Version bump

Package-Manager: portage-HEAD/cvs/Linux x86_64
Manifest-Sign-Key: 0x13CB1360

6 files changed, 194 insertions, 33 deletions

diff --git a/sci-libs/hdf5/ChangeLog b/sci-libs/hdf5/ChangeLog
index 15c930ec0885..f13d1019c107 100644
--- a/sci-libs/hdf5/ChangeLog
+++ b/sci-libs/hdf5/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-libs/hdf5
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/ChangeLog,v 1.117 2013/11/15 15:49:14 xarthisius Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/ChangeLog,v 1.118 2014/06/04 16:05:55 bicatali Exp $
+
+*hdf5-1.8.13 (04 Jun 2014)
+
+  04 Jun 2014; Sébastien Fabbro <bicatali@gentoo.org>
+  +files/hdf5-1.8.13-implicits.patch,
+  +files/hdf5-1.8.13-no-messing-ldpath.patch, +hdf5-1.8.13.ebuild, metadata.xml:
+  Version bump
 
 *hdf5-1.8.12 (15 Nov 2013)
 
diff --git a/sci-libs/hdf5/Manifest b/sci-libs/hdf5/Manifest
index 9bab58779284..775461c1facf 100644
--- a/sci-libs/hdf5/Manifest
+++ b/sci-libs/hdf5/Manifest
@@ -6,6 +6,8 @@ AUX hdf5-1.8.10-comments.patch 1584 SHA256 d8a7e54546d4571b1a494d3426ac56b0e32cd
 AUX hdf5-1.8.10-implicits.patch 1424 SHA256 7c733026322ac3fbc86af9983c81b87ba87fc6ac1149c3befb30141e83a79325 SHA512 f48c2ba476496ed137e03b49afe4c12c29a85dd8144558ad21bbef2845eb80574f59def56d4df8d339e884cb8d8662bcf800e9ace2f0b1ab50a811c4bbdd54fc WHIRLPOOL 458b385b8b6a4acd9a581e6e26ee5e582b9c8685464e9240cda75dce7f2a0be69f9011ac54df773546b18d501e092133eb7ef106f8bf1d59fd95a036c5cf026c
 AUX hdf5-1.8.10_p1-comments.patch 1014 SHA256 dd0dc78b4b431868040cb86c16b2a75e9794f9f1152c87d46ead6850649ce49c SHA512 09bd427fb73c5485362ae036b35bb68b6ecd5439d88c131bc2ccc9af86142c87f085a18a4b0f40f0fafaba2e06d677fcfa25519ef219d75c93ded2faa5a91bdf WHIRLPOOL 6a12fcda0d84420a456457a20ca9d3c0c3bb088d56ff5e2d63beace56296348ef5a1075ad19a532d955a0b469a39e50a91897215871f43c89ca83065d46919a7
 AUX hdf5-1.8.11-implicits.patch 1238 SHA256 2139c1f88573a59391de1d49f56455a0012311b34620d63eb5c946467bae7a29 SHA512 27fb12b32f53585732fcc8ce174189ab40e8e631553b657d7953fea59856aa7cdceac74746f001b02e22a87a393ded73e54e3ed6f9aadff2cf4a17042200339a WHIRLPOOL f52e42db4c492fcbf41786abb986010f1be435c68535dce2af6cb895c649e5cffb3cf72d43cfc25922afe3b5f95b154232e3b2eda64d1fd63b18136320cf0cd4
+AUX hdf5-1.8.13-implicits.patch 1034 SHA256 0b53f6295b0b4cd627ac302fdd9a06425abb0f0e2f7d66cba94fcb6058deec78 SHA512 b6b715e330dd08b357cd21ab1848dfd78b0e4e7f2284aa689aaad0b4dc8d7c6b71a07b28b62acc2c2334ba2f000fd6dccfb33c90fdcb654563a0a34b7e1a87a6 WHIRLPOOL 1d93a8766e65940c1a5a138fc62d1a0f94854f324df9995e4bd1990a732c7a306252d8eeb7a39393e9d0518372660060dc1599552620cd68373fc73a6cf71291
