[gentoo-commits] proj/sci:master commit in: sci-libs/hdf5/files/, sci-libs/hdf5/

["Sebastien Fabbro" <bicatali@gentoo.org>]

commit:     aa8d1629a74fa1d78d505fee76946c82d828e111
Author:     Sebastien Fabbro <sfabbro <AT> uvic <DOT> ca>
AuthorDate: Fri Jul  6 17:50:07 2012 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Fri Jul  6 17:50:07 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=aa8d1629

sci-libs/hdf5: in main tree

---
 sci-libs/hdf5/files/hdf5-1.8.8-array_bounds.patch |   22 -----
 sci-libs/hdf5/files/hdf5-1.8.8-buildsystem.patch  |   33 -------
 sci-libs/hdf5/files/hdf5-1.8.9-implicits.patch    |   55 -----------
 sci-libs/hdf5/hdf5-1.8.9_pre14.ebuild             |  101 ---------------------
 sci-libs/hdf5/metadata.xml                        |   19 ----
 5 files changed, 0 insertions(+), 230 deletions(-)

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
deleted file mode 100644
index 042d012..0000000
--- a/sci-libs/hdf5/files/hdf5-1.8.8-array_bounds.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- 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
deleted file mode 100644
index 0f85cf5..0000000
--- a/sci-libs/hdf5/files/hdf5-1.8.8-buildsystem.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-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
deleted file mode 100644
index 43e4f07..0000000
--- a/sci-libs/hdf5/files/hdf5-1.8.9-implicits.patch
+++ /dev/null
@@ -1,55 +0,0 @@
---- 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_pre14.ebuild b/sci-libs/hdf5/hdf5-1.8.9_pre14.ebuild
deleted file mode 100644
index 702301a..0000000
--- a/sci-libs/hdf5/hdf5-1.8.9_pre14.ebuild
+++ /dev/null
@@ -1,101 +0,0 @@
-# Copyright 1999-2012 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
deleted file mode 100644
index 6b6f687..0000000
--- a/sci-libs/hdf5/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?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>