From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id DBD3B1381F3 for ; Wed, 19 Jun 2013 06:53:42 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 5C879E0946; Wed, 19 Jun 2013 06:53:42 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id AD67DE0946 for ; Wed, 19 Jun 2013 06:53:41 +0000 (UTC) Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 9F41D33E5B9 for ; Wed, 19 Jun 2013 06:53:40 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id 436FCE5459 for ; Wed, 19 Jun 2013 06:53:39 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1371563669.83a6f8e906f3701f214c034c05285f7106cc5413.jlec@gentoo> Subject: [gentoo-commits] proj/sci:ccp4 commit in: / X-VCS-Repository: proj/sci X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 83a6f8e906f3701f214c034c05285f7106cc5413 X-VCS-Branch: ccp4 Date: Wed, 19 Jun 2013 06:53:39 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: cedde816-fc73-47c9-9a01-9920e7c3416a X-Archives-Hash: 125b7926f586317050c2b3e18ef79301 commit: 83a6f8e906f3701f214c034c05285f7106cc5413 Author: Honza Macháček centrum cz> AuthorDate: Tue Jun 18 13:54:29 2013 +0000 Commit: Justin Lecher gentoo org> CommitDate: Tue Jun 18 13:54:29 2013 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=83a6f8e9 The dependency of several packages on sci-libs/libxc modified to reflect correctly the recent change in the upgrade of sci-physics/abinit & friends. profiles/package.mask | 6 +++ sci-chemistry/freeon/freeon-2012.05.03.ebuild | 7 +-- sci-chemistry/freeon/freeon-9999.ebuild | 7 +-- sci-chemistry/mics/ChangeLog | 10 ++++ sci-chemistry/mics/Manifest | 1 + .../{mgltools-autodocktools => mics}/metadata.xml | 0 sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild | 51 +++++++++++++++++++ sci-chemistry/modeller/ChangeLog | 6 +++ ...odeller-9.12.ebuild => modeller-9.12-r1.ebuild} | 2 +- sci-chemistry/talosn/ChangeLog | 10 ++++ sci-chemistry/talosn/Manifest | 1 + .../metadata.xml | 0 .../talosn/talosn-4.01.2013.148.15.55.ebuild | 59 ++++++++++++++++++++++ sci-libs/bigdft-abi/ChangeLog | 4 ++ sci-libs/bigdft-abi/Manifest | 2 - sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild | 5 +- sci-libs/libxc/Manifest | 2 +- sci-libs/libxc/libxc-9999.ebuild | 27 ++++++---- sci-libs/mumps/ChangeLog | 5 +- sci-libs/mumps/mumps-4.10.0-r2.ebuild | 5 +- sci-physics/abinit/ChangeLog | 3 ++ sci-physics/abinit/Manifest | 3 +- sci-physics/abinit/abinit-7.2.2.ebuild | 2 +- sci-physics/bigdft/ChangeLog | 5 ++ sci-physics/bigdft/bigdft-1.7_pre24.ebuild | 2 +- sci-physics/elk/ChangeLog | 4 ++ sci-physics/elk/elk-1.4.22.ebuild | 2 +- 27 files changed, 196 insertions(+), 35 deletions(-) diff --cc profiles/package.mask index 0c270df,0c270df..f354cdf --- a/profiles/package.mask +++ b/profiles/package.mask @@@ -68,6 -68,6 +68,12 @@@ >=sci-chemistry/coot-9999 >=sci-chemistry/pymol-9999 ++# Honza Macháček (17 June 2013) ++# bigdft moved from sci-libs to sci-physics ++# sci-physics/abinit now uses sci-libs/bigdft-abi instead ++# sci-libs/bigdft should be deleted in 30 days ++sci-libs/bigdft ++ # Justin Lecher (03 March 2013) # Missing deps sci-biology/gbrowse diff --cc sci-chemistry/freeon/freeon-2012.05.03.ebuild index 99805e0,99805e0..5a9cc6a --- a/sci-chemistry/freeon/freeon-2012.05.03.ebuild +++ b/sci-chemistry/freeon/freeon-2012.05.03.ebuild @@@ -33,11 -33,11 +33,8 @@@ DEPEND="${DEPEND S="${WORKDIR}/${REAL_PN}-${REAL_PV}" src_prepare() { -- # Get rid of the obsolete internal hdf5 -- rm -r "${S}"/hdf5-1.8.3 -- # as well as of the internal lapack -- rm -r "${S}"/lapack -- epatch "${FILESDIR}"/"${P}"-no_internal_libs.patch ++ # Prevent the obsolete internal hdf5 breaking autoconf ++ epatch "${FILESDIR}"/"${P}"-no_internal_hdf5.patch eautoreconf } diff --cc sci-chemistry/freeon/freeon-9999.ebuild index 369e063,369e063..6d02d93 --- a/sci-chemistry/freeon/freeon-9999.ebuild +++ b/sci-chemistry/freeon/freeon-9999.ebuild @@@ -31,11 -31,11 +31,8 @@@ DEPEND="${DEPEND virtual/pkgconfig" src_prepare() { -- # Get rid of the obsolete internal hdf5 -- rm -r "${S}"/Modules/hdf5-1.8.3 -- # as well as of the internal lapack -- rm -r "${S}"/Modules/lapack -- epatch "${FILESDIR}"/"${P}"-no_internal_libs.patch ++ # Prevent the obsolete internal hdf5 breaking autoconf ++ epatch "${FILESDIR}"/"${P}"-no_internal_hdf5.patch eautoreconf } diff --cc sci-libs/bigdft-abi/ChangeLog index 4c48008,4c48008..10ecead --- a/sci-libs/bigdft-abi/ChangeLog +++ b/sci-libs/bigdft-abi/ChangeLog @@@ -2,6 -2,6 +2,10 @@@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ ++ 18 Jun 2013; Honza Macháček ++ bigdft-abi-1.0.4.ebuild: ++ The dependency on sci-libs/libxc modified to allow for 1.2.0-r1. ++ *bigdft-abi-1.0.4 (17 Jun 2013) 17 Jun 2013; Honza Macháček diff --cc sci-libs/bigdft-abi/Manifest index bd17fc5,bd17fc5..e8a8b97 --- a/sci-libs/bigdft-abi/Manifest +++ b/sci-libs/bigdft-abi/Manifest @@@ -1,3 -1,3 +1,1 @@@ --AUX bigdft-abi-1.0.4-tests.tar.bz2 402968 SHA256 11144208456b001f63b75cadce0e9b685054ef8bbc39a76cb08af61d5c86c4fb SHA512 3594d11a8d5834916f44bf6f049630ac9d092df6a7a3171701ef65e5ab56e9d039c2bb4603698cb4935a95189c65d7bf77f44b50617ea8c971a844a2757b3202 