Version bump. Important update mainly for netcdf4 users

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

6 files changed, 65 insertions, 491 deletions

diff --git a/sci-libs/hdf5/ChangeLog b/sci-libs/hdf5/ChangeLog
index ec8cd73c65de..de9fbe7588b3 100644
--- a/sci-libs/hdf5/ChangeLog
+++ b/sci-libs/hdf5/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-libs/hdf5
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/ChangeLog,v 1.53 2010/02/10 17:21:57 bicatali Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/ChangeLog,v 1.54 2010/05/04 18:38:13 bicatali Exp $
+
+*hdf5-1.8.4_p1 (04 May 2010)
+
+  04 May 2010; Sébastien Fabbro <bicatali@gentoo.org>
+  -hdf5-1.6.5-r1.ebuild, -hdf5-1.6.6.ebuild, -hdf5-1.8.3-r1.ebuild,
+  files/hdf5-1.8.3-as-needed.patch, +hdf5-1.8.4_p1.ebuild:
+  Version bump. Important update mainly for netcdf4 users
 
   10 Feb 2010; Sébastien Fabbro <bicatali@gentoo.org> hdf5-1.8.4-r1.ebuild:
   Added some warnings for mpi
diff --git a/sci-libs/hdf5/Manifest b/sci-libs/hdf5/Manifest
index cee3d68c5a4f..8b1acc1827c9 100644
--- a/sci-libs/hdf5/Manifest
+++ b/sci-libs/hdf5/Manifest
@@ -2,7 +2,7 @@
 Hash: SHA1
 
