science/hdf5-18: upgrade to 1.8.23

This fixes the build with recent clang.

14 files changed, 219 insertions, 354 deletions

diff --git a/science/hdf5-18/Makefile b/science/hdf5-18/Makefile
index 3c24f9321138..22467f05d507 100644
--- a/science/hdf5-18/Makefile
+++ b/science/hdf5-18/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	hdf5
-PORTVERSION=	1.8.21 # When PORTVERSION changes, please update french/med/files/patch-configure
-PORTREVISION=	4
+PORTVERSION=	1.8.23
 CATEGORIES=	science archivers graphics
 MASTER_SITES=	https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/${PORTNAME}-${PORTVERSION}/src/	\
 		http://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/${PORTNAME}-${PORTVERSION}/src/	\
@@ -14,46 +13,29 @@ WWW=		https://www.hdfgroup.org/HDF5/
 LICENSE=	BSD4CLAUSE
 LICENSE_FILE=	${WRKSRC}/COPYING
 
-OPTIONS_DEFINE=	DEBUG EXAMPLES FORTRAN SZIP
+OPTIONS_DEFINE=	EXAMPLES FORTRAN SZIP
 
-USES=		cpe libtool:keepla localbase tar:bzip2
+USES=		cmake:testing cpe libtool:keepla localbase pkgconfig tar:bzip2
 CPE_VENDOR=	hdfgroup
 USE_LDCONFIG=	yes
-GNU_CONFIGURE=	yes
 PORTSUFF=	${PORTNAME}${PKGNAMESUFFIX}
-CONFIGURE_ARGS=	--enable-cxx \
-		--enable-instrument \
-		--enable-strict-format-checks \
-		--with-pthread=/usr \
-		--with-zlib=/usr \
-		--program-suffix=${PKGNAMESUFFIX} \
-		--includedir=${PREFIX}/include/${PORTSUFF}
+CMAKE_ARGS=	-DHDF5_LIB_INFIX:STRING="-18"
 EXAMPLESDIR=	${PREFIX}/share/examples/${PORTSUFF}
 
-SUFF2FIX=	tools/misc/h5cc.in tools/misc/h5redeploy.in	\
-		c++/src/h5c++.in fortran/src/h5fc.in
+SHRFILES=	COPYING RELEASE.txt USING_HDF5_CMake.txt
 
-.include <bsd.port.options.mk>
+SUFF2FIX=	c++/src/h5c++.in fortran/src/h5fc.in
 
-.if ${PORT_OPTIONS:MDEBUG}
-CONFIGURE_ARGS+=--disable-production --enable-debug=all
-.endif
+FORTRAN_USES=		fortran
+FORTRAN_CMAKE_BOOL=	HDF5_BUILD_FORTRAN
+FORTRAN_PLIST_SUB=	FORTRAN=""
+FORTRAN_PLIST_SUB_OFF=	FORTRAN="@comment "
+FORTRAN__VARS=		FCFLAGS_f90="${FCFLAGS}" LIBS="-lstdc++"
 
-.if ${PORT_OPTIONS:MFORTRAN}
-USES+=		fortran
-CONFIGURE_ARGS+=--enable-fortran
-CONFIGURE_ENV+=	F9X=${FC}
-PLIST_SUB+=	FORTRAN=""
-FCFLAGS_f90=	${FCFLAGS}
-LIBS+=		-lstdc++
-.else
-PLIST_SUB+=	FORTRAN="@comment "
-.endif
+SZIP_CMAKE_BOOL=	HDF5_ENABLE_SZIP_SUPPORT
+SZIP_LIB_DEPENDS=	libsz.so:science/libaec
 
-.if ${PORT_OPTIONS:MSZIP}
-LIB_DEPENDS+=	libsz.so:science/libaec
-CONFIGURE_ARGS+=--with-szlib=${LOCALBASE}
-.endif
+EXAMPLES_CMAKE_BOOL=	HDF5_BUILD_EXAMPLES
 
 pre-configure:
 	${REINPLACE_CMD} -e 's|-lpthread|${PTHREAD_LIBS}|g' ${WRKSRC}/configure
@@ -64,9 +46,6 @@ pre-configure:
 		-e 's|(INSTALL)|(INSTALL_DATA)|' \
 			`${FIND} ${WRKSRC} -regex '.*/examples/Makefile.in'`
 	${REINPLACE_CMD} -e 's|\[ -a|\[ -f|g' `${FIND} ${WRKSRC} -name \*.sh\*`
-.if !${PORT_OPTIONS:MEXAMPLES}
-	${REINPLACE_CMD} -e '/^install:/ s|install-examples||' ${WRKSRC}/Makefile.in
-.endif
 	${FIND} ${WRKSRC} -name Makefile.in | ${XARGS} \
 		${REINPLACE_CMD} -e 's|libhdf5|libhdf5${PKGNAMESUFFIX}|g'
 	${REINPLACE_CMD} -e 's|libhdf5|libhdf5${PKGNAMESUFFIX}|g'	\
@@ -74,16 +53,38 @@ pre-configure:
 .for pf in ${SUFF2FIX}
 	${REINPLACE_CMD} -e 's|%%SUFF%%|${PKGNAMESUFFIX}|g' ${WRKSRC}/${pf}
 .endfor
+	${CP} ${WRKSRC}/src/libhdf5.settings.in	\
+		${WRKSRC}/src/libhdf5-18.settings.in
 
