upgrade to 1.6.1

PR:		58335
Submitted by:	AMAKAWA Shuhei <sa264@cam.ac.uk>

10 files changed, 184 insertions, 20 deletions

diff --git a/science/hdf5-18/Makefile b/science/hdf5-18/Makefile
index 86a7fb1f095d..044c72cee4b6 100644
--- a/science/hdf5-18/Makefile
+++ b/science/hdf5-18/Makefile
@@ -7,7 +7,7 @@
 #
 
 PORTNAME=	hdf5
-PORTVERSION=	1.4.5
+PORTVERSION=	1.6.1
 CATEGORIES=	graphics
 MASTER_SITES=	http://fresh.t-systems-sfr.com/unix/src/misc/
 
@@ -33,11 +33,11 @@ post-patch:
 		 s|[\$$]LDFLAGS -pthread|\$$LDFLAGS ${PTHREAD_LIBS}|g ; \
 		 s|-lcipher||g' \
 			${WRKSRC}/config/freebsd
-	@${REINPLACE_CMD} -e 's|-O2||g' ${WRKSRC}/config/gnu-flags
+	@${REINPLACE_CMD} -e 's|-O3||g' ${WRKSRC}/config/gnu-flags
 
 post-install:
-.for file in gif2h5 h52gif h5debug h5dump h5import h5ls h5perf h5repart
-	@${STRIP_CMD} ${PREFIX}/bin/${file}
+.for i in gif2h5 h52gif h5createU8 h5debug h5diff h5dump h5import h5ls h5repart
+	@${STRIP_CMD} ${PREFIX}/bin/${i}
 .endfor
 
 .include <bsd.port.mk>
diff --git a/science/hdf5-18/distinfo b/science/hdf5-18/distinfo
index f9a9f7cefae7..f8f88c898a18 100644
--- a/science/hdf5-18/distinfo
+++ b/science/hdf5-18/distinfo
@@ -1 +1 @@
-MD5 (hdf5-1.4.5.tar.gz) = 573b9001b00c3ba78f681babd4fe7520
+MD5 (hdf5-1.6.1.tar.gz) = db1ea5374572412b6e75f7916effe064
diff --git a/science/hdf5-18/files/patch-c++::commence.in b/science/hdf5-18/files/patch-c++::commence.in
new file mode 100644
index 000000000000..393adc30cc0f
--- /dev/null
+++ b/science/hdf5-18/files/patch-c++::commence.in
@@ -0,0 +1,31 @@
+--- 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=$(docdir)/examples/hdf5/c++
+ LIB=
+ LIB_SRC=
+ LIB_OBJ=
diff --git a/science/hdf5-18/files/patch-commence.in b/science/hdf5-18/files/patch-commence.in
index 8da9308386cd..0795dcb37f66 100644
--- a/science/hdf5-18/files/patch-commence.in
+++ b/science/hdf5-18/files/patch-commence.in
@@ -1,5 +1,5 @@
---- config/commence.in.orig	Sun Jul  7 20:15:36 2002
-+++ config/commence.in	Sun Jul  7 20:15:58 2002
+--- config/commence.in.orig	Tue Jul 22 23:39:43 2003
++++ config/commence.in	Mon Oct 20 23:45:00 2003
 @@ -26,7 +26,7 @@
  RM=rm -f
  CP=cp
@@ -9,3 +9,24 @@
  INSTALL_DATA=@INSTALL_DATA@
  RUNSERIAL=@RUNSERIAL@
  RUNPARALLEL=@RUNPARALLEL@
+@@ -39,7 +39,7 @@
+ bindir=@bindir@
+ libdir=@libdir@
+ includedir=@includedir@
+-docdir=@exec_prefix@/doc
++docdir=@exec_prefix@/share