 AUX hdf5-1.6.6-gcc4.3.patch 355 RMD160 109811c4e4d434bfa09ea156e67623e50b0f89a5 SHA1 c0fe43c262723e117572b687d9f3c94910e4fddc SHA256 ca1a16f1df4c58410001ca4b06886f9df47b475100078c5e9208ff7a21ca22c1
-AUX hdf5-1.8.3-as-needed.patch 1909 RMD160 86c153a302d2730d94ab2c741fb71eb66de6b271 SHA1 aafc558d4a5bf58d78ff807f79a81b0f2ef8f8f3 SHA256 11d4fba2970b68666d65e31178f2a07630c0c1f46ef7b18bfa16d49de776a649
+AUX hdf5-1.8.3-as-needed.patch 1821 RMD160 a20e65447625134132cb3e8e19917eb499a463e8 SHA1 b295f26b8d39fae21201449441a8ac3c0c699048 SHA256 6f03f955186e2e2870517580bd14a637e2cf0206e7547184948653e04c464bb3
 AUX hdf5-1.8.3-destdir.patch 1475 RMD160 78bc020b5b8aaef070bafd4a99a2e57f41e5e06b SHA1 7ddfa5d47759d1f7637d0c558cead7a7af63f23d SHA256 866a431b36a5998c1930af6384ff8cd11241af1f488ac5910d247b724eedd309
 AUX hdf5-1.8.3-gnutools.patch 1352 RMD160 a0a51a484f1ab926f13618093c809b6582da8e7f SHA1 e4121383f2876dea4ba09356ca7d233fe6ac5b2e SHA256 0e6720e736d7103f39edcf8d3fb4a14f40bbee67363e8f167d9b594ef348f197
 AUX hdf5-1.8.3-includes.patch 398 RMD160 5112dd05bebbc702f24fa22aeebc67209a4e6611 SHA1 339137d04a803e25a0cafaa4f4d167a4cbc9a7ae SHA256 cd82d8b3817d83d59054a2a32ce44aca060157095875f6e91c560ab830b32561
@@ -16,24 +16,20 @@ AUX hdf5-mpich2.patch 488 RMD160 f8ab476eed88267c4b79cc56ae683dc485255921 SHA1 a
 AUX mpd.conf 48 RMD160 289de9bb40759e3f71229cf47e4d2af83703a85f SHA1 244eee76dbf4ff269e4489d5cc7c3577c6c1fa6b SHA256 ae740cacaf2cb798921cb2092f5af98de67445e27af3f88858f3e6d2bbb127f4
 DIST hdf5-1.6.2.tar.gz 3879147 RMD160 75678e8859e783dbb274cdabee3d916724c46780 SHA1 1afa977b371c01e53dd6e0bd3a0d879a3f2ae5a2 SHA256 aabc23cb2c744c25b71416e25bdca3b9ca8dadb9248f22314330a33d91c599ba
 DIST hdf5-1.6.4.tar.gz 4862437 RMD160 8175af3153bb0a5a1278c01af2d3940f4fd5084f SHA1 e419e81097b8093d16d96708b764bd85db053e86 SHA256 11ab0d81575f333067ae091d39c28fbf446c8ecafdfe70cf92b3c35ceffbfc97
-DIST hdf5-1.6.5.tar.gz 4930666 RMD160 70db16a832f77aa6d0c97da517353665304b7b27 SHA1 c5b7b375c0eb23dcab0c66d39b1b06c263048546 SHA256 85b7cfc1e34db544fa93f5bf7effe189a5e1eb97f0cfa7b212adc11915a756b2
-DIST hdf5-1.6.6.tar.gz 5299558 RMD160 e7cf3f8d6aa5f34ef10cabf650ed43d644e54f1b SHA1 c8a9ec598cf0debb694a1d7034fd85bbd67f173b SHA256 432d02f2d6988999d3d18caa6680af3cef14c8a7537c98e7adbaa8f873fba2a7
 DIST hdf5-1.6.7.tar.gz 5299219 RMD160 2dbbcccd32986dcd66ce804c5e90ac6c949b71f6 SHA1 9c26fe09cdad269c9a6757933f70ca164a47b8e8 SHA256 9d9a98204f8c7d82f767f27f84db2520c04f5c73a4a6348c781a0d91a296e9a2
-DIST hdf5-1.8.3.tar.gz 7175884 RMD160 7b279306b5458f39dc7343c14a7c7c88459823a3 SHA1 0bf66eb5d964472eae4b6c2bb26e669dcd188140 SHA256 2e124dfd59ca00dee693c06cf2517d14b361769e65edbc1c3940063437d0a5e3
+DIST hdf5-1.8.4-patch1.tar.gz 7180426 RMD160 69fbb9d58890abe36a19167b1511bd1073cc1935 SHA1 dd2f815d5145216fac93d0e5bf22316a2a7cc558 SHA256 8893a6e773e9140230ca638d592408a61bd1726c13784e4bdf048e8ed3591bd9
 DIST hdf5-1.8.4.tar.gz 7181176 RMD160 e448e2326b55aa89ff0bd7488cd4291d6c5485ee SHA1 37877e29c49a6af3e23aa9ad798ef12b8ba1c05c SHA256 a992fce9387a17f175b3b188dc2a42f545a3057aeb141beb3fc3361c7521f465
 EBUILD hdf5-1.6.2.ebuild 1837 RMD160 2c7e527ade607fd3d98222787db400bc86c28d37 SHA1 a1b5e54d886d09074665512428c7a1ea23f28437 SHA256 612db1a50d632dd5b0d1c63d557888c4e5765a0debf774552443cdb1dde3a49c
 EBUILD hdf5-1.6.4.ebuild 2098 RMD160 348a6f05d7677e372688ca5ecdcdea36c90df7c9 SHA1 aaeed445389bad0630f518e0778f900af9614fb1 SHA256 469176113ea60bc95a7efa63ca24e6d53baeab71660a44eaa23088fedfd911af
-EBUILD hdf5-1.6.5-r1.ebuild 6638 RMD160 b19d0ec9f56fa0ba1423a494798ab79bccc1380d SHA1 ca0a6106c94fd1745e6852b89f4e119d7d10f461 SHA256 c59e90e1383173906eb59d78bb48a57acebc94530e596501db8f6d5ee8268226
-EBUILD hdf5-1.6.6.ebuild 7782 RMD160 2ee70cea539827f28e08f18638703d9a0a87a40e SHA1 cbe8ba966c6435269a84bc120189fb63ac559f8a SHA256 ab6325efffbf410230cf8df6391e33d925c6b0ed9f7b0fcaddf57c8d174ed8fd
 EBUILD hdf5-1.6.7.ebuild 7799 RMD160 992a00257e2e94d2933d61950b1a85155ce995f3 SHA1 1d51c88dc85b13f658bbfde4676de013b23da2d5 SHA256 a3cacbfed63bd26c0f9346d3e0e424b0444ce1dc6e38e2fd4fa5a87f2c9f403b
-EBUILD hdf5-1.8.3-r1.ebuild 2435 RMD160 ee9b11586a1515abfd0d3182cf119b8f6b1a4011 SHA1 41e03d5c7ee325af7843e701930d216517845f3b SHA256 eb220cc4691c19ba0ade57d30f619013440d11c6be50194d15c8c9027481e09e
 EBUILD hdf5-1.8.4-r1.ebuild 3109 RMD160 c37975d36839d34448e29248f7597183094e1acf SHA1 8b4b11069045137e1409255f4567a8114594d84e SHA256 1c24728311d46b40eee9aee22866e0afbfb9427cce67b052fcaacc8879158f0b
-MISC ChangeLog 11636 RMD160 0b86d260365bf41af1618de7ee37500a548e4351 SHA1 e025843b19835b52ed76580ac5921da8a5e54406 SHA256 ba0fc559dbb8aab95adbe2de110760c73419297f60c1cc6908e20bc42831087b
+EBUILD hdf5-1.8.4_p1.ebuild 3101 RMD160 2770fb98edcf6986af4d3ef5cd47c7f4c028d297 SHA1 c0390a6a7c814211d75b2172d5b37cc925b1d060 SHA256 da11216f31d31e2910156810dd9248960a2e0a56994557217099676c2eabafc2
+MISC ChangeLog 11907 RMD160 243794b028c313cae1e5523e1839f37734a769b4 SHA1 05bd21d1193fe44bb38a8fc0d818ac0071cbae73 SHA256 585150ded489b7130435dfea05ee258d5fc94e3e9c70885ed2eaa692fc313c1a
 MISC metadata.xml 649 RMD160 08065c3c8adc0f0254c2c2d341b375b98837d6b1 SHA1 10e4f63c12adf0853081bd55dddc6b72ddf897a1 SHA256 c72b0032f2aa35ccb361af5bc256667a46ecf6ac3e6c84786c0291f286862780
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.14 (GNU/Linux)
+Version: GnuPG v2.0.15 (GNU/Linux)
 
