Version bump

Package-Manager: portage-2.2.0_alpha138/cvs/Linux x86_64
Manifest-Sign-Key: 0x5D21B852895192F9

5 files changed, 223 insertions, 2 deletions

diff --git a/sci-libs/hdf5/ChangeLog b/sci-libs/hdf5/ChangeLog
index 54540e8651cc..15523d49c0c2 100644
--- a/sci-libs/hdf5/ChangeLog
+++ b/sci-libs/hdf5/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-libs/hdf5
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/ChangeLog,v 1.97 2012/11/04 14:09:16 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/ChangeLog,v 1.98 2012/11/06 19:56:41 xarthisius Exp $
+
+*hdf5-1.8.10 (06 Nov 2012)
+
+  06 Nov 2012; Kacper Kowalik <xarthisius@gentoo.org>
+  +files/hdf5-1.8.10-buildsystem.patch, +files/hdf5-1.8.10-implicits.patch,
+  +hdf5-1.8.10.ebuild:
+  Version bump
 
   04 Nov 2012; Agostino Sarubbo <ago@gentoo.org> hdf5-1.8.9-r2.ebuild:
   Stable for amd64, wrt bug #440682
diff --git a/sci-libs/hdf5/Manifest b/sci-libs/hdf5/Manifest
index 05436855d353..cc45660904db 100644
--- a/sci-libs/hdf5/Manifest
+++ b/sci-libs/hdf5/Manifest
@@ -1,3 +1,8 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA256
+
+AUX hdf5-1.8.10-buildsystem.patch 1489 SHA256 7fb52e8187009180ea0d5d45c7a48e7680c8ed49533fb2c3d48eaab979956d73 SHA512 8363e983685d7124d8a5ad528786d208d81ecc241ca325c6357eb79d1d39357cdc74c9a283d78f3d3b2a09a59ccee0cd1fb48b92f3cdd2df97b25599e79147d7 WHIRLPOOL a6b24607bf9b651bbbd05be0c755d4eb8ee463550e458940ff6b971a9533a51715a57744a3dcd3159410b88721b909863ac4469e5b3d8dd48834186269f80779
+AUX hdf5-1.8.10-implicits.patch 1424 SHA256 7c733026322ac3fbc86af9983c81b87ba87fc6ac1149c3befb30141e83a79325 SHA512 f48c2ba476496ed137e03b49afe4c12c29a85dd8144558ad21bbef2845eb80574f59def56d4df8d339e884cb8d8662bcf800e9ace2f0b1ab50a811c4bbdd54fc WHIRLPOOL 458b385b8b6a4acd9a581e6e26ee5e582b9c8685464e9240cda75dce7f2a0be69f9011ac54df773546b18d501e092133eb7ef106f8bf1d59fd95a036c5cf026c
 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
@@ -5,9 +10,28 @@ AUX hdf5-1.8.9-implicits.patch 1387 SHA256 7d62dc53f2769aef1025fb128d4e2d11a5a17
 AUX hdf5-1.8.9-mpicxx.patch 494 SHA256 b8412a94dcc88b520f28ea119694dd3037ab6bd2c2bc064ab0ab868b1eb970bb SHA512 8b4c39e40591860652547ea8ff205230da7d67488233e911cbcb3416eab561f2529c65bc5e7c9c812bf4298812346f47f9209e5f69f7e8f66ad587306a5b477b WHIRLPOOL a345a591813303a0ee87f08de2b9b96a2e80246be671dc7854307767abdc6f6db9684a7c298478090ef4e5bd9d2891e1f097cd77bae736bd39b6353c26bd80ea