WHIRLPOOL 492b92805a4eecb5bb204dbf76acf9a40c790b39708a914e38628a2f4dadc3377eed79f8d986231c006bc8c5be0167af60c36f72212005156e8fe3a3c619281c DIST bigdft-abi-1.0.4.tar.gz 8982260 SHA256 345cf49da92275710252d50b4ac8364f2f3c33e8f28d84d7b13ccf6fd0c69310 SHA512 556001d1ffd08be70b97f07a8a150d5d033a4611957180a7a25b41963754e0e3d2bb2a4e9d5b6beb8ff6fb1eb6f4ae9b51633cfe3d7f5a8ed20a85be21031c35 WHIRLPOOL b7c58732b538306f2b9b89b1310d9212cc1bb038fded782e6707e54679013ebc8376d54b5bd1bd51464dc7878fa05102fcba8f70a5d38b4571720c8d57ee3af1 --EBUILD bigdft-abi-1.0.4.ebuild 4232 SHA256 006484b64a83d7971efc05670b77d26114eed87f0d062c39e9b9bf01a4a005ce SHA512 bc34310bf3b4b3999574be8f67db51072a53b2a14fbf340edb72d046989f088b3c12b65f98a781fb5791263ce4c947786ee250dcbe4c162dcd194711321db4b5 WHIRLPOOL 28a1b685e427500acda0e210c9d2e72bbcd24bfe2be1b09112a1aab829d1efe9a896e28b45b42ec7db29c4908bc7cb3b73c83d0ad77accf9269ee9774e310537 diff --cc sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild index c285d63,c285d63..91e3bac --- a/sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild +++ b/sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild @@@ -19,7 -19,7 +19,7 @@@ KEYWORDS="~amd64 ~x86 ~amd64-linux IUSE="cuda doc etsf_io mpi netcdf openmp opencl test" RDEPEND=" -- >=sci-libs/libxc-2.0.1[fortran] ++ >=sci-libs/libxc-1.2.0-r1[fortran] virtual/blas virtual/fortran virtual/lapack @@@ -75,9 -75,9 +75,6 @@@ pkg_setup() } src_prepare() { --# epatch \ --# "${FILESDIR}"/"${P}"-nolib_mods.patch --# tar -xjf "${FILESDIR}"/"${P}"-tests.tar.bz2 -C "${S}"/tests/DFT/ eautoreconf } diff --cc sci-libs/libxc/Manifest index fa863cf,fa863cf..a85ebc8 --- a/sci-libs/libxc/Manifest +++ b/sci-libs/libxc/Manifest @@@ -1,2 -1,2 +1,2 @@@ --DIST libxc-1.1.0.tar.gz 543168 SHA256 b75fb2a73a9e2d75e250cc77b71d5485c8e9b11c3b25c91899c366e217283c57 SHA512 a5ed3a4a7a7abaa11321fe877d01ff00132eab976205213e578cd57fbd2073eea00ce3a3afc188e30ebbd31deb32468c4472313df9992e8d9e3148e6f619936b WHIRLPOOL 8ff70acb2ee65b3373942b71e350fe146f1c205aa4c09dbb22adc04227ba6888482ce412b3e843a9402efd51f9cf6f478f9c65b97305b2035185e59b35484d9f DIST libxc-1.2.0.tar.gz 895527 SHA256 ee441c3cde2e2bd87828186aa17f6e4438d17b38634c5d29bb12d3b7554461fb SHA512 3ac0fd07e40db4feb0f0a4ebe1358fdd4de0fff21f6dd369895c658a14cd3bafedbbc374b89f68320401dfcfe16a6230e05403fdaccfcbebb98349ca06593125 WHIRLPOOL 66439bf65a656567c0e52a4ee20b206658a9185bdbd3e045daca00bf01ba0199ccbedea3e5034cf90fbc36dbc04d9666cde8bde46e2577ffd160800f1718bd2a ++DIST libxc-2.0.1.tar.gz 1062846 SHA256 c332f08648ec2bc7ccce83e45a84776215aa5dfebc64fae2a23f2ac546d41ea4 SHA512 c7d87134911fdfd91d985397a3fa990a63cc05d0752f0e2522e41dae0c2f39c43f9bd87ee6eb1972ab92b1aedeefad55a33ad84b1c66032e61ca03c87db02c5b WHIRLPOOL 16a5b999bb60177fde1371421f41f35736af4fcf8df123318ea438ffd34f487dcbadc95124ab9cf6ab2edeadd7983c56e0ca9d84bf528254de1f2a003addd402 diff --cc sci-libs/libxc/libxc-9999.ebuild index baf29d4,baf29d4..2432915 --- a/sci-libs/libxc/libxc-9999.ebuild +++ b/sci-libs/libxc/libxc-9999.ebuild @@@ -1,8 -1,8 +1,8 @@@ --# Copyright 1999-2012 Gentoo Foundation ++# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ --EAPI=4 ++EAPI=5 inherit autotools-utils fortran-2 multilib subversion @@@ -14,7 -14,7 +14,7 @@@ ESVN_BOOTSTRAP="eautoreconf -i LICENSE="LGPL-3" SLOT="0" KEYWORDS="" --IUSE="fortran static-libs" ++IUSE="fortran static-libs -test" MAKEOPTS+=" -j1" @@@ -31,14 -31,14 +31,21 @@@ src_configure() autotools-utils_src_configure } ++## Upstream recommends not running the test suite because it requires ++## human expert interpretation to determine whether output is an error or ++## expected under certain circumstances. Nevertheless, experts might want the option. ++# The autotools src_test function modified not to die. Runs emake check in build directory. ++src_test() { ++ debug-print-function ${FUNCNAME} "$@" ++ ++ _check_build_dir ++ pushd "${BUILD_DIR}" > /dev/null || die ++ make check || ewarn "Make check failed. See above for details." ++ einfo "emake check done" ++ popd > /dev/null || die ++} ++ src_install() { autotools-utils_src_install -- if use fortran; then -- insinto /usr/$(get_libdir)/finclude -- pushd "${AUTOTOOLS_BUILD_DIR}"/src >/dev/null -- doins *.mod || die -- rm -f "${D}"/usr/include/*.mod || die -- popd >/dev/null -- fi } diff --cc sci-physics/abinit/ChangeLog index a4f623b,a4f623b..2f76ad0 --- a/sci-physics/abinit/ChangeLog +++ b/sci-physics/abinit/ChangeLog @@@ -2,6 -2,6 +2,9 @@@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ ++ 18 Jun 2013; Honza Macháček abinit-7.2.2.ebuild: ++ The dependency on sci-libs/libxc modified to allow for 1.2.0-r1. ++ *abinit-7.2.2 (17 Jun 2013) 17 Jun 2013; Honza Macháček -abinit-7.0.4.ebuild, diff --cc sci-physics/abinit/Manifest index dee0365,dee0365..f000cdc --- a/sci-physics/abinit/Manifest +++ b/sci-physics/abinit/Manifest @@@ -1,2 -1,2 +1,1 @@@ --DIST abinit-7.0.4.tar.gz 61715030 SHA256 b3ad895b75b92b3ff05e873d42d0b26f6e6113b9de4579966f7b6d1b49d6004e SHA512 8edfe4019c968e6f912d0678fe331fc8a6ce2848f1b16973336d4181d010a776ed1ea2c5500499dac895d9d773d72165e20524705cf8928f91ede873272b0417 