-iEYEARECAAYFAkuZc4cACgkQdz7hIScOURHTrgCgg8grUqb7Rp+LgbZ12eLIM5kV
-8vIAoIS47zudx/k4c2IXtUvSBUD+aZ6x
-=a7g2
+iEYEARECAAYFAkvgc+QACgkQ1ycZbhPLE2B8EACeKzVlcHjmn8Vqps8ACmqO3OCu
+Q+cAnRHoHvsBC6smmXWtH/uoC9azCyf/
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diff --git a/sci-libs/hdf5/files/hdf5-1.8.3-as-needed.patch b/sci-libs/hdf5/files/hdf5-1.8.3-as-needed.patch
index 677264b22b53..6b1f43835aed 100644
--- a/sci-libs/hdf5/files/hdf5-1.8.3-as-needed.patch
+++ b/sci-libs/hdf5/files/hdf5-1.8.3-as-needed.patch
@@ -1,5 +1,5 @@
---- hdf5-1.8.3.orig/fortran/src/Makefile.am	2009-04-15 19:10:01.053733251 +0100
-+++ hdf5-1.8.3/fortran/src/Makefile.am	2009-04-15 19:12:49.874557795 +0100
+--- fortran/src/Makefile.am.orig	2009-04-15 19:10:01.053733251 +0100
++++ fortran/src/Makefile.am	2009-04-15 19:12:49.874557795 +0100
 @@ -66,6 +66,8 @@
           H5If.c H5Lf.c H5Of.c H5Pf.c H5Rf.c H5Sf.c H5Tf.c H5Zf.c        \
           $(PARALLEL_COND_SRC)
@@ -9,8 +9,8 @@
  # h5fc is generated during configure.
  # Remove it only when distclean.
  DISTCLEANFILES=h5fc
---- hdf5-1.8.3.orig/hl/fortran/src/Makefile.am	2009-04-15 19:10:01.245748616 +0100
-+++ hdf5-1.8.3/hl/fortran/src/Makefile.am	2009-04-15 19:30:56.042226227 +0100
+--- hl/fortran/src/Makefile.am.orig	2009-04-15 19:10:01.245748616 +0100
++++ hl/fortran/src/Makefile.am	2009-04-15 19:30:56.042226227 +0100
 @@ -43,6 +43,7 @@
  
  libhdf5hl_fortran_la_SOURCES=H5LTfc.c  H5IMfc.c H5IMcc.c H5TBfc.c H5LTff.f90  \
@@ -19,8 +19,8 @@
  
  # Fortran module files can have different extensions and different names
  # (e.g., different capitalizations) on different platforms.  Write rules
---- hdf5-1.8.3.orig/hl/c++/src/Makefile.am	2009-04-15 19:10:01.249750013 +0100
-+++ hdf5-1.8.3/hl/c++/src/Makefile.am	2009-04-15 20:16:08.812068687 +0100
+--- hl/c++/src/Makefile.am.orig	2009-04-15 19:10:01.249750013 +0100
++++ hl/c++/src/Makefile.am	2009-04-15 20:16:08.812068687 +0100
 @@ -35,6 +35,7 @@
  # Source files for the library
  # At the moment, only the H5PT Packet Table has a C++ API.
@@ -29,8 +29,8 @@
  
