- Update science/netcdf4 to 4.0.1

- Bump PORTREVISION for dependent ports

PR:		ports/136377
Submitted by:	Sunpoet Po-Chuan Hsieh <sunpoet at sunpoet.net> (maintainer)
Feature safe:	yes

8 files changed, 35 insertions, 14 deletions

diff --git a/math/p5-NetCDF/Makefile b/math/p5-NetCDF/Makefile
index 62032540632b..5315684c820b 100644
--- a/math/p5-NetCDF/Makefile
+++ b/math/p5-NetCDF/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	NetCDF
 PORTVERSION=	1.2.3
+PORTREVISION=	1
 CATEGORIES=	math perl5
 MASTER_SITES=	ftp://ftp.unidata.ucar.edu/pub/netcdf-perl/
 PKGNAMEPREFIX=	p5-
@@ -19,7 +20,7 @@ COMMENT=	Perl5 module to read and write netCDF files
 NETCDF_VER?=	4
 
 .if (${NETCDF_VER} == 4)
-LIB_DEPENDS=	netcdf.5:${PORTSDIR}/science/netcdf4
+LIB_DEPENDS=	netcdf.6:${PORTSDIR}/science/netcdf4
 .else
 LIB_DEPENDS=	netcdf.4:${PORTSDIR}/science/netcdf
 .endif
diff --git a/math/p5-NetCDF/files/patch-perl-NetCDF.xs b/math/p5-NetCDF/files/patch-perl-NetCDF.xs
new file mode 100644
index 000000000000..c3fd58c8c600
--- /dev/null
+++ b/math/p5-NetCDF/files/patch-perl-NetCDF.xs
@@ -0,0 +1,13 @@
+--- perl/NetCDF.xs.orig	2003-01-10 00:09:14.000000000 +0800
++++ perl/NetCDF.xs	2009-09-26 06:10:36.000000000 +0800
+@@ -23,6 +23,10 @@
+ #include <assert.h>
+ #include "netcdf.h"
+ 
++#if !defined(MAX_NC_OPEN)
++#define MAX_NC_OPEN sysconf(_SC_OPEN_MAX)
++#endif
++
+ /*
+  * Macro for setting a scalar value either directly or through a reference:
+  */
diff --git a/science/cdo/Makefile b/science/cdo/Makefile
index 167624d08e2a..86ba89cb2b60 100644
--- a/science/cdo/Makefile
+++ b/science/cdo/Makefile
@@ -8,6 +8,7 @@
 
 PORTNAME=		cdo
 PORTVERSION=		1.3.1
+PORTREVISION=		1
 CATEGORIES=		science
 MASTER_SITES=		http://www.mpimet.mpg.de/fileadmin/software/cdo/ \
 			http://sunpoet.net/distfiles/
@@ -47,7 +48,7 @@ EXTRA_PATCHES+=		${FILESDIR}/extra-patch-src-Makefile.in
 .if (${NETCDF_VER} == 4)
 HDF5_VER=		18
 WITH_HDF5=		yes
-LIB_DEPENDS+=		netcdf.5:${PORTSDIR}/science/netcdf4
+LIB_DEPENDS+=		netcdf.6:${PORTSDIR}/science/netcdf4
 .else
 LIB_DEPENDS+=		netcdf.4:${PORTSDIR}/science/netcdf
 .endif
diff --git a/science/netcdf4/Makefile b/science/netcdf4/Makefile
index 34a9ef8bb392..b417a782b278 100644
--- a/science/netcdf4/Makefile
+++ b/science/netcdf4/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	netcdf
-PORTVERSION=	4.0
+PORTVERSION=	4.0.1
 CATEGORIES=	science
 MASTER_SITES=	http://www.unidata.ucar.edu/downloads/netcdf/ftp/ \
 		ftp://ftp.unidata.ucar.edu/pub/netcdf/ \
@@ -19,8 +19,8 @@ CONFLICTS=	hdf-4.* netcdf-3.*
 LATEST_LINK=	netcdf4
 
 CONFIGURE_ARGS=	--disable-f77 --disable-f90 \
-		--enable-cxx --enable-cxx-4 --enable-netcdf-4 --enable-shared \
-		--with-hdf5=${LOCALBASE} --with-zlib=/usr
+		--enable-cxx --enable-cxx-4 --enable-ncgen4 --enable-netcdf-4 \
+		--enable-shared --with-hdf5=${LOCALBASE} --with-zlib=/usr
 CONFIGURE_ENV+=	CPPFLAGS="${CPPFLAGS} -I${LOCALBASE}/include -fPIC -DPIC -Df2cFortran"
 MAKE_ENV+=	MAKEINFOFLAGS="--no-split" INFODIR="${PREFIX}/${INFO_PATH}"
 
@@ -32,7 +32,7 @@ LIB_DEPENDS+=	hdf5.6:${PORTSDIR}/science/hdf5-18
 INFO=		netcdf netcdf-c netcdf-cxx netcdf-cxx4 netcdf-f77 \
 		netcdf-f90 netcdf-install netcdf-tutorial
 