-post-configure:
-	${CP} -p ${WRKSRC}/src/libhdf5.settings.in	\
-		${WRKSRC}/src/libhdf5${PKGNAMESUFFIX}.settings.in
-	${CP} -p ${WRKSRC}/src/libhdf5.settings		\
-		${WRKSRC}/src/libhdf5${PKGNAMESUFFIX}.settings
 post-stage:
-.if ${PORT_OPTIONS:MFORTRAN}
-	${MV} ${STAGEDIR}${PREFIX}/bin/h5fc ${STAGEDIR}${PREFIX}/bin/h5fc${PKGNAMESUFFIX}
-.endif
+	cd ${STAGEDIR}${PREFIX}/bin && ( \
+		for f in `${FIND} . -type f`; do \
+			${MV} $$f $${f}-18; \
+		done; \
+	)
+	${MKDIR} ${STAGEDIR}${PREFIX}/include/hdf5-18
+	${MV} ${STAGEDIR}${PREFIX}/include/*.h	\
+		${STAGEDIR}${PREFIX}/include/hdf5-18/
+	@${MKDIR} ${STAGEDIR}${DATADIR}-18 ${STAGEDIR}${PREFIX}/lib/cmake/hdf5-18
+	${MV} ${STAGEDIR}${PREFIX}/cmake/* ${STAGEDIR}${PREFIX}/lib/cmake/hdf5-18
+.for f in ${SHRFILES}
+	${MV} ${STAGEDIR}${PREFIX}/share/${f} ${STAGEDIR}${DATADIR}-18
+.endfor
+	${MV} ${STAGEDIR}${PREFIX}/lib/libhdf5.settings	\
+		${STAGEDIR}${PREFIX}/lib/libhdf5-18.settings
+	${RMDIR} ${STAGEDIR}${PREFIX}/cmake
+
+post-stage-FORTRAN-on:
+.for ext in mod f90
+	${MV} ${STAGEDIR}${PREFIX}/include/*.${ext}	\
+		${STAGEDIR}${PREFIX}/include/hdf5-18/
+.endfor
+	${MV} ${STAGEDIR}${PREFIX}/mod/* ${STAGEDIR}${PREFIX}/include/hdf5-18/
+	${RMDIR} ${STAGEDIR}${PREFIX}/mod
+
+post-install-EXAMPLES-on:
+	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
+	cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}
 
 regression-test test: build
 	cd ${WRKSRC}/ && ${SETENV} ${MAKE_ENV} ${MAKE} check
diff --git a/science/hdf5-18/distinfo b/science/hdf5-18/distinfo
index c94096ef1d50..ec5713db6a55 100644
--- a/science/hdf5-18/distinfo
+++ b/science/hdf5-18/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1541674750
-SHA256 (hdf5-1.8.21.tar.bz2) = e5b1b1dee44a64b795a91c3321ab7196d9e0871fe50d42969761794e3899f40d
-SIZE (hdf5-1.8.21.tar.bz2) = 6872822
+TIMESTAMP = 1678016444
+SHA256 (hdf5-1.8.23.tar.bz2) = 69ac1f7e28de5a96b45fd597f18b2ce1e1c47f4b2b64dc848a64be66722da64e
+SIZE (hdf5-1.8.23.tar.bz2) = 7683643
diff --git a/science/hdf5-18/files/patch-c++_src_h5c++.in b/science/hdf5-18/files/patch-c++_src_h5c++.in
index 09034d28c9d6..b2719e334fbc 100644
--- a/science/hdf5-18/files/patch-c++_src_h5c++.in
+++ b/science/hdf5-18/files/patch-c++_src_h5c++.in
@@ -1,4 +1,4 @@
---- c++/src/h5c++.in.orig	2017-06-15 15:46:52 UTC
+--- c++/src/h5c++.in.orig	2023-01-30 14:52:50 UTC
 +++ c++/src/h5c++.in
 @@ -159,7 +159,7 @@ usage() {
  # libhdf5.settings file reside in the lib directory.
@@ -11,7 +11,7 @@
  