  # Public headers
  include_HEADERS=H5PacketTable.h
---- hdf5-1.8.3.orig/hl/src/Makefile.am	2009-05-13 17:03:11.000000000 +0200
-+++ hdf5-1.8.3/hl/src/Makefile.am	2009-09-10 19:22:57.489698969 +0200
+--- hl/src/Makefile.am.orig	2009-05-13 17:03:11.000000000 +0200
++++ hl/src/Makefile.am	2009-09-10 19:22:57.489698969 +0200
 @@ -31,6 +31,7 @@
  libhdf5_hl_la_LDFLAGS= -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE)
  
diff --git a/sci-libs/hdf5/hdf5-1.6.5-r1.ebuild b/sci-libs/hdf5/hdf5-1.6.5-r1.ebuild
deleted file mode 100644
index 00425284b721..000000000000
--- a/sci-libs/hdf5/hdf5-1.6.5-r1.ebuild
+++ /dev/null
@@ -1,197 +0,0 @@
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/hdf5-1.6.5-r1.ebuild,v 1.7 2008/06/06 15:04:44 markusle Exp $
-
-inherit fortran eutils toolchain-funcs
-
-DESCRIPTION="General purpose library and file format for storing scientific data"
-HOMEPAGE="http://hdf.ncsa.uiuc.edu/HDF5/"
-SRC_URI="ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/src/${P}.tar.gz"
-
-LICENSE="NCSA-HDF"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86"
-# need to update szip to get alpha, ia64, etc back in here,
-IUSE="cxx f90 fortran hlapi mpi ssl szip threads zlib static debug"
-
-DEPEND="mpi? ( virtual/mpi )
-	ssl? ( dev-libs/openssl )
-	szip? ( sci-libs/szip )
-	zlib? ( sys-libs/zlib )
-	sys-apps/coreutils
-	sys-apps/which
-	sys-process/time"
-
-RDEPEND="${DEPEND}
-	dev-lang/perl"
-
-pkg_setup() {
-	# The above gcc dep is a hack to insure at least one Fortran 90
-	# compiler is installed if the user enables fortran support.  Feel
-	# free to improve it...
-	if use fortran ; then
-	    if [ $(gcc-major-version) -ge 4 ] \
-		&& built_with_use sys-devel/gcc fortran ; then
-	    	    FORTRAN="gfortran"
-		    fortran_pkg_setup
-		    einfo "Configuring for GNU fortran..."
-	    elif
-		test -d /opt/intel/fortran90 ; then
-		    FORTRAN="ifc"
-		    fortran_pkg_setup
-		    einfo "Configuring for Intel fortran..."
-	    elif use f90 ; then
-		einfo "Relying on H5Detect to configure Fortran compiler..."
-		FORTRAN=""
-	    else
-		einfo "No F90 compiler found; please install either gcc 4 with"
-		einfo "fortran support or some other Fortran 90 compiler such"
-		einfo "as ifc or pgf90 (or disable fortran support)."
-		die "No usable Fortran 90 compiler found."
-	    fi
-	fi
-}
-
-src_compile() {
-	local myconf="--with-pic"
-
-	# --disable-static conflicts with --enable-cxx, so we have to do either
-	# or here.  --enable-cxx also conflicts with parallel (mpi) support.
-	# fortran needs f90 support and requires static and mpi (for gfortran).
-	if use static ; then
-	    if use cxx && ! use mpi ; then
-		myconf="${myconf} --enable-cxx"
-	    elif use cxx && use mpi ; then
-		ewarn "C++ support is not compatible with the mpi interface."
-		die "Please disable either cxx or mpi."
-	    else
-		myconf="${myconf} --disable-cxx"
-	    fi
-	    if use fortran && use mpi ; then
-		ewarn "Requires Fortran 90 support in your mpi library..."
-		myconf="${myconf} --enable-fortran --enable-static"
-	    elif use fortran && use f90 ; then
-		ewarn "Relying on configure to detect Fortran 90 compiler..."
-		myconf="${myconf} --enable-fortran --enable-static"
-	    elif
-		use fortran && ! use mpi && ! use f90 ; then
-		ewarn "Configure fortran will probably fail without mpi, if all"
-		ewarn "you have is gfortran installed.  Please enable mpi or"
-		ewarn "install another Fortran compiler.  Fortran support is"
-		ewarn "not enabled for this build..."
-		myconf="${myconf} --disable-fortran --enable-static"
-	    else
-		myconf="${myconf} --disable-fortran --enable-static"
-	    fi
-	else
-	    einfo "C++ support cannot be enabled without both enabling static"
-	    einfo "library support and disabling mpi.  Fortran9X support needs"
-	    einfo "both static and mpi enabled to work with GNU fortran."
-	    echo
-	    einfo "Suggested USE flags for fortran and mpi using gfortran:"
-	    einfo "USE=\"fortran mpi static -cxx\""
