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authorMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2013-09-25 14:30:09 +0200
committerMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2013-09-25 14:30:09 +0200
commit30141b35ea5b62b066b29bcc7c903097990777a3 (patch)
treeb0f656e1c3735748a726922044d0cb61ba6a5fd8
parentUpstream accidentally dropped some of my patch chunks while preparing 1.62 re... (diff)
parentPreviously announced change of sci-libs/bigdft-abi actually done. Added a met... (diff)
downloadsci-30141b35ea5b62b066b29bcc7c903097990777a3.tar.gz
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sci-30141b35ea5b62b066b29bcc7c903097990777a3.zip
Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-rw-r--r--dev-perl/Bio-BigFile/Bio-BigFile-1.07.ebuild (renamed from dev-perl/Bio-BigFile/Bio-BigFile-1.06.ebuild)9
-rw-r--r--dev-perl/Bio-BigFile/ChangeLog6
-rw-r--r--dev-perl/Bio-BigFile/Manifest2
-rw-r--r--dev-perl/Bio-BigFile/metadata.xml10
-rw-r--r--sci-chemistry/coot/ChangeLog3
-rw-r--r--sci-chemistry/coot/coot-9999.ebuild8
-rw-r--r--sci-chemistry/freeon/ChangeLog14
-rw-r--r--sci-chemistry/freeon/Manifest2
-rw-r--r--sci-chemistry/freeon/freeon-1.0.2.ebuild26
-rw-r--r--sci-chemistry/freeon/freeon-1.0.3.ebuild33
-rw-r--r--sci-chemistry/freeon/metadata.xml3
-rw-r--r--sci-chemistry/modeller/ChangeLog4
-rw-r--r--sci-chemistry/modeller/modeller-9.12-r3.ebuild (renamed from sci-chemistry/modeller/modeller-9.12-r2.ebuild)7
-rw-r--r--sci-libs/bigdft-abi/ChangeLog11
-rw-r--r--sci-libs/bigdft-abi/bigdft-abi-1.0.4-r2.ebuild (renamed from sci-libs/bigdft-abi/bigdft-abi-1.0.4-r1.ebuild)5
-rw-r--r--sci-libs/bigdft-abi/metadata.xml24
-rw-r--r--sci-libs/bigdft/ChangeLog139
-rw-r--r--sci-libs/bigdft/Manifest2
-rw-r--r--sci-libs/bigdft/bigdft-1.6.0-r2.ebuild122
-rw-r--r--sci-libs/bigdft/bigdft-1.7_pre12.ebuild147
-rw-r--r--sci-libs/bigdft/files/bigdft-1.6-tuto.1-GPUlibs-1.patch26
-rw-r--r--sci-libs/bigdft/files/bigdft-1.6-tuto.1-bigdft.pc-1.patch207
-rw-r--r--sci-libs/bigdft/files/bigdft-1.6-tuto.1-gcc-4.6.patch67
-rw-r--r--sci-libs/bigdft/files/bigdft-1.6-tuto.1-libxc_dir_include.patch50
-rw-r--r--sci-libs/bigdft/files/bigdft-1.6.0-libxc_dir_include.patch50
-rw-r--r--sci-libs/bigdft/files/bigdft-1.7-dev.12-GPUlink.patch12
-rw-r--r--sci-libs/bigdft/files/bigdft-1.7-dev.12-libxc_dir_include.patch50
-rw-r--r--sci-libs/bigdft/files/bigdft-1.7-dev.12-nolib_mods.patch25
-rw-r--r--sci-libs/bigdft/files/bigdft-1.7-dev.12-tests.tar.bz2bin22103 -> 0 bytes
-rw-r--r--sci-libs/bigdft/metadata.xml10
-rw-r--r--sci-libs/modglue/ChangeLog14
-rw-r--r--sci-libs/modglue/Manifest2
-rw-r--r--sci-libs/modglue/files/modglue-1.16-ldflags.patch13
-rw-r--r--sci-libs/modglue/files/modglue-1.16-lib64.patch61
-rw-r--r--sci-libs/modglue/files/modglue-1.16-parallelmake.patch53
-rw-r--r--sci-libs/modglue/files/modglue-1.19-Makefiles.patch113
-rw-r--r--sci-libs/modglue/modglue-1.19.ebuild (renamed from sci-libs/modglue/modglue-1.16.ebuild)11
-rw-r--r--sci-libs/scikits_image/ChangeLog7
-rw-r--r--sci-libs/scikits_image/metadata.xml16
-rw-r--r--sci-libs/scikits_image/scikits_image-9999.ebuild6
-rw-r--r--sci-libs/wannier90/ChangeLog6
-rw-r--r--sci-libs/wannier90/wannier90-1.2-r2.ebuild (renamed from sci-libs/wannier90/wannier90-1.2-r1.ebuild)5
-rw-r--r--sci-mathematics/cadabra/ChangeLog8
-rw-r--r--sci-mathematics/cadabra/Manifest2
-rw-r--r--sci-mathematics/cadabra/cadabra-1.33.ebuild (renamed from sci-mathematics/cadabra/cadabra-1.31.ebuild)18
-rw-r--r--sci-mathematics/cadabra/files/cadabra-1.21-no-stripping.patch30
-rw-r--r--sci-mathematics/cadabra/files/cadabra-1.25-xcadabra-flags.patch11
-rw-r--r--sci-mathematics/cadabra/files/cadabra-1.33-FLAGS.patch171
-rw-r--r--sci-physics/abinit/ChangeLog15
-rw-r--r--sci-physics/abinit/Manifest2
-rw-r--r--sci-physics/abinit/abinit-7.4.2.ebuild (renamed from sci-physics/abinit/abinit-7.2.2.ebuild)277
-rw-r--r--sci-physics/abinit/files/7.4.2-levmar_diag_scaling.patch21
-rw-r--r--sci-physics/abinit/files/7.4.2-syntax.patch21
-rw-r--r--sci-physics/abinit/metadata.xml36
-rw-r--r--sci-physics/openmx/ChangeLog6
-rw-r--r--sci-physics/openmx/Manifest2
-rw-r--r--sci-physics/openmx/openmx-3.7.6.ebuild (renamed from sci-physics/openmx/openmx-3.7.4.ebuild)12
57 files changed, 732 insertions, 1281 deletions
diff --git a/dev-perl/Bio-BigFile/Bio-BigFile-1.06.ebuild b/dev-perl/Bio-BigFile/Bio-BigFile-1.07.ebuild
index 7da661606..c9264eaf6 100644
--- a/dev-perl/Bio-BigFile/Bio-BigFile-1.06.ebuild
+++ b/dev-perl/Bio-BigFile/Bio-BigFile-1.07.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
MODULE_AUTHOR="LDS"
@@ -15,7 +15,10 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
-RDEPEND="sci-biology/ucsc-genome-browser"
+RDEPEND="
+ dev-perl/IO-String
+ sci-biology/bioperl
+ sci-biology/ucsc-genome-browser[static-libs]"
DEPEND="${RDEPEND}
virtual/perl-Module-Build"
diff --git a/dev-perl/Bio-BigFile/ChangeLog b/dev-perl/Bio-BigFile/ChangeLog
index d899200ff..3af2a5639 100644
--- a/dev-perl/Bio-BigFile/ChangeLog
+++ b/dev-perl/Bio-BigFile/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for dev-perl/Bio-BigFile
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 Sep 2013; Justin Lecher <jlec@gentoo.org> -Bio-BigFile-1.06.ebuild,
+ +Bio-BigFile-1.07.ebuild, metadata.xml:
+ Version BUmp, fix deps
+
22 May 2012; Justin Lecher <jlec@gentoo.org> Bio-BigFile-1.06.ebuild:
Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
diff --git a/dev-perl/Bio-BigFile/Manifest b/dev-perl/Bio-BigFile/Manifest
index e4ed7f064..cec303381 100644
--- a/dev-perl/Bio-BigFile/Manifest
+++ b/dev-perl/Bio-BigFile/Manifest
@@ -1 +1 @@
-DIST Bio-BigFile-1.06.tar.gz 603786 SHA256 15f1ece2563096a301cff533a9ac91b8fc31af7643b4c4d7fd5d4fa75d4cb5ef SHA512 c018eb0787c4912e777721cd8f863c48e933dce179a0f223820648ecda736ca7e2d6647bb46b51fe500d8f5712b6ce0d2df98bebdfed7cffc7c58933e55a5387 WHIRLPOOL a13cb43f8f897fbf872e798828750e3f196b8710be8a389e4f4a315b5a63fab9abf2de27e565a196a8403a3ef5e3181c8e6579d5ffb7df07290bd7c18c6a5f78
+DIST Bio-BigFile-1.07.tar.gz 605804 SHA256 277b66ce8acbdd52399e2c5a0cf4e3bd5c74c12b94877cd383d0c4c97740d16d SHA512 2a65556b52c220881c3f0534b324889d3ac5284fc62f6a8fffe301be9bef7c8f3278e50bd6af11ac5bbb22a5c928b08442c427e3931aec8422c0fbff3fcba314 WHIRLPOOL 0713ad699b4f2fbc13a3a29a0e3fb22c6d73ae06ef784508bcd0b071b24166e858b591b8d87c79ed133fb95d78662582ed91cb65e4b13dd407211313227e1963
diff --git a/dev-perl/Bio-BigFile/metadata.xml b/dev-perl/Bio-BigFile/metadata.xml
index 07b525505..2bc893037 100644
--- a/dev-perl/Bio-BigFile/metadata.xml
+++ b/dev-perl/Bio-BigFile/metadata.xml
@@ -1,9 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci-biology</herd>
- <maintainer>
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index a8ab290f1..43da81892 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 19 Sep 2013; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild:
+ Clean for latest HEAD
+
28 Aug 2013; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild:
Install missing syminfo, #482734
diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index 3d39cf95a..dcebce6a6 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -18,7 +18,7 @@ MY_P=${PN}-${MY_PV}
DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
HOMEPAGE="http://www.biop.ox.ac.uk/coot/"
-SRC_URI="test? ( http://www.biop.ox.ac.uk/coot/devel/greg-data.tar.gz )"
+SRC_URI="test? ( http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/data/greg-data.tar.gz )"
ESVN_REPO_URI="http://coot.googlecode.com/svn/trunk"
SLOT="0"
@@ -175,9 +175,3 @@ src_test() {
"${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
"${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die
}
-
-src_install() {
- autotools-utils_src_install
- insinto /usr/share/${PN}
- doins syminfo.lib
-}
diff --git a/sci-chemistry/freeon/ChangeLog b/sci-chemistry/freeon/ChangeLog
index e9013eff9..ccc74ddae 100644
--- a/sci-chemistry/freeon/ChangeLog
+++ b/sci-chemistry/freeon/ChangeLog
@@ -2,6 +2,20 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 20 Sep 2013; Nicolas Bock <nicolasbock@gmail.com> freeon-1.0.3.ebuild:
+ sci-chemistry/freeon-1.0.3: Fixed broken ebuild.
+
+*freeon-1.0.3 (20 Sep 2013)
+
+ 20 Sep 2013; Nicolas Bock <nicolasbock@gmail.com> +freeon-1.0.3.ebuild,
+ metadata.xml:
+ sci-chemistry/freeon-1.0.3: Version bump.
+
+*freeon-1.0.2 (18 Sep 2013)
+
+ 18 Sep 2013; Nicolas Bock <nicolasbock@gmail.com> +freeon-1.0.2.ebuild:
+ sci-chemistry/freeon-1.0.2: Version bump
+
*freeon-1.0.1 (18 Sep 2013)
18 Sep 2013; Nicolas Bock <nicolasbock@gmail.com> +freeon-1.0.1.ebuild:
diff --git a/sci-chemistry/freeon/Manifest b/sci-chemistry/freeon/Manifest
index 3845b633d..c11115d32 100644
--- a/sci-chemistry/freeon/Manifest
+++ b/sci-chemistry/freeon/Manifest
@@ -1,4 +1,6 @@
DIST freeon-1.0.1.tar.bz2 6081683 SHA256 91832ebf84bcaf7f3cfacee0bad45745b1f77839c8ef6d1fa9118abee73c0910 SHA512 4971bece35d32d680f2b2d57f366695d7f46a78e24a55840db71e492ccb7bf8ba0001e3c5fba9a6f8aea2bb5a231c02b9aac0722574e0fddc169089b2d84c43e WHIRLPOOL 3509bd6e8a76b8fb72b701abceda2ab44a7587aa5ddd41b3a7eec294f6989bf37b0045b268e8d1af355ad88e5445598c4c6bc31a5442e8f0b84779cb6782070b
+DIST freeon-1.0.2.tar.bz2 6081976 SHA256 d391f3648f0d795a836eddddf70ed4b43b91e94cb18823f03f8c999fad1491ed SHA512 e3169dd3a2c543d44c7a7e7c8b32af0055832a11239175581c38294904f43a0c2f3a567172841b977497325a9bdd9f1634b57606d4054bda106bdf632b31956f WHIRLPOOL 28bc95853a6cd2d99ac1550112fb2ec44920915ba183eb4f6c5cd3152388ceaad093f72628052a5eb4ceb4838d5ee5e111484ea3b594f7abeed4ef3b05c4160c
+DIST freeon-1.0.3.tar.bz2 6094060 SHA256 d17cf00e8b861a3c8d12d562d436fdf4cbf5e75e2e130af0b0b659c91a6b38a8 SHA512 b86979471b1f8c3d1af59f2562ec6f7b71ffe44d28276483db6ab2b9aef20de4c4edbdf9d4c7f6d0ad25e216e23a6ef0e1e5e4e5487d06c5d7268fc18b4da6b9 WHIRLPOOL 6a44726558ecb85e5bd21e8c201f1c01527ef1c06632b1f042a8f6d9539225914830688b7ac100c9322f0c543aa609881eb91c3a2258ac4d9cc929b6696f575b
DIST freeon-1.0.tar.bz2 6053346 SHA256 4cd7618402cea91eba90377546001e975b81b7e5ff533c36f650f9e2b5c1363c SHA512 4161f020beb5e55ed1d352c8c309c1ae6237d982a858cef61c1343f379d0142890fa45eb5de8cb8a93591cfec74485ed50b51d663038e4496febb9673a6bf646 WHIRLPOOL 6da7320e730359e4599a8312037b2e276e68835d0b05aedd913f1dbcb529dfb22c38cb76f0fd8c5eb96060a6c3bfe0b8bd70d5388a21fbcafab2f09b42b79d1c
DIST freeon-2013-09-12.tar.bz2 6058108 SHA256 5a2b76f590110e960885369f158c828d3b1c4ae28308940b620ce78b59550dd1 SHA512 5946b6add17dc753a0a249ef640ec6eb6df5ce48d25fd3ed086da5a23b16d3c5d63fbaf26543ac27dedf7f2f1376525a10a1c6b41ad66bdddd82364951d4faa0 WHIRLPOOL 1bc739f6d6dbeaef486da282a4bf225553b108e5896674b252ee61a1dd66f44db72531f5c1e632cfe6fc54c655e312856f86b78dbb48a138941d0787b9ea441f
DIST freeon-2013-09-16.tar.bz2 6057203 SHA256 0d213d419265030cee4eed8b43a35d39467ee1d1d1df9a7efc5ad4df15b9ca59 SHA512 cef0687aa5febbb1270719696c807b8438f18cb7c000b87f51b3562af644ed2604f57ecf9f43a92f16c2e337e8c487d0bcb13d9626ce638c5ccc313d5e681bf4 WHIRLPOOL d9d76712920152803a5aae59de70776e124f3e93d6102b50aa6f51ba06f6175946cbd24494945d60fbfa90c3580e5bb02fadf64a78cbe4c4c49abfa60c41e9d1
diff --git a/sci-chemistry/freeon/freeon-1.0.2.ebuild b/sci-chemistry/freeon/freeon-1.0.2.ebuild
new file mode 100644
index 000000000..1832c7f4d
--- /dev/null
+++ b/sci-chemistry/freeon/freeon-1.0.2.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=1
+FORTRAN_STANDARD=90
+
+inherit autotools-utils fortran-2
+
+DESCRIPTION="An experimental suite of programs for linear scaling quantum chemistry."
+HOMEPAGE="http://www.freeon.org"
+SRC_URI="http://download.savannah.gnu.org/releases/${PN}/${PN}-${PV}.tar.bz2"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+RDEPEND="
+ sci-libs/hdf5
+ virtual/blas
+ virtual/lapack"
+DEPEND="${DEPEND}
+ virtual/pkgconfig"
diff --git a/sci-chemistry/freeon/freeon-1.0.3.ebuild b/sci-chemistry/freeon/freeon-1.0.3.ebuild
new file mode 100644
index 000000000..91f6cd97d
--- /dev/null
+++ b/sci-chemistry/freeon/freeon-1.0.3.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=1
+FORTRAN_STANDARD=90
+
+inherit autotools-utils fortran-2
+
+DESCRIPTION="An experimental suite of programs for linear scaling quantum chemistry."
