[sci-libs/hdf5] add developement snapshot

6 files changed, 231 insertions, 0 deletions

diff --git a/sci-libs/hdf5/Manifest b/sci-libs/hdf5/Manifest
new file mode 100644
index 000000000..412651171
--- /dev/null
+++ b/sci-libs/hdf5/Manifest
@@ -0,0 +1 @@
+DIST hdf5-1.8.9-snap13.tar.bz2 5835537 SHA256 870465412642e71291ecd94cee998e3b874de0c6fe63197589f744becca94a1f SHA512 1d976e42cef9c6b7f96066bc1e21112e13c6f497c313532cc64afa80c28d4f675176d718d6ffb8ffdd6a88c147a99b108fdaa63fd68736a1d3c049518c433543 WHIRLPOOL c076ab336cbb2aa2638ab3156a4657351b81812d1bc10c45fa0466e7af6b9ec1897638974d0ec5ac2f41e43927b65affd1c860fd462a32a44b20de3754b0623d
diff --git a/sci-libs/hdf5/files/hdf5-1.8.8-array_bounds.patch b/sci-libs/hdf5/files/hdf5-1.8.8-array_bounds.patch
new file mode 100644
index 000000000..042d012d1
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.8.8-array_bounds.patch
@@ -0,0 +1,22 @@
+--- a/perform/pio_engine.c
++++ b/perform/pio_engine.c
+@@ -454,7 +454,7 @@
+         subdir = (user ? user : login);
+ 
+         if (subdir) {
+-            for (i = 0; i < size && prefix[i]; i++)
++            for (i = 0; i < size-1 && prefix[i]; i++)
+                 fullname[i] = prefix[i];
+ 
+             fullname[i++] = '/';
+--- a/perform/sio_engine.c
++++ b/perform/sio_engine.c
+@@ -353,7 +353,7 @@
+     subdir = (user ? user : login);
+ 
+     if (subdir) {
+-        for (i = 0; i < size && prefix[i]; i++)
++        for (i = 0; i < size-1 && prefix[i]; i++)
+         fullname[i] = prefix[i];
+ 
+         fullname[i++] = '/';
diff --git a/sci-libs/hdf5/files/hdf5-1.8.8-buildsystem.patch b/sci-libs/hdf5/files/hdf5-1.8.8-buildsystem.patch
new file mode 100644
index 000000000..0f85cf5ed
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.8.8-buildsystem.patch
@@ -0,0 +1,33 @@
+Prevent build system with messing up LD_LIBRARY_PATH
+
+--- a/configure.in
++++ b/configure.in
+@@ -2328,8 +2328,6 @@
+ dnl
+ AC_MSG_CHECKING([how to print long long])
+ AC_CACHE_VAL([hdf5_cv_printf_ll],
+-LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo $AM_LDFLAGS $LDFLAGS | sed -e 's/-L/:/g' -e 's/ //g'`"
+-export LD_LIBRARY_PATH
+ 
+ for hdf5_cv_printf_ll in l ll L q unknown; do
+    AC_TRY_RUN([
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -125,8 +125,6 @@
+ # Remove the generated .c file if errors occur unless HDF5_Make_Ignore
+ # is set to ignore the error.
+ H5Tinit.c: H5detect$(EXEEXT)
+-	LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) |                  \
+-		sed -e 's/-L/:/g' -e 's/ //g'`"                               \
+ 	$(RUNSERIAL) ./H5detect$(EXEEXT) > $@  ||                               \
+ 	    (test $$HDF5_Make_Ignore && echo "*** Error ignored") ||          \
+ 	    ($(RM) $@ ; exit 1)
+@@ -137,8 +135,6 @@
+ # Remove the generated .c file if errors occur unless HDF5_Make_Ignore
+ # is set to ignore the error.