 @@ -313,9 +313,9 @@ if test "x$do_link" = "xyes"; then
    shared_link=""
-   # conditionnaly link with the hl library  
+   # conditionally link with the hl library  
    if test "X$HL" = "Xhl"; then
 -   libraries=" $libraries -lhdf5_hl_cpp -lhdf5_cpp -lhdf5_hl -lhdf5 "
 +   libraries=" $libraries -lhdf5%%SUFF%%_hl_cpp -lhdf5%%SUFF%%_cpp -lhdf5%%SUFF%%_hl -lhdf5%%SUFF%% "
diff --git a/science/hdf5-18/files/patch-c++_test_Makefile.in b/science/hdf5-18/files/patch-c++_test_Makefile.in
deleted file mode 100644
index b8ac4a5f78e0..000000000000
--- a/science/hdf5-18/files/patch-c++_test_Makefile.in
+++ /dev/null
@@ -1,12 +0,0 @@
---- c++/test/Makefile.in.orig	2017-06-15 17:14:28 UTC
-+++ c++/test/Makefile.in
-@@ -408,8 +408,7 @@ AMTAR = @AMTAR@
- AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
- 
- # Include src, test, and c++/src directories
--AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@ -I$(top_srcdir)/src \
--	-I$(top_srcdir)/test -I$(top_srcdir)/c++/src
-+AM_CPPFLAGS =  -I$(top_srcdir)/src -I$(top_srcdir)/test -I$(top_srcdir)/c++/src @AM_CPPFLAGS@ @H5_CPPFLAGS@
- AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
- AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
- AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
diff --git a/science/hdf5-18/files/patch-fortran_src_Makefile.in b/science/hdf5-18/files/patch-fortran_src_Makefile.in
deleted file mode 100644
index 1a6e4dae5586..000000000000
--- a/science/hdf5-18/files/patch-fortran_src_Makefile.in
+++ /dev/null
@@ -1,11 +0,0 @@
---- fortran/src/Makefile.in.orig	2017-06-15 17:14:28 UTC
-+++ fortran/src/Makefile.in
-@@ -244,7 +244,7 @@ am__v_FC_1 = 
- FCLD = $(FC)
- FCLINK = $(LIBTOOL) $(AM_V_lt) --tag=FC $(AM_LIBTOOLFLAGS) \
- 	$(LIBTOOLFLAGS) --mode=link $(FCLD) $(AM_FCFLAGS) $(FCFLAGS) \
--	$(AM_LDFLAGS) $(LDFLAGS) -o $@
-+	$(LDFLAGS) -o $@
- AM_V_FCLD = $(am__v_FCLD_@AM_V@)
- am__v_FCLD_ = $(am__v_FCLD_@AM_DEFAULT_V@)
- am__v_FCLD_0 = @echo "  FCLD    " $@;
diff --git a/science/hdf5-18/files/patch-fortran_src_h5fc.in b/science/hdf5-18/files/patch-fortran_src_h5fc.in
index b6527043c60f..7ba1b0320ef9 100644
--- a/science/hdf5-18/files/patch-fortran_src_h5fc.in
+++ b/science/hdf5-18/files/patch-fortran_src_h5fc.in
@@ -1,6 +1,6 @@
---- fortran/src/h5fc.in.orig	2017-06-15 15:46:52 UTC
+--- fortran/src/h5fc.in.orig	2023-01-30 14:52:50 UTC
 +++ fortran/src/h5fc.in
-@@ -151,10 +151,10 @@ usage() {
+@@ -152,10 +152,10 @@ usage() {
  }
  
  # Show the configuration summary of the library recorded in the
@@ -13,9 +13,9 @@
    status=$?
  }
  
-@@ -300,9 +300,9 @@ if test "x$do_link" = "xyes"; then
+@@ -301,9 +301,9 @@ if test "x$do_link" = "xyes"; then
    shared_link=""
- # conditionnaly link with the hl library
+ # conditionally link with the hl library
    if test "X$HL" = "Xhl"; then
 -   libraries=" $libraries -lhdf5hl_fortran -lhdf5_hl -lhdf5_fortran -lhdf5 "
 +   libraries=" $libraries -lhdf5%%SUFF%%hl_fortran -lhdf5%%SUFF%%_hl -lhdf5%%SUFF%%_fortran -lhdf5%%SUFF%% "
@@ -25,7 +25,7 @@
    fi
    link_args="$link_args -L${libdir}"
  
-@@ -320,22 +320,22 @@ if test "x$do_link" = "xyes"; then
+@@ -321,22 +321,22 @@ if test "x$do_link" = "xyes"; then
    fi
  