+HOMEPAGE="http://www.freeon.org"
+SRC_URI="http://download.savannah.gnu.org/releases/${PN}/${PN}-${PV}.tar.bz2"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="standalone-BCSR static-libs"
+
+RDEPEND="
+ sci-libs/hdf5
+ virtual/blas
+ virtual/lapack"
+DEPEND="${DEPEND}
+ virtual/pkgconfig"
+
+src_configure() {
+ local myeconfargs=(
+ $(use_enable standalone-BCSR)
+ )
+ autotools-utils_src_configure
+}
diff --git a/sci-chemistry/freeon/metadata.xml b/sci-chemistry/freeon/metadata.xml
index bf041ec0c..5f6f63b37 100644
--- a/sci-chemistry/freeon/metadata.xml
+++ b/sci-chemistry/freeon/metadata.xml
@@ -9,4 +9,7 @@
<email>nicolasbock@gmail.com</email>
<name>Nicolas Bock</name>
</maintainer>
+ <use>
+ <flag name="standalone-BCSR">Enables a self-contained BCSR file format</flag>
+ </use>
</pkgmetadata>
diff --git a/sci-chemistry/modeller/ChangeLog b/sci-chemistry/modeller/ChangeLog
index cedd72b92..01374fb4e 100644
--- a/sci-chemistry/modeller/ChangeLog
+++ b/sci-chemistry/modeller/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 20 Sep 2013; Justin Lecher <jlec@gentoo.org> -modeller-9.12-r2.ebuild,
+ +modeller-9.12-r3.ebuild:
+ Mask lib dir for revdep-rebuild, #474696
+
26 Jun 2013; Justin Lecher <jlec@gentoo.org> -modeller-9.12-r1.ebuild,
+modeller-9.12-r2.ebuild:
Fix lib position, #474696
diff --git a/sci-chemistry/modeller/modeller-9.12-r2.ebuild b/sci-chemistry/modeller/modeller-9.12-r3.ebuild
index 9cfd2e3d3..a01b74960 100644
--- a/sci-chemistry/modeller/modeller-9.12-r2.ebuild
+++ b/sci-chemistry/modeller/modeller-9.12-r3.ebuild
@@ -42,6 +42,7 @@ pkg_setup() {
python_prepare_all(){
sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die
+ distutils-r1_python_prepare_all
}
python_compile(){
@@ -92,6 +93,12 @@ python_install_all(){
insinto /usr/share/${PN}/
doins -r examples
fi
+
+ insinto /etc/revdep-rebuild
+ cat >> "${T}"/40-${PN} <<- EOF
+ SEARCH_DIRS_MASK="${EPREFIX}/opt/modeller/lib/"
+ EOF
+ doins "${T}"/40-${PN}
}
pkg_postinst() {
diff --git a/sci-libs/bigdft-abi/ChangeLog b/sci-libs/bigdft-abi/ChangeLog
index b1fc75cb5..c44387008 100644
--- a/sci-libs/bigdft-abi/ChangeLog
+++ b/sci-libs/bigdft-abi/ChangeLog
@@ -2,6 +2,17 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 23 Sep 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
+ bigdft-abi-1.0.4-r2.ebuild, +metadata.xml:
+ Previously announced change actually done. Added a metadata file. Dealing
+ with more complaints of repoman posponed.
+
+*bigdft-abi-1.0.4-r2 (19 Sep 2013)
+
+ 19 Sep 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
+ -bigdft-abi-1.0.4-r1.ebuild, +bigdft-abi-1.0.4-r2.ebuild:
+ Avoid sandbox violation when generating TeX fonts.
+
*bigdft-abi-1.0.4-r1 (27 Jun 2013)
27 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
diff --git a/sci-libs/bigdft-abi/bigdft-abi-1.0.4-r1.ebuild b/sci-libs/bigdft-abi/bigdft-abi-1.0.4-r2.ebuild
index f466e9078..8187e463e 100644
--- a/sci-libs/bigdft-abi/bigdft-abi-1.0.4-r1.ebuild
+++ b/sci-libs/bigdft-abi/bigdft-abi-1.0.4-r2.ebuild
@@ -148,7 +148,10 @@ src_compile() {
popd > /dev/null
#autotools-utils_src_compile
- use doc && autotools-utils_src_compile doc
+ if use doc; then
+ VARTEXFONTS="${T}/fonts"
+ autotools-utils_src_compile doc
+ fi
}
src_test() {
diff --git a/sci-libs/bigdft-abi/metadata.xml b/sci-libs/bigdft-abi/metadata.xml
new file mode 100644
index 000000000..f3d127448
--- /dev/null
+++ b/sci-libs/bigdft-abi/metadata.xml
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-physics</herd>
+ <longdescription lang="en">
+BigDFT is a package whose main program allows one to find the total energy,
+charge density and electronic structure of systems made of electrons and nuclei
+(molecules and periodic solids) within Density Functional Theory (DFT), using
+pseudopotentials and a wavelets basis. BigDFT-ABI is its fork by ABINIT developers
+to serve as a library for sci-physics/abinit.
+</longdescription>
+ <use>
+ <flag name="cuda">Enable support for nVidia CUDA</flag>
+ </use>
+ <use>
+ <flag name="etsf_io">
+ Enable support for reading and writing the European Theoretical
+ Spectroscopy facility (ETSF) file format.
+ </flag>
+ </use>
+ <use>
+ <flag name="opencl">Enable support for OpenCL GPU acceleration.</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-libs/bigdft/ChangeLog b/sci-libs/bigdft/ChangeLog
deleted file mode 100644
index 812748003..000000000
--- a/sci-libs/bigdft/ChangeLog
+++ /dev/null
@@ -1,139 +0,0 @@
-# ChangeLog for sci-libs/bigdft
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
- 03 Mar 2013; Justin Lecher <jlec@gentoo.org> bigdft-1.7_pre12.ebuild:
- Fix issue 52
-
- 03 Mar 2013; Justin Lecher <jlec@gentoo.org> bigdft-1.7_pre12.ebuild:
- Fix issue 52
-
- 22 Feb 2013; Justin Lecher <jlec@gentoo.org> -bigdft-1.6_pre1-r4.ebuild,
- bigdft-1.6.0-r2.ebuild, bigdft-1.7_pre12.ebuild, metadata.xml:
- Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config;
- drop old
-
- 20 Feb 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
- bigdft-1.7_pre12.ebuild:
- The setup of python for the compilation of the GPU support in
- bigdft-1.7_pre12 improved.
-
- 20 Feb 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
- bigdft-1.7_pre12.ebuild, +files/bigdft-1.7-dev.12-GPUlink.patch:
- Compilation of GPU support in bigdft-1.7_pre12 improved. Yet to be tested.
-
-*bigdft-1.7_pre12 (17 Jan 2013)
-
- 17 Jan 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
- +bigdft-1.7_pre12.ebuild, +files/bigdft-1.7-dev.12-libxc_dir_include.patch,
- +files/bigdft-1.7-dev.12-nolib_mods.patch,
- +files/bigdft-1.7-dev.12-tests.tar.bz2:
- New version 1.7-dev.12 (1.7_pre12) from the Abinit site added; used by
- sci-physics/abinit-7.0.4 but apparently segfaults it.
-
-*bigdft-1.6_pre1-r4 (01 Sep 2012)
-
- 01 Sep 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
- -bigdft-1.6_pre1-r3.ebuild, +bigdft-1.6_pre1-r4.ebuild,
- -files/bigdft-1.6-tuto.1-GPUlibs.patch,
- +files/bigdft-1.6-tuto.1-GPUlibs-1.patch,
- -files/bigdft-1.6-tuto.1-bigdft.pc.patch,
- +files/bigdft-1.6-tuto.1-bigdft.pc-1.patch:
- Patches to install GPU support corrected not to break linking against the
- compiled libraries
-
- 10 Jul 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
- files/bigdft-1.6-tuto.1-GPUlibs.patch:
- bigdft-1.6-tuto.1-GPUlibs.patch updated not to forget the pkg-config file
-
-*bigdft-1.6_pre1-r3 (04 Jul 2012)
-
- 04 Jul 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
- -bigdft-1.6_pre1-r2.ebuild, +bigdft-1.6_pre1-r3.ebuild,
- +files/bigdft-1.6-tuto.1-GPUlibs.patch,
- +files/bigdft-1.6-tuto.1-gcc-4.6.patch:
- bigdft-1.6_pre1 from -r2 to -r3: patched to install necessary libraries for
- GPU support and to compile with gcc-4.6
-
- 22 Jun 2012; Alexey Shvetsov <alexxy@gentoo.org> bigdft-1.6.0-r2.ebuild,
- bigdft-1.6_pre1-r2.ebuild:
- [sci-libs/bigdft] add ~amd64-linux
-
-*bigdft-1.6.0-r2 (19 Jun 2012)
-*bigdft-1.6_pre1-r2 (19 Jun 2012)
-
- 19 Jun 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
- -bigdft-1.6_pre1-r1.ebuild, +bigdft-1.6_pre1-r2.ebuild,
- -bigdft-1.6.0-r1.ebuild, +bigdft-1.6.0-r2.ebuild:
- Reflect the split of the fortran interface out of sci-libs/netcdf
-
- 22 May 2012; Justin Lecher <jlec@gentoo.org> bigdft-1.6_pre1-r1.ebuild,
- bigdft-1.6.0-r1.ebuild:
- Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
-
-*bigdft-1.6.0-r1 (15 May 2012)
-*bigdft-1.6_pre1-r1 (15 May 2012)
-
- 15 May 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
- -bigdft-1.6_pre1.ebuild, +bigdft-1.6_pre1-r1.ebuild, -bigdft-1.6.0.ebuild,
- +bigdft-1.6.0-r1.ebuild:
- pkg-config file corrected
-
- 30 Mar 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
- -bigdft-1.2.0.2.ebuild, -files/bigdft-1.2.0.2-0001.patch,
- -files/bigdft-1.2.0.2-0002.patch, -files/bigdft-1.2.0.2-0003.patch,
- -files/bigdft-1.2.0.2-0004.patch, -files/bigdft-1.2.0.2-testH.patch,
- -bigdft-1.2.0.5.ebuild, -files/bigdft-1.2.0.5-0001.patch,
- -bigdft-1.6_pre0.ebuild, -files/bigdft-1.6-tuto-bigdft.pc.patch,
- -files/bigdft-1.6-tuto-libxc_dir_include.patch:
- Clean-up.
-
-*bigdft-1.6_pre1 (22 Mar 2012)
-*bigdft-1.6_pre0 (22 Mar 2012)
-
- 22 Mar 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
- +bigdft-1.2.0.2.ebuild, +bigdft-1.2.0.5.ebuild, +bigdft-1.6_pre0.ebuild,
- +bigdft-1.6_pre1.ebuild, bigdft-1.6.0.ebuild,
- +files/bigdft-1.6.0-libxc_dir_include.patch,
- +files/bigdft-1.6-tuto.1-bigdft.pc.patch,
- +files/bigdft-1.6-tuto.1-libxc_dir_include.patch,
- +files/bigdft-1.6-tuto-bigdft.pc.patch,
- +files/bigdft-1.6-tuto-libxc_dir_include.patch:
- Old versions used by old versions of abinit ressurected. May be removed
- forever if nobody complains about the latest abinit. 1.6.0 corrected,
- 1.6_pre0 and 1.6_pre1 added; 1.6_pre1 is used by sci-physics/abinit-6.12.1.
-
-*bigdft-1.6.0 (18 Feb 2012)
-
- 18 Feb 2012; Justin Lecher <jlec@gentoo.org> -bigdft-1.2.0.2.ebuild,
- -bigdft-1.2.0.5.ebuild, +bigdft-1.6.0.ebuild, metadata.xml:
- Move to EAPI=4 and autotools-util.eclass
-
-*bigdft-1.2.0.5 (14 Dec 2011)
-
- 14 Dec 2011; Honza Macháček <Hloupy.Honza@centrum.cz>
- bigdft-1.2.0.2.ebuild, +bigdft-1.2.0.5.ebuild,
- +files/bigdft-1.2.0.5-0001.patch:
- Version bump to 1.2.0.5 for sci-physics/abinit-6.10.3; still not much
- progress towards the current version (1.5.2 and 1.6-tuto)
-
- 11 Jul 2011; Honza Macháček <Hloupy.Honza@centrum.cz>
- bigdft-1.2.0.2.ebuild:
- The MPI support, broken by fortran-2.eclass usage, made work again.
-
- 24 Jun 2011; Justin Lecher <jlec@gentoo.org> bigdft-1.2.0.2.ebuild:
- Streamlined fortran-2 eclass usage
-
- 21 Jun 2011; Justin Lecher <jlec@gentoo.org> bigdft-1.2.0.2.ebuild,
- +metadata.xml:
- Added fortran-2.eclass support
-
-*bigdft-1.2.0.2 (17 Jan 2011)
-
- 17 Jan 2011; Honza Macháček <Hloupy.Honza@centrum.cz>
- +bigdft-1.2.0.2.ebuild, +files/bigdft-1.2.0.2-0001.patch,
- +files/bigdft-1.2.0.2-0002.patch, +files/bigdft-1.2.0.2-0003.patch,
- +files/bigdft-1.2.0.2-0004.patch, +files/bigdft-1.2.0.2-testH.patch:
- A bigDFT ebuild for sci-physics/abinit; not the latest version but the abinit
- compatible one.