+ PUB_LIB=$(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/hdf5-18/pkg-plist b/science/hdf5-18/pkg-plist
index 302c6e510524..2f6647a1c46a 100644
--- a/science/hdf5-18/pkg-plist
+++ b/science/hdf5-18/pkg-plist
@@ -1,16 +1,17 @@
 bin/gif2h5
 bin/h52gif
+bin/h5c++
 bin/h5cc
+bin/h5createU8
 bin/h5debug
+bin/h5diff
 bin/h5dump
 bin/h5import
 bin/h5ls
-bin/h5perf
 bin/h5redeploy
 bin/h5repart
 include/H5ACpublic.h
 include/H5AbstractDs.h
-include/H5Alltypes.h
 include/H5Apublic.h
 include/H5AtomType.h
 include/H5Attribute.h
@@ -30,6 +31,7 @@ include/H5Epublic.h
 include/H5Exception.h
 include/H5FDcore.h
 include/H5FDfamily.h
+include/H5FDfphdf5.h
 include/H5FDgass.h
 include/H5FDlog.h
 include/H5FDmpio.h
@@ -40,6 +42,7 @@ include/H5FDsec2.h
 include/H5FDsrb.h
 include/H5FDstdio.h
 include/H5FDstream.h
+include/H5FPpublic.h
 include/H5FaccProp.h
 include/H5FcreatProp.h
 include/H5File.h
@@ -50,7 +53,6 @@ include/H5Group.h
 include/H5HGpublic.h
 include/H5HLpublic.h
 include/H5IdComponent.h
-include/H5Idtemplates.h
 include/H5Include.h
 include/H5IntType.h
 include/H5Ipublic.h
@@ -76,3 +78,31 @@ lib/libhdf5.settings
 lib/libhdf5.so
 lib/libhdf5.so.0
 lib/libhdf5_cpp.a
+share/examples/hdf5/c/h5_attribute.c
+share/examples/hdf5/c/h5_chunk_read.c
+share/examples/hdf5/c/h5_compound.c
+share/examples/hdf5/c/h5_drivers.c
+share/examples/hdf5/c/h5_extend_write.c
+share/examples/hdf5/c/h5_group.c
+share/examples/hdf5/c/h5_mount.c
+share/examples/hdf5/c/h5_read.c
+share/examples/hdf5/c/h5_reference.c
+share/examples/hdf5/c/h5_select.c
+share/examples/hdf5/c/h5_write.c
+share/examples/hdf5/c/ph5example.c
+share/examples/hdf5/c++/Attributes.h5
+share/examples/hdf5/c++/Group.h5
+share/examples/hdf5/c++/SDS.h5
+share/examples/hdf5/c++/SDScompound.h5
+share/examples/hdf5/c++/SDSextendible.h5
+share/examples/hdf5/c++/Select.h5
+share/examples/hdf5/c++/chunks.cpp
+share/examples/hdf5/c++/compound.cpp
+share/examples/hdf5/c++/create.cpp
+share/examples/hdf5/c++/extend_ds.cpp
+share/examples/hdf5/c++/h5group.cpp
+share/examples/hdf5/c++/readdata.cpp
+share/examples/hdf5/c++/writedata.cpp
+@dirrm share/examples/hdf5/c
+@dirrm share/examples/hdf5/c++
+@dirrm share/examples/hdf5
diff --git a/science/hdf5/Makefile b/science/hdf5/Makefile
index 86a7fb1f095d..044c72cee4b6 100644
--- a/science/hdf5/Makefile
+++ b/science/hdf5/Makefile
@@ -7,7 +7,7 @@
 #
 