-	    echo
-	    if use fortran || use cxx ; then
-		die "Please adjust your use flags."
-	    else
-		einfo "Disabling fortran, C++, and static library support..."
-		myconf="${myconf} --disable-static --disable-fortran \
-		    --disable-cxx"
-	    fi
-	fi
-	use threads && myconf="${myconf} --with-pthread"
-	use debug && myconf="${myconf} --enable-debug=all"
-	use mpi && myconf="${myconf} --enable-parallel --enable-gpfs"
-	use hlapi || myconf="${myconf} --disable-hl"
-
-	# NOTE: the hdf5 configure script has its own interpretation of
-	# the ARCH environment variable which conflicts with that of
-	# ebuild/emerge. As a work around, we save the ARCH variable as
-	# EBUILD_ARCH and restore it when we are done.
-	EBUILD_ARCH=${ARCH}
-	unset ARCH
-
-	if use mpi ; then
-	    export CC="/usr/bin/mpicc"
-	fi
-	./configure --prefix=/usr ${myconf} \
-		$(use_enable zlib) \
-		$(use_with ssl) \
-		--enable-linux-lfs  \
-		--sysconfdir=/etc \
-		--infodir=/usr/share/info \
-		--libdir=/usr/$(get_libdir) \
-		--mandir=/usr/share/man || die "configure failed"
-
-	# restore the ARCH environment variable
-	ARCH=${EBUILD_ARCH}
-
-	# emake has occasional segfaults
-	make || die "make failed"
-}
-
-src_test() {
-	# make test is not reliable, and the mpi tests have a weird failure
-	export HDF5_Make_Ignore=yes
-	install -g portage -o portage -m 0600 "${FILESDIR}"/mpd.conf ${HOME}/.mpd.conf
-	/usr/bin/mpd --daemon
-	make check || die "make test failed"
-	/usr/bin/mpdallexit
-	export HDF5_Make_Ignore=no
-}
-
-src_install() {
-	make \
-		prefix="${D}"usr \
-		mandir="${D}"usr/share/man \
-		docdir="${D}"usr/share/doc/${PF} \
-		libdir="${D}"usr/$(get_libdir) \
-		infodir="${D}"usr/share/info \
-		install || die "make install failed"
-
-	dolib.so "${S}"/test/.libs/lib*so* || die "dolib.so failed"
-
-	if use static ; then
-	    dolib.a "${S}"/tools/lib/.libs/libh5tools.a \
-		"${S}"/test/.libs/libh5test.a || die "dolib.a failed"
-	    insinto /usr/$(get_libdir)
-	    doins "${S}"/tools/lib/libh5tools.la \
-		 "${S}"/test/libh5test.la || die "doins failed"
-	fi
-
-	dobin "${S}"/bin/iostats || die "dobin failed"
-	dodoc README.txt MANIFEST
-	dohtml doc/html/*
-
-	if use mpi ; then
-	    mv "${D}"usr/bin/h5pcc "${D}"usr/bin/h5cc
-	fi
-	if use fortran ; then
-	    mv "${D}"usr/bin/h5pfc "${D}"usr/bin/h5fc
-	fi
-	# change the SHLIB default for C
-	if ! use static ; then
-	    dosed "s/SHLIB:-no/SHLIB:-yes/g" "${D}"usr/bin/h5cc || die "dosed failed"
-	fi
-}
-
-pkg_postinst() {
-	echo
-	einfo "Use the fortran flag for gfortran or ifc, and add the f90"
-	einfo "flag to override the fortran flag if you have a different"
-	einfo "f90 compiler installed (gfortran requires gcc 4.x). Note that"
-	einfo "gfortran only works as mpif90 and is not detected properly by"
-	einfo "configure without the mpi wrapper."
-	echo
-	einfo "There are currently 2 non-fatal test errors in the mpi tests,"
-	einfo "however, all C++, Fortran, and other tests pass successfully."
-	einfo "The only expected failure is currently in the PHDF5 section"
-	einfo "under MPI functionality tests. The second section using the"
-	einfo "MPIPOSIX driver should work, along with all other tests."
-	echo
-	einfo "Suggested USE flags for fortran and mpi support using gfortran:"
-	einfo "USE=\"fortran mpi static -cxx\""
-	echo
-	ewarn "Note: currently untested on a virtual (parallel) filesystem."
-	echo
-}
diff --git a/sci-libs/hdf5/hdf5-1.6.6.ebuild b/sci-libs/hdf5/hdf5-1.6.6.ebuild
deleted file mode 100644
index 756ec552c1a2..000000000000
--- a/sci-libs/hdf5/hdf5-1.6.6.ebuild
+++ /dev/null
@@ -1,251 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/hdf5-1.6.6.ebuild,v 1.12 2009/09/23 20:11:51 patrick Exp $
-
-inherit eutils fixheadtails flag-o-matic fortran toolchain-funcs
-
-DESCRIPTION="General purpose library and file format for storing scientific data"
-HOMEPAGE="http://hdf.ncsa.uiuc.edu/HDF5/"
-SRC_URI="ftp://ftp.hdfgroup.org/HDF5/current/src/${P}.tar.gz"
-
-LICENSE="NCSA-HDF"