-
diff --git a/sci-libs/bigdft/Manifest b/sci-libs/bigdft/Manifest
deleted file mode 100644
index a828ad66e..000000000
--- a/sci-libs/bigdft/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST bigdft-1.6.0.tar.gz 8876759 SHA256 2d3212ef5f1ebc10fe7c627397ac6282ad41e1433ec6e66905f9d39a302913c0 SHA512 facbb78d126885dd04fed6451aa9cd1f5c755055e146cda1d2d4e90e3310fc3066b661635477db96d5b143ffaaa3ebb01107681437fd9965f3c764cf1b034361 WHIRLPOOL 97bc6c28296a92b09139e3a65266daa583011620fad5aed208e0e48627ab1d9c0ef9993d6c4c3cce5696d5c707bcdfb4b8ca7e64379909b3cf073206e32f9572
-DIST bigdft-1.7-dev.12.tar.gz 8904633 SHA256 2f899f287dd508dc616fb798cc9d01d1c79951dc68c277fb0ce19ea0ad690332 SHA512 35efe93edd7e6fb08abe919c59913c173f23e17a50104ad92e510dba5ba35ba8117012249d620896affc8acc05c9d85c6c61a411bc903750db6593456e9e8142 WHIRLPOOL 94a8d6d25fe82f3f1b89d15b4e23293d018bfb66c96fd1061a09e6352fb6811e79a15161bd3ca92e5f544253c8fa9f919d41fe069635ac07f33e21cc70878719
diff --git a/sci-libs/bigdft/bigdft-1.6.0-r2.ebuild b/sci-libs/bigdft/bigdft-1.6.0-r2.ebuild
deleted file mode 100644
index e43d7e45b..000000000
--- a/sci-libs/bigdft/bigdft-1.6.0-r2.ebuild
+++ /dev/null
@@ -1,122 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-inherit autotools-utils eutils flag-o-matic fortran-2 toolchain-funcs
-
-REAL_P="${P/_pre0/-tuto}"
-
-DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
-HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
-SRC_URI="http://inac.cea.fr/L_Sim/BigDFT/${REAL_P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="cuda doc etsf_io mpi netcdf opencl test"
-
-RDEPEND="
- =sci-libs/libxc-1*[fortran]
- virtual/blas
- virtual/fortran
- virtual/lapack
- mpi? ( virtual/mpi )
- cuda? ( dev-util/nvidia-cuda-sdk )
- opencl? (
- || (
- dev-util/nvidia-cuda-sdk
- dev-util/amdstream
- )
- )
- etsf_io? ( sci-libs/etsf_io )
- netcdf? ( || (
- sci-libs/netcdf[fortran]
- sci-libs/netcdf-fortran
- )
- )"
-DEPEND="${RDEPEND}
- virtual/pkgconfig
- >=sys-devel/autoconf-2.59
- doc? ( virtual/latex-base )"
-
-S="${WORKDIR}/${REAL_P}"
-
-DOCS=( README INSTALL ChangeLog AUTHORS NEWS )
-
-FORTRAN_STANDARD=90
-
-pkg_setup() {
- # fortran-2.eclass does not handle mpi wrappers
- if use mpi; then
- export FC="mpif90"
- export F77="mpif77"
- export CC="mpicc"
- else
- tc-export FC F77 CC
- fi
-
- fortran-2_pkg_setup
-}
-
-src_prepare() {
- epatch "${FILESDIR}"/"${REAL_P}"-libxc_dir_include.patch
- eautoreconf
-}
-
-src_configure() {
- local modules="${EPREFIX}/usr/$(get_libdir)/finclude"
- local netcdff_libs="-lnetcdff"
- filter-flags '-m*' '-O*' "-pipe"
- local nvcflags="${CFLAGS}"
-# _filter-var nvcflags '-m*' '-O*' "-pipe"
- local myeconfargs=(
- $(use_enable mpi)
- --enable-optimised-convolution
- --enable-pseudo
- --enable-libbigdft
- --enable-binaries
- --disable-minima-hopping
- --with-moduledir="${modules}"
- --with-ext-linalg="$($(tc-getPKG_CONFIG) --libs-only-l lapack) \
- $($(tc-getPKG_CONFIG) --libs-only-l blas)"
- --with-ext-linalg-path="$($(tc-getPKG_CONFIG) --libs-only-L lapack) \
- $($(tc-getPKG_CONFIG) --libs-only-L blas)"
- --disable-internal-libxc
- --with-libxc-path="/usr"
- --with-libxc-include="${modules}"
- $(use_enable cuda cuda-gpu)
- $(use_with cuda cuda-path /opt/cuda)
- $(use_with cuda nvcc-flags "${nvcflags}")
- $(use_enable opencl)
- $(use_with opencl ocl-path "${EPREFIX}/usr")
- $(use_with etsf_io etsf-io)
- $(use_with etsf_io etsf-io-path "${EPREFIX}/usr")
- $(use_with etsf_io netcdf-path "$($(tc-getPKG_CONFIG) --libs-only-L netcdf)")
- "$(use etsf_io && echo "--with-netcdf-libs=$($(tc-getPKG_CONFIG) --libs netcdf) ${netcdff_libs}")"
- FCFLAGS+=" -I${modules}"
- LD="$(tc-getLD)"
- CPP="$(tc-getCPP)"
- )
- autotools-utils_src_configure
-}
-
-src_compile() {
- #autotools-utils_src_compile() expanded
- _check_build_dir
- pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
- emake -j1
- sed -i -e's%\$(top_builddir)/[^ ]*/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc
- popd > /dev/null
-
- use doc && autotools-utils_src_compile doc
-}
-
-src_test() {
- use test && autotools-utils_src_test
-}
-
-src_install() {
- autotools-utils_src_install HAVE_LIBXC=1
-}
diff --git a/sci-libs/bigdft/bigdft-1.7_pre12.ebuild b/sci-libs/bigdft/bigdft-1.7_pre12.ebuild
deleted file mode 100644
index 8ff693ea1..000000000
--- a/sci-libs/bigdft/bigdft-1.7_pre12.ebuild
+++ /dev/null
@@ -1,147 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_5 python2_6 python2_7 )
-
-inherit autotools-utils eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs
-
-REAL_P="${P/_pre/-dev.}"
-
-DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
-HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
-SRC_URI="http://forge.abinit.org/fallbacks/${REAL_P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="cuda doc etsf_io mpi netcdf openmp opencl test"
-
-RDEPEND="
- =sci-libs/libxc-1*[fortran]
- virtual/blas
- virtual/fortran
- virtual/lapack
- dev-libs/libyaml
- mpi? ( virtual/mpi )
- cuda? ( dev-util/nvidia-cuda-sdk )
- opencl? (
- || (
- dev-util/nvidia-cuda-sdk
- dev-util/amdstream
- )
- )
- etsf_io? ( sci-libs/etsf_io )
- netcdf? ( || (
- sci-libs/netcdf[fortran]
- sci-libs/netcdf-fortran
- )
- )"
-DEPEND="${RDEPEND}
- virtual/pkgconfig
- >=sys-devel/autoconf-2.59
- doc? ( virtual/latex-base )
- cuda? ( ${PYTHON_DEPS} )
- opencl? ( ${PYTHON_DEPS} )
- app-arch/tar
- app-arch/gzip"
-
-S="${WORKDIR}/${REAL_P}"
-
-DOCS=( README INSTALL ChangeLog AUTHORS NEWS )
-
-FORTRAN_STANDARD=90
-
-pkg_setup() {
- # fortran-2.eclass does not handle mpi wrappers
- if use mpi; then
- export FC="mpif90"
- export F77="mpif77"
- export CC="mpicc"
- else
- tc-export FC F77 CC
- fi
-
- fortran-2_pkg_setup
- if use openmp && [[ $(tc-getCC)$ == *gcc* ]] && ! tc-has-openmp; then
- die "Please select an openmp capable compiler like gcc[openmp]"
- fi
- python-any-r1_pkg_setup
-}
-
-src_prepare() {
- epatch \
- "${FILESDIR}"/"${REAL_P}"-libxc_dir_include.patch \
- "${FILESDIR}"/"${REAL_P}"-GPUlink.patch \
- "${FILESDIR}"/"${REAL_P}"-nolib_mods.patch
- tar -xjf "${FILESDIR}"/"${REAL_P}"-tests.tar.bz2 -C "${S}"/tests/DFT/postSCF/
- eautoreconf
-}
-
-src_configure() {
- local openmp=""
- use openmp && openmp="-fopenmp"
- local modules="${EPREFIX}/usr/$(get_libdir)/finclude"
- local netcdff_libs="-lnetcdff"
- filter-flags '-m*' '-O*' "-pipe"
- local nvcflags="${CFLAGS}"
- _filter-var nvcflags '-m*' '-O*' "-pipe"
- local myeconfargs=(
- $(use_enable mpi)
- --enable-optimised-convolution
- --enable-pseudo
- --enable-libbigdft
- --enable-binaries
- --disable-minima-hopping
- --disable-internal-libyaml
- --enable-internal-libabinit
- --with-moduledir="${modules}"
- --with-ext-linalg="$($(tc-getPKG_CONFIG) --libs-only-l lapack) \
- $($(tc-getPKG_CONFIG) --libs-only-l blas)"
- --with-ext-linalg-path="$($(tc-getPKG_CONFIG) --libs-only-L lapack) \
- $($(tc-getPKG_CONFIG) --libs-only-L blas)"
- --enable-libxc
- --disable-internal-libxc
- --with-libxc-include="${modules}"
- $(use_enable cuda cuda-gpu)
- $(use_with cuda cuda-path /opt/cuda)
- $(use_with cuda nvcc-flags "${nvcflags}")
- $(use_enable opencl)
- $(use_with etsf_io etsf-io)
- "$(use etsf_io && echo "--with-netcdf-libs=$($(tc-getPKG_CONFIG) --libs netcdf) ${netcdff_libs}")"
- FCFLAGS="${FCFLAGS} ${openmp} -I${modules}"
- LD="$(tc-getLD)"
- CPP="$(tc-getCPP)"
- )
- autotools-utils_src_configure
-}
-
-src_compile() {
- #autotools-utils_src_compile() expanded
- _check_build_dir
- pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
- emake -j1
- sed -i -e's%\$(top_builddir)/[^ ]*/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc
- popd > /dev/null
-
- #autotools-utils_src_compile
- use doc && autotools-utils_src_compile doc
-}
-
-src_test() {
- if use test; then
- #autotools-utils_src_test() expanded
- _check_build_dir
- pushd "${BUILD_DIR}" > /dev/null || die
- # Run default src_test as defined in ebuild.sh
- cd tests
- emake -j1 check
- popd > /dev/null
- fi
-}
-
-src_install() {
- autotools-utils_src_install HAVE_LIBXC=1
-}
diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-GPUlibs-1.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-GPUlibs-1.patch
deleted file mode 100644
index 386e39dc7..000000000
--- a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-GPUlibs-1.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-diff -Naur orig/bigdft-1.6-tuto.1.orig/src/CUDA/Makefile.am patched/bigdft-1.6-tuto.1/src/CUDA/Makefile.am
---- bigdft-1.6-tuto.1.orig/src/CUDA/Makefile.am 2011-09-27 12:43:06.000000000 +0000
-+++ bigdft-1.6-tuto.1/src/CUDA/Makefile.am 2012-07-04 12:08:27.000000000 +0000
-@@ -43,7 +43,8 @@
- # Not used anymore, to be removed
- #INC_CUDA = -I@LIB_CUTIL_PATH@
- EXTRA_PROGRAMS = conv_check
--noinst_LIBRARIES = libGPU.a libbasef.a
-+lib_LIBRARIES = libGPU.a
-+noinst_LIBRARIES = libbasef.a
-
- libGPU_a_SOURCES = $(SOURCES_CU_CONV1) $(SOURCES_SHARED) $(SOURCES_CONV)
- AM_CPPFLAGS = $(INC_CUDA) -I. -I$(top_builddir) -I@CUDA_PATH@/include/ @LIBSGPU_INCLUDE@ -DCUBLAS_USE_THUNKING
-diff -Naur orig/bigdft-1.6-tuto.1.orig/src/OpenCL/Makefile.am patched/bigdft-1.6-tuto.1/src/OpenCL/Makefile.am
---- bigdft-1.6-tuto.1.orig/src/OpenCL/Makefile.am 2011-09-27 12:43:06.000000000 +0000
-+++ bigdft-1.6-tuto.1/src/OpenCL/Makefile.am 2012-07-04 12:09:02.000000000 +0000
-@@ -26,7 +26,8 @@
-
- EXTRA_PROGRAMS = conv_check conv_check_fft bench_conv bench_conv_quick bench_zgemm stream_check
-
--noinst_LIBRARIES = libbasef.a libbasec.a libOCL.a libStream.a
-+lib_LIBRARIES = libOCL.a
-+noinst_LIBRARIES = libbasef.a libbasec.a libStream.a
-
- libbasef_a_SOURCES = $(mpi_source)
- libbasef_a_LIBADD = ../modules/defs.o ../modules/base.o \
diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-bigdft.pc-1.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-bigdft.pc-1.patch
deleted file mode 100644
index 7c3380a9b..000000000
--- a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-bigdft.pc-1.patch
+++ /dev/null
@@ -1,207 +0,0 @@
-diff -Naur bigdft-1.6-tuto_orig/Makefile.am bigdft-1.6-tuto/Makefile.am
---- Makefile.am 2011-10-18 07:39:52.000000000 +0000
-+++ Makefile.am 2012-03-21 10:08:44.000000000 +0000
-@@ -4,7 +4,10 @@
-
- ACLOCAL_AMFLAGS = -I config/m4
-
--DISTCLEANFILES = config.inc
-+DISTCLEANFILES = config.inc bigdft.pc
-+
-+pkgconfigdir = $(libdir)/pkgconfig
-+pkgconfig_DATA = bigdft.pc
-
- if BUILD_LIBABINIT
- libABINIT_dir = libABINIT/src
-diff -Naur bigdft-1.6-tuto_orig/Makefile.in bigdft-1.6-tuto/Makefile.in
---- Makefile.in 2012-03-21 10:03:28.000000000 +0000
-+++ Makefile.in 2012-03-21 10:20:48.000000000 +0000
-@@ -33,7 +33,7 @@
- POST_UNINSTALL = :
- subdir = .
- DIST_COMMON = README $(am__configure_deps) $(srcdir)/Makefile.am \
-- $(srcdir)/Makefile.in $(srcdir)/config.h.in \
-+ $(srcdir)/Makefile.in $(srcdir)/bigdft.pc.in $(srcdir)/config.h.in \
- $(top_srcdir)/config/Doxyfile.in $(top_srcdir)/configure \
- AUTHORS COPYING ChangeLog INSTALL NEWS config/depcomp \
- config/install-sh config/missing
-@@ -48,7 +48,7 @@
- configure.lineno config.status.lineno
- mkinstalldirs = $(install_sh) -d
- CONFIG_HEADER = config.h
--CONFIG_CLEAN_FILES = config/Doxyfile
-+CONFIG_CLEAN_FILES = bigdft.pc config/Doxyfile
- CONFIG_CLEAN_VPATH_FILES =
- SOURCES =
- DIST_SOURCES =
-@@ -59,6 +59,35 @@
- install-pdf-recursive install-ps-recursive install-recursive \
- installcheck-recursive installdirs-recursive pdf-recursive \
- ps-recursive uninstall-recursive
-+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
-+am__vpath_adj = case $$p in \
-+ $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
-+ *) f=$$p;; \
-+ esac;
-+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
-+am__install_max = 40
-+am__nobase_strip_setup = \
-+ srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
-+am__nobase_strip = \
-+ for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
-+am__nobase_list = $(am__nobase_strip_setup); \
-+ for p in $$list; do echo "$$p $$p"; done | \
-+ sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
-+ $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
-+ if (++n[$$2] == $(am__install_max)) \
-+ { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
-+ END { for (dir in files) print dir, files[dir] }'
-+am__base_list = \
-+ sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
-+ sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
-+am__uninstall_files_from_dir = { \
-+ test -z "$$files" \
-+ || { test ! -d "$$dir" && test ! -f "$$dir" && test ! -r "$$dir"; } \
-+ || { echo " ( cd '$$dir' && rm -f" $$files ")"; \
-+ $(am__cd) "$$dir" && rm -f $$files; }; \
-+ }
-+am__installdirs = "$(DESTDIR)$(pkgconfigdir)"
-+DATA = $(pkgconfig_DATA)
- RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \
- distclean-recursive maintainer-clean-recursive
- AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
-@@ -232,7 +261,9 @@
- config/m4
-
- ACLOCAL_AMFLAGS = -I config/m4
--DISTCLEANFILES = config.inc
-+DISTCLEANFILES = config.inc bigdft.pc
-+pkgconfigdir = $(libdir)/pkgconfig
-+pkgconfig_DATA = bigdft.pc
- @BUILD_LIBABINIT_FALSE@libABINIT_dir =
- @BUILD_LIBABINIT_TRUE@libABINIT_dir = libABINIT/src
- @BUILD_LIBXC_FALSE@libXC_dir =
-@@ -307,8 +338,28 @@
-
- distclean-hdr:
- -rm -f config.h stamp-h1
-+bigdft.pc: $(top_builddir)/config.status $(srcdir)/bigdft.pc.in
-+ cd $(top_builddir) && $(SHELL) ./config.status $@
- config/Doxyfile: $(top_builddir)/config.status $(top_srcdir)/config/Doxyfile.in
- cd $(top_builddir) && $(SHELL) ./config.status $@
-+install-pkgconfigDATA: $(pkgconfig_DATA)
-+ @$(NORMAL_INSTALL)
-+ test -z "$(pkgconfigdir)" || $(MKDIR_P) "$(DESTDIR)$(pkgconfigdir)"
-+ @list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \
-+ for p in $$list; do \
-+ if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
-+ echo "$$d$$p"; \
-+ done | $(am__base_list) | \
-+ while read files; do \
-+ echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(pkgconfigdir)'"; \
-+ $(INSTALL_DATA) $$files "$(DESTDIR)$(pkgconfigdir)" || exit $$?; \
-+ done
-+
-+uninstall-pkgconfigDATA:
-+ @$(NORMAL_UNINSTALL)
-+ @list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \
-+ files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
-+ dir='$(DESTDIR)$(pkgconfigdir)'; $(am__uninstall_files_from_dir)
-
- # This directory's subdirectories are mostly independent; you can cd
- # into them and run `make' without going through this Makefile.
