14 files changed, 78 insertions, 114 deletions

diff --git a/science/gnudatalanguage/Makefile b/science/gnudatalanguage/Makefile
index cf0fabbecc1d..ea67e9859bef 100644
--- a/science/gnudatalanguage/Makefile
+++ b/science/gnudatalanguage/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	gnudatalanguage
 DISTVERSION=	0.9.4
-PORTREVISION=	4
+PORTREVISION=	5
 CATEGORIES=	science lang
 MASTER_SITES=	SF/${PORTNAME}/gdl/${DISTVERSION}
 .if defined(BUILD_PYTHON_MODULE)
diff --git a/science/kst2/Makefile b/science/kst2/Makefile
index 73d010bb61aa..c59f935609ed 100644
--- a/science/kst2/Makefile
+++ b/science/kst2/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	kst
 DISTVERSION=	2.0.6
-PORTREVISION=	3
+PORTREVISION=	4
 CATEGORIES=	science kde
 MASTER_SITES=	SF/${PORTNAME}/Kst%20${DISTVERSION:C/-r.*//}/
 
diff --git a/science/minc/Makefile b/science/minc/Makefile
index 799a03c7e423..9e90efc3bba2 100644
--- a/science/minc/Makefile
+++ b/science/minc/Makefile
@@ -12,13 +12,14 @@
 
 PORTNAME=	minc
 PORTVERSION=	1.5.1
+PORTREVISION=	1
 CATEGORIES=	science biology
 MASTER_SITES=	http://www.nitrc.org/frs/downloadlink.php/400/
 
 MAINTAINER=	jwbacon@tds.net
 COMMENT=	Medical Imaging NetCDF
 
-LIB_DEPENDS=	netcdf.4:${PORTSDIR}/science/netcdf
+LIB_DEPENDS=	libnetcdf.so:${PORTSDIR}/science/netcdf
 
 USE_AUTOTOOLS=	libtool
 USE_LDCONFIG=	yes
diff --git a/science/minc2/Makefile b/science/minc2/Makefile
index 7963920933db..672e367e1b5a 100644
--- a/science/minc2/Makefile
+++ b/science/minc2/Makefile
@@ -12,7 +12,7 @@
 
 PORTNAME=	minc
 PORTVERSION=	2.0.18
-PORTREVISION=	1
+PORTREVISION=	2
 PORTEPOCH=	1
 CATEGORIES=	science biology
 MASTER_SITES=	http://packages.bic.mni.mcgill.ca/tgz/ \
@@ -24,7 +24,7 @@ COMMENT=	Medical Imaging NetCDF
 
 LICENSE=	BSD
 
-LIB_DEPENDS=	libnetcdf.so.4:${PORTSDIR}/science/netcdf \
+LIB_DEPENDS=	libnetcdf.so:${PORTSDIR}/science/netcdf \
 		libhdf5.so:${PORTSDIR}/science/hdf5
 
 USE_AUTOTOOLS=	libtool
diff --git a/science/netcdf/Makefile b/science/netcdf/Makefile
index 19f9e1b9336f..e9c2389584a3 100644
--- a/science/netcdf/Makefile
+++ b/science/netcdf/Makefile
@@ -1,65 +1,65 @@
-# Created by: Thomas Gellekum <tg@FreeBSD.org>
+# Created by: Sunpoet Po-Chuan Hsieh <sunpoet@sunpoet.net>
 # $FreeBSD$
 
 PORTNAME=	netcdf
-PORTVERSION=	3.6.3
-PORTREVISION?=	7
+PORTVERSION=	4.3.2
 CATEGORIES=	science
 MASTER_SITES=	http://www.unidata.ucar.edu/downloads/netcdf/ftp/ \
 		ftp://ftp.unidata.ucar.edu/pub/netcdf/ \
 		LOCAL/sunpoet
-PKGNAMESUFFIX?=	3
 