-SLOT="0"
-KEYWORDS="~amd64 ~hppa ~ppc ~ppc64 ~x86 ~sparc"
-# need to update szip to get alpha, ia64, etc back in here,
-IUSE="cxx debug fortran mpi ssl szip threads tools zlib "
-
-DEPEND="mpi? ( >=sys-cluster/mpich2-1.0.6
-		net-fs/nfs-utils )
-	ssl? ( dev-libs/openssl )
-	szip? ( sci-libs/szip )
-	zlib? ( sys-libs/zlib )
-	sys-apps/coreutils
-	sys-apps/which
-	sys-process/time"
-
-RDEPEND="${DEPEND}
-	dev-lang/perl"
-
-pkg_setup() {
-	if has test ${FEATURES} && use mpi ; then
-	    elog ""
-	    elog "Parallel tests will launch 3 mpd processes on this box,"
-	    elog "so it may take some time on a slow machine (only a few"
-	    elog "minutes on a reasonably fast machine).  Hit Ctl-C now"
-	    elog "and emerge with FEATURES=-test if you'd rather not..."
-	    elog ""
-	    epause 9
-	fi
-
-	# The above gcc dep is a hack to insure at least one Fortran 90
-	# compiler is installed if the user enables fortran support.  Feel
-	# free to improve it...
-	if use fortran ; then
-	    fortran_pkg_setup
-	    case "${FORTRANC}" in
-		gfortran|ifc|ifort|f95|pgf90)
-		    export F9X="${FORTRANC}"
-		    ;;
-		g77|f77|f2c)
-		    export F9X=""
-		    ;;
-	    esac
-	fi
-
-	# if anyone knows of a better way to do this...
-	if use mpi && ! built_with_use sys-cluster/mpich2 pvfs2 ; then
-	    ewarn "Your MPI library needs parallel IO support for HDF5. You"
-	    ewarn "must re-emerge mpich2 with USE=pvfs2."
-	    die "requires parallel IO support"
-	fi
-}
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	epatch "${FILESDIR}"/${P}-gcc4.3.patch
-	if use mpi; then
-	    # this is required for mpich2, and should be safe otherwise
-	    epatch "${FILESDIR}/${PN}-mpich2.patch"
-	fi
-
-	# fix test script stuff
-	ht_fix_file "${S}"/bin/release "${S}"/tools/h5dump/testh5dump.sh.in
-	sed -i -e "s:+4l:+4:g" tools/h5dump/testh5dump.sh.in || die "oops"
-
-	# fix sort key
-	sed -i -e "s:sort +2:sort -k 2:g" bin/ltmain.sh || die "sed failed"
-
-}
-
-src_compile() {
-	local myconf
-
-	# a better way to do this would also be nice, but i can't think of one
-	if use cxx && ! use mpi ; then
-	    myconf="${myconf} --enable-cxx"
-	elif use cxx && use mpi ; then
-	    ewarn "C++ support is not compatible with the mpi interface."
-	    die "Please disable either cxx or mpi."
-	else
-	    myconf="${myconf} --disable-cxx"
-	fi
-
-	if use fortran && use mpi ; then
-	    ewarn "Requires Fortran 90 support in your mpi library..."
-	    myconf="${myconf} --enable-fortran --enable-parallel"
-	fi
-
-	use threads && myconf="${myconf} --with-pthread --enable-threadsafe"
-
-	if use debug ; then
-	    myconf="${myconf} --enable-debug=all"
-	else
-	    myconf="${myconf} --enable-production"
-	fi
-
-	# NOTE: the hdf5 configure script has its own interpretation of
-	# the ARCH environment variable which conflicts with that of
-	# ebuild/emerge. As a work around, we save the ARCH variable as
-	# EBUILD_ARCH and restore it when we are done.
-	EBUILD_ARCH="${ARCH}"
-
-	unset ARCH
-
-	if use mpi ; then
-	    EBUILD_CC="${CC}"
-	    # set NPROCS explicitly if needed
-	    export NPROCS=${NPROCS:=2}
-	    export CC="$(which mpicc)"
-	    if [[ ${FORTRANC} == gfortran ]] ; then
-		export F9X="$(which mpif90)"
-	    fi
-	    if built_with_use sys-cluster/mpich2 pvfs2 ; then
-		export LIBS="${LIBS} $(sh pvfs2-config --libs) -lmpich"
-	    else
-		export LIBS="${LIBS} -lmpich"
-	    fi
-	    append-ldflags "${LIBS}"
-	fi
-
-	econf --prefix=/usr \
-		$(use_enable zlib) \
-		$(use_enable fortran) \
-		$(use_enable mpi parallel) \
-		$(use_with ssl) \
-		--enable-linux-lfs  \
-		--sysconfdir=/etc \
-		--infodir=/usr/share/info \
-		--libdir=/usr/$(get_libdir) \
-		--mandir=/usr/share/man \
-		--enable-shared --with-pic \
-		${myconf} || die "configure failed"
-
-	# restore the ARCH environment variable
-	ARCH="${EBUILD_ARCH}"
-
-	# emake has occasional segfaults
-	make || die "make failed"
-	use mpi && CC="${EBUILD_CC}"
-}
-
-src_test() {
-	# all tests pass; a few are skipped, and MPI skips parts if it sees
