- Update to 1.8.12 (from science/hdf5-18)

- Add LICENSE - Convert to new LIB_DEPENDS format - Convert to new options helper - Use NOT_FOR_ARCHS - Strip shared library - Remove deprecated PTHREAD_* - Use MAKE_CMD - Bump PORTREVISION for science/hdf5 shlib change [1] Changes: http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.12-RELEASE.txt http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html Approved by: portmgr (bapt) [1]
svn path=/head/; revision=352854
2014-05-03 00:55:30 +00:00 · 2014-05-03 00:55:30 +00:00 · 095fbe3e1a · 2021-03-31 03:12:20 +00:00
commit 095fbe3e1a
parent b7c8fa8138
34 changed files with 176 additions and 351 deletions
--- a/devel/py-tables/Makefile
+++ b/devel/py-tables/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	tables
 PORTVERSION=	3.0.0
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	devel python
 MASTER_SITES=	SF/py${PORTNAME:L}/py${PORTNAME}/${PORTVERSION}
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@ -16,9 +16,9 @@ COMMENT=	Hierarchical database for Python
 BUILD_DEPENDS=	${PYNUMPY} \
 		${LOCALBASE}/bin/cython:${PORTSDIR}/lang/cython \
 		${PYTHON_PKGNAMEPREFIX}numexpr>=1.4.1:${PORTSDIR}/math/py-numexpr
-LIB_DEPENDS=	hdf5:${PORTSDIR}/science/hdf5-18 \
-		lzo2:${PORTSDIR}/archivers/lzo2 \
-		ucl:${PORTSDIR}/archivers/ucl
+LIB_DEPENDS=	libhdf5.so:${PORTSDIR}/science/hdf5 \
+		liblzo2.so:${PORTSDIR}/archivers/lzo2 \
+		libucl.so:${PORTSDIR}/archivers/ucl
 RUN_DEPENDS:=	${BUILD_DEPENDS}

 USE_PYTHON=		yes
--- a/french/aster/Makefile
+++ b/french/aster/Makefile
@ -3,6 +3,7 @@

 PORTNAME=		aster
 DISTVERSION=		${ASTER_DISTVERSION}
+PORTREVISION=	1
 CATEGORIES=		french cad

 MAINTAINER=	thierry@FreeBSD.org
@ -35,7 +36,7 @@ BUILD_DEPENDS+=	${LOCALBASE}/aster/ASTK/ASTK_SERV:${PORTSDIR}/cad/astk-serveur	\
 		${SHELL_INSTALL_ASTER}:${PORTSDIR}/shells/${SHIADEP}		\
 		${LOCALBASE}/lib/libscotch.a:${PORTSDIR}/cad/scotch		\
 		${PYNUMPY}
-LIB_DEPENDS+=	libhdf5.so.7:${PORTSDIR}/science/hdf5-18			\
+LIB_DEPENDS+=	libhdf5.so:${PORTSDIR}/science/hdf5				\
 		libmed.so:${PORTSDIR}/french/med				\
 		libmetis.so.0:${PORTSDIR}/math/metis-edf
 RUN_DEPENDS+=	${PYTHON_SITELIBDIR}/Gnuplot:${PORTSDIR}/math/py-gnuplot	\
--- a/french/med/Makefile
+++ b/french/med/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	med
 DISTVERSION=	3.0.7
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	french science

 MAINTAINER=	thierry@FreeBSD.org
@ -11,7 +11,7 @@ COMMENT=	Modelisation et Echanges de Donnees

 LICENSE=	GPLv3

-LIB_DEPENDS=	libhdf5.so.7:${PORTSDIR}/science/hdf5-18
+LIB_DEPENDS=	libhdf5.so:${PORTSDIR}/science/hdf5

 WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}

--- a/graphics/gdal/Makefile
+++ b/graphics/gdal/Makefile
@ -3,6 +3,7 @@

 PORTNAME=	gdal
 PORTVERSION=	1.11.0
+PORTREVISION=	1
 CATEGORIES=	graphics geography
 MASTER_SITES=	http://download.osgeo.org/gdal/${PORTVERSION}/ \
 		ftp://ftp.remotesensing.org/pub/gdal/${PORTVERSION}/ \
@ -68,7 +69,7 @@ GTA_CONFIGURE_ON=	--with-gta=${LOCALBASE}
 GTA_LIB_DEPENDS=	libgta.so:${PORTSDIR}/devel/libgta
 HDF5_CONFIGURE_OFF=	--with-hdf5=no
 HDF5_CONFIGURE_ON=	--with-hdf5=${LOCALBASE}
-HDF5_LIB_DEPENDS=	libhdf5.so:${PORTSDIR}/science/hdf5-18
+HDF5_LIB_DEPENDS=	libhdf5.so:${PORTSDIR}/science/hdf5
 ICONV_CONFIGURE_OFF=	--with-libiconv-prefix=no
 ICONV_CONFIGURE_ON=	${ICONV_CONFIGURE_ARG}
 ICONV_LDFLAGS=		-L${ICONV_PREFIX}/lib ${ICONV_LIB}
--- a/graphics/openimageio/Makefile
+++ b/graphics/openimageio/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	openimageio
 PORTVERSION=	1.3.9
-PORTREVISION?=	1
+PORTREVISION?=	2
 CATEGORIES?=	graphics multimedia

 MAINTAINER?=	FreeBSD@Shaneware.biz
@ -39,7 +39,7 @@ OCIO_DESC=		Colour management support
 .if ${SLAVE_PORT} == no
 LIB_DEPENDS=	libIlmImf.so:${PORTSDIR}/graphics/OpenEXR \
 		libboost_thread.so:${PORTSDIR}/devel/boost-libs \
-		libhdf5.so:${PORTSDIR}/science/hdf5-18 \
+		libhdf5.so:${PORTSDIR}/science/hdf5 \
 		libopencv_legacy.so:${PORTSDIR}/graphics/opencv \
 		libopenjpeg.so:${PORTSDIR}/graphics/openjpeg \
 		libwebp.so:${PORTSDIR}/graphics/webp
--- a/graphics/vigra/Makefile
+++ b/graphics/vigra/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	vigra
 PORTVERSION=	1.9.0
-PORTREVISION=	5
+PORTREVISION=	6
 CATEGORIES=	graphics
 MASTER_SITES=	http://hci.iwr.uni-heidelberg.de/vigra/
 DISTNAME=	${PORTNAME}-${PORTVERSION}-src
@ -29,7 +29,7 @@ NUMPY_DESC=		NumPy mathematical computing (USE Fortran/GCC46+)