 MAINTAINER=	sunpoet@FreeBSD.org
-COMMENT?=	Library for machine-independent, array-oriented data access
+COMMENT=	C library for machine-independent, array-oriented data access
 
-CONFLICTS=	hdf-4.* netcdf-4.*
-PORTSCOUT=	limit:^3\.
+LIB_DEPENDS=	libhdf5.so:${PORTSDIR}/science/hdf5
 
-CONFIGURE_ARGS=	--enable-shared
-CPPFLAGS+=	-I${LOCALBASE}/include -fPIC -DPIC
-GNU_CONFIGURE=	yes
-USES=		gmake libtool:keepla
+CONFLICTS_INSTALL=	hdf-4.[0-9]* netcdf-3.[0-9]* netcdf3-3.[0-9]*
+PORTSCOUT=	limit:^4\.
+
+OPTIONS_DEFINE=	DAP DOCS DOXYGEN SZIP
+OPTIONS_DEFAULT=DAP SZIP
+DAP_DESC=	Build DAP client and remote testing
+SZIP_DESC=	SZIP support (required if HDF5 was built with SZIP)
+
+CFLAGS+=	-I${WRKSRC}/include -I${LOCALBASE}/include -fPIC -DPIC
+CMAKE_ARGS=	-DHDF5_INCLUDE_DIRS=${LOCALBASE} -DUSE_HDF5=ON -DZLIB_INCLUDE_DIRS=/usr
+LDFLAGS+=	-L${LOCALBASE}/lib
 USE_LDCONFIG=	yes
+USES=		cmake pathfix
 
-INFO=		netcdf netcdf-c netcdf-cxx netcdf-f77 netcdf-f90 \
-		netcdf-install netcdf-tutorial
+PLIST_SUB=	PORTVERSION=${PORTVERSION}
+PORTDOCS=	*
 
-OPTIONS_DEFINE=	FORTRAN DOCS
-FORTRAN_DESC=	Build library for Fortran
+DAP_CMAKE_OFF=		-DENABLE_DAP=OFF -DENABLE_DAP_REMOTE_TESTS=OFF
+DAP_CMAKE_ON=		-DCURL_INCLUDE_DIRS=${LOCALBASE} -DENABLE_DAP=ON
+DAP_LIB_DEPENDS=	libcurl.so:${PORTSDIR}/ftp/curl
+DOXYGEN_BUILD_DEPENDS=	${LOCALBASE}/bin/doxygen:${PORTSDIR}/devel/doxygen
+DOXYGEN_CMAKE_OFF=	-DENABLE_DOXYGEN=OFF
+DOXYGEN_CMAKE_ON=	-DENABLE_DOXYGEN=ON
+SZIP_CMAKE_OFF=		-DUSE_SZIP=OFF
+SZIP_CMAKE_ON=		-DSZIP_DIR=${LOCALBASE} -DSZIP_INCLUDE_DIRS=${LOCALBASE} -DUSE_SZIP=ON
+SZIP_LDFLAGS=		-lsz
+SZIP_LIB_DEPENDS=	libsz.so:${PORTSDIR}/science/szip
 
 .include <bsd.port.options.mk>
 
-.if ${PORT_OPTIONS:MDOCS}
-CONFIGURE_ARGS+=--enable-docs-install
-.else
-CONFIGURE_ARGS+=--disable-docs-install
-.endif
+post-patch:
+	@${REINPLACE_CMD} -e '/man4/d; s|share/cmake|&/Modules|; s|$${CMAKE_INSTALL_LIBDIR}/pkgconfig|libdata/pkgconfig|' ${WRKSRC}/CMakeLists.txt
+	@${REINPLACE_CMD} -e 's|share/man|man|' ${WRKSRC}/libsrc/CMakeLists.txt ${WRKSRC}/ncdump/CMakeLists.txt ${WRKSRC}/ncgen/CMakeLists.txt ${WRKSRC}/ncgen3/CMakeLists.txt
+	@${REINPLACE_CMD} -e 's|mmap|_&|g' ${WRKSRC}/nc_test/tst_diskless.c ${WRKSRC}/nc_test/tst_diskless3.c
 