 AUX hdf5-1.8.9-static_libgfortran.patch 429 SHA256 7802a4535f456c951fb4162850edd53f667ac29fc4838fce960a18f23d2dfc0d SHA512 af97c54469a90bf3b0e8ec1218d4ca95822ac0cbc7120114979fc467fe3114743c74f4d4e16f0c10b1cd82d40880ef482f6fd34e1effc7c621b981ad466204f9 WHIRLPOOL 08e6f90b86ee3020eab9c3e02caf315ff77b57365f96175c1aea6c52b254dd59d2e7bf647a6458ef51147fdb3a20622bd31bdbc82e69b0bbb689178edb6768f4
 AUX mpd.conf 48 SHA256 ae740cacaf2cb798921cb2092f5af98de67445e27af3f88858f3e6d2bbb127f4 SHA512 82eafba82e93066ee2faea52b08f59c2231a5bb1a5e64551d399dceb7e48cdb5edda51c264a2e2b6016826613dff50aa2b7d4e946eb0732e2a260332b87f2ec7 WHIRLPOOL 3fc71bb16abbc090549af95912e0945e15abf3c303d6e89bad77d6064acf30fb26067fe95f26f707cd13274f30a8ab090f9b1bf1fc26dd018e652c280dbecb54
+DIST hdf5-1.8.10.tar.bz2 6024645 SHA256 fa6e6b37b7976edac860732b87c50370e3beba3ae784d05f16f298c033a45a44 SHA512 de9269eb21142bc92214f05293a5fb7f77eb74e4a9293f4fb26e346842ebfff340b1a13cd631082548b6fabfe9a0b670bad28e35b58675d4db55061e91a59955 WHIRLPOOL baf65f79da563de94403d34141d7e7e28cd121b693772948ed91ca5ba71c57ac7b0b292e09e0189a90dc9af3bd7a717437496752a3f9c3daa82f327f226d5023
 DIST hdf5-1.8.8.tar.bz2 5827394 SHA256 b0ebb0b5478c6c0427631d4ad08f96e39f1b09fde615aa98d2a1b8fb7f6dced3 SHA512 cfa5b31e06a42308519d440a6c5792f26fea6ce27cc3624658acf4499930ac45e596c5b61c9e59d7f4d610a3a04851966929cb8da1f1d12a94b73a1f2562ed17 WHIRLPOOL 8ad9d2b79c0adf3c31db2d13e0e4df4c532e8ff583501df61af7e8bbcdcfd9d503d6816a40fc747ce61482caa8f913a6ed1550dafdb0efab4a42933f5b2933f5
 DIST hdf5-1.8.9.tar.bz2 6006715 SHA256 fafe54856b00f0d6531629f66e2c476ab6ee03458803088f270bbfc4a60966c7 SHA512 08d916c37baa14896f51492559b298bf94e8ba9a6b19ac16ff63ec5814cfc788b522386c2392abbc9d24839aac7fb4585246bd1ff57e6030a2c6d5377f719eee WHIRLPOOL 424f6e2052a8b6beaa9f37865904849419ec1155a7adf4d19aa87633315061775ca970723d8c2284456b8b4972590ce8581fac7efe687160001903afe53a9903
+EBUILD hdf5-1.8.10.ebuild 3126 SHA256 e0983e1ec4563aeb3a3686de6d48efa5eef43c2af466444ac4d8f23f0a199a82 SHA512 d617556598091067ad908b592e6984c8ce9fa62950d2cc2decd083af518ac064075d004a1b52bfccfe76ac5cd5baa91b985964b3637188d273afb2eca05a0498 WHIRLPOOL 4c774495d2c6473a132e459c78bb88aa69358edff5a754c9fdee4d15ade19aa7d0e1a6631792371febad977724d16cfed525626b27f848a0ad86f1246c8ab6b7
 EBUILD hdf5-1.8.8-r1.ebuild 2834 SHA256 f28d79faf3ccdfb132a9a1e719982b41eba7036641ff1d688fac042e4dfbaddd SHA512 6ddf7979f5dbf9800bad67b7f0cca1218d94fd67465e414fb70fe3204ddff0158729bc9a6ebe4beac3d7099db3d97b5bb49166516f84aa578dd2f1d948f63922 WHIRLPOOL bf93d43a72e59c0659479380a653bd72ea5c0a8decd6744eea551ba82e4394cdac1927a6117f41e722d33b20f396fbae64340b0e273dfbfd0a9842ad6b058c82