WHIRLPOOL 35da8681a68e435b460a11112e6cf6990fdf141d53d5849be45225d50e803e2bfc65cb05e5e576c704411be5734e47ed2e4ccca1fd1689311bd4febea937f0f8 --DIST abinit-7.0.5.tar.gz 61711550 SHA256 b16556aa05448781d872ab18f76ca6446a52be9eeed8d22015a0b63f4adf0f54 SHA512 007292cc7cdf459a5d62e907b29009d9496955952b5f491fa9183a5abb86dbf48020eb435b784d74037e381d65d2255a2b9a130322ee9bfecbff8ca075488ecd WHIRLPOOL 74d83a3a05817eaca402ace1b7ec3c3a6db3697a7ca0166549aee8155edfa2a7c8d516e2ae210a6f0e855f72617d704785bbb10e3a3ee262140964913608a307 ++DIST abinit-7.2.2.tar.gz 63683267 SHA256 96f83e3af63e993cb886d9d6cd1c4fac04d50b5e460d5620330441050a909533 SHA512 fbc4898ae4625e12ea22d8f2da63e037eb947320fedf800bd40bd7e0015633ce54b7cb224cee3fc931d015774c51df5f8594ebe26a409cb0325e7a3ab0bf5e4a WHIRLPOOL a149d7ecea9b2b19b94b4e873f1924ce5fe221e037c642d6428727b552dc0c428b288551dda708286995da26080171c385a3ef3ad3766e065073139d4ef0f2e8 diff --cc sci-physics/abinit/abinit-7.2.2.ebuild index 0a2b49b,0a2b49b..a420f51 --- a/sci-physics/abinit/abinit-7.2.2.ebuild +++ b/sci-physics/abinit/abinit-7.2.2.ebuild @@@ -16,7 -16,7 +16,7 @@@ KEYWORDS="~amd64 ~x86 IUSE="cuda cuda-double -debug +etsf_io +fftw +fftw-threads +fox gsl gui +hdf5 libabinit mpi +netcdf openmp python -test +threads -vdwxc" RDEPEND="~sci-libs/bigdft-abi-1.0.4 -- >=sci-libs/libxc-2.0.1[fortran] ++ >=sci-libs/libxc-1.2.0-r1[fortran] >=sci-physics/atompaw-3.0.1.9-r1[libxc] etsf_io? ( >=sci-libs/etsf_io-1.0.3-r2 ) fox? ( >=sci-libs/fox-4.1.2-r2[sax] ) diff --cc sci-physics/bigdft/ChangeLog index 0c32817,0c32817..3e78db9 --- a/sci-physics/bigdft/ChangeLog +++ b/sci-physics/bigdft/ChangeLog @@@ -2,6 -2,6 +2,11 @@@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ ++ 18 Jun 2013; Honza Macháček ++ bigdft-1.7_pre24.ebuild: ++ The dependency on sci-libs/libxc corrected to reflect the recent change in ++ the upgrade of sci-physics/abinit & friends. ++ *bigdft-1.7_pre24 (17 Jun 2013) 17 Jun 2013; Honza Macháček diff --cc sci-physics/bigdft/bigdft-1.7_pre24.ebuild index d74906a,d74906a..4a354aa --- a/sci-physics/bigdft/bigdft-1.7_pre24.ebuild +++ b/sci-physics/bigdft/bigdft-1.7_pre24.ebuild @@@ -20,7 -20,7 +20,7 @@@ KEYWORDS="~amd64 ~x86 ~amd64-linux IUSE="cuda doc etsf_io mpi netcdf openmp opencl test" RDEPEND=" -- >=sci-libs/libxc-1.0[fortran] ++ >=sci-libs/libxc-1.2.0-r1[fortran] virtual/blas virtual/fortran virtual/lapack diff --cc sci-physics/elk/ChangeLog index 28ac97d,28ac97d..2a837bc --- a/sci-physics/elk/ChangeLog +++ b/sci-physics/elk/ChangeLog @@@ -2,6 -2,6 +2,10 @@@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ ++ 18 Jun 2013; Honza Macháček elk-1.4.22.ebuild: ++ The dependency on sci-libs/libxc adapted to its recent change in the upgrade ++ of sci-physics/abinit & friends. ++ 21 Feb 2013; Justin Lecher elk-1.4.22.ebuild: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; add missing dep on virtual/pkgconfig; cleaning of ebuild diff --cc sci-physics/elk/elk-1.4.22.ebuild index ab7cd8d,ab7cd8d..5e99d05 --- a/sci-physics/elk/elk-1.4.22.ebuild +++ b/sci-physics/elk/elk-1.4.22.ebuild @@@ -19,7 -19,7 +19,7 @@@ RDEPEND= lapack? ( virtual/blas virtual/lapack ) -- libxc? ( =sci-libs/libxc-1*[fortran] ) ++ libxc? ( >=sci-libs/libxc-1.2.0-r1[fortran] ) mpi? ( virtual/mpi )" DEPEND="${RDEPEND} perl? ( dev-lang/perl ) From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 1F8BE1381F3 for ; Wed, 26 Jun 2013 07:09:56 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 6E060E0A5E; Wed, 26 Jun 2013 07:09:55 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id C0C79E080A for ; Wed, 26 Jun 2013 07:09:54 +0000 (UTC) Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id B40A333E73E for ; Wed, 26 Jun 2013 07:09:53 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id 5D430E5458 for ; Wed, 26 Jun 2013 07:09:52 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1371563669.83a6f8e906f3701f214c034c05285f7106cc5413.jlec@gentoo> Subject: [gentoo-commits] proj/sci:jlec commit in: / X-VCS-Repository: proj/sci X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 83a6f8e906f3701f214c034c05285f7106cc5413 X-VCS-Branch: jlec Date: Wed, 26 Jun 2013 07:09:52 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 7eb0bba7-a124-4f9e-8a4d-2dfa449ae90c X-Archives-Hash: a804e43cf2d366e9848cc807ca1a6db3 Message-ID: <20130626070952.XjRaTTK39hgjvVjEzjP1KoFT1sumCuy0puuP1orAvEE@z> commit: 83a6f8e906f3701f214c034c05285f7106cc5413 Author: Honza Macháček centrum cz> AuthorDate: Tue Jun 18 13:54:29 2013 +0000 Commit: Justin Lecher gentoo org> CommitDate: Tue Jun 18 13:54:29 2013 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=83a6f8e9 The dependency of several packages on sci-libs/libxc modified to reflect correctly the recent change in the upgrade of sci-physics/abinit & friends. profiles/package.mask | 6 +++ sci-chemistry/freeon/freeon-2012.05.03.ebuild | 7 +-- sci-chemistry/freeon/freeon-9999.ebuild | 7 +-- sci-chemistry/mics/ChangeLog | 10 ++++ sci-chemistry/mics/Manifest | 1 + .../{mgltools-autodocktools => mics}/metadata.xml | 0 sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild | 51 +++++++++++++++++++ sci-chemistry/modeller/ChangeLog | 6 +++ ...odeller-9.12.ebuild => modeller-9.12-r1.ebuild} | 2 +- sci-chemistry/talosn/ChangeLog | 10 ++++ sci-chemistry/talosn/Manifest | 1 + .../metadata.xml | 0 .../talosn/talosn-4.01.2013.148.15.55.ebuild | 59 ++++++++++++++++++++++ sci-libs/bigdft-abi/ChangeLog | 4 ++ sci-libs/bigdft-abi/Manifest | 2 - sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild | 5 +- sci-libs/libxc/Manifest | 2 +- sci-libs/libxc/libxc-9999.ebuild | 27 ++++++---- sci-libs/mumps/ChangeLog | 5 +- sci-libs/mumps/mumps-4.10.0-r2.ebuild | 5 +- sci-physics/abinit/ChangeLog | 3 ++ sci-physics/abinit/Manifest | 3 +- sci-physics/abinit/abinit-7.2.2.ebuild | 2 +- sci-physics/bigdft/ChangeLog | 5 ++ sci-physics/bigdft/bigdft-1.7_pre24.ebuild | 2 +- sci-physics/elk/ChangeLog | 4 ++ sci-physics/elk/elk-1.4.22.ebuild | 2 +- 27 files changed, 196 insertions(+), 35 deletions(-) diff --cc profiles/package.mask index 0c270df,0c270df..f354cdf --- a/profiles/package.mask +++ b/profiles/package.mask @@@ -68,6 -68,6 +68,12 @@@ >=sci-chemistry/coot-9999 >=sci-chemistry/pymol-9999 ++# Honza Macháček (17 June 2013) ++# bigdft moved from sci-libs to sci-physics ++# sci-physics/abinit now uses sci-libs/bigdft-abi instead ++# sci-libs/bigdft should be deleted in 30 days ++sci-libs/bigdft ++ # Justin Lecher (03 March 2013) # Missing deps sci-biology/gbrowse diff --cc sci-chemistry/freeon/freeon-2012.05.03.ebuild index 99805e0,99805e0..5a9cc6a --- a/sci-chemistry/freeon/freeon-2012.05.03.ebuild +++ b/sci-chemistry/freeon/freeon-2012.05.03.ebuild @@@ -33,11 -33,11 +33,8 @@@ DEPEND="${DEPEND S="${WORKDIR}/${REAL_PN}-${REAL_PV}" src_prepare() { -- # Get rid of the obsolete internal hdf5 -- rm -r "${S}"/hdf5-1.8.3 -- # as well as of the internal lapack -- rm -r "${S}"/lapack -- epatch "${FILESDIR}"/"${P}"-no_internal_libs.patch ++ # Prevent the obsolete internal hdf5 breaking autoconf ++ epatch "${FILESDIR}"/"${P}"-no_internal_hdf5.patch eautoreconf } diff --cc sci-chemistry/freeon/freeon-9999.ebuild index 369e063,369e063..6d02d93 --- a/sci-chemistry/freeon/freeon-9999.ebuild +++ b/sci-chemistry/freeon/freeon-9999.ebuild @@@ -31,11 -31,11 +31,8 @@@ DEPEND="${DEPEND virtual/pkgconfig" src_prepare() { -- # Get rid of the obsolete internal hdf5 -- rm -r "${S}"/Modules/hdf5-1.8.3 -- # as well as of the internal lapack -- rm -r "${S}"/Modules/lapack -- epatch "${FILESDIR}"/"${P}"-no_internal_libs.patch ++ # Prevent the obsolete internal hdf5 breaking autoconf ++ epatch "${FILESDIR}"/"${P}"-no_internal_hdf5.patch eautoreconf } diff --cc sci-libs/bigdft-abi/ChangeLog index 4c48008,4c48008..10ecead --- a/sci-libs/bigdft-abi/ChangeLog +++ b/sci-libs/bigdft-abi/ChangeLog @@@ -2,6 -2,6 +2,10 @@@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ ++ 18 Jun 2013; Honza Macháček ++ bigdft-abi-1.0.4.ebuild: ++ The dependency on sci-libs/libxc modified to allow for 1.2.0-r1. ++ *bigdft-abi-1.0.4 (17 Jun 2013) 17 Jun 2013; Honza Macháček diff --cc sci-libs/bigdft-abi/Manifest index bd17fc5,bd17fc5..e8a8b97 --- a/sci-libs/bigdft-abi/Manifest +++ b/sci-libs/bigdft-abi/Manifest @@@ -1,3 -1,3 +1,1 @@@ --AUX bigdft-abi-1.0.4-tests.tar.bz2 402968 SHA256 11144208456b001f63b75cadce0e9b685054ef8bbc39a76cb08af61d5c86c4fb SHA512 3594d11a8d5834916f44bf6f049630ac9d092df6a7a3171701ef65e5ab56e9d039c2bb4603698cb4935a95189c65d7bf77f44b50617ea8c971a844a2757b3202 WHIRLPOOL 492b92805a4eecb5bb204dbf76acf9a40c790b39708a914e38628a2f4dadc3377eed79f8d986231c006bc8c5be0167af60c36f72212005156e8fe3a3c619281c DIST bigdft-abi-1.0.4.tar.gz 8982260 SHA256 345cf49da92275710252d50b4ac8364f2f3c33e8f28d84d7b13ccf6fd0c69310 SHA512 556001d1ffd08be70b97f07a8a150d5d033a4611957180a7a25b41963754e0e3d2bb2a4e9d5b6beb8ff6fb1eb6f4ae9b51633cfe3d7f5a8ed20a85be21031c35 WHIRLPOOL b7c58732b538306f2b9b89b1310d9212cc1bb038fded782e6707e54679013ebc8376d54b5bd1bd51464dc7878fa05102fcba8f70a5d38b4571720c8d57ee3af1 --EBUILD bigdft-abi-1.0.4.ebuild 4232 SHA256 006484b64a83d7971efc05670b77d26114eed87f0d062c39e9b9bf01a4a005ce SHA512 bc34310bf3b4b3999574be8f67db51072a53b2a14fbf340edb72d046989f088b3c12b65f98a781fb5791263ce4c947786ee250dcbe4c162dcd194711321db4b5 WHIRLPOOL 28a1b685e427500acda0e210c9d2e72bbcd24bfe2be1b09112a1aab829d1efe9a896e28b45b42ec7db29c4908bc7cb3b73c83d0ad77accf9269ee9774e310537 diff --cc sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild index c285d63,c285d63..91e3bac --- a/sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild +++ b/sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild @@@ -19,7 -19,7 +19,7 @@@ KEYWORDS="~amd64 ~x86 ~amd64-linux IUSE="cuda doc etsf_io mpi netcdf openmp opencl test" RDEPEND=" -- >=sci-libs/libxc-2.0.1[fortran] ++ >=sci-libs/libxc-1.2.0-r1[fortran] virtual/blas virtual/fortran virtual/lapack @@@ -75,9 -75,9 +75,6 @@@ pkg_setup() } src_prepare() { --# epatch \ --# "${FILESDIR}"/"${P}"-nolib_mods.patch --# tar -xjf "${FILESDIR}"/"${P}"-tests.tar.bz2 -C "${S}"/tests/DFT/ eautoreconf } diff --cc sci-libs/libxc/Manifest index fa863cf,fa863cf..a85ebc8 --- a/sci-libs/libxc/Manifest +++ b/sci-libs/libxc/Manifest @@@ -1,2 -1,2 +1,2 @@@ --DIST libxc-1.1.0.tar.gz 543168 SHA256 b75fb2a73a9e2d75e250cc77b71d5485c8e9b11c3b25c91899c366e217283c57 SHA512 a5ed3a4a7a7abaa11321fe877d01ff00132eab976205213e578cd57fbd2073eea00ce3a3afc188e30ebbd31deb32468c4472313df9992e8d9e3148e6f619936b WHIRLPOOL 8ff70acb2ee65b3373942b71e350fe146f1c205aa4c09dbb22adc04227ba6888482ce412b3e843a9402efd51f9cf6f478f9c65b97305b2035185e59b35484d9f DIST libxc-1.2.0.tar.gz 895527 SHA256 ee441c3cde2e2bd87828186aa17f6e4438d17b38634c5d29bb12d3b7554461fb SHA512 3ac0fd07e40db4feb0f0a4ebe1358fdd4de0fff21f6dd369895c658a14cd3bafedbbc374b89f68320401dfcfe16a6230e05403fdaccfcbebb98349ca06593125 WHIRLPOOL 66439bf65a656567c0e52a4ee20b206658a9185bdbd3e045daca00bf01ba0199ccbedea3e5034cf90fbc36dbc04d9666cde8bde46e2577ffd160800f1718bd2a ++DIST libxc-2.0.1.tar.gz 1062846 SHA256 c332f08648ec2bc7ccce83e45a84776215aa5dfebc64fae2a23f2ac546d41ea4 SHA512 c7d87134911fdfd91d985397a3fa990a63cc05d0752f0e2522e41dae0c2f39c43f9bd87ee6eb1972ab92b1aedeefad55a33ad84b1c66032e61ca03c87db02c5b WHIRLPOOL 16a5b999bb60177fde1371421f41f35736af4fcf8df123318ea438ffd34f487dcbadc95124ab9cf6ab2edeadd7983c56e0ca9d84bf528254de1f2a003addd402 diff --cc sci-libs/libxc/libxc-9999.ebuild index baf29d4,baf29d4..2432915 --- a/sci-libs/libxc/libxc-9999.ebuild +++ b/sci-libs/libxc/libxc-9999.ebuild @@@ -1,8 -1,8 +1,8 @@@ --# Copyright 1999-2012 Gentoo Foundation ++# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ --EAPI=4 ++EAPI=5 inherit autotools-utils fortran-2 multilib subversion @@@ -14,7 -14,7 +14,7 @@@ ESVN_BOOTSTRAP="eautoreconf -i LICENSE="LGPL-3" SLOT="0" KEYWORDS="" --IUSE="fortran static-libs" ++IUSE="fortran static-libs -test" MAKEOPTS+=" -j1" @@@ -31,14 -31,14 +31,21 @@@ src_configure() autotools-utils_src_configure } ++## Upstream recommends not running the test suite because it requires ++## human expert interpretation to determine whether output is an error or ++## expected under certain circumstances. Nevertheless, experts might want the option. ++# The autotools src_test function modified not to die. Runs emake check in build directory. ++src_test() { ++ debug-print-function ${FUNCNAME} "$@" ++ ++ _check_build_dir ++ pushd "${BUILD_DIR}" > /dev/null || die ++ make check || ewarn "Make check failed. See above for details." ++ einfo "emake check done" ++ popd > /dev/null || die ++} ++ src_install() { autotools-utils_src_install -- if use fortran; then -- insinto /usr/$(get_libdir)/finclude -- pushd "${AUTOTOOLS_BUILD_DIR}"/src >/dev/null -- doins *.mod || die -- rm -f "${D}"/usr/include/*.mod || die -- popd >/dev/null -- fi } diff --cc sci-physics/abinit/ChangeLog index a4f623b,a4f623b..2f76ad0 --- a/sci-physics/abinit/ChangeLog +++ b/sci-physics/abinit/ChangeLog @@@ -2,6 -2,6 +2,9 @@@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ ++ 18 Jun 2013; Honza Macháček abinit-7.2.2.ebuild: ++ The dependency on sci-libs/libxc modified to allow for 1.2.0-r1. ++ *abinit-7.2.2 (17 Jun 2013) 17 Jun 2013; Honza Macháček -abinit-7.0.4.ebuild, diff --cc sci-physics/abinit/Manifest index dee0365,dee0365..f000cdc --- a/sci-physics/abinit/Manifest +++ b/sci-physics/abinit/Manifest @@@ -1,2 -1,2 +1,1 @@@ --DIST abinit-7.0.4.tar.gz 61715030 SHA256 b3ad895b75b92b3ff05e873d42d0b26f6e6113b9de4579966f7b6d1b49d6004e SHA512 8edfe4019c968e6f912d0678fe331fc8a6ce2848f1b16973336d4181d010a776ed1ea2c5500499dac895d9d773d72165e20524705cf8928f91ede873272b0417 WHIRLPOOL 35da8681a68e435b460a11112e6cf6990fdf141d53d5849be45225d50e803e2bfc65cb05e5e576c704411be5734e47ed2e4ccca1fd1689311bd4febea937f0f8 --DIST abinit-7.0.5.tar.gz 61711550 SHA256 b16556aa05448781d872ab18f76ca6446a52be9eeed8d22015a0b63f4adf0f54 SHA512 007292cc7cdf459a5d62e907b29009d9496955952b5f491fa9183a5abb86dbf48020eb435b784d74037e381d65d2255a2b9a130322ee9bfecbff8ca075488ecd WHIRLPOOL 74d83a3a05817eaca402ace1b7ec3c3a6db3697a7ca0166549aee8155edfa2a7c8d516e2ae210a6f0e855f72617d704785bbb10e3a3ee262140964913608a307 ++DIST abinit-7.2.2.tar.gz 63683267 SHA256 96f83e3af63e993cb886d9d6cd1c4fac04d50b5e460d5620330441050a909533 SHA512 fbc4898ae4625e12ea22d8f2da63e037eb947320fedf800bd40bd7e0015633ce54b7cb224cee3fc931d015774c51df5f8594ebe26a409cb0325e7a3ab0bf5e4a WHIRLPOOL a149d7ecea9b2b19b94b4e873f1924ce5fe221e037c642d6428727b552dc0c428b288551dda708286995da26080171c385a3ef3ad3766e065073139d4ef0f2e8 diff --cc sci-physics/abinit/abinit-7.2.2.ebuild index 0a2b49b,0a2b49b..a420f51 --- a/sci-physics/abinit/abinit-7.2.2.ebuild +++ b/sci-physics/abinit/abinit-7.2.2.ebuild @@@ -16,7 -16,7 +16,7 @@@ KEYWORDS="~amd64 ~x86 IUSE="cuda cuda-double -debug +etsf_io +fftw +fftw-threads +fox gsl gui +hdf5 libabinit mpi +netcdf openmp python -test +threads -vdwxc" RDEPEND="~sci-libs/bigdft-abi-1.0.4 -- >=sci-libs/libxc-2.0.1[fortran] ++ >=sci-libs/libxc-1.2.0-r1[fortran] >=sci-physics/atompaw-3.0.1.9-r1[libxc] etsf_io? ( >=sci-libs/etsf_io-1.0.3-r2 ) fox? ( >=sci-libs/fox-4.1.2-r2[sax] ) diff --cc sci-physics/bigdft/ChangeLog index 0c32817,0c32817..3e78db9 --- a/sci-physics/bigdft/ChangeLog +++ b/sci-physics/bigdft/ChangeLog @@@ -2,6 -2,6 +2,11 @@@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ ++ 18 Jun 2013; Honza Macháček ++ bigdft-1.7_pre24.ebuild: ++ The dependency on sci-libs/libxc corrected to reflect the recent change in ++ the upgrade of sci-physics/abinit & friends. ++ *bigdft-1.7_pre24 (17 Jun 2013) 17 Jun 2013; Honza Macháček diff --cc sci-physics/bigdft/bigdft-1.7_pre24.ebuild index d74906a,d74906a..4a354aa --- a/sci-physics/bigdft/bigdft-1.7_pre24.ebuild +++ b/sci-physics/bigdft/bigdft-1.7_pre24.ebuild @@@ -20,7 -20,7 +20,7 @@@ KEYWORDS="~amd64 ~x86 ~amd64-linux IUSE="cuda doc etsf_io mpi netcdf openmp opencl test" RDEPEND=" -- >=sci-libs/libxc-1.0[fortran] ++ >=sci-libs/libxc-1.2.0-r1[fortran] virtual/blas virtual/fortran virtual/lapack diff --cc sci-physics/elk/ChangeLog index 28ac97d,28ac97d..2a837bc --- a/sci-physics/elk/ChangeLog +++ b/sci-physics/elk/ChangeLog @@@ -2,6 -2,6 +2,10 @@@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ ++ 18 Jun 2013; Honza Macháček elk-1.4.22.ebuild: ++ The dependency on sci-libs/libxc adapted to its recent change in the upgrade ++ of sci-physics/abinit & friends. ++ 21 Feb 2013; Justin Lecher elk-1.4.22.ebuild: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; add missing dep on virtual/pkgconfig; cleaning of ebuild diff --cc sci-physics/elk/elk-1.4.22.ebuild index ab7cd8d,ab7cd8d..5e99d05 --- a/sci-physics/elk/elk-1.4.22.ebuild +++ b/sci-physics/elk/elk-1.4.22.ebuild @@@ -19,7 -19,7 +19,7 @@@ RDEPEND= lapack? ( virtual/blas virtual/lapack ) -- libxc? ( =sci-libs/libxc-1*[fortran] ) ++ libxc? ( >=sci-libs/libxc-1.2.0-r1[fortran] ) mpi? ( virtual/mpi )" DEPEND="${RDEPEND} perl? ( dev-lang/perl ) From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 52444138200 for ; Sat, 22 Jun 2013 10:49:26 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id BBF1FE0A45; Sat, 22 Jun 2013 10:49:25 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 30B3DE0A10 for ; Sat, 22 Jun 2013 10:49:25 +0000 (UTC) Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id F1DFA33E643 for ; Sat, 22 Jun 2013 10:49:23 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id 8BD13E468F for ; Sat, 22 Jun 2013 10:49:22 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1371563669.83a6f8e906f3701f214c034c05285f7106cc5413.jlec@gentoo> Subject: [gentoo-commits] proj/sci:fixing commit in: / X-VCS-Repository: proj/sci X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 83a6f8e906f3701f214c034c05285f7106cc5413 X-VCS-Branch: fixing Date: Sat, 22 Jun 2013 10:49:22 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 03767a82-9d8a-4794-a9c8-25c2fd5133ce X-Archives-Hash: 407e6e7a01bfe275fb6ea9b7286b8ce7 Message-ID: <20130622104922.4_njh0jGIn0hsCjPRVuFRin40-LAdQUomYSXERIOfpY@z> commit: 83a6f8e906f3701f214c034c05285f7106cc5413 Author: Honza Macháček centrum cz> AuthorDate: Tue Jun 18 13:54:29 2013 +0000 Commit: Justin Lecher gentoo org> CommitDate: Tue Jun 18 13:54:29 2013 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=83a6f8e9 The dependency of several packages on sci-libs/libxc modified to reflect correctly the recent change in the upgrade of sci-physics/abinit & friends. profiles/package.mask | 6 +++ sci-chemistry/freeon/freeon-2012.05.03.ebuild | 7 +-- sci-chemistry/freeon/freeon-9999.ebuild | 7 +-- sci-chemistry/mics/ChangeLog | 10 ++++ sci-chemistry/mics/Manifest | 1 + .../{mgltools-autodocktools => mics}/metadata.xml | 0 sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild | 51 +++++++++++++++++++ sci-chemistry/modeller/ChangeLog | 6 +++ ...odeller-9.12.ebuild => modeller-9.12-r1.ebuild} | 2 +- sci-chemistry/talosn/ChangeLog | 10 ++++ sci-chemistry/talosn/Manifest | 1 + .../metadata.xml | 0 .../talosn/talosn-4.01.2013.148.15.55.ebuild | 59 ++++++++++++++++++++++ sci-libs/bigdft-abi/ChangeLog | 4 ++ sci-libs/bigdft-abi/Manifest | 2 - sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild | 5 +- sci-libs/libxc/Manifest | 2 +- sci-libs/libxc/libxc-9999.ebuild | 27 ++++++---- sci-libs/mumps/ChangeLog | 5 +- sci-libs/mumps/mumps-4.10.0-r2.ebuild | 5 +- sci-physics/abinit/ChangeLog | 3 ++ sci-physics/abinit/Manifest | 3 +- sci-physics/abinit/abinit-7.2.2.ebuild | 2 +- sci-physics/bigdft/ChangeLog | 5 ++ sci-physics/bigdft/bigdft-1.7_pre24.ebuild | 2 +- sci-physics/elk/ChangeLog | 4 ++ sci-physics/elk/elk-1.4.22.ebuild | 2 +- 27 files changed, 196 insertions(+), 35 deletions(-) diff --cc profiles/package.mask index 0c270df,0c270df..f354cdf --- a/profiles/package.mask +++ b/profiles/package.mask @@@ -68,6 -68,6 +68,12 @@@ >=sci-chemistry/coot-9999 >=sci-chemistry/pymol-9999 ++# Honza Macháček (17 June 2013) ++# bigdft moved from sci-libs to sci-physics ++# sci-physics/abinit now uses sci-libs/bigdft-abi instead ++# sci-libs/bigdft should be deleted in 30 days ++sci-libs/bigdft ++ # Justin Lecher (03 March 2013) # Missing deps sci-biology/gbrowse diff --cc sci-chemistry/freeon/freeon-2012.05.03.ebuild index 99805e0,99805e0..5a9cc6a --- a/sci-chemistry/freeon/freeon-2012.05.03.ebuild +++ b/sci-chemistry/freeon/freeon-2012.05.03.ebuild @@@ -33,11 -33,11 +33,8 @@@ DEPEND="${DEPEND