-@@ -622,9 +673,12 @@
- exit 1; } >&2
- check-am: all-am
- check: check-recursive
--all-am: Makefile config.h
-+all-am: Makefile $(DATA) config.h
- installdirs: installdirs-recursive
- installdirs-am:
-+ for dir in "$(DESTDIR)$(pkgconfigdir)"; do \
-+ test -z "$$dir" || $(MKDIR_P) "$$dir"; \
-+ done
- install: install-recursive
- install-exec: install-exec-recursive
- install-data: install-data-recursive
-@@ -672,7 +726,7 @@
-
- info-am:
-
--install-data-am:
-+install-data-am: install-pkgconfigDATA
-
- install-dvi: install-dvi-recursive
-
-@@ -718,7 +772,7 @@
-
- ps-am:
-
--uninstall-am:
-+uninstall-am: uninstall-pkgconfigDATA
-
- .MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all \
- ctags-recursive install-am install-strip tags-recursive
-@@ -733,10 +787,10 @@
- install-data-am install-dvi install-dvi-am install-exec \
- install-exec-am install-html install-html-am install-info \
- install-info-am install-man install-pdf install-pdf-am \
-- install-ps install-ps-am install-strip installcheck \
-+ install-pkgconfigDATA install-ps install-ps-am install-strip installcheck \
- installcheck-am installdirs installdirs-am maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
-- pdf-am ps ps-am tags tags-recursive uninstall uninstall-am
-+ pdf-am ps ps-am tags tags-recursive uninstall uninstall-am uninstall-pkgconfigDATA
-
- configure
-
-diff -Naur bigdft-1.6-tuto_orig/bigdft.pc.in bigdft-1.6-tuto/bigdft.pc.in
---- bigdft.pc.in 1970-01-01 00:00:00.000000000 +0000
-+++ bigdft.pc.in 2012-02-01 09:43:59.000000000 +0000
-@@ -0,0 +1,15 @@
-+@USE_CUDA_GPU_FALSE@libs_cuda=
-+@USE_CUDA_GPU_TRUE@libs_cuda=$(top_builddir)/src/CUDA/libGPU.a
-+@USE_OCL_FALSE@libs_ocl=
-+@USE_OCL_TRUE@libs_ocl=$(top_builddir)/src/OpenCL/libOCL.a -lstdc++
-+prefix=@prefix@
-+exec_prefix=@exec_prefix@
-+libdir=@libdir@
-+includedir=@includedir@
-+
-+Name: libbigdft
-+Description: Library for DFT calculation over wavelets.
-+Requires:
-+Version: @VERSION@
-+Libs: -L${libdir} -lbigdft -lpoissonsolver ${libs_cuda} ${libs_ocl} @LIBS@ @FCLIBS@
-+Cflags: -I${includedir}
-diff -Naur bigdft-1.6-tuto_orig/configure bigdft-1.6-tuto/configure
---- configure 2012-03-21 10:03:26.000000000 +0000
-+++ configure 2012-03-21 11:04:52.000000000 +0000
-@@ -8512,7 +8512,7 @@
- docdir="${docdir}"
-
-
--ac_config_files="$ac_config_files Makefile libABINIT/src/Makefile config/Doxyfile src/Makefile src/modules/Makefile src/modules/configure.inc src/profiling/Makefile src/PSolver/Makefile src/convolutions/Makefile src/CUDA/Makefile src/OpenCL/Makefile src/dgemmsy/Makefile src/convolutions-c/Makefile src/art/Makefile src/tools/Makefile src/tools/bader/Makefile utils/Makefile utils/PSPfiles/Makefile pseudo/Makefile pseudo/src/Makefile pseudo/tests/Makefile doc/Makefile tests/Makefile tests/fft/Makefile tests/PSolver/Makefile tests/H2-freq/Makefile tests/MINHOP/Makefile tests/NEB/Makefile tests/NEB/input tests/NEB/NEB_include.sh tests/XabsCheb/Makefile tests/SPLSAD/Makefile tests/TDDFT/Makefile tests/OP2P/Makefile tests/DFT/Makefile tests/OpenCL/Makefile tests/CUDA/Makefile tests/ETSF_IO/Makefile tests/tutorials/Makefile tests/xc/Makefile"
-+ac_config_files="$ac_config_files Makefile bigdft.pc libABINIT/src/Makefile config/Doxyfile src/Makefile src/modules/Makefile src/modules/configure.inc src/profiling/Makefile src/PSolver/Makefile src/convolutions/Makefile src/CUDA/Makefile src/OpenCL/Makefile src/dgemmsy/Makefile src/convolutions-c/Makefile src/art/Makefile src/tools/Makefile src/tools/bader/Makefile utils/Makefile utils/PSPfiles/Makefile pseudo/Makefile pseudo/src/Makefile pseudo/tests/Makefile doc/Makefile tests/Makefile tests/fft/Makefile tests/PSolver/Makefile tests/H2-freq/Makefile tests/MINHOP/Makefile tests/NEB/Makefile tests/NEB/input tests/NEB/NEB_include.sh tests/XabsCheb/Makefile tests/SPLSAD/Makefile tests/TDDFT/Makefile tests/OP2P/Makefile tests/DFT/Makefile tests/OpenCL/Makefile tests/CUDA/Makefile tests/ETSF_IO/Makefile tests/tutorials/Makefile tests/xc/Makefile"
-
-
- # Call libXC ./configure script recursively.
-@@ -9349,6 +9349,7 @@
- "config.h") CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;;
- "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
- "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
-+ "bigdft.pc") CONFIG_FILES="$CONFIG_FILES bigdft.pc" ;;
- "libABINIT/src/Makefile") CONFIG_FILES="$CONFIG_FILES libABINIT/src/Makefile" ;;
- "config/Doxyfile") CONFIG_FILES="$CONFIG_FILES config/Doxyfile" ;;
- "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
-diff -Naur bigdft-1.6-tuto_orig/configure.ac bigdft-1.6-tuto/configure.ac
---- configure.ac 2012-03-21 10:03:02.000000000 +0000
-+++ configure.ac 2012-03-21 10:48:53.000000000 +0000
-@@ -715,6 +715,7 @@
- dnl Give the name of file.in to transform to file
- AC_CONFIG_FILES([
- Makefile
-+bigdft.pc
- libABINIT/src/Makefile
- config/Doxyfile
- src/Makefile
diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-gcc-4.6.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-gcc-4.6.patch
deleted file mode 100644
index e89da2546..000000000
--- a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-gcc-4.6.patch
+++ /dev/null
@@ -1,67 +0,0 @@
-diff -Naurp bigdft-1.6-tuto.1.orig/src/art/art_lanczos.f90 bigdft-1.6-tuto.1/src/art/art_lanczos.f90
---- bigdft-1.6-tuto.1.orig/src/art/art_lanczos.f90 2011-10-17 08:46:50.000000000 +0000
-+++ bigdft-1.6-tuto.1/src/art/art_lanczos.f90 2012-06-22 13:03:49.000000000 +0000
-@@ -80,11 +80,30 @@ subroutine lanczos( maxvec, new_projecti
- integer :: i_min
- real(kind=8) :: e_min
- !_______________________
-+
-+ interface
-+ !> ART center
-+ !! @author
-+ !! Written by EM 2010, see ~/AUTHORS
-+ !! It places the center of mass of a 3D vector at (0,0,0).
-+ subroutine center( vector, vecsize )
-+
-+ use defs, only : natoms, constr
-+ use bigdft_forces, only : in_system
-+ implicit none
-+
-+ !Arguments
-+ integer, intent(in) :: vecsize
-+ real(kind=8), dimension(vecsize), intent(inout), target :: vector
-+
-+ end subroutine center
-+ end interface
-+
- newpos = 0.0d0
- diag = 0.0d0
- offdiag = 0.0d0
- lanc = 0.0d0
--
-+
- boxl = box * scala
- ! We now take the current position as the
- ! reference point and will make a displacement
-diff -Naurp bigdft-1.6-tuto.1.orig/src/art/calcfo_sw.f90 bigdft-1.6-tuto.1/src/art/calcfo_sw.f90
---- bigdft-1.6-tuto.1.orig/src/art/calcfo_sw.f90 2011-10-17 08:46:50.000000000 +0000
-+++ bigdft-1.6-tuto.1/src/art/calcfo_sw.f90 2012-06-22 12:58:35.000000000 +0000
-@@ -475,6 +475,28 @@ function diff_square_force_one(P,numnei,
- integer :: trash_evalf
- real(8), dimension(3*natoms,configs_to_fit) :: force_tempo,tmp_force
-
-+interface
-+! subroutine to compute forces of one atom
-+subroutine SWcalczone(nat,posa,boxl,tmp_force, this_atom,numnei,nei)
-+
-+
-+ use SWpotential
-+ use defs, only : boundary,maxnei,iproc,MPI_COMM_WORLD
-+
-+ implicit none
-+
-+ integer, intent(in) :: nat
-+ real(kind=8), intent(in), dimension(3*nat) :: posa
-+ real(kind=8), dimension(3), intent(inout) :: boxl
-+ integer, intent(in) :: this_atom
-+ real(8), intent(out), dimension(3*nat), target:: tmp_force
-+
-+
-+ integer, dimension(nat),intent(in) :: numnei
-+ integer, dimension(nat,maxnei),intent(in) :: nei
-+end subroutine SWcalczone
-+end interface
-+
- trash_evalf = 0
- my_counter = 0
- force_tempo = force_work_fit
diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-libxc_dir_include.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-libxc_dir_include.patch
deleted file mode 100644
index 6d0f6046a..000000000
--- a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-libxc_dir_include.patch
+++ /dev/null
@@ -1,50 +0,0 @@
---- configure.ac.orig 2011-11-23 14:02:15.000000000 +0000
-+++ configure.ac 2011-11-23 14:09:19.000000000 +0000
-@@ -551,14 +551,17 @@
- ac_build_libxc="no"
- AC_ARG_ENABLE(libxc, AS_HELP_STRING([--disable-libxc], [Do not link with libXC library (default = yes).]), ac_use_libxc=$enableval, ac_use_libxc="yes")
- AC_ARG_ENABLE(internal-libxc, AS_HELP_STRING([--disable-internal-libxc], [Do not build and link with internal libXC library (default = yes).]), ac_internal_libxc=$enableval, ac_internal_libxc="yes")
--AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib and module files (default = None).]),
-+AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib files (default = None).]),
- ac_libxc_dir=$withval, ac_libxc_dir=)
-+AC_ARG_WITH(libxc-include, AS_HELP_STRING([--with-libxc-include], [Give the path for an external libXC library module files (default = None).]),
-+ ac_libxc_dir_include=$withval, ac_libxc_dir_include=)
- if test x"$ac_use_libxc" = x"yes" ; then
- ac_build_libxc=$ac_internal_libxc
- if test "$ac_internal_libxc" = "yes" ; then
- ac_build_libxc="yes"
- ac_use_libxc="yes"
- ac_libxc_dir="$top_builddir"/libxc-1.1.0/src
-+ ac_libxc_dir_include="$ac_libxc_dir"/include
- AC_SUBST(LIBXC_DIR, "\$(top_builddir)"/libxc-1.1.0/src)
- AC_SUBST(LIBXC_INCLUDE, "-I\$(top_builddir)"/libxc-1.1.0/src)
- LDFLAGS="$LDFLAGS -L\$(top_builddir)/libxc-1.1.0/src/.libs"
-@@ -566,6 +569,9 @@
- else
- if test -n "$ac_libxc_dir" ; then
- LDFLAGS="$LDFLAGS -L$ac_libxc_dir/lib"
-+ if test x"$ac_libxc_dir_include" = x ; then
-+ ac_libxc_dir_include="$ac_libxc_dir"/include
-+ fi
-
- dnl Test the given implementation of libXC.
- ac_libxc_libname="xc"
-@@ -574,13 +580,13 @@
- ac_libxc_libname="dft_xc"
- AC_CHECK_LIB($ac_libxc_libname, xc_f90_lda_vxc, withlibxc=yes, withlibxc=no)
- fi
-- AC_CHECK_FILE($ac_libxc_dir/include/libxc_funcs_m.$capitalize_module_ext, funcs="yes", funcs="no")
-- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_lib_m.$capitalize_module_ext, lib="yes", lib="no")
-- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_types_m.$capitalize_module_ext, types="yes", types="no")
-+ AC_CHECK_FILE($ac_libxc_dir_include/libxc_funcs_m.$capitalize_module_ext, funcs="yes", funcs="no")
-+ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_lib_m.$capitalize_module_ext, lib="yes", lib="no")
-+ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_types_m.$capitalize_module_ext, types="yes", types="no")
- if test "$withlibxc" = "yes" -a "$funcs" = "yes" -a "$lib" = "yes" -a "$types" = "yes"; then
- ac_use_libxc="yes"
-- AC_SUBST(LIBXC_DIR, $ac_libxc_dir/include)
-- AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir/include)
-+ AC_SUBST(LIBXC_DIR, $ac_libxc_dir_include)
-+ AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir_include)
- LIBXC_LIBS="-l"$ac_libxc_libname
- fi
- else
diff --git a/sci-libs/bigdft/files/bigdft-1.6.0-libxc_dir_include.patch b/sci-libs/bigdft/files/bigdft-1.6.0-libxc_dir_include.patch
deleted file mode 100644
index 7179fcb0f..000000000
--- a/sci-libs/bigdft/files/bigdft-1.6.0-libxc_dir_include.patch
+++ /dev/null
@@ -1,50 +0,0 @@
---- configure.ac.orig 2011-11-23 14:02:15.000000000 +0000
-+++ configure.ac 2011-11-23 14:09:19.000000000 +0000
-@@ -604,14 +604,17 @@
- ac_build_libxc="no"
- AC_ARG_WITH(libxc, AS_HELP_STRING([--without-libxc], [Do not link with libXC library (default = yes).]), ac_use_libxc=$enableval, ac_use_libxc="yes")
- AC_ARG_ENABLE(internal-libxc, AS_HELP_STRING([--disable-internal-libxc], [Do not build and link with internal libXC library (default = yes).]), ac_internal_libxc=$enableval, ac_internal_libxc="yes")
--AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib and module files (default = None).]),
-+AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib files (default = None).]),
- ac_libxc_dir=$withval, ac_libxc_dir=)
-+AC_ARG_WITH(libxc-include, AS_HELP_STRING([--with-libxc-include], [Give the path for an external libXC library module files (default = None).]),
-+ ac_libxc_dir_include=$withval, ac_libxc_dir_include=)
- if test x"$ac_use_libxc" = x"yes" ; then
- ac_build_libxc=$ac_internal_libxc
- if test "$ac_internal_libxc" = "yes" ; then
- ac_build_libxc="yes"
- ac_use_libxc="yes"
- ac_libxc_dir="$top_builddir"/libxc-1.1.0/src
-+ ac_libxc_dir_include="$ac_libxc_dir"/include
- AC_SUBST(LIBXC_DIR, "\$(top_builddir)"/libxc-1.1.0/src)
- AC_SUBST(LIBXC_INCLUDE, "-I\$(top_builddir)"/libxc-1.1.0/src)
- LDFLAGS="$LDFLAGS -L\$(top_builddir)/libxc-1.1.0/src/.libs"
-@@ -619,6 +622,9 @@
- else
- if test -n "$ac_libxc_dir" ; then
- LDFLAGS="$LDFLAGS -L$ac_libxc_dir/lib"
-+ if test x"$ac_libxc_dir_include" = x ; then
-+ ac_libxc_dir_include="$ac_libxc_dir"/include
-+ fi
-
- dnl Test the given implementation of libXC.