-.if ${PORT_OPTIONS:MFORTRAN}
-CPPFLAGS+=	-DpgiFortran
-CONFLICTS+=	netcdf-3.*
-PLIST_SUB+=	FORTRAN=""
-USES+=		fortran
-.else
-CONFIGURE_ARGS+=--disable-f77 --disable-f90
-CONFLICTS+=	netcdf-ftn-3.*
-PLIST_SUB+=	FORTRAN="@comment "
+post-build:
+.if ${PORT_OPTIONS:MDOCS} && ${PORT_OPTIONS:MDOXYGEN}
+	@cd ${WRKSRC}/man4 && ${LOCALBASE}/bin/doxygen .
 .endif
 
-post-patch:
-	@${REINPLACE_CMD} -e \
-		'291 s/\(html_docs)\).*/\1/' \
-		${WRKSRC}/man/Makefile.in
-	@${REINPLACE_CMD} -e \
-		'271 s/\(info_docs\).*/html_docs\)/' \
-		${WRKSRC}/man4/Makefile.in
-.if ! ${PORT_OPTIONS:MDOCS}
-	@${REINPLACE_CMD} -e '790 s/install-docDATA //' \
-		${WRKSRC}/man/Makefile.in
+post-install:
+.if ${PORT_OPTIONS:MDOCS} && ${PORT_OPTIONS:MDOXYGEN}
+	${MKDIR} ${STAGEDIR}${DOCSDIR}/
+	cd ${WRKSRC}/man4/html/ && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR}
 .endif
 
-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.mk>
diff --git a/science/netcdf/distinfo b/science/netcdf/distinfo
index cca29d29a70f..71fc034f6aa7 100644
--- a/science/netcdf/distinfo
+++ b/science/netcdf/distinfo
@@ -1,2 +1,2 @@
-SHA256 (netcdf-3.6.3.tar.gz) = afa1a0fa82b9ea33b035257b6e9662b22e135f98b2fd93d5cf030320dfc3ffa1
-SIZE (netcdf-3.6.3.tar.gz) = 11572512
+SHA256 (netcdf-4.3.2.tar.gz) = 57086b4383ce9232f05aad70761c2a6034b1a0c040260577d369b3bbfe6d248e
+SIZE (netcdf-4.3.2.tar.gz) = 5013938
diff --git a/science/netcdf/pkg-descr b/science/netcdf/pkg-descr
index fa18f64fac06..08839b648c08 100644
--- a/science/netcdf/pkg-descr
+++ b/science/netcdf/pkg-descr
@@ -6,4 +6,6 @@ library, and format support the creation, access, and sharing of
 scientific data. The netCDF software was developed at the Unidata
 Program Center in Boulder, Colorado.
 