    if test "x$USE_SHARED_LIB" != "xyes"; then
diff --git a/science/hdf5-18/files/patch-fortran_test_Makefile.in b/science/hdf5-18/files/patch-fortran_test_Makefile.in
deleted file mode 100644
index 99931e76f95f..000000000000
--- a/science/hdf5-18/files/patch-fortran_test_Makefile.in
+++ /dev/null
@@ -1,20 +0,0 @@
---- fortran/test/Makefile.in.orig	2017-06-15 17:14:28 UTC
-+++ fortran/test/Makefile.in
-@@ -153,7 +153,7 @@ fortranlib_test_DEPENDENCIES = libh5test
- 	$(LIBH5F) $(LIBHDF5)
- fortranlib_test_LINK = $(LIBTOOL) $(AM_V_lt) --tag=FC \
- 	$(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(FCLD) \
--	$(fortranlib_test_FCFLAGS) $(FCFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-+	$(fortranlib_test_FCFLAGS) $(FCFLAGS) $(LDFLAGS) \
- 	-o $@
- am_fortranlib_test_1_8_OBJECTS = tH5O.$(OBJEXT) tH5A_1_8.$(OBJEXT) \
- 	tH5G_1_8.$(OBJEXT) tH5MISC_1_8.$(OBJEXT) tHDF5_1_8.$(OBJEXT) \
-@@ -222,7 +222,7 @@ am__v_FC_1 = 
- FCLD = $(FC)
- FCLINK = $(LIBTOOL) $(AM_V_lt) --tag=FC $(AM_LIBTOOLFLAGS) \
- 	$(LIBTOOLFLAGS) --mode=link $(FCLD) $(AM_FCFLAGS) $(FCFLAGS) \
--	$(AM_LDFLAGS) $(LDFLAGS) -o $@
-+	$(LDFLAGS) -o $@
- AM_V_FCLD = $(am__v_FCLD_@AM_V@)
- am__v_FCLD_ = $(am__v_FCLD_@AM_DEFAULT_V@)
- am__v_FCLD_0 = @echo "  FCLD    " $@;
diff --git a/science/hdf5-18/files/patch-hl_c++_test_Makefile.in b/science/hdf5-18/files/patch-hl_c++_test_Makefile.in
deleted file mode 100644
index 52a141401b2a..000000000000
--- a/science/hdf5-18/files/patch-hl_c++_test_Makefile.in
+++ /dev/null
@@ -1,16 +0,0 @@
---- hl/c++/test/Makefile.in.orig	2017-06-15 17:14:28 UTC
-+++ hl/c++/test/Makefile.in
-@@ -404,10 +404,11 @@ AMTAR = @AMTAR@
- AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
- 
- # Include directories
--AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@ -I$(top_srcdir)/src \
-+AM_CPPFLAGS = -I$(top_srcdir)/src \
- 	-I$(top_srcdir)/c++/src -I$(top_srcdir)/hl/src \
- 	-I$(top_srcdir)/hl/c++/src -I$(top_srcdir)/test \
--	-I$(top_builddir)/hl/test -I$(top_srcdir)/hl/test
-+	-I$(top_builddir)/hl/test -I$(top_srcdir)/hl/test \
-+	@AM_CPPFLAGS@ @H5_CPPFLAGS@
- AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
- AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
- AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
diff --git a/science/hdf5-18/files/patch-hl_fortran_test_Makefile.in b/science/hdf5-18/files/patch-hl_fortran_test_Makefile.in
deleted file mode 100644
index 3222e5943938..000000000000
--- a/science/hdf5-18/files/patch-hl_fortran_test_Makefile.in
+++ /dev/null
@@ -1,11 +0,0 @@
---- hl/fortran/test/Makefile.in.orig	2017-06-15 17:14:28 UTC
-+++ hl/fortran/test/Makefile.in
-@@ -165,7 +165,7 @@ am__v_FC_1 = 
- FCLD = $(FC)
- FCLINK = $(LIBTOOL) $(AM_V_lt) --tag=FC $(AM_LIBTOOLFLAGS) \
- 	$(LIBTOOLFLAGS) --mode=link $(FCLD) $(AM_FCFLAGS) $(FCFLAGS) \
--	$(AM_LDFLAGS) $(LDFLAGS) -o $@
-+	$(LDFLAGS) -o $@
- AM_V_FCLD = $(am__v_FCLD_@AM_V@)
- am__v_FCLD_ = $(am__v_FCLD_@AM_DEFAULT_V@)
- am__v_FCLD_0 = @echo "  FCLD    " $@;
diff --git a/science/hdf5-18/files/patch-src-H5FDdirect.c b/science/hdf5-18/files/patch-src-H5FDdirect.c
index e98164e3f10b..055e931da400 100644
--- a/science/hdf5-18/files/patch-src-H5FDdirect.c
+++ b/science/hdf5-18/files/patch-src-H5FDdirect.c
@@ -1,4 +1,4 @@
---- src/H5FDdirect.c.orig	2017-06-15 15:47:13 UTC
+--- src/H5FDdirect.c.orig	2023-01-30 14:52:51 UTC
 +++ src/H5FDdirect.c
 @@ -27,6 +27,8 @@
   * this file. */
@@ -6,6 +6,6 @@
  