- ac_libxc_libname="xc"
-@@ -587,13 +593,13 @@
- ac_libxc_libname="dft_xc"
- AC_CHECK_LIB($ac_libxc_libname, xc_f90_lda_vxc, withlibxc=yes, withlibxc=no)
- fi
-- AC_CHECK_FILE($ac_libxc_dir/include/libxc_funcs_m.$ax_fc_mod_ext, funcs="yes", funcs="no")
-- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_lib_m.$ax_fc_mod_ext, lib="yes", lib="no")
-- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_types_m.$ax_fc_mod_ext, types="yes", types="no")
-+ AC_CHECK_FILE($ac_libxc_dir_include/libxc_funcs_m.$ax_fc_mod_ext, funcs="yes", funcs="no")
-+ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_lib_m.$ax_fc_mod_ext, lib="yes", lib="no")
-+ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_types_m.$ax_fc_mod_ext, types="yes", types="no")
- if test "$withlibxc" = "yes" -a "$funcs" = "yes" -a "$lib" = "yes" -a "$types" = "yes"; then
- ac_use_libxc="yes"
-- AC_SUBST(LIBXC_DIR, $ac_libxc_dir/include)
-- AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir/include)
-+ AC_SUBST(LIBXC_DIR, $ac_libxc_dir_include)
-+ AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir_include)
- LIBXC_LIBS="-l"$ac_libxc_libname
- fi
- else
diff --git a/sci-libs/bigdft/files/bigdft-1.7-dev.12-GPUlink.patch b/sci-libs/bigdft/files/bigdft-1.7-dev.12-GPUlink.patch
deleted file mode 100644
index f4b0e18a9..000000000
--- a/sci-libs/bigdft/files/bigdft-1.7-dev.12-GPUlink.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naurp bigdft-1.7-dev.12.orig/S_GPU/src/Makefile.in bigdft-1.7-dev.12/S_GPU/src/Makefile.in
---- bigdft-1.7-dev.12.orig/S_GPU/src/Makefile.in 2012-07-16 08:24:00.000000000 +0000
-+++ bigdft-1.7-dev.12/S_GPU/src/Makefile.in 2013-02-19 15:59:06.142835878 +0000
-@@ -88,7 +88,7 @@ am__objects_1 = libs_gpu_la-s_gpu_C.lo \
- libs_gpu_la-s_gpu_F.lo
- am_libs_gpu_la_OBJECTS = $(am__objects_1)
- libs_gpu_la_OBJECTS = $(am_libs_gpu_la_OBJECTS)
--libs_gpu_la_LINK = $(LIBTOOL) --tag=CXX $(libs_gpu_la_LIBTOOLFLAGS) \
-+libs_gpu_la_LINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) \
- $(LIBTOOLFLAGS) --mode=link $(CXXLD) $(AM_CXXFLAGS) \
- $(CXXFLAGS) $(libs_gpu_la_LDFLAGS) $(LDFLAGS) -o $@
- DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)
diff --git a/sci-libs/bigdft/files/bigdft-1.7-dev.12-libxc_dir_include.patch b/sci-libs/bigdft/files/bigdft-1.7-dev.12-libxc_dir_include.patch
deleted file mode 100644
index 9084d08e5..000000000
--- a/sci-libs/bigdft/files/bigdft-1.7-dev.12-libxc_dir_include.patch
+++ /dev/null
@@ -1,50 +0,0 @@
---- configure.ac.orig 2011-11-23 14:02:15.000000000 +0000
-+++ configure.ac 2011-11-23 14:09:19.000000000 +0000
-@@ -743,14 +743,17 @@
- ac_build_libxc="no"
- AC_ARG_ENABLE(libxc, AS_HELP_STRING([--without-libxc], [Do not link with libXC library (default = yes).]), ac_use_libxc=$enableval, ac_use_libxc="yes")
- AC_ARG_ENABLE(internal-libxc, AS_HELP_STRING([--disable-internal-libxc], [Do not build and link with internal libXC library (default = yes).]), ac_internal_libxc=$enableval, ac_internal_libxc="yes")
--AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib and module files (default = None).]),
-+AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib files (default = None).]),
- ac_libxc_dir=$withval, ac_libxc_dir=)
-+AC_ARG_WITH(libxc-include, AS_HELP_STRING([--with-libxc-include], [Give the path for an external libXC library module files (default = None).]),
-+ ac_libxc_dir_include=$withval, ac_libxc_dir_include=)
- if test x"$ac_use_libxc" = x"yes" ; then
- ac_build_libxc=$ac_internal_libxc
- if test "$ac_internal_libxc" = "yes" ; then
- ac_build_libxc="yes"
- ac_use_libxc="yes"
- ac_libxc_dir="$top_builddir"/libxc-1.1.0/src
-+ ac_libxc_dir_include="$ac_libxc_dir"/include
- AC_SUBST(LIBXC_DIR, "\$(top_builddir)"/libxc-1.1.0/src)
- AC_SUBST(LIBXC_INCLUDE, "-I\$(top_builddir)"/libxc-1.1.0/src)
- LDFLAGS="$LDFLAGS -L\$(top_builddir)/libxc-1.1.0/src/.libs"
-@@ -758,6 +761,9 @@
- else
- if test -n "$ac_libxc_dir" ; then
- LDFLAGS="$LDFLAGS -L$ac_libxc_dir/lib"
-+ if test x"$ac_libxc_dir_include" = x ; then
-+ ac_libxc_dir_include="$ac_libxc_dir"/include
-+ fi
-
- dnl Test the given implementation of libXC.
- ac_libxc_libname="xc"
-@@ -766,13 +772,13 @@
- ac_libxc_libname="dft_xc"
- AC_CHECK_LIB($ac_libxc_libname, xc_f90_lda_vxc, withlibxc=yes, withlibxc=no)
- fi
-- AC_CHECK_FILE($ac_libxc_dir/include/libxc_funcs_m.$ax_fc_mod_ext, funcs="yes", funcs="no")
-- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_lib_m.$ax_fc_mod_ext, lib="yes", lib="no")
-- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_types_m.$ax_fc_mod_ext, types="yes", types="no")
-+ AC_CHECK_FILE($ac_libxc_dir_include/libxc_funcs_m.$ax_fc_mod_ext, funcs="yes", funcs="no")
-+ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_lib_m.$ax_fc_mod_ext, lib="yes", lib="no")
-+ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_types_m.$ax_fc_mod_ext, types="yes", types="no")
- if test "$withlibxc" = "yes" -a "$funcs" = "yes" -a "$lib" = "yes" -a "$types" = "yes"; then
- ac_use_libxc="yes"
-- AC_SUBST(LIBXC_DIR, $ac_libxc_dir/include)
-- AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir/include)
-+ AC_SUBST(LIBXC_DIR, $ac_libxc_dir_include)
-+ AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir_include)
- LIBXC_LIBS="-l"$ac_libxc_libname
- fi
- else
diff --git a/sci-libs/bigdft/files/bigdft-1.7-dev.12-nolib_mods.patch b/sci-libs/bigdft/files/bigdft-1.7-dev.12-nolib_mods.patch
deleted file mode 100644
index 8137a48ab..000000000
--- a/sci-libs/bigdft/files/bigdft-1.7-dev.12-nolib_mods.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-diff -Naurp bigdft-1.7-dev.12.orig/src/Makefile.am bigdft-1.7-dev.12/src/Makefile.am
---- bigdft-1.7-dev.12.orig/src/Makefile.am 2012-07-16 07:46:11.000000000 +0000
-+++ bigdft-1.7-dev.12/src/Makefile.am 2013-01-09 14:09:58.198905489 +0000
-@@ -45,6 +45,9 @@ EXTRA_DIST = \
- # -------------
- if BUILD_LIB_BIGDFT
- lib_bigdft = libbigdft.a libdft_common.a
-+else
-+lib_bigdft =
-+endif
- PS_SOURCES = PSolver/Build_Kernel.f90 \
- PSolver/xcenergy.f90 \
- PSolver/3Dgradient.f90 \
-@@ -53,11 +56,6 @@ PS_SOURCES = PSolver/Build_Kernel.f90 \
- PSolver/wofz.f90 \
- lib/fft/fft3d.f90
- PS_MODULES = PSolver/Poisson_Solver.f90
--else
--lib_bigdft =
--PS_SOURCES =
--PS_MODULES =
--endif
- if BUILD_BINARIES
- binaries_sources = bigdft memguess splsad NEB frequencies MDanalysis $(minima_hopping_sources) bart abscalc BigDFT2Wannier WaCo
- local_binaries = test_forces
diff --git a/sci-libs/bigdft/files/bigdft-1.7-dev.12-tests.tar.bz2 b/sci-libs/bigdft/files/bigdft-1.7-dev.12-tests.tar.bz2
deleted file mode 100644
index d74c56176..000000000
--- a/sci-libs/bigdft/files/bigdft-1.7-dev.12-tests.tar.bz2
+++ /dev/null
Binary files differ
diff --git a/sci-libs/bigdft/metadata.xml b/sci-libs/bigdft/metadata.xml
deleted file mode 100644
index fcc220851..000000000
--- a/sci-libs/bigdft/metadata.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci</herd>
-<use>
- <flag name="cuda">Add cuda support</flag>
- <flag name="etsf_io">Undocumented USE</flag>
- <flag name="opencl">Undocumented USE</flag>
-</use>
-</pkgmetadata>
diff --git a/sci-libs/modglue/ChangeLog b/sci-libs/modglue/ChangeLog
index eb811e97d..36095f3ef 100644
--- a/sci-libs/modglue/ChangeLog
+++ b/sci-libs/modglue/ChangeLog
@@ -2,6 +2,20 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 19 Sep 2013; François Bissey <francois.bissey@canterbury.ac.nz>
+ +files/modglue-1.19-Makefiles.patch, -files/modglue-1.16-lib64.patch,
+ -files/modglue-1.19-ldflags.patch, -files/modglue-1.19-parallelmake.patch,
+ modglue-1.19.ebuild:
+ Fixing sandbox violations
+
+*modglue-1.19 (18 Sep 2013)
+
+ 18 Sep 2013; François Bissey <francois.bissey@canterbury.ac.nz>
+ +files/modglue-1.19-ldflags.patch, +files/modglue-1.19-parallelmake.patch,
+ +modglue-1.19.ebuild, -files/modglue-1.16-ldflags.patch,
+ -files/modglue-1.16-parallelmake.patch, -modglue-1.16.ebuild:
+ Bump modglue to 1.19
+
03 Sep 2013; François Bissey <francois.bissey@canterbury.ac.nz>
modglue-1.16.ebuild:
Fix PATCHES definition, it shouldn't include 'epatch'
diff --git a/sci-libs/modglue/Manifest b/sci-libs/modglue/Manifest
index 9c45f3be3..1f7db367c 100644
--- a/sci-libs/modglue/Manifest
+++ b/sci-libs/modglue/Manifest
@@ -1 +1 @@
-DIST modglue-1.16.tar.gz 89987 SHA256 1da62910d7171cb5547c0757c366e5338f889c0155c33375e891df75e2ee429e SHA512 2ac93f771f99b33f6339ceb55ba95c034c37d84b3d8ee6a56a8c75e7b6129cf3a218adb5539df37da2c5f645983eb7c141c9716ad5c94699e2f44396609d7f2a WHIRLPOOL 39f399b30c3762fa6522444051f81bb8d484448681735e8e1c0d304f0f8ebc5e281853257dffc506ab3f864025cab373b608720e0645ed8397ec7fc2fe8625af
+DIST modglue-1.19.tar.gz 94435 SHA256 f228e6666e328a44472a3b8755aba317d38330af322023ce404146d504544f73 SHA512 cdf069dd28674076f9f7275112b4bd96b58c1bfd238ec9570a29a13bca1d8fcdad8c1b8d1fd78aca3ece95890a54d4a8d13db2a3299f4ec6f6475d13145599bf WHIRLPOOL 7b3ae11d18737b859a32a65787e1c445a9e63eaa66cd1a93f06828ec875891f50fcdb069bf7e1173e61e3f04ccbf9e55f071a26ffbe0936030df3a6c24ee2ef5
diff --git a/sci-libs/modglue/files/modglue-1.16-ldflags.patch b/sci-libs/modglue/files/modglue-1.16-ldflags.patch
deleted file mode 100644
index 4c2bbbc27..000000000
--- a/sci-libs/modglue/files/modglue-1.16-ldflags.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- src/Makefile.in.orig 2010-08-19 23:38:00.081085063 +1200
-+++ src/Makefile.in 2010-08-19 23:38:56.018083508 +1200
-@@ -15,8 +15,8 @@
- LTRELEASE = `echo ${RELEASE} | sed -e "s/\./:/g"`
-
- CPHASE = ${LIBTOOL} --tag=CXX --mode=compile @CXX@ -c @CFLAGS@
--LPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ -version-info ${LTRELEASE} -rpath @prefix@/@libdir@ @LIBS@
--MPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@
-+LPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ -version-info ${LTRELEASE} @LDFLAGS@ -rpath @prefix@/@libdir@ @LIBS@
-+MPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ @LDFLAGS@
- IPHASE = ${LIBTOOL} --mode=install @INSTALL@
- FPHASE = ${LIBTOOL} --mode=finish @prefix@/@libdir@
-
diff --git a/sci-libs/modglue/files/modglue-1.16-lib64.patch b/sci-libs/modglue/files/modglue-1.16-lib64.patch
deleted file mode 100644
index e67adba2e..000000000
--- a/sci-libs/modglue/files/modglue-1.16-lib64.patch
+++ /dev/null
@@ -1,61 +0,0 @@
---- Makefile.in.orig 2010-03-04 10:34:54.000000000 +1300
-+++ Makefile.in 2010-08-23 23:21:34.931886424 +1200
-@@ -3,6 +3,9 @@
-
- .PHONY: all install library static examples uninstall clean distclean
-
-+prefix = @prefix@
-+exec_prefix = @exec_prefix@
-+
- all: library
- #examples
-
-@@ -17,8 +20,8 @@
-
- install:
- ( cd src && $(MAKE) install );
-- @INSTALL@ -d -m 755 ${DESTDIR}@prefix@/@libdir@/pkgconfig
-- @INSTALL@ -m 644 modglue.pc ${DESTDIR}@prefix@/@libdir@/pkgconfig/
-+ @INSTALL@ -d -m 755 ${DESTDIR}@libdir@/pkgconfig
-+ @INSTALL@ -m 644 modglue.pc ${DESTDIR}@libdir@/pkgconfig/
- @INSTALL@ -d -m 755 ${DESTDIR}@prefix@/share/man/man1
- @INSTALL@ man/man1/prompt.1 ${DESTDIR}@prefix@/share/man/man1
- @INSTALL@ man/man1/ptywrap.1 ${DESTDIR}@prefix@/share/man/man1
---- src/Makefile.in.orig 2010-03-04 10:34:54.000000000 +1300
-+++ src/Makefile.in 2010-08-23 23:21:41.165883457 +1200
-@@ -1,6 +1,8 @@
-
-
- MACTEST= @MAC_OS_X@
-+prefix = @prefix@
-+exec_prefix = @exec_prefix@
-
- ifeq ($(strip $(MACTEST)),)
- LIBTOOL = libtool
-@@ -18,7 +20,7 @@
- LPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ -version-info ${LTRELEASE} -rpath @prefix@/@libdir@ @LIBS@
- MPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@
- IPHASE = ${LIBTOOL} --mode=install @INSTALL@
--FPHASE = ${LIBTOOL} --mode=finish @prefix@/@libdir@
-+FPHASE = ${LIBTOOL} --mode=finish @libdir@
-
- TIMESTAMP = -D"DATETIME=\"`date | sed -e 's/ / /'`\"" -DHOSTNAME=\"`hostname`\"
-
-@@ -98,13 +100,13 @@
-
- install: library tools
- @INSTALL@ -m 755 -d ${DESTDIR}@prefix@
-- @INSTALL@ -m 755 -d ${DESTDIR}@prefix@/@libdir@
-- @INSTALL@ -m 755 -d ${DEVDESTDIR}@prefix@/@libdir@
-+ @INSTALL@ -m 755 -d ${DESTDIR}@libdir@
-+ @INSTALL@ -m 755 -d ${DEVDESTDIR}@libdir@
- @INSTALL@ -m 755 -d ${DESTDIR}@prefix@/bin
- @INSTALL@ -m 755 -d ${DEVDESTDIR}@prefix@/include/modglue
-- ${IPHASE} libmodglue.la ${DESTDIR}@prefix@/@libdir@
-+ ${IPHASE} libmodglue.la ${DESTDIR}@libdir@
- ifneq ($(DESTDIR),$(DEVDESTDIR))
-- mv ${DESTDIR}@prefix@/@libdir@/libmodglue*.so ${DEVDESTDIR}@prefix@/@libdir@
-+ mv ${DESTDIR}@libdir@/libmodglue*.so ${DEVDESTDIR}@libdir@
- endif
- # ${IPHASE} libmid.la ${DESTDIR}@prefix@/lib
- ${FPHASE}
diff --git a/sci-libs/modglue/files/modglue-1.16-parallelmake.patch b/sci-libs/modglue/files/modglue-1.16-parallelmake.patch
deleted file mode 100644
index b6d675084..000000000
--- a/sci-libs/modglue/files/modglue-1.16-parallelmake.patch
+++ /dev/null
@@ -1,53 +0,0 @@
---- Makefile.in.orig 2010-08-21 22:04:51.877629329 +1200
-+++ Makefile.in 2010-08-21 22:06:12.887628815 +1200
-@@ -7,7 +7,7 @@
- #examples
-
- library:
-- ( cd src && $(MAKE) );
-+ ( cd src && $(MAKE) library tools );
-
- static:
- ( cd src && $(MAKE) static );
---- src/Makefile.in.orig 2010-08-21 22:05:26.411630332 +1200
-+++ src/Makefile.in 2010-08-21 22:08:20.961629492 +1200
-@@ -49,21 +49,21 @@
-
- #------- Tests ----------------------------------------
-
--test_child_process: test_child_process.o
-+test_child_process: library test_child_process.o
- ${MPHASE} -o test_child_process $< libmodglue.la
-
--test_ext_process: test_ext_process.o
-+test_ext_process: library test_ext_process.o
- ${MPHASE} -o test_ext_process $< libmodglue.la
-
--test_pipe: test_pipe.o
-+test_pipe: library test_pipe.o
- ${MPHASE} -o test_pipe $< libmodglue.la
-
--test_writes: test_writes.o
-+test_writes: library test_writes.o
- ${MPHASE} -o test_writes $< libmodglue.la
-
- #------- Tools ----------------------------------------
-
--prompt: prompt.o
-+prompt: library prompt.o
- ${MPHASE} -o prompt prompt.o `pkg-config sigc++-2.0 --libs` libmodglue.la
-
- prompt_static: prompt.cc library
-@@ -77,10 +77,10 @@
- endif
-
-
--ptywrap: ptywrap.o
-+ptywrap: library ptywrap.o
- ${MPHASE} -o ptywrap ptywrap.o @LINK_UTIL@
-
--ptywrap_static: ptywrap.o
-+ptywrap_static: library ptywrap.o
- ${CPHASE} ${TIMESTAMP} -o ptywrap.o \
- -I@top_srcdir@/include -DSTATICBUILD ptywrap.cc
- ifeq ($(strip $(MACTEST)),)
diff --git a/sci-libs/modglue/files/modglue-1.19-Makefiles.patch b/sci-libs/modglue/files/modglue-1.19-Makefiles.patch
new file mode 100644
index 000000000..a1dae99f0
--- /dev/null
+++ b/sci-libs/modglue/files/modglue-1.19-Makefiles.patch
@@ -0,0 +1,113 @@
+--- Makefile.in.orig 2013-02-24 11:18:44.000000000 +1300
++++ Makefile.in 2013-09-20 10:05:25.316018672 +1200
+@@ -3,12 +3,15 @@
+
+ .PHONY: all install library static examples uninstall clean distclean
+
++prefix = @prefix@
++exec_prefix = @exec_prefix@
++
+ all: library
+ #examples
+
+ library:
+ echo @libdir@
+- ( cd src && $(MAKE) );
++ ( cd src $(MAKE) library tools );
+
+ static:
+ ( cd src && $(MAKE) static );
+@@ -18,8 +21,8 @@
+
+ install:
+ ( cd src && $(MAKE) install );
+- @INSTALL@ -d -m 755 ${DESTDIR}@prefix@/@libdir@/pkgconfig
+- @INSTALL@ -m 644 modglue.pc ${DESTDIR}@prefix@/@libdir@/pkgconfig/
++ @INSTALL@ -d -m 755 ${DESTDIR}@libdir@/pkgconfig
++ @INSTALL@ -m 644 modglue.pc ${DESTDIR}@libdir@/pkgconfig/
+ @INSTALL@ -d -m 755 ${DESTDIR}@prefix@/share/man/man1
+ @INSTALL@ man/man1/prompt.1 ${DESTDIR}@prefix@/share/man/man1
+ @INSTALL@ man/man1/ptywrap.1 ${DESTDIR}@prefix@/share/man/man1
+--- src/Makefile.in.orig 2013-02-24 11:18:44.000000000 +1300
++++ src/Makefile.in 2013-09-20 10:07:56.956164930 +1200
+@@ -1,6 +1,8 @@
+
+
+ MACTEST= @MAC_OS_X@
++prefix = @prefix@
++exec_prefix = @exec_prefix@
+
+ ifeq ($(strip $(MACTEST)),)
+ LIBTOOL = libtool
+@@ -21,11 +23,11 @@
+ LTRELEASE = `echo ${RELEASE} | sed -e "s/\./:/g"`
+
+ CPHASE = ${LIBTOOL} --tag=CXX --mode=compile @CXX@ -c @CFLAGS@
+-LPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ -version-info ${LTRELEASE} -rpath @prefix@@libdir@ @LIBS@
++LPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ -version-info ${LTRELEASE} -rpath @libdir@ @LIBS@
+ #LPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ -version-info ${LTRELEASE} @LIBS@
+ MPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@
+ IPHASE = ${LIBTOOL} --mode=install @INSTALL@
+-FPHASE = ${LIBTOOL} --mode=finish @prefix@/@libdir@
++FPHASE = ${LIBTOOL} --mode=finish ${DESTDIR}@libdir@
+
+ TIMESTAMP = -D"DATETIME=\"`date | sed -e 's/ / /'`\"" -DHOSTNAME=\"`hostname`\"
+
+@@ -56,21 +58,21 @@
+
+ #------- Tests ----------------------------------------
+
+-test_child_process: test_child_process.o
++test_child_process: library test_child_process.o
+ ${MPHASE} -o test_child_process $< libmodglue.la
+
+-test_ext_process: test_ext_process.o
++test_ext_process: library test_ext_process.o
+ ${MPHASE} -o test_ext_process $< libmodglue.la
+
+-test_pipe: test_pipe.o
++test_pipe: library test_pipe.o
+ ${MPHASE} -o test_pipe $< libmodglue.la
+
+-test_writes: test_writes.o
++test_writes: library test_writes.o
+ ${MPHASE} -o test_writes $< libmodglue.la
+
+ #------- Tools ----------------------------------------
+
+-prompt: prompt.o
++prompt: library prompt.o
+ ${MPHASE} -o prompt prompt.o `pkg-config sigc++-2.0 --libs` libmodglue.la
+ # chrpath -d .libs/prompt
+
+@@ -85,10 +87,10 @@
+ endif
+
+
+-ptywrap: ptywrap.o
++ptywrap: library ptywrap.o
+ ${MPHASE} -o ptywrap ptywrap.o @LINK_UTIL@
+
+-ptywrap_static: ptywrap.o
++ptywrap_static: library ptywrap.o
+ ${CPHASE} ${TIMESTAMP} -o ptywrap.o \
+ -I@top_srcdir@/include -DSTATICBUILD ptywrap.cc
+ ifeq ($(strip $(MACTEST)),)
+@@ -109,13 +111,13 @@
+ DEVDESTDIR=${DESTDIR}
+ endif
+ @INSTALL@ -m 755 -d ${DESTDIR}@prefix@
+- @INSTALL@ -m 755 -d ${DESTDIR}@prefix@/@libdir@
+- @INSTALL@ -m 755 -d ${DEVDESTDIR}@prefix@/@libdir@
++ @INSTALL@ -m 755 -d ${DESTDIR}@libdir@
++ @INSTALL@ -m 755 -d ${DEVDESTDIR}@libdir@
+ @INSTALL@ -m 755 -d ${DESTDIR}@prefix@/bin
+ @INSTALL@ -m 755 -d ${DEVDESTDIR}@prefix@/include/modglue
+- ${IPHASE} libmodglue.la ${DESTDIR}@prefix@/@libdir@
++ ${IPHASE} libmodglue.la ${DESTDIR}@libdir@
+ ifneq ($(DESTDIR),$(DEVDESTDIR))
+- mv ${DESTDIR}@prefix@/@libdir@/libmodglue*.so ${DEVDESTDIR}@prefix@/@libdir@
++ mv ${DESTDIR}@libdir@/libmodglue*.so ${DEVDESTDIR}@libdir@
+ endif
+ # ${IPHASE} libmid.la ${DESTDIR}@prefix@/lib
+ ${FPHASE}
diff --git a/sci-libs/modglue/modglue-1.16.ebuild b/sci-libs/modglue/modglue-1.19.ebuild
index ab4602cd4..022049ce8 100644
--- a/sci-libs/modglue/modglue-1.16.ebuild
+++ b/sci-libs/modglue/modglue-1.19.ebuild
@@ -24,14 +24,9 @@ DEPEND="${RDEPEND}
AUTOTOOLS_IN_SOURCE_BUILD=1
PATCHES=(
- # Respect LDFLAGS
- "${FILESDIR}"/${P}-ldflags.patch
- # fix parallel make. test are made at the same time as the library??
- "${FILESDIR}"/${P}-parallelmake.patch
- # take care of the lib/lib64 problem. Without this modglue installs
- # stuff in /usr/usr/lib64 on 64bits systems.
- "${FILESDIR}"/${P}-lib64.patch
-)
+ # consolidated (src/)Makefile.in patch
+ "${FILESDIR}"/${PN}-1.19-Makefiles.patch
+ )
src_install() {
use doc && HTML_DOCS=( "${S}"/doc/. )
diff --git a/sci-libs/scikits_image/ChangeLog b/sci-libs/scikits_image/ChangeLog
index 2b3abdf68..116468d3f 100644
--- a/sci-libs/scikits_image/ChangeLog
+++ b/sci-libs/scikits_image/ChangeLog
@@ -2,6 +2,13 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 20 Sep 2013; Justin Lecher <jlec@gentoo.org> scikits_image-9999.ebuild:
+ Merge tree changes
+
+ 18 Sep 2013; Justin Lecher <jlec@gentoo.org> scikits_image-9999.ebuild,
+ metadata.xml:
+ Drop KEYWORDS from live ebuild
+
17 Sep 2013; Sébastien Fabbro <bicatali@gentoo.org> +metadata.xml,
scikits_image-9999.ebuild:
sci-libs/scikits_image: Fix source directory, update dependencies, cleanup
diff --git a/sci-libs/scikits_image/metadata.xml b/sci-libs/scikits_image/metadata.xml
index 51476ec31..4e57c7f06 100644
--- a/sci-libs/scikits_image/metadata.xml
+++ b/sci-libs/scikits_image/metadata.xml
@@ -1,17 +1,17 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
-<herd>sci</herd>
-<longdescription lang="en">
+ <herd>sci</herd>
+ <longdescription lang="en">
This SciKit (toolkit for SciPy) includes useful image processing
algorithms for use with Python and NumPy. While SciPy’s ndimage
provides low-level manipulation, scikits.image centres around
algorithms and applications.
</longdescription>
-<use>
- <flag name="freeimage">Enable support for image i/o via <pkg>media-libs/freeimage</pkg></flag>
-</use>
-<upstream>
- <remote-id type="pypi">scikit-image</remote-id>
-</upstream>
+ <use>
+ <flag name="freeimage">Enable support for image i/o via <pkg>media-libs/freeimage</pkg></flag>
+ </use>
+ <upstream>
+ <remote-id type="pypi">scikit-image</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-libs/scikits_image/scikits_image-9999.ebuild b/sci-libs/scikits_image/scikits_image-9999.ebuild
index bcb232c18..ebedf7b5d 100644
--- a/sci-libs/scikits_image/scikits_image-9999.ebuild
+++ b/sci-libs/scikits_image/scikits_image-9999.ebuild
@@ -16,7 +16,7 @@ EGIT_REPO_URI="https://github.com/scikit-image/scikit-image.git"
LICENSE="BSD"
SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS=""
IUSE="doc freeimage gtk qt4 test"
RDEPEND="
@@ -40,8 +40,8 @@ python_test() {
# distutils_install_for_testing not working here
esetup.py \
install --root="${T}/test-${EPYTHON}" \
- --no-compile || die "install test failed"
+ --no-compile
cd "${T}/test-${EPYTHON}/$(python_get_sitedir)" || die
- echo "backend: Agg" > matplotlibrc
+ echo "backend: Agg" > matplotlibrc || die
MPLCONFIGDIR=. nosetests -v skimage || die
}
diff --git a/sci-libs/wannier90/ChangeLog b/sci-libs/wannier90/ChangeLog
index bb0da8817..ff8ee508f 100644
--- a/sci-libs/wannier90/ChangeLog
+++ b/sci-libs/wannier90/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*wannier90-1.2-r2 (19 Sep 2013)
+
+ 19 Sep 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
+ -wannier90-1.2-r1.ebuild, +wannier90-1.2-r2.ebuild:
+ Avoid sandbox violation when generating TeX fonts.
+
*wannier90-1.2-r1 (17 Jun 2013)
17 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
diff --git a/sci-libs/wannier90/wannier90-1.2-r1.ebuild b/sci-libs/wannier90/wannier90-1.2-r2.ebuild
index 252792245..481ce2b9a 100644
--- a/sci-libs/wannier90/wannier90-1.2-r1.ebuild
+++ b/sci-libs/wannier90/wannier90-1.2-r2.ebuild
@@ -48,7 +48,10 @@ src_configure() {
src_compile() {
emake -j1 wannier
emake -j1 lib
- use doc & emake -j1 doc
+ if use doc; then
+ VARTEXFONTS="${T}/fonts"
+ emake -j1 doc
+ fi
}
src_test() {
diff --git a/sci-mathematics/cadabra/ChangeLog b/sci-mathematics/cadabra/ChangeLog
index fc95a0fae..e630f20a8 100644
--- a/sci-mathematics/cadabra/ChangeLog
+++ b/sci-mathematics/cadabra/ChangeLog
@@ -2,6 +2,14 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*cadabra-1.33 (19 Sep 2013)
+
+ 19 Sep 2013; François Bissey <francois.bissey@canterbury.ac.nz>
+ +cadabra-1.33.ebuild, +files/cadabra-1.33-FLAGS.patch, -cadabra-1.31.ebuild,
+ -files/cadabra-1.21-no-stripping.patch,
+ -files/cadabra-1.25-xcadabra-flags.patch:
+ Bump to 1.33 and solve issue #113
+
13 Jun 2013; Justin Lecher <jlec@gentoo.org> -cadabra-1.25.ebuild,
-cadabra-1.28.ebuild, -cadabra-1.29.ebuild, cadabra-1.31.ebuild,
metadata.xml:
diff --git a/sci-mathematics/cadabra/Manifest b/sci-mathematics/cadabra/Manifest
index 96690ef40..2c7e3d931 100644
--- a/sci-mathematics/cadabra/Manifest
+++ b/sci-mathematics/cadabra/Manifest
@@ -1 +1 @@
-DIST cadabra-1.31.tar.gz 853016 SHA256 97be19dfce98a91d133dd60cebe58029ffbba3108dd1ae6b8e201f1d1791aad2 SHA512 a1e77b5e5c099b3eecd27ec06721acd1054815d987b405265a9e31348ca0b12ab5c6be437417e8783a34a6bf3ee55cebfaf92a12621bc72d8ede559af4e2ef40 WHIRLPOOL 22a99e61afc8b40b9bc314ad9481199dcf09cf5c6ec8dd43dfbc82177f4b3d1d9756c602713f0e5e099f026f3ef8dfbe0fecc4a94da57562f325ed064fc200d1
+DIST cadabra-1.33.tar.gz 855777 SHA256 075dad3a1a9fd8774473f6d28f036f65629a286304c02f0ac1e10be3cb2ebd12 SHA512 3add8e2dd94c51ac68ed6a7243769b256c873a8f86eb58a7a7c24680b5333eb6849103c0bfd4cd0cc55290fb78fdcd4686065693e815eb4c2f62099bedbcdb6c WHIRLPOOL cd922d21e752acda08e23678b970162b561830d4d8def717dfb4d4bf2625090b8c3b02be4ff25fac731942b28d6f0d07c77066bb75c7a2e11901adce9a300380
diff --git a/sci-mathematics/cadabra/cadabra-1.31.ebuild b/sci-mathematics/cadabra/cadabra-1.33.ebuild
index f56d98121..ca222daad 100644
--- a/sci-mathematics/cadabra/cadabra-1.31.ebuild
+++ b/sci-mathematics/cadabra/cadabra-1.33.ebuild
@@ -13,7 +13,7 @@ SRC_URI="http://cadabra.phi-sci.com/${P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="doc examples X"
+IUSE="doc examples X test"
CDEPEND="
sci-libs/modglue
@@ -28,18 +28,20 @@ CDEPEND="
DEPEND="${CDEPEND}
doc? (
app-doc/doxygen
- || ( app-text/texlive-core dev-tex/pdftex ) )"
+ || ( app-text/texlive-core dev-tex/pdftex ) )
+ test? ( sys-process/time )"
RDEPEND="${CDEPEND}
virtual/latex-base
- dev-tex/mh"
+ dev-texlive/texlive-latexrecommended"
src_prepare(){
- # xcadabra doesn't respect LDFLAGS (cadabra does!)
- epatch "${FILESDIR}/${PN}-1.25-xcadabra-flags.patch"
+ # fixing the flag mess
+ epatch "${FILESDIR}/${PN}-1.33-FLAGS.patch"
}
src_configure(){
- econf $(use_enable X gui)
+ econf $(use_enable X gui) \
+ --disable-runtime-dependency-check
}
src_compile() {
@@ -54,7 +56,9 @@ src_compile() {
}
src_install() {
- emake DESTDIR="${D}" DEVDESTDIR="${D}" install
+ # cadabra strip binaries unless you are on OS X.
+ # So faking it to avoid outright stripping.
+ emake DESTDIR="${D}" DEVDESTDIR="${D}" MACTEST=1 install
dodoc AUTHORS ChangeLog INSTALL
diff --git a/sci-mathematics/cadabra/files/cadabra-1.21-no-stripping.patch b/sci-mathematics/cadabra/files/cadabra-1.21-no-stripping.patch
deleted file mode 100644
index d21047f72..000000000
--- a/sci-mathematics/cadabra/files/cadabra-1.21-no-stripping.patch
+++ /dev/null
@@ -1,30 +0,0 @@
---- src/Makefile.in.orig 2010-03-28 23:01:45.367865648 +1300
-+++ src/Makefile.in 2010-03-28 23:02:11.518865659 +1300
-@@ -146,9 +146,9 @@
- # Installation and cleanup.