S="${WORKDIR}/${REAL_PN}-${REAL_PV}" src_prepare() { -- # Get rid of the obsolete internal hdf5 -- rm -r "${S}"/hdf5-1.8.3 -- # as well as of the internal lapack -- rm -r "${S}"/lapack -- epatch "${FILESDIR}"/"${P}"-no_internal_libs.patch ++ # Prevent the obsolete internal hdf5 breaking autoconf ++ epatch "${FILESDIR}"/"${P}"-no_internal_hdf5.patch eautoreconf } diff --cc sci-chemistry/freeon/freeon-9999.ebuild index 369e063,369e063..6d02d93 --- a/sci-chemistry/freeon/freeon-9999.ebuild +++ b/sci-chemistry/freeon/freeon-9999.ebuild @@@ -31,11 -31,11 +31,8 @@@ DEPEND="${DEPEND virtual/pkgconfig" src_prepare() { -- # Get rid of the obsolete internal hdf5 -- rm -r "${S}"/Modules/hdf5-1.8.3 -- # as well as of the internal lapack -- rm -r "${S}"/Modules/lapack -- epatch "${FILESDIR}"/"${P}"-no_internal_libs.patch ++ # Prevent the obsolete internal hdf5 breaking autoconf ++ epatch "${FILESDIR}"/"${P}"-no_internal_hdf5.patch eautoreconf } diff --cc sci-libs/bigdft-abi/ChangeLog index 4c48008,4c48008..10ecead --- a/sci-libs/bigdft-abi/ChangeLog +++ b/sci-libs/bigdft-abi/ChangeLog @@@ -2,6 -2,6 +2,10 @@@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ ++ 18 Jun 2013; Honza Macháček ++ bigdft-abi-1.0.4.ebuild: ++ The dependency on sci-libs/libxc modified to allow for 1.2.0-r1. ++ *bigdft-abi-1.0.4 (17 Jun 2013) 17 Jun 2013; Honza Macháček diff --cc sci-libs/bigdft-abi/Manifest index bd17fc5,bd17fc5..e8a8b97 --- a/sci-libs/bigdft-abi/Manifest +++ b/sci-libs/bigdft-abi/Manifest @@@ -1,3 -1,3 +1,1 @@@ --AUX bigdft-abi-1.0.4-tests.tar.bz2 402968 SHA256 11144208456b001f63b75cadce0e9b685054ef8bbc39a76cb08af61d5c86c4fb SHA512 3594d11a8d5834916f44bf6f049630ac9d092df6a7a3171701ef65e5ab56e9d039c2bb4603698cb4935a95189c65d7bf77f44b50617ea8c971a844a2757b3202 WHIRLPOOL 492b92805a4eecb5bb204dbf76acf9a40c790b39708a914e38628a2f4dadc3377eed79f8d986231c006bc8c5be0167af60c36f72212005156e8fe3a3c619281c DIST bigdft-abi-1.0.4.tar.gz 8982260 SHA256 345cf49da92275710252d50b4ac8364f2f3c33e8f28d84d7b13ccf6fd0c69310 SHA512 556001d1ffd08be70b97f07a8a150d5d033a4611957180a7a25b41963754e0e3d2bb2a4e9d5b6beb8ff6fb1eb6f4ae9b51633cfe3d7f5a8ed20a85be21031c35 WHIRLPOOL b7c58732b538306f2b9b89b1310d9212cc1bb038fded782e6707e54679013ebc8376d54b5bd1bd51464dc7878fa05102fcba8f70a5d38b4571720c8d57ee3af1 --EBUILD bigdft-abi-1.0.4.ebuild 4232 SHA256 006484b64a83d7971efc05670b77d26114eed87f0d062c39e9b9bf01a4a005ce SHA512 bc34310bf3b4b3999574be8f67db51072a53b2a14fbf340edb72d046989f088b3c12b65f98a781fb5791263ce4c947786ee250dcbe4c162dcd194711321db4b5 WHIRLPOOL 28a1b685e427500acda0e210c9d2e72bbcd24bfe2be1b09112a1aab829d1efe9a896e28b45b42ec7db29c4908bc7cb3b73c83d0ad77accf9269ee9774e310537 diff --cc sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild index c285d63,c285d63..91e3bac --- a/sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild +++ b/sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild @@@ -19,7 -19,7 +19,7 @@@ KEYWORDS="~amd64 ~x86 ~amd64-linux IUSE="cuda doc etsf_io mpi netcdf openmp opencl test" RDEPEND=" -- >=sci-libs/libxc-2.0.1[fortran] ++ >=sci-libs/libxc-1.2.0-r1[fortran] virtual/blas virtual/fortran virtual/lapack @@@ -75,9 -75,9 +75,6 @@@ pkg_setup() } src_prepare() { --# epatch \ --# "${FILESDIR}"/"${P}"-nolib_mods.patch --# tar -xjf "${FILESDIR}"/"${P}"-tests.tar.bz2 -C "${S}"/tests/DFT/ eautoreconf } diff --cc sci-libs/libxc/Manifest index fa863cf,fa863cf..a85ebc8 --- a/sci-libs/libxc/Manifest +++ b/sci-libs/libxc/Manifest @@@ -1,2 -1,2 +1,2 @@@ --DIST libxc-1.1.0.tar.gz 543168 SHA256 b75fb2a73a9e2d75e250cc77b71d5485c8e9b11c3b25c91899c366e217283c57 SHA512 a5ed3a4a7a7abaa11321fe877d01ff00132eab976205213e578cd57fbd2073eea00ce3a3afc188e30ebbd31deb32468c4472313df9992e8d9e3148e6f619936b WHIRLPOOL 8ff70acb2ee65b3373942b71e350fe146f1c205aa4c09dbb22adc04227ba6888482ce412b3e843a9402efd51f9cf6f478f9c65b97305b2035185e59b35484d9f DIST libxc-1.2.0.tar.gz 895527 SHA256 ee441c3cde2e2bd87828186aa17f6e4438d17b38634c5d29bb12d3b7554461fb SHA512 3ac0fd07e40db4feb0f0a4ebe1358fdd4de0fff21f6dd369895c658a14cd3bafedbbc374b89f68320401dfcfe16a6230e05403fdaccfcbebb98349ca06593125 WHIRLPOOL 66439bf65a656567c0e52a4ee20b206658a9185bdbd3e045daca00bf01ba0199ccbedea3e5034cf90fbc36dbc04d9666cde8bde46e2577ffd160800f1718bd2a ++DIST libxc-2.0.1.tar.gz 1062846 SHA256 c332f08648ec2bc7ccce83e45a84776215aa5dfebc64fae2a23f2ac546d41ea4 SHA512 c7d87134911fdfd91d985397a3fa990a63cc05d0752f0e2522e41dae0c2f39c43f9bd87ee6eb1972ab92b1aedeefad55a33ad84b1c66032e61ca03c87db02c5b WHIRLPOOL 16a5b999bb60177fde1371421f41f35736af4fcf8df123318ea438ffd34f487dcbadc95124ab9cf6ab2edeadd7983c56e0ca9d84bf528254de1f2a003addd402 diff --cc sci-libs/libxc/libxc-9999.ebuild index baf29d4,baf29d4..2432915 --- a/sci-libs/libxc/libxc-9999.ebuild +++ b/sci-libs/libxc/libxc-9999.ebuild @@@ -1,8 -1,8 +1,8 @@@ --# Copyright 1999-2012 Gentoo Foundation ++# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ --EAPI=4 ++EAPI=5 inherit autotools-utils fortran-2 multilib subversion @@@ -14,7 -14,7 +14,7 @@@ ESVN_BOOTSTRAP="eautoreconf -i LICENSE="LGPL-3" SLOT="0" KEYWORDS="" --IUSE="fortran