 .if ${PORT_OPTIONS:MHDF5}
 CMAKE_ARGS+=	-DWITH_HDF5=1
-LIB_DEPENDS+=	libhdf5.so.7:${PORTSDIR}/science/hdf5-18
+LIB_DEPENDS+=	libhdf5.so:${PORTSDIR}/science/hdf5
 .else
 CMAKE_ARGS+=	-DWITH_HDF5=0
 .endif
@ -50,7 +50,7 @@ USE_PYTHON=	2
 BUILD_DEPENDS+=	nosetests:${PORTSDIR}/devel/py-nose
 BUILD_DEPENDS+=	${PYTHON_SITELIBDIR}/numpy/core/numeric.py:${PORTSDIR}/math/py-numpy
 #BUILD_DEPENDS+=	sphinx-build:${PORTSDIR}/textproc/py-sphinx
-LIB_DEPENDS=	libboost_python.so:${PORTSDIR}/devel/boost-python-libs
+LIB_DEPENDS+=	libboost_python.so:${PORTSDIR}/devel/boost-python-libs
 RUN_DEPENDS:=	${BUILD_DEPENDS}
 PLIST_SUB+=	PYTHON=""
 .else
--- a/math/labplot/Makefile
+++ b/math/labplot/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	labplot
 DISTVERSION=	2.0.0.beta2
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	math kde
 MASTER_SITES=	SF/${PORTNAME}/${PORTNAME}/${PORTVERSION:R}

--- a/math/matio/Makefile
+++ b/math/matio/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	matio
 PORTVERSION=	1.5.2
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 MASTER_SITES=	SF

@ -21,7 +21,7 @@ OPTIONS_DEFINE=	HDF5
 OPTIONS_DEFAULT=	HDF5

 HDF5_DESC=	Support for MAT file version 7.3
-HDF5_LIB_DEPENDS=	libhdf5.so:${PORTSDIR}/science/hdf5-18
+HDF5_LIB_DEPENDS=	libhdf5.so:${PORTSDIR}/science/hdf5
 HDF5_CONFIGURE_ON=	--enable-mat73=yes \
 			--with-hdf5=${LOCALBASE}

--- a/math/octave/Makefile
+++ b/math/octave/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	octave
 PORTVERSION=	3.8.0
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	math
 MASTER_SITES=	${MASTER_SITE_GNU}
 MASTER_SITE_SUBDIR=	octave
@ -27,7 +27,7 @@ LIB_DEPENDS=	GraphicsMagick.14:${PORTSDIR}/graphics/GraphicsMagick13 \
 		fftw3f:${PORTSDIR}/math/fftw3-float \
 		fltk.1:${PORTSDIR}/x11-toolkits/fltk \
 		ftgl:${PORTSDIR}/graphics/ftgl \
-		hdf5:${PORTSDIR}/science/hdf5-18 \
+		libhdf5.so:${PORTSDIR}/science/hdf5 \
 		pcre.3:${PORTSDIR}/devel/pcre \
 		qhull.5:${PORTSDIR}/math/qhull5 \
 		qrupdate:${PORTSDIR}/math/qrupdate \
--- a/science/cgnslib/Makefile
+++ b/science/cgnslib/Makefile
@ -3,6 +3,7 @@

 PORTNAME=	cgnslib
 DISTVERSION=	3.2.1
+PORTREVISION=	1
 PORTEPOCH=	1
 CATEGORIES=	science
 MASTER_SITES=	SF/cgns/${PORTNAME}_${PORTVERSION:R}/
@ -31,7 +32,7 @@ OPTIONS_DEFAULT=HDF5 TESTS TOOLS
 .include <bsd.port.options.mk>

 .if ${PORT_OPTIONS:MHDF5}
-LIB_DEPENDS+=	libhdf5.so.7:${PORTSDIR}/science/hdf5-18
+LIB_DEPENDS+=	libhdf5.so:${PORTSDIR}/science/hdf5
 CMAKE_ARGS+=	-DCGNS_ENABLE_HDF5:BOOL=TRUE -DHDF5_NEED_ZLIB:BOOL=TRUE	\
 		-DHDF5_INCLUDE_PATH:PATH="${LOCALBASE}/include"
 PLIST_SUB=	HDF5=""
--- a/science/ecs/Makefile
+++ b/science/ecs/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	ecs
 PORTVERSION=	2.0.2
-PORTREVISION=	5
+PORTREVISION=	6
 CATEGORIES=	science
 MASTER_SITES=	http://research.edf.com/fichiers/fckeditor/Commun/Innovation/logiciels/code_saturne/Releases/
 DISTNAME=	${PORTNAME}-${PORTVERSION:S/.//g}
@ -15,7 +15,7 @@ LICENSE=	GPLv2

 LIB_DEPENDS=	libmed.so:${PORTSDIR}/french/med	\
 		libbft.so:${PORTSDIR}/science/bft	\
-		libhdf5.so.7:${PORTSDIR}/science/hdf5-18\
+		libhdf5.so:${PORTSDIR}/science/hdf5	\
 		libcgns.so:${PORTSDIR}/science/cgnslib

 WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
--- a/science/fvm/Makefile
+++ b/science/fvm/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	fvm
 PORTVERSION=	0.15.3
-PORTREVISION=	5
+PORTREVISION=	6
 CATEGORIES=	science parallel
 MASTER_SITES=	http://research.edf.com/fichiers/fckeditor/Commun/Innovation/logiciels/code_saturne/Releases/
 DISTNAME=	${PORTNAME}-${PORTVERSION:S/.//g}
@ -15,7 +15,7 @@ LICENSE=	LGPL21

 LIB_DEPENDS=	libmed.so:${PORTSDIR}/french/med	\
 		libbft.so:${PORTSDIR}/science/bft	\
-		libhdf5.so.7:${PORTSDIR}/science/hdf5-18\
+		libhdf5.so:${PORTSDIR}/science/hdf5	\
 		libcgns.so:${PORTSDIR}/science/cgnslib

 WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
--- a/science/gnudatalanguage/Makefile
+++ b/science/gnudatalanguage/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	gnudatalanguage
 DISTVERSION=	0.9.4
-PORTREVISION=	3
+PORTREVISION=	4
 CATEGORIES=	science lang
 MASTER_SITES=	SF/${PORTNAME}/gdl/${DISTVERSION}
 .if defined(BUILD_PYTHON_MODULE)
@ -16,8 +16,6 @@ COMMENT?=	GDL, a free IDL compatible incremental compiler

 LICENSE=	GPLv2

-#NO_STAGE=	yes
-
 #---------------------------------------------------------------------------
 # You may define these options:
 #
@ -72,7 +70,7 @@ CMAKE_ARGS+=	-DGRAPHICSMAGICK:BOOL=NO
 .endif

 .if !defined(WITHOUT_HDF5)
-LIB_DEPENDS+=	libhdf5.so.7:${PORTSDIR}/science/hdf5-18
+LIB_DEPENDS+=	libhdf5.so:${PORTSDIR}/science/hdf5
 CMAKE_ARGS+=	-DHDF5:BOOL=YES
 .else
 CMAKE_ARGS+=	-DHDF5:BOOL=NO
--- a/science/h5utils/Makefile
+++ b/science/h5utils/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	h5utils
 PORTVERSION=	1.12.1
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	science
 MASTER_SITES=	http://ab-initio.mit.edu/${PORTNAME}/

@ -21,9 +21,9 @@ CFLAGS +=	-L${LOCALBASE}/lib -I${LOCALBASE}/include \
 		-I${LOCALBASE}/include/libpng15 ${PTHREAD_LIBS}

 BUILD_DEPENDS+=	gawk:${PORTSDIR}/lang/gawk
-LIB_DEPENDS +=	hdf5:${PORTSDIR}/science/hdf5 \
-		png15:${PORTSDIR}/graphics/png \
-		matheval.1:${PORTSDIR}/devel/libmatheval
+LIB_DEPENDS+=	libhdf5.so:${PORTSDIR}/science/hdf5 \
+		libpng15.so:${PORTSDIR}/graphics/png \
+		libmatheval.so:${PORTSDIR}/devel/libmatheval

 NO_STAGE=	yes
 .include <bsd.port.mk>
--- a/science/hdf-java/Makefile
+++ b/science/hdf-java/Makefile
@ -3,6 +3,7 @@

 PORTNAME=	hdf-java
 PORTVERSION=	2.10
+PORTREVISION=	1
 CATEGORIES=	science java
 MASTER_SITES=	http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdf-java-${PORTVERSION}/src/
 DISTNAME=	${PORTNAME}-${PORTVERSION}-source
@ -10,7 +11,7 @@ DISTNAME=	${PORTNAME}-${PORTVERSION}-source
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Java interface to HDF5

-LIB_DEPENDS=	libhdf5.so:${PORTSDIR}/science/hdf5-18 \
+LIB_DEPENDS=	libhdf5.so:${PORTSDIR}/science/hdf5 \
 		libjpeg.so:${PORTSDIR}/graphics/jpeg

 USE_JAVA=	yes
@ -33,7 +34,7 @@ CONFIGURE_ARGS=	--with-jdk=${JAVA_HOME}/include,${JAVA_HOME}/jre/lib/ \
 USE_LDCONFIG=	yes

 OPTIONS_DEFINE=	SZIP DOCS
-SZIP_DESC=	SZIP support (must match with science/hdf5-18)
+SZIP_DESC=	SZIP support (must match with science/hdf5)

 .include <bsd.port.options.mk>

--- a/science/hdf5/Makefile
+++ b/science/hdf5/Makefile
@ -2,74 +2,61 @@
 # $FreeBSD$

 PORTNAME=	hdf5
-PORTVERSION=	1.6.9
-PORTREVISION=	2
+PORTVERSION=	1.8.12
 CATEGORIES=	science archivers graphics
-MASTER_SITES=	ftp://ftp.hdfgroup.org/HDF5/current16/src/ \
-		ftp://ftp.hdfgroup.org/HDF5/prev-releases/ \
-		ftp://ftp.hdfgroup.org/HDF5/prev-releases/hdf5-${PORTVERSION}/src/ \
-		LOCAL/chinsan
+MASTER_SITES=	http://www.hdfgroup.org/ftp/HDF5/current/src/ \
+		ftp://ftp.hdfgroup.org/HDF5/current/src/ \
+		http://www.hdfgroup.org/ftp/HDF5/releases/${DISTNAME}/src/ \
+		ftp://ftp.hdfgroup.org/HDF5/releases/${DISTNAME}/src/
+#DISTNAME=	${PORTNAME}-${PORTVERSION}-patch1

 MAINTAINER=	sunpoet@FreeBSD.org
 COMMENT=	Hierarchical Data Format library (from NCSA)