 +#define O_DIRECT	0x00010000
 +
- #include "H5private.h"    /* Generic Functions      */
- #include "H5Eprivate.h"    /* Error handling        */
- #include "H5Fprivate.h"    /* File access        */
+ #include "H5private.h"   /* Generic Functions        */
+ #include "H5Eprivate.h"  /* Error handling           */
+ #include "H5Fprivate.h"  /* File access              */
diff --git a/science/hdf5-18/files/patch-tools_misc_Makefile.in b/science/hdf5-18/files/patch-tools_misc_Makefile.in
deleted file mode 100644
index 5ca7142d4e43..000000000000
--- a/science/hdf5-18/files/patch-tools_misc_Makefile.in
+++ /dev/null
@@ -1,25 +0,0 @@
---- tools/misc/Makefile.in.orig	2017-06-15 17:14:30 UTC
-+++ tools/misc/Makefile.in
-@@ -684,7 +684,7 @@ LIBH5CPP_HL = $(top_builddir)/hl/c++/src
- # Scripts used to build examples
- # If only shared libraries have been installed, have h5cc build examples with
- # shared libraries instead of static libraries
--H5CC = ${DESTDIR}$(bindir)/h5cc
-+H5CC = ${DESTDIR}$(bindir)/$(H5CC_NAME)
- H5CC_PP = ${DESTDIR}$(bindir)/h5pcc
- H5FC = ${DESTDIR}$(bindir)/h5fc
- H5FC_PP = ${DESTDIR}$(bindir)/h5pfc
-@@ -725,11 +725,11 @@ DISTCLEANFILES = h5cc testh5repart.sh
- 
- # All programs rely on hdf5 library and h5tools library
- LDADD = $(LIBH5TOOLS) $(LIBHDF5)
--@BUILD_PARALLEL_CONDITIONAL_FALSE@H5CC_NAME = h5cc
-+@BUILD_PARALLEL_CONDITIONAL_FALSE@H5CC_NAME = h5cc-18
- 
- # h5cc needs custom install and uninstall rules, since it may be
- # named h5pcc if hdf5 is being built in parallel mode.
--@BUILD_PARALLEL_CONDITIONAL_TRUE@H5CC_NAME = h5pcc
-+@BUILD_PARALLEL_CONDITIONAL_TRUE@H5CC_NAME = h5pcc-18
- 
- # Automake needs to be taught how to build lib, dyn, progs, and tests targets.
- # These will be filled in automatically for the most part (e.g.,
diff --git a/science/hdf5-18/files/patch-tools_misc_h5cc.in b/science/hdf5-18/files/patch-tools_misc_h5cc.in
deleted file mode 100644
index d096cd7a5ea0..000000000000
--- a/science/hdf5-18/files/patch-tools_misc_h5cc.in
+++ /dev/null
@@ -1,36 +0,0 @@
---- tools/misc/h5cc.in.orig	2017-06-15 15:47:13 UTC
-+++ tools/misc/h5cc.in
-@@ -170,7 +170,7 @@ usage() {
- # libhdf5.settings file reside in the lib directory.
- showconfigure()
- {
--  cat ${libdir}/libhdf5.settings
-+  cat ${libdir}/libhdf5%%SUFF%%.settings
-   status=$?
- }
- 
-@@ -327,9 +327,9 @@ if test "x$do_link" = "xyes"; then
-   shared_link=""
- # conditionnaly link with the hl library  
-   if test "X$HL" = "Xhl"; then
--   libraries=" $libraries -lhdf5_hl -lhdf5 "
-+   libraries=" $libraries -lhdf5%%SUFF%%_hl -lhdf5%%SUFF%% "
-   else
--   libraries=" $libraries  -lhdf5 "
-+   libraries=" $libraries  -lhdf5%%SUFF%% "
-   fi
-   link_args="$link_args -L${libdir}"
- 
-@@ -360,10 +360,10 @@ if test "x$do_link" = "xyes"; then
-     for lib in $libraries; do
-       case "$lib" in
-         -lhdf5)
--          new_libraries="$new_libraries ${libdir}/libhdf5.a"
-+          new_libraries="$new_libraries ${libdir}/libhdf5%%SUFF%%.a"
-           ;;
-         -lhdf5_hl)
--          new_libraries="$new_libraries ${libdir}/libhdf5_hl.a"
-+          new_libraries="$new_libraries ${libdir}/libhdf5%%SUFF%%_hl.a"
-           ;;
-         *)
-           new_libraries="$new_libraries $lib"
diff --git a/science/hdf5-18/files/patch-tools_misc_h5redeploy.in b/science/hdf5-18/files/patch-tools_misc_h5redeploy.in
deleted file mode 100644
index d51ee4720ab9..000000000000
--- a/science/hdf5-18/files/patch-tools_misc_h5redeploy.in
+++ /dev/null
@@ -1,11 +0,0 @@
---- tools/misc/h5redeploy.in.orig	2017-06-15 15:47:13 UTC
-+++ tools/misc/h5redeploy.in
-@@ -145,7 +145,7 @@ if [ -z "$includedir" ]; then
-     includedir='${prefix}'/include # use single quotes to prevent expansion of $
- fi
- 
--for x in $h5tools; do
-+for x in $h5tools%%SUFF%%; do
-     if [ -f $x ]; then
- 	foundtools="$foundtools $x"
- 	if [ ! -w $x ]; then
diff --git a/science/hdf5-18/pkg-plist b/science/hdf5-18/pkg-plist
index 12adce530109..f860ea7ce01a 100644
--- a/science/hdf5-18/pkg-plist
+++ b/science/hdf5-18/pkg-plist
@@ -1,97 +1,82 @@
 bin/gif2h5-18
+bin/gif2h5-shared-18
 bin/h52gif-18
-bin/h5c++-18
+bin/h52gif-shared-18