-
- install:
--ifeq ($(strip $(MACTEST)),)
-- strip cadabra
--endif
-+#ifeq ($(strip $(MACTEST)),)
-+# strip cadabra
-+#endif
- # strip -S cadabra
- #endif
- @INSTALL@ -m 0755 -d ${DESTDIR}@prefix@/bin
---- gui/Makefile.in.orig 2010-03-28 23:01:34.485865848 +1300
-+++ gui/Makefile.in 2010-03-28 23:02:30.490865700 +1300
-@@ -30,9 +30,9 @@
- @CXX@ -o test_texit `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` $+
-
- install:
--ifeq ($(strip $(MACTEST)),)
-- strip xcadabra
--endif
-+#ifeq ($(strip $(MACTEST)),)
-+# strip xcadabra
-+#endif
- install -d ${DESTDIR}@prefix@/bin
- install -m 0755 xcadabra ${DESTDIR}@prefix@/bin
- install -d ${DESTDIR}@prefix@/share/texmf/tex/latex/cadabra
diff --git a/sci-mathematics/cadabra/files/cadabra-1.25-xcadabra-flags.patch b/sci-mathematics/cadabra/files/cadabra-1.25-xcadabra-flags.patch
deleted file mode 100644
index 0d1beaa2d..000000000
--- a/sci-mathematics/cadabra/files/cadabra-1.25-xcadabra-flags.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- gui/Makefile.in.orig 2010-08-20 22:59:47.208483158 +1200
-+++ gui/Makefile.in 2010-08-20 23:00:51.888482426 +1200
-@@ -19,7 +19,7 @@
- main.o: $(OBJS) Makefile
-
- xcadabra: $(OBJS)
-- @CXX@ -o xcadabra $+ `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` -lpcrecpp
-+ @CXX@ @CFLAGS@ @LDFLAGS@ -o xcadabra $+ `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` -lpcrecpp
-
- xcadabra_static: $(OBJS)
- @CXX@ -o xcadabra -static $+ -L@prefix@/lib `pkg-config modglue --libs` \
diff --git a/sci-mathematics/cadabra/files/cadabra-1.33-FLAGS.patch b/sci-mathematics/cadabra/files/cadabra-1.33-FLAGS.patch
new file mode 100644
index 000000000..2d78e9327
--- /dev/null
+++ b/sci-mathematics/cadabra/files/cadabra-1.33-FLAGS.patch
@@ -0,0 +1,171 @@
+--- Makefile.in.orig 2013-09-05 21:45:20.026339263 +1200
++++ Makefile.in 2013-09-05 21:48:20.859739672 +1200
+@@ -24,7 +24,7 @@
+ ( cd src && $(MAKE) static );
+
+ profile:
+- ( export CFLAGS=-pg && export LDFLAGS=-pg && cd src && $(MAKE) );
++ ( export CFLAGS="$(CFLAGS) -pg" && CXXFLAGS="$(CXXFLAGS) -pg" && cd src && $(MAKE) );
+
+ doc:
+ ( cd doc && $(MAKE) );
+--- src/Makefile.in.orig 2013-09-05 21:45:35.546373837 +1200
++++ src/Makefile.in 2013-09-05 21:53:51.146459582 +1200
+@@ -22,12 +22,13 @@
+
+ SRCS = `find . -name "*.cc"`
+ MCFLAGS = @CFLAGS@ -I. -I@top_srcdir@/src `pkg-config modglue --cflags`
++MCXXFLAGS = @CXXFLAGS@ -I. -I@top_srcdir@/src `pkg-config modglue --cflags`
+ TIMESTAMP = -D"RELEASE=\"${RELEASE}\"" -D"DATETIME=\"`date | sed -e 's/ / /'`\"" -DHOSTNAME=\"`hostname`\"
+
+
+
+ %.o: %.cc
+- @CXX@ ${MCFLAGS} ${TIMESTAMP} -c -o $@ $<
++ @CXX@ ${MCXXFLAGS} ${TIMESTAMP} -c -o $@ $<
+
+ modules/xperm.o: modules/xperm.c
+ @CC@ @NESTED@ ${MCFLAGS} ${TIMESTAMP} -c -o $@ $<
+@@ -42,10 +43,10 @@
+
+ ifeq ($(strip $(MACTEST)),)
+ cadabra: $(OBJS) $(MOBJS)
+- @CXX@ -o cadabra ${LDFLAGS} -Wl,--as-needed $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp
++ @CXX@ -o cadabra ${MCXXFLAGS} ${LDFLAGS} -Wl,--as-needed $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp
+ else
+ cadabra: $(OBJS) $(MOBJS)
+- @CXX@ -o cadabra ${LDFLAGS} -Wl,-dead_strip_dylibs $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp
++ @CXX@ -o cadabra ${MCXXFLAGS} ${LDFLAGS} -Wl,-dead_strip_dylibs $+ `pkg-config modglue --libs` -lgmpxx -lpcrecpp -lgmp
+ endif
+
+ #`pkg-config glib-2.0 --libs`
+@@ -53,15 +54,15 @@
+
+ cadabra_static: $(OBJS) $(MOBJS)
+ rm -f main.o
+- @CXX@ -Wall -g ${MCFLAGS} ${TIMESTAMP} -DSTATICBUILD -c -o main.o main.cc
++ @CXX@ -Wall -g ${MCXXFLAGS} ${TIMESTAMP} -DSTATICBUILD -c -o main.o main.cc
+ ifeq ($(strip $(MACTEST)),)
+- @CXX@ -o cadabra -static $+ ${LDFLAGS} `pkg-config modglue --libs` -lmodglue \
++ @CXX@ -o cadabra -static ${MCXXFLAGS} $+ ${LDFLAGS} `pkg-config modglue --libs` -lmodglue \
+ -lgmpxx -lgmp -lpcrecpp -lpcre \
+ `pkg-config sigc++-2.0 --libs` -lsigc-2.0 -lutil
+
+ else
+ export MACOSX_DEPLOYMENT_TARGET=10.3
+- @CXX@ -o cadabra $+ ${LDFLAGS} `pkg-config modglue --libs` \
++ @CXX@ -o cadabra ${MCXXFLAGS} $+ ${LDFLAGS} `pkg-config modglue --libs` \
+ -lgmp -lgmpxx -lpcre++ -lpcre -lexpect
+ endif
+
+@@ -77,32 +78,32 @@
+ # @CXX@ -c -o defaults.o defaults.cc
+
+ test_tree: test_tree.o
+- @CXX@ -o test_tree test_tree.o
++ @CXX@ ${MCXXFLAGS} -o test_tree test_tree.o
+
+ test_lie: test_lie.o modules/lie.o
+ ifeq ($(strip $(MACTEST)),)
+- @CXX@ -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue`
++ @CXX@ ${MCXXFLAGS} -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue`
+ else
+- @CXX@ -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue`
++ @CXX@ ${MCXXFLAGS} -o test_lie test_lie.o modules/lie.o `pkg-config --libs modglue`
+ endif
+
+ tree_regression_tests: tree_regression_tests.o
+- @CXX@ -o tree_regression_tests tree_regression_tests.o
++ @CXX@ ${MCXXFLAGS} -o tree_regression_tests tree_regression_tests.o
+
+ test_xperm: test_xperm.o modules/xperm.o
+- @CXX@ -o test_xperm test_xperm.o modules/xperm.o
++ @CXX@ ${MCXXFLAGS} -o test_xperm test_xperm.o modules/xperm.o
+
+ tree_example: tree_example.o tree.hh
+- @CXX@ -o tree_example tree_example.o
++ @CXX@ ${MCXXFLAGS} -o tree_example tree_example.o
+
+ test_combinatorics: test_combinatorics.o combinatorics.o
+- @CXX@ -o test_combinatorics test_combinatorics.o combinatorics.o
++ @CXX@ ${MCXXFLAGS} -o test_combinatorics test_combinatorics.o combinatorics.o
+
+ test_young: test_young.o youngtab.o combinatorics.o
+- @CXX@ -o test_young test_young.o youngtab.o combinatorics.o ${LDFLAGS} -lgmpxx -lgmp
++ @CXX@ ${MCXXFLAGS} -o test_young test_young.o youngtab.o combinatorics.o ${LDFLAGS} -lgmpxx -lgmp
+
+ test_preprocessor: test_preprocessor.o preprocessor.o
+- @CXX@ -o test_preprocessor test_preprocessor.o preprocessor.o ${LDFLAGS} -lgmpxx -lgmp
++ @CXX@ ${MCXXFLAGS} -o test_preprocessor test_preprocessor.o preprocessor.o ${LDFLAGS} -lgmpxx -lgmp
+
+ mpi_pass_tree: mpi_pass_tree.o
+ @CXX@ -o mpi_pass_tree mpi_pass_tree.o -L/usr/lib/mpich/lib -lmpich++ -lpmpich -lmpich
+@@ -133,13 +134,13 @@
+ # Then the actual compilation.
+
+ lex.yy.o: lex.yy.c parser2.tab.h
+- @CXX@ -c -o lex.yy.o lex.yy.c
++ @CXX@ ${MCXXFLAGS} -c -o lex.yy.o lex.yy.c
+
+ parser2.tab.o: parser2.tab.c
+- @CXX@ -c -o parser2.tab.o parser2.tab.c
++ @CXX@ ${MCXXFLAGS} -c -o parser2.tab.o parser2.tab.c
+
+ parser2: parser2.tab.o lex.yy.o storage.o props.o
+- @CXX@ -o parser2 $+ -ll -ly -lgmpxx -lgmp -lpcrecpp
++ @CXX@ ${MCXXFLAGS} -o parser2 $+ -ll -ly -lgmpxx -lgmp -lpcrecpp
+
+
+
+@@ -170,7 +171,7 @@
+ .depend:
+ rm -f .depend
+ for i in ${SRCS}; \
+- do @CXX@ ${MCFLAGS} -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${CFLAGS} $$i >> .depend; \
++ do @CXX@ ${MCXXFLAGS} -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${CXXFLAGS} $$i >> .depend; \
+ done
+
+ include .depend
+--- gui/Makefile.in.orig 2013-09-05 21:45:50.989408184 +1200
++++ gui/Makefile.in 2013-09-05 21:57:17.495902104 +1200
+@@ -8,26 +8,26 @@
+ static: xcadabra_static
+
+ OBJS = help.o widgets.o window.o main.o ../src/stopwatch.o
+-CFLAGS = -O2 -I. -I@top_srcdir@/include `pkg-config modglue --cflags` `pkg-config --cflags gtkmm-2.4` \
++MCXXFLAGS = -O2 $(CXXFLAGS) -I. -I@top_srcdir@/include `pkg-config modglue --cflags` `pkg-config --cflags gtkmm-2.4` \
+ `pkg-config --cflags pango`
+ SRCS = `find . -name "*.cc"`
+ TIMESTAMP = -D"RELEASE=\"${RELEASE}\"" -D"DATETIME=\"`date | sed -e 's/ / /'`\"" -DHOSTNAME=\"`hostname`\"
+
+ %.o: %.cc
+- @CXX@ -Wall @CFLAGS@ -D"DESTDIR=\"@prefix@\"" ${TIMESTAMP} ${CFLAGS} -c -o $@ $<
++ @CXX@ -Wall $(MCXXFLAGS) -D"DESTDIR=\"@prefix@\"" ${TIMESTAMP} -c -o $@ $<
+
+ main.o: $(OBJS) Makefile
+
+ xcadabra: $(OBJS)
+- @CXX@ -o xcadabra $+ `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` -lpcrecpp
++ @CXX@ $(MCXXFLAGS) -o xcadabra $+ $(LDFLAGS) `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` -lpcrecpp
+
+ xcadabra_static: $(OBJS)
+- @CXX@ -o xcadabra -static $+ -L@prefix@/lib `pkg-config modglue --libs` \
++ @CXX@ $(MCXXFLAGS) -o xcadabra -static $+ $(LDFLAGS) -L@prefix@/lib `pkg-config modglue --libs` \
+ `pkg-config --libs gtkmm-2.4` `pkg-config libxml++-2.6` \
+ -lpthread -lexpat
+
+ test_texit: texit.o test_texit.o
+- @CXX@ -o test_texit `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` $+
++ @CXX@ $(MCXXFLAGS) -o test_texit `pkg-config modglue --libs` `pkg-config --libs gtkmm-2.4` $+
+
+ install:
+ ifeq ($(strip $(MACTEST)),)
+@@ -50,7 +50,7 @@
+ .depend:
+ rm -f .depend
+ for i in ${SRCS}; \
+- do g++ -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${CFLAGS} $$i >> .depend; \
++ do g++ -E -MM -MT `echo $$i | sed -e 's/\.\///' -e 's/\.cc/\.o/'` ${MCXXFLAGS} $$i >> .depend; \
+ done
+
+ include .depend
diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog
index a46d8e53a..4cde21a8f 100644
--- a/sci-physics/abinit/ChangeLog
+++ b/sci-physics/abinit/ChangeLog
@@ -2,6 +2,20 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 19 Sep 2013; Honza Macháček <Hloupy.Honza@centrum.cz> metadata.xml:
+ The metadata of sci-physics/abinit augmented by the description of the etsf_io
+ USE flag.
+
+*abinit-7.4.2 (19 Sep 2013)
+
+ 19 Sep 2013; Honza Macháček <Hloupy.Honza@centrum.cz> -abinit-7.2.2.ebuild,
+ +abinit-7.4.2.ebuild, +files/7.4.2-levmar_diag_scaling.patch,
+ +files/7.4.2-syntax.patch, metadata.xml:
+ Updated to 7.4.2, the new way of testing adopted. Use of atompaw, bigdft,
+ libxc, and wannier90 made optional, driven by USE flags (atompaw, bigdft,
+ libxc, wannier). USE flag levmar for the new optional Levenberg-Marquardt
+ least-squares algorithm support added. Ebuild cleaned up a bit.
+
20 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
+files/6.12.3-gui-makefiles.tbz:
files/6.12.3-gui-makefiles.tbz put back, its deletion was a mistake.
@@ -203,4 +217,3 @@
An ebuild for abinit-6.4.2 using external dependencies as proper Gentoo
packages. Based on bug 249493, still work in progress. With USE="smp"
compiles, but crashes.
-
diff --git a/sci-physics/abinit/Manifest b/sci-physics/abinit/Manifest
index f000cdcd5..fe8168fdc 100644
--- a/sci-physics/abinit/Manifest
+++ b/sci-physics/abinit/Manifest
@@ -1 +1 @@
-DIST abinit-7.2.2.tar.gz 63683267 SHA256 96f83e3af63e993cb886d9d6cd1c4fac04d50b5e460d5620330441050a909533 SHA512 fbc4898ae4625e12ea22d8f2da63e037eb947320fedf800bd40bd7e0015633ce54b7cb224cee3fc931d015774c51df5f8594ebe26a409cb0325e7a3ab0bf5e4a WHIRLPOOL a149d7ecea9b2b19b94b4e873f1924ce5fe221e037c642d6428727b552dc0c428b288551dda708286995da26080171c385a3ef3ad3766e065073139d4ef0f2e8
+DIST abinit-7.4.2.tar.gz 69150549 SHA256 26fcc60e18071b7579843f43cbe44e79db50466dbaae8b862ad96a8986733f63 SHA512 55132cfbfb26bf22ae486ada7e721188bd436a48299da3a386928776f6d0652d8a19a5e5b70261b84afc6cb6b058fe711171fa09aff637bdb2da11e8df032543 WHIRLPOOL add34b50d2c6843064254a3caffbfa4d9fef644ae98513a1b7681ffb8f2c0f4d31b5b995920a97fa656d82a38aeec313f98e1f91c06166ea83ed6ba87192292d
diff --git a/sci-physics/abinit/abinit-7.2.2.ebuild b/sci-physics/abinit/abinit-7.4.2.ebuild
index a420f51cf..41441a68f 100644
--- a/sci-physics/abinit/abinit-7.2.2.ebuild
+++ b/sci-physics/abinit/abinit-7.4.2.ebuild
@@ -4,7 +4,9 @@
EAPI=5
-inherit autotools-utils eutils flag-o-matic fortran-2 multilib toolchain-funcs
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools-utils eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs
DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory"
HOMEPAGE="http://www.abinit.org/"
@@ -13,45 +15,47 @@ SRC_URI="http://ftp.abinit.org/${P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
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"
+IUSE="atompaw bigdft cuda cuda-double -debug +etsf_io +fftw +fftw-threads +fox gsl +hdf5 levmar -libabinit libxc -lotf mpi +netcdf openmp python scripts -test +threads -vdwxc wannier"
+
+REQUIRED_USE="scripts? ( ${PYTHON_REQUIRED_USE} )
+ test? ( ${PYTHON_REQUIRED_USE} )"
-RDEPEND="~sci-libs/bigdft-abi-1.0.4
- >=sci-libs/libxc-1.2.0-r1[fortran]
- >=sci-physics/atompaw-3.0.1.9-r1[libxc]
+RDEPEND="virtual/blas
+ virtual/lapack
+ atompaw? ( >=sci-physics/atompaw-3.0.1.9-r1[libxc?] )
+ bigdft? ( ~sci-libs/bigdft-abi-1.0.4 )
+ cuda? ( dev-util/nvidia-cuda-sdk )
etsf_io? ( >=sci-libs/etsf_io-1.0.3-r2 )
+ fftw? (
+ sci-libs/fftw:3.0
+ fftw-threads? ( sci-libs/fftw:3.0[threads] )
+ )
fox? ( >=sci-libs/fox-4.1.2-r2[sax] )
+ gsl? ( sci-libs/gsl )
+ hdf5? ( sci-libs/hdf5[fortran] )
+ levmar? ( sci-libs/levmar )
+ libxc? ( >=sci-libs/libxc-2.0.1[fortran] )
netcdf? (
+ sci-libs/netcdf[hdf5?]