-CONFLICTS=	hdf5-1.8.*
+LICENSE=	BSD4CLAUSE

-USE_LDCONFIG=	yes
-USE_AUTOTOOLS=	libtool
-GNU_CONFIGURE=	yes
-LIBTOOLFILES=	configure c++/configure
-CONFIGURE_ARGS=	--disable-debug \
-		--enable-cxx \
+CONFLICTS_INSTALL=	hdf-4.[0-9]* hdf5-1.6.[0-9]*
+
+OPTIONS_DEFINE=	DEBUG EXAMPLES FORTRAN SZIP
+OPTIONS_SUB=	yes
+
+CFLAGS+=	-D__BSD_VISIBLE
+CONFIGURE_ARGS=	--enable-cxx \
+		--enable-hl \
 		--enable-instrument \
-		--enable-production \
 		--enable-strict-format-checks \
-		--enable-threadsafe \
 		--with-pthread=/usr \
-		--with-ssl=/usr \
 		--with-zlib=/usr
-ALL_TARGET=	lib progs
-MAKE_JOBS_UNSAFE=	yes
+GNU_CONFIGURE=	yes
+MAKE_ENV=	INSTALL_STRIP_FLAG=${STRIP}
+USE_LDCONFIG=	yes
+USES=		libtool tar:bzip2

-.include <bsd.port.pre.mk>
+PORTEXAMPLES=	*

-.if defined(WITH_FORTRAN)
-LIBTOOLFILES+=		fortran/configure
-USES+=			fortran
-CONFIGURE_ENV+=		F9X=${FC}
-CONFIGURE_ARGS+=	--enable-fortran
-PLIST_SUB+=		FORTRAN=""
-.else
-PLIST_SUB+=		FORTRAN="@comment "
-.endif
+NOT_FOR_ARCHS=	sparc64
+NOT_FOR_ARCHS_REASON=	does not compile

-.if ${ARCH} == "sparc64"
-BROKEN=		Does not compile on ${ARCH}
-.endif
+DEBUG_CONFIGURE_OFF=	--enable-production
+DEBUG_CONFIGURE_ON=	--disable-production --enable-debug=all
+FORTRAN_CONFIGURE_ENV=	F9X=${FC}
+FORTRAN_CONFIGURE_OFF=	--disable-fortran --disable-fortran2003
+FORTRAN_CONFIGURE_ON=	--enable-fortran --enable-fortran2003
+FORTRAN_USES=		fortran
+SZIP_CONFIGURE_ARGS=	--with-szlib=${LOCALBASE}
+SZIP_LIB_DEPENDS=	libsz.so:${PORTSDIR}/science/szip

 post-patch:
-	@${REINPLACE_CMD} -e 's|-lpthread|${PTHREAD_LIBS}|g' ${WRKSRC}/configure
-	@${REINPLACE_CMD} -e 's|-D_THREAD_SAFE|${PTHREAD_CFLAGS}|g' \
-		-e 's|[\$$]LDFLAGS -pthread|\$$LDFLAGS ${PTHREAD_LIBS}|g'  \
-			${WRKSRC}/config/freebsd ${WRKSRC}/c++/config/freebsd
+	@${REINPLACE_CMD} -e 's|-lpthread|-pthread|g' ${WRKSRC}/configure
 	@${REINPLACE_CMD} -e 's|-O3||g' ${WRKSRC}/config/gnu-flags
-	@${REINPLACE_CMD} -e 's|objformat=|#objformat=|g' \
-		-e 's|\(version_type=freebsd\)-.*|\1-elf|g' \
-			${WRKSRC}/aclocal.m4 ${WRKSRC}/configure
-.if defined(NOPORTEXAMPLES)
-.for i in . c++ hl fortran
 	@${REINPLACE_CMD} \
-		-e 's,\((cd examples && $$(MAKE) $$@) || exit 1;\),#\1,g' \
-			${WRKSRC}/${i}/Makefile.in
-.endfor
-.endif
+		-e '/LD_LIBRARY_PATH/ s|^|#|' \
+		-e 's|/share/hdf5_examples|/${EXAMPLESDIR_REL}|' \
+		-e 's|(INSTALL)|(INSTALL_DATA)|' \
+			`${FIND} ${WRKSRC} -regex '.*/examples/Makefile.in'`
+	@${REINPLACE_CMD} -e 's|\[ -a|\[ -f|g' `${FIND} ${WRKSRC} -name \*.sh\*`

-post-install:
-.for i in gif2h5 h52gif h5debug h5diff h5dump h5import h5jam h5ls h5repack h5repart h5unjam
-	@${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/${i}
-.endfor
+regression-test test: build
+	cd ${WRKSRC}/ && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} check