 bin/h5cc-18
 bin/h5copy-18
+bin/h5copy-shared-18
 bin/h5debug-18
+bin/h5debug-shared-18
 bin/h5diff-18
+bin/h5diff-shared-18
 bin/h5dump-18
+bin/h5dump-shared-18
 %%FORTRAN%%bin/h5fc-18
+bin/h5hlcc-18
+%%FORTRAN%%bin/h5hlfc-18
 bin/h5import-18
+bin/h5import-shared-18
 bin/h5jam-18
+bin/h5jam-shared-18
 bin/h5ls-18
+bin/h5ls-shared-18
 bin/h5mkgrp-18
-bin/h5perf_serial-18
-bin/h5redeploy-18
+bin/h5mkgrp-shared-18
 bin/h5repack-18
+bin/h5repack-shared-18
 bin/h5repart-18
+bin/h5repart-shared-18
+bin/h5repart_test-18
 bin/h5stat-18
+bin/h5stat-shared-18
 bin/h5unjam-18
-include/hdf5-18/H5AbstractDs.h
+bin/h5unjam-shared-18
 include/hdf5-18/H5ACpublic.h
-include/hdf5-18/H5AcreatProp.h
-include/hdf5-18/H5api_adpt.h
 include/hdf5-18/H5Apublic.h
-include/hdf5-18/H5ArrayType.h
-include/hdf5-18/H5AtomType.h
-include/hdf5-18/H5Attribute.h
-include/hdf5-18/H5Classes.h
-include/hdf5-18/H5CommonFG.h
-include/hdf5-18/H5CompType.h
-include/hdf5-18/H5Cpp.h
-include/hdf5-18/H5CppDoc.h
 include/hdf5-18/H5Cpublic.h
-include/hdf5-18/H5DataSet.h
-include/hdf5-18/H5DataSpace.h
-include/hdf5-18/H5DataType.h
-include/hdf5-18/H5DcreatProp.h
 include/hdf5-18/H5DOpublic.h
-include/hdf5-18/H5Dpublic.h
 include/hdf5-18/H5DSpublic.h
-include/hdf5-18/H5DxferProp.h
-include/hdf5-18/H5EnumType.h
+include/hdf5-18/H5Dpublic.h
 include/hdf5-18/H5Epubgen.h
 include/hdf5-18/H5Epublic.h
-include/hdf5-18/H5Exception.h
-include/hdf5-18/H5FaccProp.h
-include/hdf5-18/H5FcreatProp.h
 include/hdf5-18/H5FDcore.h
 include/hdf5-18/H5FDdirect.h
 include/hdf5-18/H5FDfamily.h
+include/hdf5-18/H5FDhdfs.h
 include/hdf5-18/H5FDlog.h
 include/hdf5-18/H5FDmpi.h
 include/hdf5-18/H5FDmpio.h
 include/hdf5-18/H5FDmulti.h
 include/hdf5-18/H5FDpublic.h
+include/hdf5-18/H5FDros3.h
+include/hdf5-18/H5FDs3comms.h
 include/hdf5-18/H5FDsec2.h
 include/hdf5-18/H5FDstdio.h
-include/hdf5-18/H5File.h
-include/hdf5-18/H5FloatType.h
+include/hdf5-18/H5FDwindows.h
 include/hdf5-18/H5Fpublic.h
 include/hdf5-18/H5Gpublic.h
-include/hdf5-18/H5Group.h
-include/hdf5-18/H5IdComponent.h
 include/hdf5-18/H5IMpublic.h
-include/hdf5-18/H5Include.h
-include/hdf5-18/H5IntType.h
 include/hdf5-18/H5Ipublic.h
-include/hdf5-18/H5LaccProp.h
-include/hdf5-18/H5LcreatProp.h
-include/hdf5-18/H5Library.h
-include/hdf5-18/H5Location.h
-include/hdf5-18/H5Lpublic.h
+include/hdf5-18/H5LTparse.h
 include/hdf5-18/H5LTpublic.h
+include/hdf5-18/H5Lpublic.h
 include/hdf5-18/H5MMpublic.h
-include/hdf5-18/H5Object.h
-include/hdf5-18/H5OcreatProp.h
 include/hdf5-18/H5Opublic.h
-include/hdf5-18/H5PacketTable.h
 include/hdf5-18/H5PLextern.h
 include/hdf5-18/H5PLpublic.h
-include/hdf5-18/H5Ppublic.h
-include/hdf5-18/H5PredType.h
-include/hdf5-18/H5PropList.h
 include/hdf5-18/H5PTpublic.h
+include/hdf5-18/H5Ppublic.h
 include/hdf5-18/H5Rpublic.h
 include/hdf5-18/H5Spublic.h
-include/hdf5-18/H5StrType.h
-include/hdf5-18/H5StrcreatProp.h
 include/hdf5-18/H5TBpublic.h
 include/hdf5-18/H5Tpublic.h
-include/hdf5-18/H5VarLenType.h
 include/hdf5-18/H5Zpublic.h
+include/hdf5-18/H5api_adpt.h
+%%FORTRAN%%include/hdf5-18/H5f90.h
 %%FORTRAN%%include/hdf5-18/H5f90i.h
 %%FORTRAN%%include/hdf5-18/H5f90i_gen.h
+%%FORTRAN%%include/hdf5-18/H5f90proto.h
+%%FORTRAN%%include/hdf5-18/H5fortran_types.f90
 include/hdf5-18/H5overflow.h
 include/hdf5-18/H5pubconf.h
 include/hdf5-18/H5public.h
@@ -126,130 +111,151 @@ include/hdf5-18/H5version.h
 %%FORTRAN%%include/hdf5-18/h5t.mod
 %%FORTRAN%%include/hdf5-18/h5t_provisional.mod
 %%FORTRAN%%include/hdf5-18/h5tb.mod
-%%FORTRAN%%include/hdf5-18/h5test_kind_storage_size_mod.mod
 %%FORTRAN%%include/hdf5-18/h5z.mod
 include/hdf5-18/hdf5.h
 %%FORTRAN%%include/hdf5-18/hdf5.mod
 include/hdf5-18/hdf5_hl.h
+%%FORTRAN%%include/hdf5-18/shared/h5_dble_interface.mod
+%%FORTRAN%%include/hdf5-18/shared/h5a.mod
+%%FORTRAN%%include/hdf5-18/shared/h5a_provisional.mod
+%%FORTRAN%%include/hdf5-18/shared/h5d.mod
+%%FORTRAN%%include/hdf5-18/shared/h5d_provisional.mod
+%%FORTRAN%%include/hdf5-18/shared/h5ds.mod
+%%FORTRAN%%include/hdf5-18/shared/h5e.mod
+%%FORTRAN%%include/hdf5-18/shared/h5e_provisional.mod
+%%FORTRAN%%include/hdf5-18/shared/h5f.mod
+%%FORTRAN%%include/hdf5-18/shared/h5f_provisional.mod