-	# only one process on the build host.
-	export HDF5_Make_Ignore=yes
-	if use mpi ; then
-	    EBUILD_CC="${CC}"
-	    export HDF5_PARAPREFIX="${S}/testpar"
-	    export CC="$(which mpicc)"
-	    export MPI_UNIVERSE="localhost 4"
-	    export NPROCS=3
-	    install -g portage -o portage -m 0600 "${FILESDIR}"/mpd.conf "${HOME}"/.mpd.conf
-	    mpd --daemon --listenport=4268
-	    mpd --daemon -h localhost -p 4268 -n
-	    mpd --daemon -h localhost -p 4268 -n
-	    elog "NPROCS = ${NPROCS}"
-	    elog "mpdtrace output:"
-	    mpdtrace
-	fi
-	make check || die "make test failed"
-	use mpi && mpdallexit
-	use mpi && CC="${EBUILD_CC}"
-	export HDF5_Make_Ignore=no
-}
-
-src_install() {
-	# emake install and einstall cause sandbox violations here
-	make \
-		prefix="${D}"usr \
-		mandir="${D}"usr/share/man \
-		docdir="${D}"usr/share/doc/"${PF}" \
-		libdir="${D}"usr/$(get_libdir) \
-		infodir="${D}usr"/share/info \
-		install || die "make install failed"
-
-	if use tools ; then
-	    dolib.a "${S}"/tools/lib/.libs/libh5tools.a \
-		"${S}"/test/.libs/libh5test.a || die "dolib.a failed"
-	    insinto /usr/$(get_libdir)
-	    doins "${S}"/tools/lib/libh5tools.la \
-		"${S}"/test/libh5test.la || die "doins failed"
-	    dolib.so "${S}"/test/.libs/libh5test.so.0.0.0 \
-			"${S}"/test/.libs/libh5test.so.0 \
-			"${S}"/test/.libs/libh5test.so \
-		|| die "dolib.so failed"
-
-	    exeinto /usr/bin
-	    newexe "${S}"/bin/iostats iostats.pl || die "newexe failed"
-
-	    exeinto /usr/share/"${PN}/test-tools"
-	    cd "${S}"/test
-	    doexe big bittests fillval lheap file_handle istore set_extent \
-		srb_append cache flush1 srb_read cmpd_dset flush2 srb_write \
-		dangle gass_append links stab dsets dtypes enum extend external \
-		gass_read mount gass_write getname gheap hyperslab mtime ntypes \
-		ohdr reserved stream_test testhdf5 ttsafe unlink
-	    cd "${S}"
-	    use mpi && doexe testpar/testphdf5 testpar/t_mpi
-	fi
-
-	dodoc README.txt
-	dohtml doc/html/*
-
-	if use mpi ; then
-	    mv "${D}"usr/bin/h5pcc "${D}"usr/bin/h5cc
-	fi
-	if use fortran ; then
-	    mv "${D}"usr/bin/h5pfc "${D}"usr/bin/h5fc
-	fi
-	# change the SHLIB default for C
-	dosed "s/SHLIB:-no/SHLIB:-yes/g" "${D}"usr/bin/h5cc || die "dosed failed"
-}
-
-pkg_postinst() {
-	echo
-	elog "Use the fortran flag for gfortran or ifc, and add the f90"
-	elog "flag to override the fortran flag if you have a different"
-	elog "f90 compiler installed (gfortran requires gcc 4.x). Note that"
-	elog "gfortran only works as mpif90 and is not detected properly by"
-	elog "configure without the mpi wrapper."
-	echo
-	elog "There should not be any more test errors in the mpi tests,"
-	elog "and all C++, Fortran, and other tests pass successfully."
-	elog "Suggested USE flags for fortran and mpi support using"
-	elog "gfortran:  USE=\"fortran mpi -cxx\""
-	echo
-	ewarn "Note 1: Needs more SMP and cluster testing, as well as"
-	ewarn "more testing on a virtual (parallel) filesystem."
-	echo
-	ewarn "Note 2: currently testing pvfs2 support (with mpi).  Please"
-	ewarn "report any problems in the usual way."
-	elog
-	ewarn "Note 3: you'll need rawio support enabled in your kernel or"
-	ewarn "certain asynchronous IO operations may fail.  Either enable"
-	ewarn "the RAW driver (under Character Devices) or patch your kernel"
-	ewarn "with the new PAIO drivers and use libposix-aio.  See both:"
-	ewarn "http://sourceforge.net/projects/paiol  and"
-	ewarn "http://www.bullopensource.org/posix  for more info."
-	elog
-}
diff --git a/sci-libs/hdf5/hdf5-1.8.3-r1.ebuild b/sci-libs/hdf5/hdf5-1.8.4_p1.ebuild
index 09e26a63b89e..ee936ec1b56d 100644
--- a/sci-libs/hdf5/hdf5-1.8.3-r1.ebuild
+++ b/sci-libs/hdf5/hdf5-1.8.4_p1.ebuild
@@ -1,24 +1,23 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/hdf5-1.8.3-r1.ebuild,v 1.5 2009/10/12 19:58:35 jer Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/hdf5/hdf5-1.8.4_p1.ebuild,v 1.1 2010/05/04 18:38:13 bicatali Exp $
 