-regression-test: build
-	@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE} check
-
-.include <bsd.port.post.mk>
+.include <bsd.port.mk>
--- a/science/hdf5/distinfo
+++ b/science/hdf5/distinfo
@ -1,2 +1,2 @@
-SHA256 (hdf5-1.6.9.tar.gz) = 15ff93cbbf40c2c9a84638e53f8b0dfe7e92b142b337702a300c7db106fce89b
-SIZE (hdf5-1.6.9.tar.gz) = 5451465
+SHA256 (hdf5-1.8.12.tar.bz2) = 6d080f913a226a3ce390a11d9b571b2d5866581a2aa4434c398cd371c7063639
+SIZE (hdf5-1.8.12.tar.bz2) = 5994832
--- a/science/hdf5/files/patch-Makefile.in
+++ b/science/hdf5/files/patch-Makefile.in
@ -1,11 +0,0 @@
--- Makefile.in.orig	2009-05-01 02:23:03.000000000 +0000
-+++ Makefile.in
-@@ -93,7 +93,7 @@ uninstall-all:
- 	@$(MAKE) uninstall-doc
- 
- install:
-	@@SETX@; for d in $(SUBDIRS) perform; do			      \
-+	@@SETX@; for d in $(SUBDIRS); do			      \
- 	   (cd $$d && $(MAKE) $@) || exit 1;				      \
- 	done
- 	@$(MAKE) install-examples
--- a/science/hdf5/files/patch-c++::commence.in
+++ b/science/hdf5/files/patch-c++::commence.in
@ -1,31 +0,0 @@
--- c++/config/commence.in.orig	Mon Jun 30 16:19:35 2003
-+++ c++/config/commence.in	Mon Oct 20 23:44:08 2003
-@@ -27,7 +27,7 @@
- RM=rm -f
- CP=cp
- INSTALL=@INSTALL@
-INSTALL_PROGRAM=@INSTALL_PROGRAM@
-+INSTALL_PROGRAM=@INSTALL_SCRIPT@
- INSTALL_DATA=@INSTALL_DATA@
- TRACE=:
- 
-@@ -37,7 +37,7 @@
- bindir=@bindir@
- libdir=@libdir@
- includedir=@includedir@
-docdir=@exec_prefix@/doc
-+docdir=@exec_prefix@/share
- PUB_LIB=$(LIB)
- 
- ## Obtain default library; the current version of libtool does not fully
-@@ -60,8 +60,8 @@
- ## Optional variables. We must declare them here because Irix pmake
- ## complains if it sees a reference to a variable which has never been
- ## defined. The main makefile is free to redefine these to something else.
-DOCDIR=$(docdir)
-EXAMPLEDIR=$(docdir)/hdf5/examples/c++
-+DOCDIR=$(docdir)/doc/hdf5
-+EXAMPLEDIR=$(docdir)/examples/hdf5/c++
- LIB=
- LIB_SRC=
- LIB_OBJ=
--- a/science/hdf5/files/patch-commence.in
+++ b/science/hdf5/files/patch-commence.in
@ -1,32 +0,0 @@
--- config/commence.in.orig	Tue Jul 22 23:39:43 2003
-+++ config/commence.in	Mon Oct 20 23:45:00 2003
-@@ -26,7 +26,7 @@
- RM=rm -f
- CP=cp
- INSTALL=@INSTALL@
-INSTALL_PROGRAM=@INSTALL_PROGRAM@
-+INSTALL_PROGRAM=@INSTALL_SCRIPT@
- INSTALL_DATA=@INSTALL_DATA@
- RUNSERIAL=@RUNSERIAL@
- RUNPARALLEL=@RUNPARALLEL@
-@@ -39,7 +39,7 @@
- bindir=@bindir@
- libdir=@libdir@
- includedir=@includedir@
-docdir=@exec_prefix@/doc
-+docdir=@exec_prefix@/share
- PUB_LIB=$(LIB)
- 
- ## Shared libraries
-@@ -57,9 +57,9 @@
- ## Optional variables. We must declare them here because Irix pmake
- ## complains if it sees a reference to a variable which has never been
- ## defined. The main makefile is free to redefine these to something else.
-DOCDIR=$(docdir)
-+DOCDIR=$(docdir)/doc/hdf5
- SUBDOCDIR=
-EXAMPLEDIR=$(docdir)/hdf5/examples/c
-+EXAMPLEDIR=$(docdir)/examples/hdf5/c
- LIB=
- LIB_SRC=
- LIB_OBJ=
--- a/science/hdf5/files/patch-fortran_H5f90i.h
+++ b/science/hdf5/files/patch-fortran_H5f90i.h
@ -1,11 +0,0 @@
--- fortran/src/H5f90i.h.orig	Thu Jul 12 21:26:46 2007
-+++ fortran/src/H5f90i.h	Thu Jul 12 21:27:18 2007
-@@ -71,7 +71,7 @@
- #endif /*APPLE*/
- 
- /* LINUX definitions */
-#if (defined(linux) || defined(__gnu_linux__) || defined(__linux__))
-+#if (defined(linux) || defined(__gnu_linux__) || defined(__linux__) || defined(__FreeBSD__))
- 
- /* Common definitions */
- typedef char              *_fcd;
--- a/science/hdf5/files/patch-fortran_commence.in
+++ b/science/hdf5/files/patch-fortran_commence.in
@ -1,31 +0,0 @@
--- fortran/config/commence.in.orig	Thu Jul 12 21:28:40 2007
-+++ fortran/config/commence.in	Thu Jul 12 21:33:56 2007
-@@ -47,7 +47,7 @@
- RM=rm -f
- CP=cp
- INSTALL=@INSTALL@
-INSTALL_PROGRAM=@INSTALL_PROGRAM@
-+INSTALL_PROGRAM=@INSTALL_SCRIPT@
- INSTALL_DATA=@INSTALL_DATA@
- PARALLEL=@PARALLEL@
- RUNSERIAL=@RUNSERIAL@
-@@ -62,7 +62,7 @@
- bindir=@bindir@
- libdir=@libdir@
- includedir=@includedir@
-docdir=@exec_prefix@/doc
-+docdir=@exec_prefix@/share
- PUB_LIB=$(LIB)
- 
- ## Shared libraries
-@@ -85,8 +85,8 @@
- ## Optional variables. We must declare them here because Irix pmake
- ## complains if it sees a reference to a variable which has never been
- ## defined. The main makefile is free to redefine these to something else.
-DOCDIR=$(docdir)
-EXAMPLEDIR=$(docdir)/hdf5/examples/fortran
-+DOCDIR=$(docdir)/doc/hdf5
-+EXAMPLEDIR=$(docdir)/examples/hdf5/fortran
- LIB=
- LIB_SRC=
- LIB_OBJ=
--- a/science/hdf5/files/patch-fortran_configure
+++ b/science/hdf5/files/patch-fortran_configure
@ -1,10 +0,0 @@
--- fortran/configure.orig	Thu Jul 12 21:36:24 2007
-+++ fortran/configure	Thu Jul 12 21:36:49 2007
-@@ -7602,6 +7602,7 @@
- 
- # This can be used to rebuild libtool when needed
- LIBTOOL_DEPS="$ac_aux_dir/ltmain.sh"
-+$ac_aux_dir/ltconfig $LIBTOOL_DEPS
- 
- # Always use our own libtool.
- LIBTOOL='$(SHELL) $(top_builddir)/libtool'
--- a/science/hdf5/files/patch-fortran_freebsd
+++ b/science/hdf5/files/patch-fortran_freebsd
@ -1,23 +0,0 @@
--- fortran/config/freebsd.orig	Thu Jul 12 21:23:06 2007
-+++ fortran/config/freebsd	Thu Jul 12 21:25:09 2007
-@@ -27,3 +27,20 @@
- 
- # Figure out compiler flags
- . $srcdir/config/gnu-flags
-+
-+#
-+# HDF5 integers
-+#
-+# 	R_LARGE is the number of digits for the bigest integer supported.
-+#	R_INTEGER is the number of digits in INTEGER
-+#
-+# (for the Linux architechture)
-+#
-+R_LARGE=18
-+R_INTEGER=9
-+HADDR_T='SELECTED_INT_KIND(R_LARGE)'
-+HSIZE_T='SELECTED_INT_KIND(R_LARGE)'
-+HSSIZE_T='SELECTED_INT_KIND(R_LARGE)'
-+HID_T='SELECTED_INT_KIND(R_INTEGER)'
-+SIZE_T='SELECTED_INT_KIND(R_INTEGER)'
-+OBJECT_NAMELEN_DEFAULT_F=-1
--- a/science/hdf5/pkg-descr
+++ b/science/hdf5/pkg-descr
@ -1,17 +1,16 @@
-HDF5 is a completely new Hierarchical Data Format product consisting of a
-data format specification and a supporting library implementation. HDF5 is
-designed to address some of the limitations of the older HDF product and to
-address current and anticipated requirements of modern systems and
-applications.
+HDF5 is a completely new Hierarchical Data Format product consisting of a data
+format specification and a supporting library implementation. HDF5 is designed
+to address some of the limitations of the older HDF product and to address
+current and anticipated requirements of modern systems and applications.