+%%FORTRAN%%include/hdf5-18/shared/h5fortran_types.mod
+%%FORTRAN%%include/hdf5-18/shared/h5g.mod
+%%FORTRAN%%include/hdf5-18/shared/h5global.mod
+%%FORTRAN%%include/hdf5-18/shared/h5i.mod
+%%FORTRAN%%include/hdf5-18/shared/h5im.mod
+%%FORTRAN%%include/hdf5-18/shared/h5l.mod
+%%FORTRAN%%include/hdf5-18/shared/h5l_provisional.mod
+%%FORTRAN%%include/hdf5-18/shared/h5lib.mod
+%%FORTRAN%%include/hdf5-18/shared/h5lib_provisional.mod
+%%FORTRAN%%include/hdf5-18/shared/h5lt.mod
+%%FORTRAN%%include/hdf5-18/shared/h5o.mod
+%%FORTRAN%%include/hdf5-18/shared/h5o_provisional.mod
+%%FORTRAN%%include/hdf5-18/shared/h5p.mod
+%%FORTRAN%%include/hdf5-18/shared/h5p_provisional.mod
+%%FORTRAN%%include/hdf5-18/shared/h5r.mod
+%%FORTRAN%%include/hdf5-18/shared/h5r_provisional.mod
+%%FORTRAN%%include/hdf5-18/shared/h5s.mod
+%%FORTRAN%%include/hdf5-18/shared/h5t.mod
+%%FORTRAN%%include/hdf5-18/shared/h5t_provisional.mod
+%%FORTRAN%%include/hdf5-18/shared/h5tb.mod
+%%FORTRAN%%include/hdf5-18/shared/h5z.mod
+%%FORTRAN%%include/hdf5-18/shared/hdf5.mod
+%%FORTRAN%%include/hdf5-18/static/h5_dble_interface.mod
+%%FORTRAN%%include/hdf5-18/static/h5a.mod
+%%FORTRAN%%include/hdf5-18/static/h5a_provisional.mod
+%%FORTRAN%%include/hdf5-18/static/h5d.mod
+%%FORTRAN%%include/hdf5-18/static/h5d_provisional.mod
+%%FORTRAN%%include/hdf5-18/static/h5ds.mod
+%%FORTRAN%%include/hdf5-18/static/h5e.mod
+%%FORTRAN%%include/hdf5-18/static/h5e_provisional.mod
+%%FORTRAN%%include/hdf5-18/static/h5f.mod
+%%FORTRAN%%include/hdf5-18/static/h5f_provisional.mod
+%%FORTRAN%%include/hdf5-18/static/h5fortran_types.mod
+%%FORTRAN%%include/hdf5-18/static/h5g.mod
+%%FORTRAN%%include/hdf5-18/static/h5global.mod
+%%FORTRAN%%include/hdf5-18/static/h5i.mod
+%%FORTRAN%%include/hdf5-18/static/h5im.mod
+%%FORTRAN%%include/hdf5-18/static/h5l.mod
+%%FORTRAN%%include/hdf5-18/static/h5l_provisional.mod
+%%FORTRAN%%include/hdf5-18/static/h5lib.mod
+%%FORTRAN%%include/hdf5-18/static/h5lib_provisional.mod
+%%FORTRAN%%include/hdf5-18/static/h5lt.mod
+%%FORTRAN%%include/hdf5-18/static/h5o.mod
+%%FORTRAN%%include/hdf5-18/static/h5o_provisional.mod
+%%FORTRAN%%include/hdf5-18/static/h5p.mod
+%%FORTRAN%%include/hdf5-18/static/h5p_provisional.mod
+%%FORTRAN%%include/hdf5-18/static/h5r.mod
+%%FORTRAN%%include/hdf5-18/static/h5r_provisional.mod
+%%FORTRAN%%include/hdf5-18/static/h5s.mod
+%%FORTRAN%%include/hdf5-18/static/h5t.mod
+%%FORTRAN%%include/hdf5-18/static/h5t_provisional.mod
+%%FORTRAN%%include/hdf5-18/static/h5tb.mod
+%%FORTRAN%%include/hdf5-18/static/h5z.mod
+%%FORTRAN%%include/hdf5-18/static/hdf5.mod
+lib/cmake/hdf5-18/hdf5-config-version.cmake
+lib/cmake/hdf5-18/hdf5-config.cmake
+lib/cmake/hdf5-18/hdf5-targets-%%CMAKE_BUILD_TYPE%%.cmake
+lib/cmake/hdf5-18/hdf5-targets.cmake
 lib/libhdf5-18.a
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 lib/libhdf5-18.settings
 lib/libhdf5-18.so
 lib/libhdf5-18.so.10
-lib/libhdf5-18.so.10.3.2
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-lib/libhdf5-18_cpp.so.16
-lib/libhdf5-18_cpp.so.16.0.0
+lib/libhdf5-18.so.10.4.1
+%%FORTRAN%%lib/libhdf5-18_f90cstub.a
+%%FORTRAN%%lib/libhdf5-18_f90cstub.so
+%%FORTRAN%%lib/libhdf5-18_f90cstub.so.10
+%%FORTRAN%%lib/libhdf5-18_f90cstub.so.10.0.8
 %%FORTRAN%%lib/libhdf5-18_fortran.a
-%%FORTRAN%%lib/libhdf5-18_fortran.la
 %%FORTRAN%%lib/libhdf5-18_fortran.so
 %%FORTRAN%%lib/libhdf5-18_fortran.so.10
-%%FORTRAN%%lib/libhdf5-18_fortran.so.10.0.6
+%%FORTRAN%%lib/libhdf5-18_fortran.so.10.0.8
 lib/libhdf5-18_hl.a
-lib/libhdf5-18_hl.la
 lib/libhdf5-18_hl.so
 lib/libhdf5-18_hl.so.10
-lib/libhdf5-18_hl.so.10.2.2
-lib/libhdf5-18_hl_cpp.a
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-lib/libhdf5-18_hl_cpp.so
-lib/libhdf5-18_hl_cpp.so.11
-lib/libhdf5-18_hl_cpp.so.11.1.2
-%%FORTRAN%%lib/libhdf5-18hl_fortran.a
-%%FORTRAN%%lib/libhdf5-18hl_fortran.la
-%%FORTRAN%%lib/libhdf5-18hl_fortran.so
-%%FORTRAN%%lib/libhdf5-18hl_fortran.so.10
-%%FORTRAN%%lib/libhdf5-18hl_fortran.so.10.0.5
+lib/libhdf5-18_hl.so.10.2.4
+%%FORTRAN%%lib/libhdf5-18_hl_f90cstub.a
+%%FORTRAN%%lib/libhdf5-18_hl_f90cstub.so
+%%FORTRAN%%lib/libhdf5-18_hl_f90cstub.so.10
+%%FORTRAN%%lib/libhdf5-18_hl_f90cstub.so.10.0.7