+ H5lib_settings.c: H5make_libsettings$(EXEEXT) libhdf5.settings
+-	LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) |                  \
+-		sed -e 's/-L/:/g' -e 's/ //g'`"                               \
+ 	$(RUNSERIAL) ./H5make_libsettings$(EXEEXT) > $@  ||                               \
+ 	    (test $$HDF5_Make_Ignore && echo "*** Error ignored") ||          \
+ 	    ($(RM) $@ ; exit 1)
diff --git a/sci-libs/hdf5/files/hdf5-1.8.9-implicits.patch b/sci-libs/hdf5/files/hdf5-1.8.9-implicits.patch
new file mode 100644
index 000000000..43e4f0774
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.8.9-implicits.patch
@@ -0,0 +1,55 @@
+--- b/configure.in
++++ a/configure.in
+@@ -1499,6 +1499,9 @@
+     dnl though we do not do this as it breaks the big test on older versions
+     dnl of linux (CentOS 4.6) using newer versions of gcc (4.6.2).
+     AM_CPPFLAGS="-D_BSD_SOURCE $AM_CPPFLAGS"
++
++    dnl _GNU_SOURCE is needed for vasprintf
++    AM_CPPFLAGS="-D_GNU_SOURCE $AM_CPPFLAGS"
+     ;;
+ esac
+ 
+--- a/test/cache_common.h
++++ b/test/cache_common.h
+@@ -702,5 +702,9 @@
+                          hbool_t compare_init,
+                          int test_num);
+ 
++hbool_t resize_configs_are_equal(const H5C_auto_size_ctl_t *a,
++                                 const H5C_auto_size_ctl_t *b,
++                                 hbool_t compare_init);
++
+ #endif /* _CACHE_COMMON_H */
+ 
+--- a/tools/misc/talign.c
++++ b/tools/misc/talign.c
+@@ -23,6 +23,7 @@
+ 
+ #include "hdf5.h"
+ #include "H5private.h"
++#include "h5tools.h"
+ 
+ const char *fname = "talign.h5";
+ const char *setname = "align";
+--- a/tools/h5repack/testh5repack_detect_szip.c
++++ b/tools/h5repack/testh5repack_detect_szip.c
+@@ -17,6 +17,7 @@
+ #include "h5repack.h"
+ #include "h5tools.h"
+ #include "h5test.h"
++#include "h5tools_utils.h"
+ 
+ 
+ /* Name of tool */
+--- a/hl/src/H5LTanalyze.c
++++ b/hl/src/H5LTanalyze.c
+@@ -49,7 +49,8 @@
+ #define YY_FLEX_MINOR_VERSION 5
+ 
+ #include <stdio.h>
++#include "H5pubconf.h"
+ #ifdef H5_HAVE_UNISTD_H
+ #include <unistd.h>
+ #endif
+ 
diff --git a/sci-libs/hdf5/hdf5-1.8.9_pre13.ebuild b/sci-libs/hdf5/hdf5-1.8.9_pre13.ebuild
new file mode 100644
index 000000000..698acd5f4
--- /dev/null
+++ b/sci-libs/hdf5/hdf5-1.8.9_pre13.ebuild
@@ -0,0 +1,101 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/hdf5-1.8.8.ebuild,v 1.4 2011/12/05 16:56:26 xarthisius Exp $
+
+EAPI=4
+
+inherit autotools eutils fortran-2 toolchain-funcs versionator
+
+MY_PV=$(replace_version_separator 3 '-')
+MY_PV=${MY_PV/pre/snap}
+MYP=${PN}-${MY_PV}
+VER=$(get_version_component_range 1-2)
+VER=v${VER/./}
+
+DESCRIPTION="General purpose library and file format for storing scientific data"
+HOMEPAGE="http://www.hdfgroup.org/HDF5/"
+SRC_URI="http://www.hdfgroup.uiuc.edu/ftp/pub/outgoing/${PN}/snapshots/${VER}/${MYP}.tar.bz2"
+
+LICENSE="NCSA-HDF"
+SLOT="0"
+KEYWORDS=""
+IUSE="cxx debug examples fortran fortran2003 mpi static-libs szip threads zlib"
+REQUIRED_USE="cxx? ( !mpi ) mpi? ( !cxx )
+	threads? ( !cxx !mpi !fortran )
+	fortran2003? ( fortran )"
+
+RDEPEND="fortran? ( virtual/fortran )
+	mpi? ( virtual/mpi[romio] )
+	szip? ( >=sci-libs/szip-2.1 )
+	zlib? ( sys-libs/zlib )"
+
+DEPEND="${RDEPEND}
+	sys-devel/libtool:2"
+
+S=${WORKDIR}/${MYP}
+
+pkg_setup() {
+	tc-export CXX CC FC # workaround for bug 285148
+	if use fortran; then
+		use fortran2003 && FORTRAN_STANDARD=2003
+		fortran-2_pkg_setup
+	fi
+	if use mpi; then
+		if has_version 'sci-libs/hdf5[-mpi]'; then
+			ewarn "Installing hdf5 with mpi enabled with a previous hdf5 with mpi disabled may fail."