static-libs" ++IUSE="fortran static-libs -test" MAKEOPTS+=" -j1" @@@ -31,14 -31,14 +31,21 @@@ src_configure() autotools-utils_src_configure } ++## Upstream recommends not running the test suite because it requires ++## human expert interpretation to determine whether output is an error or ++## expected under certain circumstances. Nevertheless, experts might want the option. ++# The autotools src_test function modified not to die. Runs emake check in build directory. ++src_test() { ++ debug-print-function ${FUNCNAME} "$@" ++ ++ _check_build_dir ++ pushd "${BUILD_DIR}" > /dev/null || die ++ make check || ewarn "Make check failed. See above for details." ++ einfo "emake check done" ++ popd > /dev/null || die ++} ++ src_install() { autotools-utils_src_install -- if use fortran; then -- insinto /usr/$(get_libdir)/finclude -- pushd "${AUTOTOOLS_BUILD_DIR}"/src >/dev/null -- doins *.mod || die -- rm -f "${D}"/usr/include/*.mod || die -- popd >/dev/null -- fi } diff --cc sci-physics/abinit/ChangeLog index a4f623b,a4f623b..2f76ad0 --- a/sci-physics/abinit/ChangeLog +++ b/sci-physics/abinit/ChangeLog @@@ -2,6 -2,6 +2,9 @@@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ ++ 18 Jun 2013; Honza Macháček abinit-7.2.2.ebuild: ++ The dependency on sci-libs/libxc modified to allow for 1.2.0-r1. ++ *abinit-7.2.2 (17 Jun 2013) 17 Jun 2013; Honza Macháček -abinit-7.0.4.ebuild, diff --cc sci-physics/abinit/Manifest index dee0365,dee0365..f000cdc --- a/sci-physics/abinit/Manifest +++ b/sci-physics/abinit/Manifest @@@ -1,2 -1,2 +1,1 @@@ --DIST abinit-7.0.4.tar.gz 61715030 SHA256 b3ad895b75b92b3ff05e873d42d0b26f6e6113b9de4579966f7b6d1b49d6004e SHA512 8edfe4019c968e6f912d0678fe331fc8a6ce2848f1b16973336d4181d010a776ed1ea2c5500499dac895d9d773d72165e20524705cf8928f91ede873272b0417 WHIRLPOOL 35da8681a68e435b460a11112e6cf6990fdf141d53d5849be45225d50e803e2bfc65cb05e5e576c704411be5734e47ed2e4ccca1fd1689311bd4febea937f0f8 --DIST abinit-7.0.5.tar.gz 61711550 SHA256 b16556aa05448781d872ab18f76ca6446a52be9eeed8d22015a0b63f4adf0f54 SHA512 007292cc7cdf459a5d62e907b29009d9496955952b5f491fa9183a5abb86dbf48020eb435b784d74037e381d65d2255a2b9a130322ee9bfecbff8ca075488ecd WHIRLPOOL 74d83a3a05817eaca402ace1b7ec3c3a6db3697a7ca0166549aee8155edfa2a7c8d516e2ae210a6f0e855f72617d704785bbb10e3a3ee262140964913608a307 ++DIST abinit-7.2.2.tar.gz 63683267 SHA256 96f83e3af63e993cb886d9d6cd1c4fac04d50b5e460d5620330441050a909533 SHA512 fbc4898ae4625e12ea22d8f2da63e037eb947320fedf800bd40bd7e0015633ce54b7cb224cee3fc931d015774c51df5f8594ebe26a409cb0325e7a3ab0bf5e4a WHIRLPOOL a149d7ecea9b2b19b94b4e873f1924ce5fe221e037c642d6428727b552dc0c428b288551dda708286995da26080171c385a3ef3ad3766e065073139d4ef0f2e8 diff --cc sci-physics/abinit/abinit-7.2.2.ebuild index 0a2b49b,0a2b49b..a420f51 --- a/sci-physics/abinit/abinit-7.2.2.ebuild +++ b/sci-physics/abinit/abinit-7.2.2.ebuild @@@ -16,7 -16,7 +16,7 @@@ KEYWORDS="~amd64 ~x86 IUSE="cuda cuda-double -debug +etsf_io +fftw +fftw-threads +fox gsl gui +hdf5 libabinit mpi +netcdf openmp python -test +threads -vdwxc" RDEPEND="~sci-libs/bigdft-abi-1.0.4 -- >=sci-libs/libxc-2.0.1[fortran] ++ >=sci-libs/libxc-1.2.0-r1[fortran] >=sci-physics/atompaw-3.0.1.9-r1[libxc] etsf_io? ( >=sci-libs/etsf_io-1.0.3-r2 ) fox? ( >=sci-libs/fox-4.1.2-r2[sax] ) diff --cc sci-physics/bigdft/ChangeLog index 0c32817,0c32817..3e78db9 --- a/sci-physics/bigdft/ChangeLog +++ b/sci-physics/bigdft/ChangeLog @@@ -2,6 -2,6 +2,11 @@@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ ++ 18 Jun 2013; Honza Macháček ++ bigdft-1.7_pre24.ebuild: ++ The dependency on sci-libs/libxc corrected to reflect the recent change in ++ the upgrade of sci-physics/abinit & friends. ++ *bigdft-1.7_pre24 (17 Jun 2013) 17 Jun 2013; Honza Macháček diff --cc sci-physics/bigdft/bigdft-1.7_pre24.ebuild index d74906a,d74906a..4a354aa --- a/sci-physics/bigdft/bigdft-1.7_pre24.ebuild +++ b/sci-physics/bigdft/bigdft-1.7_pre24.ebuild @@@ -20,7 -20,7 +20,7 @@@ KEYWORDS="~amd64 ~x86 ~amd64-linux IUSE="cuda doc etsf_io mpi netcdf openmp opencl test" RDEPEND=" -- >=sci-libs/libxc-1.0[fortran] ++ >=sci-libs/libxc-1.2.0-r1[fortran] virtual/blas virtual/fortran virtual/lapack diff --cc sci-physics/elk/ChangeLog index 28ac97d,28ac97d..2a837bc --- a/sci-physics/elk/ChangeLog +++ b/sci-physics/elk/ChangeLog @@@ -2,6 -2,6 +2,10 @@@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ ++ 18 Jun 2013; Honza Macháček elk-1.4.22.ebuild: ++ The dependency on sci-libs/libxc adapted to its recent change in the upgrade ++ of sci-physics/abinit & friends. ++ 21 Feb 2013; Justin Lecher elk-1.4.22.ebuild: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; add missing dep on virtual/pkgconfig; cleaning of ebuild diff --cc sci-physics/elk/elk-1.4.22.ebuild index ab7cd8d,ab7cd8d..5e99d05 --- a/sci-physics/elk/elk-1.4.22.ebuild +++ b/sci-physics/elk/elk-1.4.22.ebuild @@@ -19,7 -19,7 +19,7 @@@ RDEPEND= lapack? ( virtual/blas virtual/lapack ) -- libxc? ( =sci-libs/libxc-1*[fortran] ) ++ libxc? ( >=sci-libs/libxc-1.2.0-r1[fortran] ) mpi? ( virtual/mpi )" DEPEND="${RDEPEND} perl? ( dev-lang/perl )