+%%FORTRAN%%lib/libhdf5-18_hl_fortran.a
+%%FORTRAN%%lib/libhdf5-18_hl_fortran.so
+%%FORTRAN%%lib/libhdf5-18_hl_fortran.so.10
+%%FORTRAN%%lib/libhdf5-18_hl_fortran.so.10.0.7
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+lib/libhdf5-18_tools.so.10
+lib/libhdf5-18_tools.so.10.0.9
+libdata/pkgconfig/hdf5-18.pc
+%%FORTRAN%%libdata/pkgconfig/hdf5-18_fortran.pc
+libdata/pkgconfig/hdf5-18_hl.pc
+%%FORTRAN%%libdata/pkgconfig/hdf5-18_hl_fortran.pc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Attributes.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CMakeLists.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CMakeTests.cmake
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Makefile.am
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Makefile.in
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Makefile.in.bak
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/README
-%%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++/h5tutr_cmprss.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/h5tutr_crtatt.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/h5tutr_crtdat.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/h5tutr_crtgrp.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/h5tutr_crtgrpar.cpp
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/h5tutr_crtgrpd.cpp
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-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/h5tutr_rdwt.cpp
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-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/readdata.cpp
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-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/writedata.cpp
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-%%FORTRAN%%%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fortran/selectele.f90
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-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hl/c/ex_ds1.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hl/c/ex_image1.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hl/c/ex_image2.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hl/c/ex_lite1.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hl/c/ex_lite2.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hl/c/ex_lite3.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hl/c/ex_table_01.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hl/c/ex_table_02.c
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-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hl/c/ex_table_04.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hl/c/ex_table_05.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hl/c/ex_table_06.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hl/c/ex_table_07.c
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hl/c/ex_table_08.c
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-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hl/c/image24pixel.txt
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-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hl/c/pal_rgb.h
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-%%FORTRAN%%%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hl/fortran/ex_ds1.f90
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-%%FORTRAN%%%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hl/fortran/run-hlfortran-ex.sh
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hl/run-hl-ex.sh
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h5_attribute.c
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+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ph5example.c
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/run-all-ex.sh
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/run-all-ex.sh.bak
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+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/run-c-ex.sh.in.bak
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/testh5cc.sh.in
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/testh5cc.sh.in.bak
+%%DATADIR%%-18/COPYING
+%%DATADIR%%-18/RELEASE.txt
+%%DATADIR%%-18/USING_HDF5_CMake.txt