+AUX hdf5-1.8.13-no-messing-ldpath.patch 1141 SHA256 cec0d9c73a0f4611c3453190a2c01ad7dce4c62feea6e0a7cd79a93c84f43e62 SHA512 e43021ceb83909ab06ba378363c192aa0f1b34cc7c2b121f5000e215516dbdea1b825a53ac4023073bf4870a5c3452c22f5535391d95af45ad63a309e1ffa5a4 WHIRLPOOL d0e75d8a05e13385aedd075cf96380a10dfeffaace5d5a8ba4926a5f7ed583bf36e17583dba6110a1ddbcf2652bed15b902a57ec157fb30412a2fd3b87a303a3
 AUX hdf5-1.8.8-array_bounds.patch 624 SHA256 849df1a9fed1d6225b0032507294fbd4eec13f7514e1175907f2c9c00aafb48c SHA512 611816451d8afb284e06082c15527aa71fbf67fd1c48c64257df751e4005ff038485f2a604289f92af106d44abda7537070fc7721e6a555724645b07058dfbde WHIRLPOOL b88a7e82e5e8b99ea76a823514b395a1bb432a019b1ccd7a052c350bb11c22ed8a6bbffab38e152de5d95cb7d2572e3e6fd195fb4ce049b66a7d0e38fef87684
 AUX hdf5-1.8.8-buildsystem.patch 1410 SHA256 a97a7a82197eb4f3c9d43836f24c2c2ae14962970a0b680e5305a977b8c611a5 SHA512 610264a578d292daef20e0b796ccdb899823ca9284321b67aede261717e2bb094116f7775ce9b7ed5d176c61ff187e1cad0ff3c1800c33662c411171b87c4391 WHIRLPOOL a7b58c1a2f08dc9291a7dc84a376135bf307749f27f323a627c6072f89ec44f6cab25a2219106b98b622ac7bcd5949c8915f345ad135d8117f15a28e63d37ae5
 AUX hdf5-1.8.8-implicits.patch 2005 SHA256 1fec9a12f20f28484a9047e39b4bb56694af394d9e591abf442046aed96d4b5c SHA512 eeae0ff2e9a2561b4494ac2d3853e13f9b07813f73688cf526bb57bdcda6e186a165a1be3d122c2bf60690aac4e07219c849ccda28dbddc0bd739986c5eb89a5 WHIRLPOOL d554083409fcb562bbfcf6a9c1f5a0ab8e80eeacb5db47f390dd6ae92f10e382fb67addf00a9deed7a75db4e5dbb54beb555c39048e4589f91bb5818ca332aec
@@ -16,25 +18,17 @@ AUX mpd.conf 48 SHA256 ae740cacaf2cb798921cb2092f5af98de67445e27af3f88858f3e6d2b
 DIST hdf5-1.8.10.tar.bz2 6024645 SHA256 fa6e6b37b7976edac860732b87c50370e3beba3ae784d05f16f298c033a45a44 SHA512 de9269eb21142bc92214f05293a5fb7f77eb74e4a9293f4fb26e346842ebfff340b1a13cd631082548b6fabfe9a0b670bad28e35b58675d4db55061e91a59955 WHIRLPOOL baf65f79da563de94403d34141d7e7e28cd121b693772948ed91ca5ba71c57ac7b0b292e09e0189a90dc9af3bd7a717437496752a3f9c3daa82f327f226d5023
 DIST hdf5-1.8.11.tar.bz2 5928553 SHA256 5ea1ba82fc77350ee628b795ae6ede05feeaf1c6b437911a9478de456600cafb SHA512 a29484d1b046be7cb6f050417f097859aba605c0ebab09ea568458a316d36c294576f2b115a098a330c544ff3e08e31d36cd9ca7d048892b234d61ba36240747 WHIRLPOOL c624837e5648012be706d9e7930ad9feea225ab8e5df00609f9b30b07038958f73385f3aec9435f7fc6ae0b25988dd5da65b7a08bee598d9ea772951314693b4
 DIST hdf5-1.8.12.tar.bz2 5994923 SHA256 10a369a4fc207bb09245f57c758e587420e06dfc0e445e337a58b0848b75a949 SHA512 99c922372cc9f777839356934509057c716a083c682422101af1815849d9b2b87ac992bc89795c947715be9b696fa002ab38f34d18945a4756604a69ffbb480a WHIRLPOOL ac92b0e5e49a8667b145b78429aea6b3aa2b593d727fa039534d9d736269900b75f6d3c7492c04f21220628a929788dd6c90d0337715639df1fca8f43c4fbcbb