-HDF5 includes the following improvements.
-   - A new file format designed to address some of the deficiencies of HDF4.x,
-     particularly the need to store larger files and more objects per file.
-   - A simpler, more comprehensive data model that includes only two basic
-     structures: a multidimensional array of record structures, and a grouping
-     structure.
-   - A simpler, better-engineered library and API, with improved support for
-     parallel I/O, threads, and other requirements imposed by modern systems
-     and applications.
+HDF5 includes the following improvements:
+- A new file format designed to address some of the deficiencies of HDF4.x,
+  particularly the need to store larger files and more objects per file.
+- A simpler, more comprehensive data model that includes only two basic
+  structures: a multidimensional array of record structures, and a grouping
+  structure.
+- A simpler, better-engineered library and API, with improved support for
+  parallel I/O, threads, and other requirements imposed by modern systems
+  and applications.

-WWW: http://hdf.ncsa.uiuc.edu/HDF5/
+WWW: http://www.hdfgroup.org/HDF5/
--- a/science/hdf5/pkg-plist
+++ b/science/hdf5/pkg-plist
@ -2,6 +2,7 @@ bin/gif2h5
 bin/h52gif
 bin/h5c++
 bin/h5cc
+bin/h5copy
 bin/h5debug
 bin/h5diff
 bin/h5dump
@ -9,9 +10,12 @@ bin/h5dump
 bin/h5import
 bin/h5jam
 bin/h5ls
+bin/h5mkgrp
+bin/h5perf_serial
 bin/h5redeploy
 bin/h5repack
 bin/h5repart
+bin/h5stat
 bin/h5unjam
 include/H5ACpublic.h
 include/H5AbstractDs.h
@ -19,13 +23,14 @@ include/H5Apublic.h
 include/H5ArrayType.h
 include/H5AtomType.h
 include/H5Attribute.h
-include/H5Bpublic.h
 include/H5Classes.h
 include/H5CommonFG.h
 include/H5CompType.h
 include/H5Cpp.h
 include/H5CppDoc.h
 include/H5Cpublic.h
+include/H5DOpublic.h
+include/H5DSpublic.h
 include/H5DataSet.h
 include/H5DataSpace.h
 include/H5DataType.h
@ -33,9 +38,11 @@ include/H5DcreatProp.h
 include/H5Dpublic.h
 include/H5DxferProp.h
 include/H5EnumType.h
+include/H5Epubgen.h
 include/H5Epublic.h
 include/H5Exception.h
 include/H5FDcore.h
+include/H5FDdirect.h
 include/H5FDfamily.h
 include/H5FDlog.h
 include/H5FDmpi.h
@ -52,115 +59,94 @@ include/H5FloatType.h
 include/H5Fpublic.h
 include/H5Gpublic.h
 include/H5Group.h
-include/H5HGpublic.h
-include/H5HLpublic.h
-include/H5IM.h
+include/H5IMpublic.h
 include/H5IdComponent.h
 include/H5Include.h
 include/H5IntType.h
 include/H5Ipublic.h
-include/H5LT.h
+include/H5LTpublic.h
 include/H5Library.h
+include/H5Location.h
+include/H5Lpublic.h
 include/H5MMpublic.h
 include/H5Object.h
 include/H5Opublic.h
+include/H5PLextern.h
+include/H5PTpublic.h
+include/H5PacketTable.h
 include/H5Ppublic.h
 include/H5PredType.h
 include/H5PropList.h
 include/H5Rpublic.h
 include/H5Spublic.h
 include/H5StrType.h
-include/H5TA.h
+include/H5TBpublic.h
 include/H5Tpublic.h
 include/H5VarLenType.h
 include/H5Zpublic.h
 include/H5api_adpt.h
-include/H5cxx_pubconf.h
+%%FORTRAN%%include/H5f90i.h
+%%FORTRAN%%include/H5f90i_gen.h
+include/H5overflow.h
 include/H5pubconf.h
-%%FORTRAN%%include/H5pubconf_fortran.h
 include/H5public.h
+include/H5version.h
+%%FORTRAN%%include/h5_dble_interface.mod
+%%FORTRAN%%include/h5a.mod
+%%FORTRAN%%include/h5a_provisional.mod
+%%FORTRAN%%include/h5d.mod
+%%FORTRAN%%include/h5d_provisional.mod
+%%FORTRAN%%include/h5ds.mod
+%%FORTRAN%%include/h5e.mod
+%%FORTRAN%%include/h5e_provisional.mod
+%%FORTRAN%%include/h5f.mod
+%%FORTRAN%%include/h5f_provisional.mod
+%%FORTRAN%%include/h5fortran_types.mod
+%%FORTRAN%%include/h5g.mod
+%%FORTRAN%%include/h5global.mod
+%%FORTRAN%%include/h5i.mod
+%%FORTRAN%%include/h5im.mod
+%%FORTRAN%%include/h5l.mod
+%%FORTRAN%%include/h5l_provisional.mod
+%%FORTRAN%%include/h5lib.mod
+%%FORTRAN%%include/h5lib_provisional.mod
+%%FORTRAN%%include/h5lt.mod
+%%FORTRAN%%include/h5o.mod
+%%FORTRAN%%include/h5o_provisional.mod
+%%FORTRAN%%include/h5p.mod
+%%FORTRAN%%include/h5p_provisional.mod
+%%FORTRAN%%include/h5r.mod
+%%FORTRAN%%include/h5r_provisional.mod
+%%FORTRAN%%include/h5s.mod
+%%FORTRAN%%include/h5t.mod
+%%FORTRAN%%include/h5t_provisional.mod
+%%FORTRAN%%include/h5tb.mod
+%%FORTRAN%%include/h5z.mod
 include/hdf5.h
-%%FORTRAN%%lib/h5a.mod
-%%FORTRAN%%lib/h5d.mod
-%%FORTRAN%%lib/h5e.mod
-%%FORTRAN%%lib/h5f.mod
-%%FORTRAN%%lib/h5fortran_flags.mod
-%%FORTRAN%%lib/h5fortran_types.mod
-%%FORTRAN%%lib/h5g.mod
-%%FORTRAN%%lib/h5global.mod
-%%FORTRAN%%lib/h5i.mod
-%%FORTRAN%%lib/h5lib.mod
-%%FORTRAN%%lib/h5p.mod
-%%FORTRAN%%lib/h5r.mod
-%%FORTRAN%%lib/h5s.mod
-%%FORTRAN%%lib/h5t.mod
-%%FORTRAN%%lib/h5z.mod
-%%FORTRAN%%lib/hdf5.mod
+%%FORTRAN%%include/hdf5.mod
+include/hdf5_hl.h
 lib/libhdf5.a
-lib/libhdf5.la
 lib/libhdf5.settings
 lib/libhdf5.so
-lib/libhdf5.so.0