-MAN1=		ncdump.1 ncgen.1
+MAN1=		ncdump.1 ncgen.1 ncgen4.1
 MAN3=		netcdf.3
 
 OPTIONS=	HDF5_CONVERT	"Do data conversion through HDF5"	off
@@ -49,14 +49,14 @@ CONFIGURE_ARGS+=--enable-hdf5-convert
 
 post-patch:
 .if defined(NOPORTDOCS)
-	@${REINPLACE_CMD} -e '814 s/install-docDATA //' \
+	@${REINPLACE_CMD} -e '829 s/install-docDATA //' \
 		${WRKSRC}/man4/Makefile.in
 .endif
 	@${REINPLACE_CMD} -e \
 		's/\(@INSTALL_DOCS_TRUE@MAN.*\)/# \1/' \
 		${WRKSRC}/Makefile.in
 	@${REINPLACE_CMD} -e \
-		'274 s/\(info_docs\).*/html_docs\)/' \
+		'288 s/\(info_docs\).*/html_docs\)/' \
 		${WRKSRC}/man4/Makefile.in
 
 post-configure:
diff --git a/science/netcdf4/distinfo b/science/netcdf4/distinfo
index 953e56308e28..77b19bff2660 100644
--- a/science/netcdf4/distinfo
+++ b/science/netcdf4/distinfo
@@ -1,3 +1,3 @@
-MD5 (netcdf-4.0.tar.gz) = afc057b07b6e6843556dcfbc4ced402c
-SHA256 (netcdf-4.0.tar.gz) = 4f6934fd862b2e0f5a6ddcd8ef5f86a03d8aebfd106bc09c97afc80fe2ad5c96
-SIZE (netcdf-4.0.tar.gz) = 11584002
+MD5 (netcdf-4.0.1.tar.gz) = a251453c5477599f050fa4e593295186
+SHA256 (netcdf-4.0.1.tar.gz) = 290e377aa2e9419bb50a2fa1038d6e77d36f239a8a9c3be9e3a9319f1e484d19
+SIZE (netcdf-4.0.1.tar.gz) = 8018998
diff --git a/science/netcdf4/pkg-descr b/science/netcdf4/pkg-descr
index a8ab96607da6..fa18f64fac06 100644
--- a/science/netcdf4/pkg-descr
+++ b/science/netcdf4/pkg-descr
@@ -6,4 +6,4 @@ 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.
 
-WWW: http://www.unidata.ucar.edu/packages/netcdf/
+WWW: http://www.unidata.ucar.edu/software/netcdf/
diff --git a/science/netcdf4/pkg-plist b/science/netcdf4/pkg-plist
index c20aa2419771..5d1a3621254a 100644
--- a/science/netcdf4/pkg-plist
+++ b/science/netcdf4/pkg-plist
@@ -1,5 +1,7 @@
+bin/nc-config
 bin/ncdump
 bin/ncgen
+bin/ncgen4
 include/ncvalues.h
 include/netcdf.h
 include/netcdf.hh
@@ -8,7 +10,7 @@ include/netcdfcpp4.h
 lib/libnetcdf.a
 lib/libnetcdf.la
 lib/libnetcdf.so
-lib/libnetcdf.so.5
+lib/libnetcdf.so.6
 lib/libnetcdf_c++.a
 lib/libnetcdf_c++.la
 lib/libnetcdf_c++.so
@@ -17,8 +19,10 @@ lib/libnetcdf_c++4.a
 lib/libnetcdf_c++4.la
 lib/libnetcdf_c++4.so
 lib/libnetcdf_c++4.so.1
+lib/pkgconfig/netcdf.pc
 %%PORTDOCS%%%%DOCSDIR%%/ncdump-man-1.html
 %%PORTDOCS%%%%DOCSDIR%%/ncgen-man-1.html
+%%PORTDOCS%%%%DOCSDIR%%/ncgen4-man-1.html
 %%PORTDOCS%%%%DOCSDIR%%/netcdf-c.html
 %%PORTDOCS%%%%DOCSDIR%%/netcdf-c.pdf
 %%PORTDOCS%%%%DOCSDIR%%/netcdf-c.ps
@@ -55,3 +59,4 @@ lib/libnetcdf_c++4.so.1
 %%PORTDOCS%%%%DOCSDIR%%/netcdf_f77-man.html
 %%PORTDOCS%%%%DOCSDIR%%/netcdf_f90-man.html
 %%PORTDOCS%%@dirrm %%DOCSDIR%%
+@dirrmtry lib/pkgconfig
diff --git a/science/py-netCDF4/Makefile b/science/py-netCDF4/Makefile
index 391b497d3960..a3c8ad6510f9 100644
--- a/science/py-netCDF4/Makefile
+++ b/science/py-netCDF4/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	netCDF4
 PORTVERSION=	0.8.1
+PORTREVISION=	1
 CATEGORIES=	science python
 MASTER_SITES=	http://netcdf4-python.googlecode.com/files/ \
 		CHEESESHOP
@@ -18,7 +19,7 @@ COMMENT=	Python Interface to the NetCDF Library(versions 3 and 4)
 BUILD_DEPENDS=	${PYTHON_SITELIBDIR}/numpy:${PORTSDIR}/math/py-numpy
 RUN_DEPENDS=	${BUILD_DEPENDS}
 LIB_DEPENDS=	hdf5.6:${PORTSDIR}/science/hdf5-18 \
-		netcdf.5:${PORTSDIR}/science/netcdf4
+		netcdf.6:${PORTSDIR}/science/netcdf4
 
 USE_PYTHON=	2.5+
 USE_PYDISTUTILS=	yes