+DIST hdf5-1.8.13.tar.bz2 9496378 SHA256 c2f5a412107aba6f99fd7a4a9db6ce5f5fc8171ec931472784e5839d26aa17ef SHA512 76dcd045c5dffe28478e9eb4ff5ff3f9d400b044c5af19d8b1040f8f0d1ecdce9c92d49f7df0450412214ff37023ea76ed031411a99dd4c2b848ebd3b332b853 WHIRLPOOL 5606cff29b21a7006467a9a19b246188aa088d042fdffcedd02782ef960b22049360c0239ec2cc932b8f1826c62c40289ff288dc33254dbbc1586c9b5212da19
 EBUILD hdf5-1.8.10.ebuild 3672 SHA256 8e6c2335caa4dfa8c0481481d3b828b4dd5f831e3d4c8d0219ca69b840af631d SHA512 26620e19aaacc5b658ef641b42a4d2fe96c18d72d8787f8245f7945b1d362fdbc608da8808da3e9c274bd9d02b327b4458a8b60a53529d18d649ca83d92aac16 WHIRLPOOL 857eec4579bd1d1889eba7a04c979835edd31f09237efb4d402950234b9fda89483f3e0306d6868031e89b3acedf83a710b18061324494397f8575436a2bc443
 EBUILD hdf5-1.8.11.ebuild 3284 SHA256 a0c80826a4dc2d0b96ba1c0efdd5d35861cea6a4a7ad36ebc1ca1f5879750986 SHA512 810909fb8550746742af71763a7e5107eb5ce54a0937c7861b7af6549a831ce261c343f2efddacd39f399f78b6644e1492d3452b57069f2ab3574c578cce64c3 WHIRLPOOL 61a47d2a9a5fd708683357b125f12e0485b7c3bbc0646ba764800da2826bd2385937196810c97268256c809525998235deaed6e809f7bb65511107753534b3f6
 EBUILD hdf5-1.8.12.ebuild 3243 SHA256 aac69a48e59dba2b3ef52c0183c6d025806a8c764845c78228a7901864bfde65 SHA512 ab9daabfcfc8a19f89c2d34776d19efe8e1ad86f83f45ea9360b4d28757951658147906f2acc17f5ec2fdeab5d18f4922e79a27eb9470a44a6d9b7f6da3af549 WHIRLPOOL 015c82f5d0d378eeb3700ac07647ab1eeefa84e16a2a77cf942b10c40d5012c366f58212e58692756fcf957c5aa190da2a2b8558cdd0630dff96d8618841f82c
-MISC ChangeLog 21874 SHA256 58719212434bc96a2862e0a3ab2216654df8cd51175e49c67ebbd5ad6bfff14c SHA512 aa92406f415ba26e0c4510f76d3a241d1525f1c637a9297dbd13bc51c429987af929835a5965774fc4e141d6e43d49daf3f8ee7a05b37d0669b395162a0b4ecc WHIRLPOOL 2436a15c1102f1d7b7410ab8dda01d5b992c28aeefa9b567a0123404fca7a9595c1fcb82bf1d9a86e601a3d0e2786806e9e2e3cf858052f4cc95c3f3fda60bbf
-MISC metadata.xml 710 SHA256 7b7f18e0b3b2975d97477a9155f7b5d1c79aeca7afa5ed03d6bd241a36a603e7 SHA512 4280f9a13672bef49ad95176d999a2d3214e2469f1cd7a50f9883755543ab74caafc53624322b6050dd066ac7d4af45f1559180d63b9d654cd1cc546f2882fd6 WHIRLPOOL e4a5effb8546579f44eaec2597d3c176ce144f099b85315d1635ffcd8598ef8035211268f898c3f72a84b8b70c6583ed11a4f35924f62c95f469f149f1277711