+			ewarn "Try to uninstall the current hdf5 prior to enabling mpi support."
+		fi
+		export CC=mpicc
+		use fortran && export FC=mpif90
+	elif has_version 'sci-libs/hdf5[mpi]'; then
+		ewarn "Installing hdf5 with mpi disabled while having hdf5 installed with mpi enabled may fail."
+		ewarn "Try to uninstall the current hdf5 prior to disabling mpi support."
+	fi
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PN}-1.8.8-buildsystem.patch \
+		"${FILESDIR}"/${PN}-1.8.8-array_bounds.patch \
+		"${FILESDIR}"/${PN}-1.8.9-implicits.patch
+	# respect gentoo examples directory
+	sed \
+		-e "s:hdf5_examples:doc/${PF}/examples:g" \
+		-i $(find . -name Makefile.am) $(find . -name "run*.sh.in") || die
+	sed \
+		-e '/docdir/d' \
+		-i config/commence.am || die
+	eautoreconf
+	# enable shared libs by default for h5cc config utility
+	sed -i -e "s/SHLIB:-no/SHLIB:-yes/g" tools/misc/h5cc.in	|| die
+}
+
+src_configure() {
+	econf \
+		--disable-sharedlib-rpath \
+		--enable-production \
+		--docdir="${EPREFIX}"/usr/share/doc/${PF} \
+		--enable-deprecated-symbols \
+		--enable-shared \
+		--disable-silent-rules \
+		$(use_enable static-libs static) \
+		$(use_enable debug debug all) \
+		$(use_enable debug codestack) \
+		$(use_enable cxx) \
+		$(use_enable fortran) \
+		$(use_enable fortran2003) \
+		$(use_enable mpi parallel) \
+		$(use_enable threads threadsafe) \
+		$(use_with szip szlib) \
+		$(use_with threads pthread) \
+		$(use_with zlib) \
+		${myconf}
+}
+
+src_install() {
+	default
+	use static-libs || find "${ED}" -name '*.la' -exec rm -f {} +
+
+	if use examples; then
+		emake DESTDIR="${D}" install-examples
+	fi
+}
diff --git a/sci-libs/hdf5/metadata.xml b/sci-libs/hdf5/metadata.xml
new file mode 100644
index 000000000..6b6f68735
--- /dev/null
+++ b/sci-libs/hdf5/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci</herd>
+    <maintainer>
+        <email>xarthisius@gentoo.org</email>
+        <name>Kacper Kowalik</name>
+    </maintainer>
+	<longdescription>
+		HDF5 is a file format and library for storing scientific data. HDF5
+		was designed and implemented to address the deficiencies of HDF4.x. It
+		has a more powerful and flexible data model, supports files larger
+		than 2 GB, and supports parallel I/O.
+	</longdescription>
+	<use>
+		<flag name="fortran2003">enable new features that require Fortran 2003 
+			(http://www.hdfgroup.org/HDF5/doc/fortran/NewFeatures_F2003.pdf)</flag>
+	</use>
+</pkgmetadata>