- 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]

24 files changed, 153 insertions, 328 deletions

diff --git a/science/cgnslib/Makefile b/science/cgnslib/Makefile
index ceeea807d19b..f38fb459be54 100644
--- 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=""
diff --git a/science/ecs/Makefile b/science/ecs/Makefile
index cdc0defe1f62..83a171190dfc 100644
--- 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}
diff --git a/science/fvm/Makefile b/science/fvm/Makefile
index 66907d0227c8..6d3e29e26d2d 100644
--- 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}
diff --git a/science/gnudatalanguage/Makefile b/science/gnudatalanguage/Makefile
index c25ef99e7da2..cf0fabbecc1d 100644
--- 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
diff --git a/science/h5utils/Makefile b/science/h5utils/Makefile
index dc10ea1afc0d..c1196c898983 100644
--- 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>
diff --git a/science/hdf-java/Makefile b/science/hdf-java/Makefile
index 2e6652d48480..f965fc2b8c9b 100644
--- 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>
 
diff --git a/science/hdf5/Makefile b/science/hdf5/Makefile
index 5d3fe73fd395..dfe2ba73614b 100644
--- 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
-
-post-install:
-.for i in gif2h5 h52gif h5debug h5diff h5dump h5import h5jam h5ls h5repack h5repart h5unjam
-	@${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/${i}
-.endfor
+		-e '/LD_LIBRARY_PATH/ s|^|#|' \
+		-e 's|/share/hdf5_examples|/${EXAMPLESDIR_REL}|' \
+		-e 's|(INSTALL)|(INSTALL_DATA)|' \
+			`${FIND} ${WRKSRC} -regex '.*/examples/Makefile.in'`
+	@${REINPLACE_CMD} -e 's|\[ -a|\[ -f|g' `${FIND} ${WRKSRC} -name \*.sh\*`
 
-regression-test: build
-	@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE} check
+regression-test test: build
+	cd ${WRKSRC}/ && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} check
 
-.include <bsd.port.post.mk>
+.include <bsd.port.mk>
diff --git a/science/hdf5/distinfo b/science/hdf5/distinfo
index c514ccfccc06..877852712bd7 100644
--- 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
diff --git a/science/hdf5/files/patch-Makefile.in b/science/hdf5/files/patch-Makefile.in
deleted file mode 100644
index f2dc8dd97cf4..000000000000
--- a/science/hdf5/files/patch-Makefile.in
+++ /dev/null
@@ -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
diff --git a/science/hdf5/files/patch-c++::commence.in b/science/hdf5/files/patch-c++::commence.in
deleted file mode 100644
index 393adc30cc0f..000000000000
--- a/science/hdf5/files/patch-c++::commence.in
+++ /dev/null
@@ -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=$(docdir)/examples/hdf5/c++
- LIB=
- LIB_SRC=
- LIB_OBJ=
diff --git a/science/hdf5/files/patch-commence.in b/science/hdf5/files/patch-commence.in
deleted file mode 100644
index 0795dcb37f66..000000000000
--- a/science/hdf5/files/patch-commence.in
+++ /dev/null
@@ -1,32 +0,0 @@
---- config/commence.in.orig	Tue Jul 22 23:39:43 2003
-+++ config/commence.in	Mon Oct 20 23:45:00 2003
-@@ -26,7 +26,7 @@
- RM=rm -f
- CP=cp
- INSTALL=@INSTALL@
--INSTALL_PROGRAM=@INSTALL_PROGRAM@
-+INSTALL_PROGRAM=@INSTALL_SCRIPT@
- INSTALL_DATA=@INSTALL_DATA@
- RUNSERIAL=@RUNSERIAL@
- RUNPARALLEL=@RUNPARALLEL@
-@@ -39,7 +39,7 @@
- bindir=@bindir@
- libdir=@libdir@
- includedir=@includedir@
--docdir=@exec_prefix@/doc
-+docdir=@exec_prefix@/share
- PUB_LIB=$(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=
diff --git a/science/hdf5/files/patch-fortran_H5f90i.h b/science/hdf5/files/patch-fortran_H5f90i.h
deleted file mode 100644
index 83f5855b8993..000000000000
--- a/science/hdf5/files/patch-fortran_H5f90i.h
+++ /dev/null
@@ -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;
diff --git a/science/hdf5/files/patch-fortran_commence.in b/science/hdf5/files/patch-fortran_commence.in
deleted file mode 100644
index 3331f07ce406..000000000000
--- a/science/hdf5/files/patch-fortran_commence.in
+++ /dev/null
@@ -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=$(docdir)/examples/hdf5/fortran
- LIB=
- LIB_SRC=
- LIB_OBJ=
diff --git a/science/hdf5/files/patch-fortran_configure b/science/hdf5/files/patch-fortran_configure
deleted file mode 100644
index 7244f4e4f10a..000000000000
--- a/science/hdf5/files/patch-fortran_configure
+++ /dev/null
@@ -1,10 +0,0 @@
---- fortran/configure.orig	Thu Jul 12 21:36:24 2007
-+++ fortran/configure	Thu Jul 12 21:36:49 2007
-@@ -7602,6 +7602,7 @@
- 
- # This can be used to rebuild libtool when needed
- LIBTOOL_DEPS="$ac_aux_dir/ltmain.sh"
-+$ac_aux_dir/ltconfig $LIBTOOL_DEPS
- 
- # Always use our own libtool.
- LIBTOOL='$(SHELL) $(top_builddir)/libtool'
diff --git a/science/hdf5/files/patch-fortran_freebsd b/science/hdf5/files/patch-fortran_freebsd
deleted file mode 100644
index 329de570663c..000000000000
--- a/science/hdf5/files/patch-fortran_freebsd
+++ /dev/null
@@ -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
diff --git a/science/hdf5/pkg-descr b/science/hdf5/pkg-descr
index 35a0fc9e23cf..2e3e3061d5c7 100644
--- 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/
diff --git a/science/hdf5/pkg-plist b/science/hdf5/pkg-plist
index ba8217caef46..c4cc3fc7c4ef 100644
--- 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
diff --git a/science/meep/Makefile b/science/meep/Makefile
index 1c1081f848db..0557de3bfd2c 100644
--- 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
diff --git a/science/minc2/Makefile b/science/minc2/Makefile
index c09439252284..7963920933db 100644
--- 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
diff --git a/science/mpb/Makefile b/science/mpb/Makefile
index 84f85b85cf5b..c7df390c07e9 100644
--- 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/
 
diff --git a/science/paraview/Makefile b/science/paraview/Makefile
index 832343b19ab0..b9d07f4076ef 100644
--- 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 \
diff --git a/science/py-h5py/Makefile b/science/py-h5py/Makefile
index cc1135cabfd6..1efd80f4e308 100644
--- 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
diff --git a/science/py-netCDF4/Makefile b/science/py-netCDF4/Makefile
index 6f7ec51944c1..97fa148fba0b 100644
--- 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}
 
diff --git a/science/silo/Makefile b/science/silo/Makefile
index 7c62ef27aa44..4b715314643b 100644
--- 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}/