 EAPI=2
 inherit eutils autotools
 
+MYP=${PN}-${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/current/src/${P}.tar.gz"
+SRC_URI="http://www.hdfgroup.org/ftp/HDF5/current/src/${MYP}.tar.gz"
 
 LICENSE="NCSA-HDF"
 SLOT="0"
-KEYWORDS="~alpha ~amd64 hppa ~ppc ~ppc64 ~sparc ~x86"
+KEYWORDS="~alpha ~amd64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86"
 
 IUSE="cxx examples fortran mpi szip threads zlib"
 
-RDEPEND="mpi? ( || (
-			sys-cluster/openmpi[romio]
-			sys-cluster/mpich2[romio]
-			>=sys-cluster/lam-mpi-7.1.4[romio] ) )
+RDEPEND="mpi? ( virtual/mpi[romio] )
 	szip? ( >=sci-libs/szip-2.1 )
 	zlib? ( sys-libs/zlib )"
 
@@ -26,29 +25,43 @@ DEPEND="${RDEPEND}
 	>=sys-devel/libtool-2.2
 	sys-process/time"
 
+S="${WORKDIR}/${MYP}"
+
 pkg_setup() {
 	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
 		if use cxx; then
 			ewarn "Simultaneous mpi and cxx is not supported by ${PN}"
 			ewarn "Will disable cxx interface"
 		fi
 		export CC=mpicc
-		use fortran && export FC=mpif90
+		if use fortran; then
+			export FC=mpif90
+		fi
+	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}-as-needed.patch
-	epatch "${FILESDIR}"/${P}-includes.patch
-	epatch "${FILESDIR}"/${P}-gnutools.patch
-	epatch "${FILESDIR}"/${P}-noreturn.patch
-	epatch "${FILESDIR}"/${P}-destdir.patch
-	epatch "${FILESDIR}"/${P}-signal.patch
+	epatch "${FILESDIR}"/${PN}-1.8.3-as-needed.patch
+	epatch "${FILESDIR}"/${PN}-1.8.3-includes.patch
+	epatch "${FILESDIR}"/${PN}-1.8.3-noreturn.patch
+	epatch "${FILESDIR}"/${PN}-1.8.4-gnutools.patch
+	epatch "${FILESDIR}"/${PN}-1.8.4-scaleoffset.patch
+	epatch "${FILESDIR}"/${PN}-1.8.4-sigbus.patch
 
-	# gentoo examples directory
+	# respect gentoo examples directory
 	sed -i \
-		-e 's:$(docdir)/hdf5:$(docdir):' \
+		-e 's:$(docdir)/hdf5:$(DESTDIR)/$(docdir):' \
 		$(find . -name Makefile.am) || die
+	sed -i \
+		-e '/docdir/d' \
+		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 \
@@ -61,17 +74,23 @@ src_configure() {
 	use threads && ! use fortran && ! use cxx && ! use mpi \
 		&& myconf="--enable-threadsafe"
 
-	if use mpi && use cxx; then
+	if use mpi; then
 		myconf="${myconf} --disable-cxx"
-	elif use cxx; then
-		myconf="${myconf} --enable-cxx"
+	else
+	# workaround for bug 285148
+		if use cxx; then
+			myconf="${myconf} $(use_enable cxx) CXX=$(tc-getCXX)"
+		fi
+		if use fortran; then
+			myconf="${myconf} FC=$(tc-getFC)"
+		fi
 	fi
 
 	econf \
-		--docdir=/usr/share/doc/${PF} \
 		--disable-sharedlib-rpath \
 		--enable-production \
 		--enable-strict-format-checks \
+		--docdir=/usr/share/doc/${PF} \
 		--enable-deprecated-symbols \
 		--enable-shared \
 		$(use_enable fortran) \
@@ -86,7 +105,7 @@ src_install() {
 	emake DESTDIR="${D}" install || die "emake install failed"
 	dodoc README.txt
 	if use examples; then
-		emake -j1 DESTDIR="${D}" install-examples \
+		emake DESTDIR="${D}" install-examples \
 			|| die "emake install examples failed"
 	fi
 }