+EBUILD hdf5-1.8.13.ebuild 3080 SHA256 719fd9f0af78d5f786a63c4104d69f3651662bd4c8f3f9e31fa56c0a4e3fe558 SHA512 e399704fa35acd6e896e53357c5241f7bb2bf140d8d4d468cbc5a7b7a370d54f9467f153cc743e5120a4a7625f7def1ed98751eeb7a42d0d22d664deb9d83f8e WHIRLPOOL 209ab603ca707c8aad7a7ba7fb1fd36c4cc87bb35589b89949278b9efa3cd66492eba12c76a8c4b98f12acfb760a7cb6afbf513b49006628983c6726b19fd1ed
+MISC ChangeLog 22090 SHA256 fb45e5dabae9b08c69c1cf375e44d49300f094f18b28165034c1692127a727e2 SHA512 7de90c6e22b7dceb6e917a03ce54fdd2c25bb07cb499888b1a5261a0d55f759aafd90bd90b971abad077a80a963dcf7f74b50d0118e9aba54be29dfd9f8608eb WHIRLPOOL 8aac3a6420838062f976343b68e4dd4fc3b8282e86ad394b72b58b9701684c40145254338a566f484ddb0caea2d67190dbee53a4181fde41ef441a4730688452
+MISC metadata.xml 702 SHA256 86c9065ba540628d3d1fca13625ed7c92e6ff09634362c5daa76c56905ca1160 SHA512 033892c6ece179fc84c08b4fd36bd1e12fe24ce36f425a0d32d79df63f11987740171648571880c2963b4d614a853d63bf475361b906fe4f66af870dcaf7b612 WHIRLPOOL 906c13b521650a53730589a13743fe91309d4a07b4c927bb8bc49b1d7fe7c87a9c2995bb00eadbccda62d98ff93528cc438c7d883c2ff6791d8aafa7b2beb425
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diff --git a/sci-libs/hdf5/files/hdf5-1.8.13-implicits.patch b/sci-libs/hdf5/files/hdf5-1.8.13-implicits.patch
new file mode 100644
index 000000000000..2061d16f71ea
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.8.13-implicits.patch
@@ -0,0 +1,35 @@
+--- a/test/cache_common.h
++++ b/test/cache_common.h
+@@ -702,5 +702,8 @@ void validate_mdc_config(hid_t file_id,
+                          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/testpar/t_span_tree.c
++++ b/testpar/t_span_tree.c
+@@ -37,6 +37,9 @@
+ #include "hdf5.h"
+ #include "H5private.h"
+ #include "testphdf5.h"
++#define H5S_PACKAGE
++#define H5S_TESTING
++#include "H5Spkg.h"
+ 
+ 
+ static void coll_write_test(int chunk_factor);
+--- a/configure.ac
++++ b/configure.ac
+@@ -1504,6 +1504,9 @@ case "$host_cpu-$host_vendor-$host_os" in
+     ## however, we do not do this since it breaks the big test on some 
+     ## older platforms.
+     AM_CPPFLAGS="-D_BSD_SOURCE $AM_CPPFLAGS"
++    
++    ## _GNU_SOURCE is needed for vasprintf
++    AM_CPPFLAGS="-D_GNU_SOURCE $AM_CPPFLAGS"
+     ;;
+ esac
+ 
diff --git a/sci-libs/hdf5/files/hdf5-1.8.13-no-messing-ldpath.patch b/sci-libs/hdf5/files/hdf5-1.8.13-no-messing-ldpath.patch
new file mode 100644
index 000000000000..82bc5d8b120a
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.8.13-no-messing-ldpath.patch
@@ -0,0 +1,21 @@
+Prevent build system with messing up LD_LIBRARY_PATH
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -125,8 +125,6 @@ settings_DATA=libhdf5.settings
+ # Remove the generated .c file if errors occur unless HDF5_Make_Ignore
+ # is set to ignore the error.