+Git repository: https://github.com/Unidata/netcdf-c
+
 WWW: http://www.unidata.ucar.edu/software/netcdf/
diff --git a/science/netcdf/pkg-plist b/science/netcdf/pkg-plist
index 3d67360110f0..a24e0519c3d4 100644
--- a/science/netcdf/pkg-plist
+++ b/science/netcdf/pkg-plist
@@ -1,63 +1,21 @@
+bin/nc-config
+bin/nccopy
 bin/ncdump
 bin/ncgen
-include/ncvalues.h
+bin/ncgen3
 include/netcdf.h
-include/netcdf.hh
-%%FORTRAN%%include/netcdf.inc
-%%FORTRAN%%include/netcdf.mod
-include/netcdfcpp.h
-%%FORTRAN%%include/typesizes.mod
-lib/libnetcdf.a
-lib/libnetcdf.la
 lib/libnetcdf.so
-lib/libnetcdf.so.4
-lib/libnetcdf.so.4.0.0
-lib/libnetcdf_c++.a
-lib/libnetcdf_c++.la
-lib/libnetcdf_c++.so
-lib/libnetcdf_c++.so.4
-lib/libnetcdf_c++.so.4.0.0
-%%FORTRAN%%lib/libnetcdff.a
-%%FORTRAN%%lib/libnetcdff.la
-%%FORTRAN%%lib/libnetcdff.so
-%%FORTRAN%%lib/libnetcdff.so.4
-%%FORTRAN%%lib/libnetcdff.so.4.0.0
+lib/libnetcdf.so.%%PORTVERSION%%
+lib/libnetcdf.so.7.2.0
+libdata/pkgconfig/netcdf.pc
+man/man1/nccopy.1.gz
 man/man1/ncdump.1.gz
 man/man1/ncgen.1.gz
+man/man1/ncgen3.1.gz
 man/man3/netcdf.3.gz
-%%FORTRAN%%man/man3/netcdf_f77.3.gz
-%%FORTRAN%%man/man3/netcdf_f90.3.gz
-%%PORTDOCS%%%%DOCSDIR%%/ncgen-man-1.html
-%%PORTDOCS%%%%DOCSDIR%%/ncdump-man-1.html
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-c.html
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-c.pdf
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-c.ps
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-c.txt
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-cxx.html
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-cxx.pdf
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-cxx.ps
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-cxx.txt
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-f77.html
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-f77.pdf
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-f77.ps
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-f77.txt
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-f90.html
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-f90.pdf
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-f90.ps
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-f90.txt
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-install.html
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-install.pdf
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-install.ps
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-install.txt
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-man-3.html
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-tutorial.html
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-tutorial.pdf
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-tutorial.ps
-%%PORTDOCS%%%%DOCSDIR%%/netcdf-tutorial.txt
-%%PORTDOCS%%%%DOCSDIR%%/netcdf_f77-man.html
-%%PORTDOCS%%%%DOCSDIR%%/netcdf_f90-man.html
-%%PORTDOCS%%%%DOCSDIR%%/netcdf.html
-%%PORTDOCS%%%%DOCSDIR%%/netcdf.pdf
-%%PORTDOCS%%%%DOCSDIR%%/netcdf.ps
-%%PORTDOCS%%%%DOCSDIR%%/netcdf.txt
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
+share/cmake/Modules/netcdf-config-version.cmake
+share/cmake/Modules/netcdf-config.cmake
+share/cmake/Modules/netcdf-targets-%%CMAKE_BUILD_TYPE%%.cmake
+share/cmake/Modules/netcdf-targets.cmake
+@dirrmtry share/cmake/Modules
+@dirrmtry share/cmake
diff --git a/science/py-netCDF4/Makefile b/science/py-netCDF4/Makefile
index 97fa148fba0b..098e0f26c7c1 100644
--- a/science/py-netCDF4/Makefile
+++ b/science/py-netCDF4/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	netCDF4
 PORTVERSION=	1.0.5
-PORTREVISION=	3
+PORTREVISION=	4
 CATEGORIES=	science python
 MASTER_SITES=	GOOGLE_CODE
 PROJECTHOST=	netcdf4-python
@@ -16,7 +16,7 @@ LICENSE=	MIT
 
 BUILD_DEPENDS=	${PYNUMPY}
 LIB_DEPENDS=	libhdf5.so:${PORTSDIR}/science/hdf5 \
-		libnetcdf.so:${PORTSDIR}/science/netcdf4
+		libnetcdf.so:${PORTSDIR}/science/netcdf
 RUN_DEPENDS=	${PYNUMPY}
 