 EBUILD hdf5-1.8.9-r2.ebuild 3111 SHA256 0ba0a3a104fd1118d4a07769fe8a71862cafb8d8850c345698059dfcf5169b7e SHA512 796a83221c1ce411f98234643b64882628d6f44b097186e09ba6cc63457d519334fee344100409d44c70b874407d4895b8034c00935dd04201faef9656da95f8 WHIRLPOOL 6ef937678dd88474f5712ac9b4724abe99819d9c87c8b99af5a37044f8cffa1a7cf8c67d63bf84119ab317042fde0899c5852e59b1637c590bbc5fab2799e30e
-MISC ChangeLog 18959 SHA256 ab1210e9a9e0b2a7b9e8df51367409e1ea92ea5b94965db2763b936f0b93e484 SHA512 25bf88cd90aa550bf836544447e9959a00688a13bfa35657fd55f05874d74752485bdc8122f30ac8711b216c65a7a8768b3bda187c1e1bf0e094752edec77434 WHIRLPOOL d868985fd96618e4a0f478bf87b67a1d5f6fdba8160f5de6fe45e623f92d0ebbb9648a4aa789a93bcd3d4e84934e3c16730893a4a62ce1d15a61b335a489efb7
+MISC ChangeLog 19163 SHA256 efeb1cf163021066aeaf3ca37fa7c4e56e07a5ddc1ed5ddd27a6e066969010e1 SHA512 1ca3a9a97ee422dd856560f847b26af7b244cc363e83f5964365037c41f3942a279bdc1abdc06bf766cbc52275ee79d47f258ac44d40e020e153f86146bd78bb WHIRLPOOL ba89d739f4a9f3999639df880644442af4b742fafcc6fe6633963dd4d82ab94d9f11cdf7dfbdae44d34340a89fffd13d71b900007d36dd928fc14c6872dad831
 MISC metadata.xml 710 SHA256 7b7f18e0b3b2975d97477a9155f7b5d1c79aeca7afa5ed03d6bd241a36a603e7 SHA512 4280f9a13672bef49ad95176d999a2d3214e2469f1cd7a50f9883755543ab74caafc53624322b6050dd066ac7d4af45f1559180d63b9d654cd1cc546f2882fd6 WHIRLPOOL e4a5effb8546579f44eaec2597d3c176ce144f099b85315d1635ffcd8598ef8035211268f898c3f72a84b8b70c6583ed11a4f35924f62c95f469f149f1277711
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diff --git a/sci-libs/hdf5/files/hdf5-1.8.10-buildsystem.patch b/sci-libs/hdf5/files/hdf5-1.8.10-buildsystem.patch
new file mode 100644
index 000000000000..58bcc500165f
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.8.10-buildsystem.patch
@@ -0,0 +1,33 @@
+Prevent build system with messing up LD_LIBRARY_PATH
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -2331,8 +2331,6 @@ AC_TRY_COMPILE(,[
+ ##
+ AC_MSG_CHECKING([how to print long long])
+ AC_CACHE_VAL([hdf5_cv_printf_ll], [
+-LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo $AM_LDFLAGS $LDFLAGS | sed -e 's/-L/:/g' -e 's/ //g'`"
+-export LD_LIBRARY_PATH
+ 
+ for hdf5_cv_printf_ll in l ll L q unknown; do
+    AC_TRY_RUN([
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -125,8 +125,6 @@ settings_DATA=libhdf5.settings
+ # Remove the generated .c file if errors occur unless HDF5_Make_Ignore
+ # is set to ignore the error.