+lib/libhdf5.so.8
+lib/libhdf5.so.8.0.1
 lib/libhdf5_cpp.a
-lib/libhdf5_cpp.la
+lib/libhdf5_cpp.so
+lib/libhdf5_cpp.so.8
+lib/libhdf5_cpp.so.8.0.1
 %%FORTRAN%%lib/libhdf5_fortran.a
-%%FORTRAN%%lib/libhdf5_fortran.la
-%%FORTRAN%%lib/libhdf5_fortran.settings
+%%FORTRAN%%lib/libhdf5_fortran.so
+%%FORTRAN%%lib/libhdf5_fortran.so.8
+%%FORTRAN%%lib/libhdf5_fortran.so.8.0.1
 lib/libhdf5_hl.a
-lib/libhdf5_hl.la
 lib/libhdf5_hl.so
-lib/libhdf5_hl.so.0
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/chunks.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/compound.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/create.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/extend_ds.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/h5group.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/readdata.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/strtype.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/writedata.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/ex_image1.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/ex_image2.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/ex_lite1.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/ex_lite2.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/ex_lite3.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/ex_table_01.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/ex_table_02.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/ex_table_03.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/ex_table_04.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/ex_table_05.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/ex_table_06.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/ex_table_07.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/ex_table_08.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/ex_table_09.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/ex_table_10.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/ex_table_11.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/ex_table_12.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/h5_attribute.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/h5_chunk_read.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/h5_compound.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/h5_drivers.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/h5_extend_write.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/h5_group.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/h5_mount.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/h5_read.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/h5_reference.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/h5_select.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/h5_write.c
-%%FORTRAN%%%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fortran/attrexample.f90
-%%FORTRAN%%%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fortran/compound.f90
-%%FORTRAN%%%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fortran/dsetexample.f90
-%%FORTRAN%%%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fortran/fileexample.f90
-%%FORTRAN%%%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fortran/groupexample.f90
-%%FORTRAN%%%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fortran/grpdsetexample.f90
-%%FORTRAN%%%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fortran/grpit.f90
-%%FORTRAN%%%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fortran/grpsexample.f90
-%%FORTRAN%%%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fortran/hyperslab.f90
-%%FORTRAN%%%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fortran/mountexample.f90
-%%FORTRAN%%%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fortran/refobjexample.f90
-%%FORTRAN%%%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fortran/refregexample.f90
-%%FORTRAN%%%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fortran/rwdsetexample.f90
-%%FORTRAN%%%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fortran/selectele.f90
-%%FORTRAN%%%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/fortran
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c++
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
+lib/libhdf5_hl.so.8
+lib/libhdf5_hl.so.8.0.1
+lib/libhdf5_hl_cpp.a
+lib/libhdf5_hl_cpp.so
+lib/libhdf5_hl_cpp.so.8
+lib/libhdf5_hl_cpp.so.8.0.1
+%%FORTRAN%%lib/libhdf5hl_fortran.a
+%%FORTRAN%%lib/libhdf5hl_fortran.so
+%%FORTRAN%%lib/libhdf5hl_fortran.so.8
+%%FORTRAN%%lib/libhdf5hl_fortran.so.8.0.1
--- a/science/meep/Makefile
+++ b/science/meep/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	meep
 PORTVERSION=	1.2
-PORTREVISION=	3
+PORTREVISION=	4
 CATEGORIES=	science
 MASTER_SITES=	http://ab-initio.mit.edu/meep/