 PORTNAME=	hdf5
-PORTVERSION=	1.4.5
+PORTVERSION=	1.6.1
 CATEGORIES=	graphics
 MASTER_SITES=	http://fresh.t-systems-sfr.com/unix/src/misc/
 
@@ -33,11 +33,11 @@ post-patch:
 		 s|[\$$]LDFLAGS -pthread|\$$LDFLAGS ${PTHREAD_LIBS}|g ; \
 		 s|-lcipher||g' \
 			${WRKSRC}/config/freebsd
-	@${REINPLACE_CMD} -e 's|-O2||g' ${WRKSRC}/config/gnu-flags
+	@${REINPLACE_CMD} -e 's|-O3||g' ${WRKSRC}/config/gnu-flags
 
 post-install:
-.for file in gif2h5 h52gif h5debug h5dump h5import h5ls h5perf h5repart
-	@${STRIP_CMD} ${PREFIX}/bin/${file}
+.for i in gif2h5 h52gif h5createU8 h5debug h5diff h5dump h5import h5ls h5repart
+	@${STRIP_CMD} ${PREFIX}/bin/${i}
 .endfor
 
 .include <bsd.port.mk>
diff --git a/science/hdf5/distinfo b/science/hdf5/distinfo
index f9a9f7cefae7..f8f88c898a18 100644
--- a/science/hdf5/distinfo
+++ b/science/hdf5/distinfo
@@ -1 +1 @@
-MD5 (hdf5-1.4.5.tar.gz) = 573b9001b00c3ba78f681babd4fe7520
+MD5 (hdf5-1.6.1.tar.gz) = db1ea5374572412b6e75f7916effe064
diff --git a/science/hdf5/files/patch-c++::commence.in b/science/hdf5/files/patch-c++::commence.in
new file mode 100644
index 000000000000..393adc30cc0f
--- /dev/null
+++ b/science/hdf5/files/patch-c++::commence.in
@@ -0,0 +1,31 @@
+--- 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=$(docdir)/examples/hdf5/c++
+ LIB=
+ LIB_SRC=
+ LIB_OBJ=
diff --git a/science/hdf5/files/patch-commence.in b/science/hdf5/files/patch-commence.in
index 8da9308386cd..0795dcb37f66 100644
--- a/science/hdf5/files/patch-commence.in
+++ b/science/hdf5/files/patch-commence.in
@@ -1,5 +1,5 @@
---- config/commence.in.orig	Sun Jul  7 20:15:36 2002
-+++ config/commence.in	Sun Jul  7 20:15:58 2002
+--- config/commence.in.orig	Tue Jul 22 23:39:43 2003
++++ config/commence.in	Mon Oct 20 23:45:00 2003
 @@ -26,7 +26,7 @@
  RM=rm -f
  CP=cp
@@ -9,3 +9,24 @@
  INSTALL_DATA=@INSTALL_DATA@
  RUNSERIAL=@RUNSERIAL@
  RUNPARALLEL=@RUNPARALLEL@
+@@ -39,7 +39,7 @@
+ bindir=@bindir@
+ libdir=@libdir@
+ includedir=@includedir@
+-docdir=@exec_prefix@/doc
++docdir=@exec_prefix@/share
+ PUB_LIB=$(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/pkg-plist b/science/hdf5/pkg-plist
index 302c6e510524..2f6647a1c46a 100644
--- a/science/hdf5/pkg-plist
+++ b/science/hdf5/pkg-plist
@@ -1,16 +1,17 @@
 bin/gif2h5
 bin/h52gif
+bin/h5c++
 bin/h5cc
+bin/h5createU8
 bin/h5debug
+bin/h5diff
 bin/h5dump
 bin/h5import
 bin/h5ls
-bin/h5perf
 bin/h5redeploy
 bin/h5repart
 include/H5ACpublic.h
 include/H5AbstractDs.h
-include/H5Alltypes.h
 include/H5Apublic.h
 include/H5AtomType.h
 include/H5Attribute.h
@@ -30,6 +31,7 @@ include/H5Epublic.h
 include/H5Exception.h
 include/H5FDcore.h
 include/H5FDfamily.h
+include/H5FDfphdf5.h
 include/H5FDgass.h
 include/H5FDlog.h
 include/H5FDmpio.h
@@ -40,6 +42,7 @@ include/H5FDsec2.h
 include/H5FDsrb.h
 include/H5FDstdio.h
 include/H5FDstream.h
+include/H5FPpublic.h
 include/H5FaccProp.h
 include/H5FcreatProp.h
 include/H5File.h
@@ -50,7 +53,6 @@ include/H5Group.h
 include/H5HGpublic.h
 include/H5HLpublic.h
 include/H5IdComponent.h
-include/H5Idtemplates.h
 include/H5Include.h
 include/H5IntType.h
 include/H5Ipublic.h
@@ -76,3 +78,31 @@ lib/libhdf5.settings
 lib/libhdf5.so
 lib/libhdf5.so.0
 lib/libhdf5_cpp.a
+share/examples/hdf5/c/h5_attribute.c
+share/examples/hdf5/c/h5_chunk_read.c
+share/examples/hdf5/c/h5_compound.c
+share/examples/hdf5/c/h5_drivers.c
+share/examples/hdf5/c/h5_extend_write.c
+share/examples/hdf5/c/h5_group.c
+share/examples/hdf5/c/h5_mount.c
+share/examples/hdf5/c/h5_read.c
+share/examples/hdf5/c/h5_reference.c
+share/examples/hdf5/c/h5_select.c
+share/examples/hdf5/c/h5_write.c
+share/examples/hdf5/c/ph5example.c
+share/examples/hdf5/c++/Attributes.h5
+share/examples/hdf5/c++/Group.h5
+share/examples/hdf5/c++/SDS.h5
+share/examples/hdf5/c++/SDScompound.h5
+share/examples/hdf5/c++/SDSextendible.h5
+share/examples/hdf5/c++/Select.h5
+share/examples/hdf5/c++/chunks.cpp
+share/examples/hdf5/c++/compound.cpp
+share/examples/hdf5/c++/create.cpp
+share/examples/hdf5/c++/extend_ds.cpp
+share/examples/hdf5/c++/h5group.cpp
+share/examples/hdf5/c++/readdata.cpp
+share/examples/hdf5/c++/writedata.cpp
+@dirrm share/examples/hdf5/c
+@dirrm share/examples/hdf5/c++
+@dirrm share/examples/hdf5