools
version 2.2.1
-revision 3
+revision 4
categories science
# Equivalent to BSD + explicitly requiring modifications to be documented
license Permissive
Modified: trunk/dports/science/h5utils/Portfile
===================================================================
--- trunk/dports/science/h5utils/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/h5utils/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -5,7 +5,7 @@
name h5utils
version 1.12.1
-revision 5
+revision 6
categories science
platforms darwin
maintainers ece.pdx.edu:higginja
Modified: trunk/dports/science/hdf5-18/Portfile
===================================================================
--- trunk/dports/science/hdf5-18/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/hdf5-18/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -10,8 +10,7 @@
set realname hdf5
name ${realname}-18
-version 1.8.12
-revision 1
+version 1.8.13
categories science
maintainers mmoll openmaintainer
@@ -32,9 +31,8 @@
http://www.hdfgroup.org/ftp/HDF5/current/src \
ftp://ftp.hdfgroup.org/HDF5/current/src/ \
ftp://ftp.hdfgroup.org/HDF5/prev-releases/hdf5-${version}/src/
-checksums \
- rmd160 b885803d35855007f2e66f1a376fff9d11d5c1ec \
- sha256 6d080f913a226a3ce390a11d9b571b2d5866581a2aa4434c398cd371c7063639
+checksums rmd160 59e690fcc8ce80c438c3d6977729e12a75b5d162 \
+ sha256 c2f5a412107aba6f99fd7a4a9db6ce5f5fc8171ec931472784e5839d26aa17ef
distname ${realname}-${version}
use_bzip2 yes
depends_lib port:zlib
Modified: trunk/dports/science/hdfeos5/Portfile
===================================================================
--- trunk/dports/science/hdfeos5/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/hdfeos5/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -6,7 +6,7 @@
name hdfeos5
version 1.14
-revision 5
+revision 6
categories science
platforms darwin
license public-domain
Modified: trunk/dports/science/nco/Portfile
===================================================================
--- trunk/dports/science/nco/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/nco/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -5,6 +5,7 @@
name nco
version 4.4.0
+revision 1
platforms darwin
maintainers takeshi
license GPL-3
Modified: trunk/dports/science/ncview/Portfile
===================================================================
--- trunk/dports/science/ncview/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/ncview/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -5,7 +5,7 @@
name ncview
version 2.1.1
-revision 4
+revision 5
maintainers nomaintainer
platforms darwin
categories science
Modified: trunk/dports/science/netcdf/Portfile
===================================================================
--- trunk/dports/science/netcdf/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/netcdf/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -14,6 +14,7 @@
#mpi.enforce_variant hdf5-18
github.setup Unidata netcdf-c 4.3.1.1 v
+revision 1
name netcdf
maintainers takeshi openmaintainer
platforms darwin
Modified: trunk/dports/science/silo/Portfile
===================================================================
--- trunk/dports/science/silo/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/silo/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -5,7 +5,7 @@
name silo
version 4.9.1
-revision 1
+revision 2
categories science
platforms darwin
maintainers nomaintainer
Modified: trunk/dports/science/splash/Portfile
===================================================================
--- trunk/dports/science/splash/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/splash/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -5,6 +5,7 @@
name splash
version 2.4.1
+revision 1
categories science graphics
platforms darwin
maintainers monash.edu:daniel.price
Modified: trunk/dports/science/stimfit/Portfile
===================================================================
--- trunk/dports/science/stimfit/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/stimfit/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -6,6 +6,7 @@
name stimfit
version 0.13.15
+revision 1
categories science
platforms darwin
license GPL-2
Modified: trunk/dports/science/swarm/Portfile
===================================================================
--- trunk/dports/science/swarm/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/swarm/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -5,7 +5,7 @@
name swarm
version 2.4.1
-revision 7
+revision 8
categories science
maintainers nomaintainer
license GPL-2
Modified: trunk/dports/science/vapor/Portfile
===================================================================
--- trunk/dports/science/vapor/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/vapor/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -4,7 +4,7 @@
PortSystem 1.0
name vapor
version 2.2.4
-revision 1
+revision 2
categories science
maintainers nomaintainer
description interactive 3D scientific visualization environment
Modified: trunk/dports/science/wgrib2/Portfile
===================================================================
--- trunk/dports/science/wgrib2/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/wgrib2/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -5,7 +5,7 @@
name wgrib2
version 1.9.9
-revision 2
+revision 3
platforms darwin
maintainers takeshi
license public-domain
Modified: trunk/dports/science/yorick-hdf5/Portfile
===================================================================
--- trunk/dports/science/yorick-hdf5/Portfile 2014-05-30 14:11:06 UTC (rev 120496)
+++ trunk/dports/science/yorick-hdf5/Portfile 2014-05-30 14:18:34 UTC (rev 120497)
@@ -6,7 +6,7 @@
set uname hdf5
github.setup frigaut yorick-${uname} 0.8.0
-revision 3
+revision 4
license GPL-2+
categories science yorick
platforms darwin
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