 OPTIONS_DEFINE=	DOCS EXAMPLES
diff --git a/science/pycdf/Makefile b/science/pycdf/Makefile
index ba994549a14e..7a14f14b273a 100644
--- a/science/pycdf/Makefile
+++ b/science/pycdf/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	pycdf
 PORTVERSION=	0.6.3
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	science python
 MASTER_SITES=	SF/pysclint/${PORTNAME}/${PORTNAME}-${PORTVERSION}b
 DISTNAME=	${PORTNAME}-0.6-3b
@@ -11,8 +11,8 @@ DISTNAME=	${PORTNAME}-0.6-3b
 MAINTAINER=	wenheping@gmail.com
 COMMENT=	A Python Interface to the Unidata NetCDF Library
 
-BUILD_DEPENDS=	${PYTHON_SITELIBDIR}/numpy:${PORTSDIR}/math/py-numpy \
-		${LOCALBASE}/lib/libnetcdf.so:${PORTSDIR}/science/netcdf
+BUILD_DEPENDS=	${PYTHON_SITELIBDIR}/numpy:${PORTSDIR}/math/py-numpy
+LIB_DEPENDS=	libnetcdf.so:${PORTSDIR}/science/netcdf
 RUN_DEPENDS:=	${BUILD_DEPENDS}
 
 LDFLAGS+=	"-L${LOCALBASE}/lib"
diff --git a/science/ruby-netcdf/Makefile b/science/ruby-netcdf/Makefile
index 69c5ad0ccd5a..541d7f153f06 100644
--- a/science/ruby-netcdf/Makefile
+++ b/science/ruby-netcdf/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	netcdf
 PORTVERSION=	0.6.6
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	science ruby
 MASTER_SITES=	http://ruby.gfd-dennou.org/products/ruby-netcdf/release/ \
 		http://dennou-h.gfd-dennou.org/library/ruby/products/ruby-netcdf/release/ \
diff --git a/science/rubygem-netcdf/Makefile b/science/rubygem-netcdf/Makefile
index a239c889b827..24b9f31c0897 100644
--- a/science/rubygem-netcdf/Makefile
+++ b/science/rubygem-netcdf/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	netcdf
 PORTVERSION=	0.6.6.1
+PORTREVISION=	1
 CATEGORIES=	science rubygems
 MASTER_SITES=	RG
 DISTNAME=	ruby-${PORTNAME}-${PORTVERSION}
diff --git a/science/v_sim/Makefile b/science/v_sim/Makefile
index ab18ec380e2f..1805a485482c 100644
--- a/science/v_sim/Makefile
+++ b/science/v_sim/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	v_sim
 PORTVERSION=	3.7.1
+PORTREVISION=	1
 CATEGORIES=	science
 MASTER_SITES=	http://www-drfmc.cea.fr/sp2m/L_Sim/V_Sim/download/
 
diff --git a/science/vmd/Makefile b/science/vmd/Makefile
index 3a64403fc9da..144e32de106c 100644
--- a/science/vmd/Makefile
+++ b/science/vmd/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=		vmd
 DISTVERSION=		1.9.1
+PORTREVISION=		1
 CATEGORIES=		science graphics python tcl tk
 MASTER_SITES=		http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.99b2/:tachyon \
 			http://www.photonlimited.com/~johns/tachyon/files/0.99b2/:tachyon \
@@ -16,10 +17,10 @@ COMMENT=		A molecular visualization program
 
 BUILD_DEPENDS=		makedepend:${PORTSDIR}/devel/makedepend \
 			${PYNUMERIC}
-LIB_DEPENDS=		tcl85:${PORTSDIR}/lang/tcl85 \
-			tk85:${PORTSDIR}/x11-toolkits/tk85 \
-			fltk.1:${PORTSDIR}/x11-toolkits/fltk \
-			netcdf:${PORTSDIR}/science/netcdf
+LIB_DEPENDS=		libtcl85.so:${PORTSDIR}/lang/tcl85 \
+			libtk85.so:${PORTSDIR}/x11-toolkits/tk85 \
+			libfltk.so:${PORTSDIR}/x11-toolkits/fltk \
+			libnetcdf.so:${PORTSDIR}/science/netcdf
 RUN_DEPENDS=		${PYNUMERIC}
 
 USES=			gmake perl5