+ H5Tinit.c: H5detect$(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) $@ ; exit 1)
diff --git a/sci-libs/hdf5/files/hdf5-1.8.10-implicits.patch b/sci-libs/hdf5/files/hdf5-1.8.10-implicits.patch
new file mode 100644
index 000000000000..a0b59b74e703
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.8.10-implicits.patch
@@ -0,0 +1,54 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -1494,6 +1494,9 @@ case "$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"
++
++    dnl _GNU_SOURCE is needed for vasprintf
++    AM_CPPFLAGS="-D_GNU_SOURCE $AM_CPPFLAGS"
+     ;;
+ esac
+ 
+--- a/hl/src/H5LTanalyze.c
++++ b/hl/src/H5LTanalyze.c
+@@ -49,6 +49,7 @@
+ #define YY_FLEX_MINOR_VERSION 5
+ 
+ #include <stdio.h>
++#include "H5pubconf.h"
+ #ifdef H5_HAVE_UNISTD_H
+ #include <unistd.h>
+ #endif
+--- a/test/cache_common.h
++++ b/test/cache_common.h
+@@ -702,5 +702,9 @@ 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/tools/h5repack/testh5repack_detect_szip.c
++++ b/tools/h5repack/testh5repack_detect_szip.c
+@@ -18,6 +18,7 @@
+ #include "h5tools.h"
+ #include "h5tools_utils.h"
+ #include "h5test.h"
++#include "h5tools_utils.h"
+ 
+ 
+ /* Name of tool */
+--- 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";
diff --git a/sci-libs/hdf5/hdf5-1.8.10.ebuild b/sci-libs/hdf5/hdf5-1.8.10.ebuild
new file mode 100644
index 000000000000..a2ba3a2d257a
--- /dev/null
+++ b/sci-libs/hdf5/hdf5-1.8.10.ebuild
@@ -0,0 +1,103 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/hdf5-1.8.10.ebuild,v 1.1 2012/11/06 19:56:41 xarthisius Exp $
+
+EAPI=4
+
+FORTRAN_NEEDED=fortran
+
+inherit autotools eutils fortran-2 flag-o-matic toolchain-funcs multilib
+
+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/${P}/src/${P}.tar.bz2"
+
+LICENSE="NCSA-HDF"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~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 )
+	zlib? ( sys-libs/zlib )"
+
+DEPEND="${RDEPEND}
+	sys-devel/libtool:2"
+
+pkg_setup() {
+	tc-export CXX CC # workaround for bug 285148
+	if use fortran; then
+		use fortran2003 && FORTRAN_STANDARD=2003
+		fortran-2_pkg_setup
+	fi
+	if use mpi; then
+		if has_version 'sci-libs/hdf5[-mpi]'; then
+			ewarn "Installing hdf5 with mpi enabled with a previous hdf5 with mpi disabled may fail."
+			ewarn "Try to uninstall the current hdf5 prior to enabling mpi support."
+		fi
+		export CC=mpicc
+		use fortran && export FC=mpif90
+	elif has_version 'sci-libs/hdf5[mpi]'; then
+		ewarn "Installing hdf5 with mpi disabled while having hdf5 installed with mpi enabled may fail."
+		ewarn "Try to uninstall the current hdf5 prior to disabling mpi support."
+	fi
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-buildsystem.patch \
+		"${FILESDIR}"/${PN}-1.8.8-array_bounds.patch \
+		"${FILESDIR}"/${P}-implicits.patch \
+		"${FILESDIR}"/${PN}-1.8.9-static_libgfortran.patch \
+		"${FILESDIR}"/${PN}-1.8.9-mpicxx.patch
+	# respect gentoo examples directory
+	sed \
+		-e "s:hdf5_examples:doc/${PF}/examples:g" \
+		-i $(find . -name Makefile.am) $(find . -name "run*.sh.in") || die
+	sed \
+		-e '/docdir/d' \
+		-i config/commence.am || die
+	if ! use examples; then
+		sed -e '/^install:/ s/install-examples//' \
+			-i Makefile.am || die #409091
+	fi
+	eautoreconf
+	# enable shared libs by default for h5cc config utility
+	sed -i -e "s/SHLIB:-no/SHLIB:-yes/g" tools/misc/h5cc.in	|| die
+	# bug #419677
+	use prefix && \
+		append-ldflags -Wl,-rpath,"${EPREFIX}"/usr/$(get_libdir) \
+		-Wl,-rpath,"${EPREFIX}"/$(get_libdir)
+}
+
+src_configure() {
+	econf \
+		--enable-production \
+		--docdir="${EPREFIX}"/usr/share/doc/${PF} \
+		--enable-deprecated-symbols \
+		--enable-shared \
+		--disable-silent-rules \
+		$(use_enable prefix sharedlib-rpath) \
+		$(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 {} +
+}