@ -16,7 +16,7 @@ BUILD_DEPENDS+=	bash:${PORTSDIR}/shells/bash \
 LIB_DEPENDS+=	libguile.so:${PORTSDIR}/lang/guile \
 		libblas.so:${PORTSDIR}/math/blas \
 		libctl.so:${PORTSDIR}/science/libctl \
-		libhdf5.so:${PORTSDIR}/science/hdf5-18
+		libhdf5.so:${PORTSDIR}/science/hdf5
 RUN_DEPENDS+=	harminv:${PORTSDIR}/science/harminv

 GNU_CONFIGURE=	yes
--- a/science/minc2/Makefile
+++ b/science/minc2/Makefile
@ -12,6 +12,7 @@

 PORTNAME=	minc
 PORTVERSION=	2.0.18
+PORTREVISION=	1
 PORTEPOCH=	1
 CATEGORIES=	science biology
 MASTER_SITES=	http://packages.bic.mni.mcgill.ca/tgz/ \
@ -24,7 +25,7 @@ COMMENT=	Medical Imaging NetCDF
 LICENSE=	BSD

 LIB_DEPENDS=	libnetcdf.so.4:${PORTSDIR}/science/netcdf \
-		libhdf5.so.0:${PORTSDIR}/science/hdf5
+		libhdf5.so:${PORTSDIR}/science/hdf5

 USE_AUTOTOOLS=	libtool
 USE_LDCONFIG=	yes
--- a/science/mpb/Makefile
+++ b/science/mpb/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	mpb
 PORTVERSION=	1.4.2
-PORTREVISION=	14
+PORTREVISION=	15
 CATEGORIES=	science
 MASTER_SITES=	http://ab-initio.mit.edu/mpb/

--- a/science/paraview/Makefile
+++ b/science/paraview/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	paraview
 PORTVERSION=	4.1.0
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	science graphics
 MASTER_SITES=	http://www.paraview.org/files/v${VERMAJORMINOR}/
 DISTNAME=	ParaView-v${PORTVERSION}-source
@ -17,7 +17,7 @@ LICENSE_FILE=	${PATCH_WRKSRC}/License_v1.2.txt
 LICENSE_PERMS=	dist-mirror dist-sell pkg-mirror pkg-sell auto-accept

 BUILD_DEPENDS=	${PYTHON_SITELIBDIR}/matplotlib/pyplot.py:${PORTSDIR}/math/py-matplotlib
-LIB_DEPENDS=	libhdf5.so.7:${PORTSDIR}/science/hdf5-18 \
+LIB_DEPENDS=	libhdf5.so:${PORTSDIR}/science/hdf5 \
 		libpng.so:${PORTSDIR}/graphics/png \
 		libjpeg.so:${PORTSDIR}/graphics/jpeg \
 		libtiff.so:${PORTSDIR}/graphics/tiff \
--- a/science/py-h5py/Makefile
+++ b/science/py-h5py/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	h5py
 PORTVERSION=	2.2.1
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	science python
 MASTER_SITES=	${MASTER_SITE_GOOGLE_CODE}
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@ -15,7 +15,7 @@ LICENSE=	BSD

 BUILD_DEPENDS=	${PYNUMPY}
 RUN_DEPENDS=	${PYNUMPY}
-LIB_DEPENDS=	libhdf5.so:${PORTSDIR}/science/hdf5-18
+LIB_DEPENDS=	libhdf5.so:${PORTSDIR}/science/hdf5

 USE_PYTHON=		yes
 USE_PYDISTUTILS=	yes
--- a/science/py-netCDF4/Makefile
+++ b/science/py-netCDF4/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	netCDF4
 PORTVERSION=	1.0.5
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	science python
 MASTER_SITES=	GOOGLE_CODE
 PROJECTHOST=	netcdf4-python
@ -15,7 +15,7 @@ COMMENT=	Python Interface to the NetCDF Library (versions 3 and 4)
 LICENSE=	MIT

 BUILD_DEPENDS=	${PYNUMPY}
-LIB_DEPENDS=	libhdf5.so:${PORTSDIR}/science/hdf5-18 \
+LIB_DEPENDS=	libhdf5.so:${PORTSDIR}/science/hdf5 \
 		libnetcdf.so:${PORTSDIR}/science/netcdf4
 RUN_DEPENDS=	${PYNUMPY}

--- a/science/silo/Makefile
+++ b/science/silo/Makefile
@ -4,6 +4,7 @@
 PORTNAME=	silo
 PORTVERSION=	4.9.1
 DISTVERSIONSUFFIX=	-bsd
+PORTREVISION=	1
 CATEGORIES=	science
 MASTER_SITES=	https://wci.llnl.gov/codes/${PORTNAME}/silo-${PORTVERSION}/

--- a/sysutils/slurm-hpc/Makefile
+++ b/sysutils/slurm-hpc/Makefile
@ -3,6 +3,7 @@

 PORTNAME=	slurm
 PORTVERSION=	2.6.4
+PORTREVISION=	1
 CATEGORIES=	sysutils
 MASTER_SITES=	http://www.schedmd.com/download/archive/ \
 		http://www.schedmd.com/download/latest/ \
@ -17,11 +18,8 @@ LICENSE=	GPLv1
 LIB_DEPENDS=	libsysinfo.so:${PORTSDIR}/devel/libsysinfo \
 		libhwloc.so:${PORTSDIR}/devel/hwloc \
 		libmunge.so:${PORTSDIR}/security/munge \
-		librrd.so:${PORTSDIR}/databases/rrdtool
-# Testing for hdf5.so is insufficient.  It will accept hdf5 1.6 and
-# slurm requires hdf5 1.8.  h5copy is present only in 1.8.
-BUILD_DEPENDS+=	${LOCALBASE}/bin/h5copy:${PORTSDIR}/science/hdf5-18
-RUN_DEPENDS+=	${BUILD_DEPENDS}
+		librrd.so:${PORTSDIR}/databases/rrdtool \
+		libhdf5.so:${PORTSDIR}/science/hdf5

 USE_BZIP2=	yes
 USE_LDCONFIG=	yes