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-rw-r--r--profiles/package.mask6
-rw-r--r--sci-chemistry/freeon/freeon-2012.05.03.ebuild7
-rw-r--r--sci-chemistry/freeon/freeon-9999.ebuild7
-rw-r--r--sci-libs/bigdft-abi/ChangeLog4
-rw-r--r--sci-libs/bigdft-abi/Manifest2
-rw-r--r--sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild5
-rw-r--r--sci-libs/libxc/Manifest2
-rw-r--r--sci-libs/libxc/libxc-9999.ebuild27
-rw-r--r--sci-physics/abinit/ChangeLog3
-rw-r--r--sci-physics/abinit/Manifest3
-rw-r--r--sci-physics/abinit/abinit-7.2.2.ebuild2
-rw-r--r--sci-physics/bigdft/ChangeLog5
-rw-r--r--sci-physics/bigdft/bigdft-1.7_pre24.ebuild2
-rw-r--r--sci-physics/elk/ChangeLog4
-rw-r--r--sci-physics/elk/elk-1.4.22.ebuild2
15 files changed, 49 insertions, 32 deletions
diff --git a/profiles/package.mask b/profiles/package.mask
index 0c270df4b..f354cdf57 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -68,6 +68,12 @@
>=sci-chemistry/coot-9999
>=sci-chemistry/pymol-9999
+# Honza Macháček <Hloupy.Honza@centrum.cz> (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 <jlec@gentoo.org> (03 March 2013)
# Missing deps
sci-biology/gbrowse
diff --git a/sci-chemistry/freeon/freeon-2012.05.03.ebuild b/sci-chemistry/freeon/freeon-2012.05.03.ebuild
index 99805e0dc..5a9cc6a94 100644
--- a/sci-chemistry/freeon/freeon-2012.05.03.ebuild
+++ b/sci-chemistry/freeon/freeon-2012.05.03.ebuild
@@ -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 --git a/sci-chemistry/freeon/freeon-9999.ebuild b/sci-chemistry/freeon/freeon-9999.ebuild
index 369e063f8..6d02d9380 100644
--- a/sci-chemistry/freeon/freeon-9999.ebuild
+++ b/sci-chemistry/freeon/freeon-9999.ebuild
@@ -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 --git a/sci-libs/bigdft-abi/ChangeLog b/sci-libs/bigdft-abi/ChangeLog
index 4c4800877..10eceadcb 100644
--- a/sci-libs/bigdft-abi/ChangeLog
+++ b/sci-libs/bigdft-abi/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
+ 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 <Hloupy.Honza@centrum.cz>
diff --git a/sci-libs/bigdft-abi/Manifest b/sci-libs/bigdft-abi/Manifest
index bd17fc562..e8a8b973e 100644
--- a/sci-libs/bigdft-abi/Manifest
+++ b/sci-libs/bigdft-abi/Manifest
@@ -1,3 +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 --git a/sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild b/sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild
index c285d6326..91e3bac69 100644
--- 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 @@ 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 +75,6 @@ pkg_setup() {
}
src_prepare() {
-# epatch \
-# "${FILESDIR}"/"${P}"-nolib_mods.patch
-#
tar -xjf "${FILESDIR}"/"${P}"-tests.tar.bz2 -C "${S}"/tests/DFT/
eautoreconf
}
diff --git a/sci-libs/libxc/Manifest b/sci-libs/libxc/Manifest
index fa863cf20..a85ebc898 100644
--- a/sci-libs/libxc/Manifest
+++ b/sci-libs/libxc/Manifest
@@ -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 --git a/sci-libs/libxc/libxc-9999.ebuild b/sci-libs/libxc/libxc-9999.ebuild
index baf29d429..2432915ed 100644
--- a/sci-libs/libxc/libxc-9999.ebuild
+++ b/sci-libs/libxc/libxc-9999.ebuild
@@ -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 @@ ESVN_BOOTSTRAP="eautoreconf -i"
LICENSE="LGPL-3"
SLOT="0"
KEYWORDS=""
-IUSE="fortran static-libs"
+IUSE="fortran static-libs -test"
MAKEOPTS+=" -j1"
@@ -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 --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog
index a4f623b87..2f76ad0d4 100644
--- a/sci-physics/abinit/ChangeLog
+++ b/sci-physics/abinit/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> 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 <Hloupy.Honza@centrum.cz> -abinit-7.0.4.ebuild,
diff --git a/sci-physics/abinit/Manifest b/sci-physics/abinit/Manifest
index dee036578..f000cdcd5 100644
--- a/sci-physics/abinit/Manifest
+++ b/sci-physics/abinit/Manifest
@@ -1,2 +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 --git a/sci-physics/abinit/abinit-7.2.2.ebuild b/sci-physics/abinit/abinit-7.2.2.ebuild
index 0a2b49b76..a420f51cf 100644
--- a/sci-physics/abinit/abinit-7.2.2.ebuild
+++ b/sci-physics/abinit/abinit-7.2.2.ebuild
@@ -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 --git a/sci-physics/bigdft/ChangeLog b/sci-physics/bigdft/ChangeLog
index 0c32817c1..3e78db982 100644
--- a/sci-physics/bigdft/ChangeLog
+++ b/sci-physics/bigdft/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
+ 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 <Hloupy.Honza@centrum.cz>
diff --git a/sci-physics/bigdft/bigdft-1.7_pre24.ebuild b/sci-physics/bigdft/bigdft-1.7_pre24.ebuild
index d74906a74..4a354aaef 100644
--- a/sci-physics/bigdft/bigdft-1.7_pre24.ebuild
+++ b/sci-physics/bigdft/bigdft-1.7_pre24.ebuild
@@ -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 --git a/sci-physics/elk/ChangeLog b/sci-physics/elk/ChangeLog
index 28ac97dff..2a837bcdd 100644
--- a/sci-physics/elk/ChangeLog
+++ b/sci-physics/elk/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> 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 <jlec@gentoo.org> 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 --git a/sci-physics/elk/elk-1.4.22.ebuild b/sci-physics/elk/elk-1.4.22.ebuild
index ab7cd8dcd..5e99d05d3 100644
--- a/sci-physics/elk/elk-1.4.22.ebuild
+++ b/sci-physics/elk/elk-1.4.22.ebuild
@@ -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 )