+ H5Tinit.c: H5detect$(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) $@ ; exit 1)
+@@ -137,8 +135,6 @@ H5Tinit.c: H5detect$(EXEEXT)
+ # 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/hdf5-1.8.13.ebuild b/sci-libs/hdf5/hdf5-1.8.13.ebuild
new file mode 100644
index 000000000000..1ef0ad197a1d
--- /dev/null
+++ b/sci-libs/hdf5/hdf5-1.8.13.ebuild
@@ -0,0 +1,104 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/hdf5-1.8.13.ebuild,v 1.1 2014/06/04 16:05:55 bicatali Exp $
+
+EAPI=5
+
+FORTRAN_NEEDED=fortran
+AUTOTOOLS_AUTORECONF=1
+
+inherit autotools-utils eutils fortran-2 flag-o-matic toolchain-funcs multilib
+
+MY_P=${PN}-${PV/_p/-patch}
+
+DESCRIPTION="General purpose library and file format for storing scientific data"
+HOMEPAGE="http://www.hdfgroup.org/HDF5/"
+SRC_URI="http://www.hdfgroup.org/ftp/HDF5/releases/${MY_P}/src/${MY_P}.tar.bz2"
+
+LICENSE="NCSA-HDF"
+SLOT="0/${PV%%_p*}"
+KEYWORDS="~alpha ~amd64 ~arm ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux"
+IUSE="cxx debug examples fortran fortran2003 mpi static-libs szip threads zlib"
+
+REQUIRED_USE="
+	cxx? ( !mpi ) mpi? ( !cxx )
+	threads? ( !cxx !mpi !fortran )
+	fortran2003? ( fortran )"
+
+RDEPEND="
+	mpi? ( virtual/mpi[romio] )
+	szip? ( >=sci-libs/szip-2.1:0= )
+	zlib? ( sys-libs/zlib:0= )"
+
+DEPEND="${RDEPEND}
+	sys-devel/libtool:2
+	>=sys-devel/autoconf-2.69"
+
+S="${WORKDIR}/${MY_P}"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.8.9-static_libgfortran.patch
+	"${FILESDIR}"/${PN}-1.8.9-mpicxx.patch
+	"${FILESDIR}"/${PN}-1.8.13-no-messing-ldpath.patch
+	"${FILESDIR}"/${PN}-1.8.13-implicits.patch
+)
+
+pkg_setup() {
+	tc-export CXX CC AR # 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() {
+	# respect gentoo examples directory
+	sed \
+		-e "s:hdf5_examples:doc/${PF}/examples:g" \
+		-i $(find . -name Makefile.am) $(find . -name "run*.sh.in") || die
+	sed \
+		-e '/docdir/d' \
+		-i config/commence.am || die
+	if ! use examples; then
+		sed -e '/^install:/ s/install-examples//' \
+			-i Makefile.am || die #409091
+	fi
+	# enable shared libs by default for h5cc config utility
+	sed -i -e "s/SHLIB:-no/SHLIB:-yes/g" tools/misc/h5cc.in	|| die
+	# bug #419677
+	use prefix && \
+		append-ldflags -Wl,-rpath,"${EPREFIX}"/usr/$(get_libdir) \
+		-Wl,-rpath,"${EPREFIX}"/$(get_libdir)
+	autotools-utils_src_prepare
+}
+
+src_configure() {
+	local myeconfargs=(
+		--enable-production
+		--docdir="${EPREFIX}"/usr/share/doc/${PF}
+		--enable-deprecated-symbols
+		$(use_enable prefix sharedlib-rpath)
+		$(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)
+	)
+	autotools-utils_src_configure
+}
diff --git a/sci-libs/hdf5/metadata.xml b/sci-libs/hdf5/metadata.xml
index 0267d6039ebe..a7c6921a2f93 100644
--- a/sci-libs/hdf5/metadata.xml
+++ b/sci-libs/hdf5/metadata.xml
@@ -1,19 +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>
+<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>