|| (
sci-libs/netcdf[fortran]
sci-libs/netcdf-fortran
)
- hdf5? (
- sci-libs/netcdf[hdf5]
- )
- )
- hdf5? ( sci-libs/hdf5[fortran] )
- >=sci-libs/wannier90-1.2-r1
- virtual/blas
- virtual/lapack
- gsl? ( sci-libs/gsl )
- fftw? (
- sci-libs/fftw:3.0
- fftw-threads? ( sci-libs/fftw:3.0[threads] )
)
mpi? ( virtual/mpi )
- python? ( dev-python/numpy )
- cuda? ( dev-util/nvidia-cuda-sdk )"
+ python? ( ${PYTHON_DEPS}
+ dev-python/numpy )
+ scripts? ( ${PYTHON_DEPS}
+ dev-python/numpy
+ dev-python/PyQt4 )
+ wannier? ( >=sci-libs/wannier90-1.2-r1 )"
DEPEND="${RDEPEND}
virtual/pkgconfig
- gui? ( >=virtual/jdk-1.6.0
- app-arch/sharutils
- sys-apps/gawk )
- dev-perl/Text-Markdown"
+ dev-perl/Text-Markdown
+ test? ( ${PYTHON_DEPS} )"
S=${WORKDIR}/${P%[a-z]}
-lat1loc=""
-
DOCS=( AUTHORS ChangeLog COPYING INSTALL KNOWN_PROBLEMS NEWS PACKAGING
README README.ChangeLog README.GPU README.xlf RELNOTES THANKS )
@@ -79,7 +83,7 @@ pkg_setup() {
# Preprocesor macross can make some lines really long
append-fflags -ffree-line-length-none
- # This should be correct.
+ # This should be correct:
# It is gcc-centric because toolchain-funcs.eclass is gcc-centric.
# Should a bug be filed against toolchain-funcs.eclass?
# if use openmp; then
@@ -87,7 +91,7 @@ pkg_setup() {
# die "Please select an openmp capable compiler like gcc[openmp]"
# fi
#
- # This is completely wrong.
+ # This is completely wrong:
# If other compilers than Gnu Compiler Collection can be used by portage,
# their support of OpenMP should be properly tested. This code limits the test
# to gcc, and blindly supposes that other compilers do support OpenMP.
@@ -103,6 +107,58 @@ pkg_setup() {
fortran-2_pkg_setup
+ if use openmp; then
+ # based on _fortran-has-openmp() of fortran-2.eclass
+ local code=ebuild-openmp-flags
+ local ret
+ local openmp
+
+ pushd "${T}"
+ cat <<- EOF > "${code}.c"
+ # include <omp.h>
+ main () {
+ int nthreads;
+ nthreads=omp_get_num_threads();
+ }
+ EOF
+
+ for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
+ ${CC} ${openmp} "${code}.c" -o "${code}.o" &>> "${T}"/_c_compile_test.log
+ ret=$?
+ (( ${ret} )) || break
+ done
+
+ rm -f "${code}.*"
+ popd
+
+ if (( ${ret} )); then
+ die "Please switch to an openmp compatible C compiler"
+ else
+ export CC="${CC} ${openmp}"
+ fi
+
+ pushd "${T}"
+ cat <<- EOF > "${code}.f"
+ 1 call omp_get_num_threads
+ 2 end
+ EOF
+
+ for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
+ ${FC} ${openmp} "${code}.f" -o "${code}.o" &>> "${T}"/_f_compile_test.log
+ ret=$?
+ (( ${ret} )) || break
+ done
+
+ rm -f "${code}.*"
+ popd
+
+ if (( ${ret} )); then
+ die "Please switch to an openmp compatible fortran compiler"
+ else
+ export FC="${FC} ${openmp}"
+ fi
+ fi
+
# Sort out some USE options
if use fftw-threads && ! use fftw; then
ewarn "fftw-threads set but fftw not used, ignored"
@@ -110,32 +166,9 @@ pkg_setup() {
if use cuda-double && ! use cuda; then
ewarn "cuda-double set but cuda not used, ignored"
fi
- if use gui; then
- lat1loc="$(locale |awk '/LC_CTYPE="(.*)"/{sub("LC_CTYPE=\"",""); sub("\" *$", ""); print}')"
- if locale charmap |grep -i "\<iso885915\?\>"; then
- einfo "Good, locale compatible with the GUI build"
- else
- ewarn "The locale ${lat1loc} incompatible with the GUI build"
- if latloc=`locale -a| grep -i "\<iso885915\?\>"`; then
- if echo "${latloc}" |grep -q "^fr"; then
- lat1loc="$(echo "${latloc}" | grep -im1 "^fr")"
- else
- lat1loc="$(echo "${latloc}" | grep -im1 "iso88591")"
- fi
- einfo "Will use ${lat1loc} to build the GUI"
- else
- ewarn "No ISO-8859-1 nor ISO-8859-15 locale available, the GUI build may crash"
- fi
- fi
- fi
-}
-src_unpack() {
- default_src_unpack
- if use gui; then
- pushd "${S}" > /dev/null
- tar -xjf "${FILESDIR}"/6.12.3-gui-makefiles.tbz
- popd > /dev/null
+ if use scripts || use test; then
+ python-single-r1_pkg_setup
fi
}
@@ -145,45 +178,32 @@ src_prepare() {
"${FILESDIR}"/6.2.2-change-default-directories.patch \
"${FILESDIR}"/6.12.1-autoconf.patch \
"${FILESDIR}"/6.12.1-xmalloc.patch \
- "${FILESDIR}"/7.0.4-test_dirs.patch
+ "${FILESDIR}"/7.4.2-levmar_diag_scaling.patch \
+ "${FILESDIR}"/7.4.2-syntax.patch
eautoreconf
sed -e"s/\(grep '\^-\)\(\[LloW\]\)'/\1\\\(\2\\\|pthread\\\)'/g" -i configure
-
- if use gui; then
- pushd gui > /dev/null
- eautoreconf
- popd > /dev/null
- fi
}
src_configure() {
- local openmp=""
- if use openmp; then
- # based on _fortran-has-openmp() of fortran-2.eclass
- local fcode=ebuild-openmp-flags.f
- local _fc=$(tc-getFC)
-
- cat <<- EOF > "${fcode}"
- 1 call omp_get_num_threads
- 2 end
- EOF
-
- for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
- ${_fc} ${openmp} "${fcode}" -o "${fcode}.x" && break
- done
-
- rm -f "${fcode}.*"
- fi
- local libs=""
local modules="$(FoX-config --sax --fcflags)"
- local FoX_libs="${libs} $(FoX-config --sax --libs)"
+ local FoX_libs="$(FoX-config --sax --libs)"
+
local trio_flavor=""
use etsf_io && trio_flavor="${trio_flavor}+etsf_io"
use fox && trio_flavor="${trio_flavor}+fox"
use netcdf && trio_flavor="${trio_flavor}+netcdf"
test "no${trio_flavor}" = "no" && trio_flavor="none"
+
local netcdff_libs="-lnetcdff"
use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran"
+
+ local dft_flavor=""
+ use atompaw && dft_flavor="${dft_flavor}+atompaw"
+ use bigdft && dft_flavor="${dft_flavor}+bigdft"
+ use libxc && dft_flavor="${dft_flavor}+libxc"
+ use wannier && dft_flavor="${dft_flavor}+wannier90"
+ test "no${dft_flavor}" = "no" && dft_flavor="none"
+
local fft_flavor="fftw3"
local fft_libs=""
# The fftw threads support is protected by black magick.
@@ -202,6 +222,7 @@ src_configure() {
fft_libs="${fft_libs} $($(tc-getPKG_CONFIG) --libs fftw3)"
fft_libs="${fft_libs} $($(tc-getPKG_CONFIG) --libs fftw3f)"
fi
+
local gpu_flavor="none"
if use cuda; then
gpu_flavor="cuda-single"
@@ -213,18 +234,20 @@ src_configure() {
local myeconfargs=(
--enable-clib
--enable-exports
- $(use_enable gui)
$(use_enable debug debug enhanced)
$(use_enable mpi)
$(use_enable mpi mpi-io)
$(use_enable openmp)
$(use_enable vdwxc)
+ $(use_enable lotf)
$(use_enable cuda gpu)
"$(use cuda && echo "--with-gpu-flavor=${gpu_flavor}")"
"$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")"
"$(use gsl && echo "--with-math-flavor=gsl")"
"$(use gsl && echo "--with-math-incs=$($(tc-getPKG_CONFIG) --cflags gsl)")"
"$(use gsl && echo "--with-math-libs=$($(tc-getPKG_CONFIG) --libs gsl)")"
+ "$(use levmar && echo "--with-algo-flavor=levmar")"
+ "$(use levmar && echo "--with-algo-libs=-llevmar")"
--with-linalg-flavor="atlas"
--with-linalg-libs="$($(tc-getPKG_CONFIG) --libs lapack)"
--with-trio-flavor="${trio_flavor}"
@@ -233,36 +256,26 @@ src_configure() {
"$(use fox && echo "--with-fox-incs=${modules}")"
"$(use fox && echo "--with-fox-libs=${FoX_libs}")"
"$(use etsf_io && echo "--with-etsf-io-incs=${modules}")"
- "$(use etsf_io && echo "--with-etsf-io-libs=${libs} -letsf_io -letsf_io_utils -letsf_io_low_level")"
- --with-dft-flavor="libxc+bigdft+atompaw+wannier90"
- --with-libxc-incs="${modules}"
- --with-libxc-libs="${libs} -lxc"
- --with-bigdft-incs="${modules}"
- --with-bigdft-libs="$($(tc-getPKG_CONFIG) --libs bigdft)"
- --with-atompaw-incs="${modules}"
- --with-atompaw-libs="${libs} -latompaw"
- --with-wannier90-bins="/usr/bin"
- --with-wannier90-incs="${modules}"
- --with-wannier90-libs="${libs} -lwannier $($(tc-getPKG_CONFIG) --libs lapack)"
+ "$(use etsf_io && echo "--with-etsf-io-libs=-letsf_io -letsf_io_utils -letsf_io_low_level")"
+ --with-dft-flavor="${dft_flavor}"
+ "$(use atompaw && echo "--with-atompaw-incs=${modules}")"
+ "$(use atompaw && echo "--with-atompaw-libs=-latompaw")"
+ "$(use bigdft && echo "--with-bigdft-incs=${modules}")"
+ "$(use bigdft && echo "--with-bigdft-libs=$($(tc-getPKG_CONFIG) --libs bigdft)")"
+ "$(use libxc && echo "--with-libxc-incs=${modules}")"
+ "$(use libxc && echo "--with-libxc-libs=-lxc")"
+ "$(use wannier && echo "--with-wannier90-bins=/usr/bin")"
+ "$(use wannier && echo "--with-wannier90-incs=${modules}")"
+ "$(use wannier && echo "--with-wannier90-libs=-lwannier $($(tc-getPKG_CONFIG) --libs lapack)")"
"$(use fftw && echo "--with-fft-flavor=${fft_flavor}")"
"$(use fftw && echo "--with-fft-incs=-I/usr/include")"
"$(use fftw && echo "--with-fft-libs=${fft_libs}")"
--with-timer-flavor="abinit"
LD="$(tc-getLD)"
- FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${openmp} ${modules} -I/usr/include"
+ FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include"
)
MARKDOWN=Markdown.pl autotools-utils_src_configure
-
- if use gui; then
- # autotools-utils_src_configure() part expanded
- _check_build_dir
- pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
- mkdir -p gui
- cd gui
- ECONF_SOURCE="${S}"/gui econf UUDECODE="uudecode"
- popd > /dev/null
- fi
}
src_compile() {
@@ -275,59 +288,22 @@ src_compile() {
# Can Abinit use external libabinit.a?
use libabinit && autotools-utils_src_compile libabinit.a
- if use gui; then
- #autotools-utils_src_compile() expanded
- # _check_build_dir has already been called
- pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
- # now what the function cannot be called to do
- cd gui
- LC_CTYPE="${lat1loc}" emake || die "Making GUI failed"
- popd > /dev/null
- fi
-
sed -i -e's/libatlas/lapack/' "${AUTOTOOLS_BUILD_DIR}"/config.pc
}
src_test() {
- einfo "The tests take quite a while, easily several hours"
+ einfo "The tests take quite a while, easily several hours or even days"
# autotools-utils_src_test() expanded
_check_build_dir
pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
# again something the autotools-utils function cannot be called to do
# now quite a lot of work actually
- cd tests
- emake tests_acc || ewarn "Accuracy tests failed"
- emake tests_paw || ewarn "PAW tests failed"
- emake tests_gw || ewarn "GW tests failed"
- emake tests_gw_paw || ewarn "GW-PAW tests failed"
- emake tests_bs || ewarn "BSE tests failed"
- emake tests_tddft || ewarn "TDDFT tests failed"
- emake tests_eph || ewarn "Elphon tests failed"
-
- local REPORT
- for REPORT in $(find . -name report); do
- REPORT=${REPORT#*/}
- elog "Parameters and unusual results for ${REPORT%%/*} tests"
- echo "Parameters and unusual results for ${REPORT%%/*} tests" >>tests_summary.txt
- while read line; do
- elog "${line}"
- echo "${line}" >>tests_summary.txt
- done \
- < <(grep -v -e succeeded -e passed ${REPORT})
- done
-
- local testdir
- find . -name "tmp-test*" -print | \
- while read testdir; do
- if [ -e summary_of_tests.tar ]; then
- tar rvf summary_of_tests.tar ${testdir}
- else tar cvf summary_of_tests.tar ${testdir}
- fi
- done
+ mkdir -p tests
+
+ python2 "${S}"/tests/runtests.py -w tests/ -b "${AUTOTOOLS_BUILD_DIR}"
+
popd > /dev/null
- elog "The full test results will be installed as summary_of_tests.tar.bz2."
- elog "Also a concise report tests_summary.txt is installed."
}
src_install() {
@@ -338,15 +314,9 @@ src_install() {
use libabinit && dolib libabinit.a
- if use gui; then
- pushd gui > /dev/null
- emake DESTDIR="${D}" install || die "The GUI install failed"
- popd > /dev/null
- fi
-
if use test; then
- for dc in tests_summary.txt summary_of_tests.tar; do
- test -e tests/"${dc}" && dodoc tests/"${dc}" || ewarn "Copying tests results failed"
+ for dc in results.tar.gz results.txt suite_report.html; do
+ test -e tests/"${dc}" && dodoc tests/"${dc}" || ewarn "Copying tests results ${dc} failed"
done
fi
@@ -369,6 +339,11 @@ src_install() {
dohtml -r "${HTML_DOCS[@]}" || die "dohtml failed"
fi
+ if use scripts; then
+ insinto /usr/share/"${P}"
+ doins -r scripts
+ fi
+
# Remove libtool files and unnecessary static libs
prune_libtool_files
}
diff --git a/sci-physics/abinit/files/7.4.2-levmar_diag_scaling.patch b/sci-physics/abinit/files/7.4.2-levmar_diag_scaling.patch
new file mode 100644
index 000000000..346146616
--- /dev/null
+++ b/sci-physics/abinit/files/7.4.2-levmar_diag_scaling.patch
@@ -0,0 +1,21 @@
+diff -Naurp abinit-7.4.2.orig/src/02_clib/calling_levmar.c abinit-7.4.2/src/02_clib/calling_levmar.c
+--- abinit-7.4.2.orig/src/02_clib/calling_levmar.c 2013-09-08 07:24:13.000000000 +0000
++++ abinit-7.4.2/src/02_clib/calling_levmar.c 2013-09-16 14:59:06.574702521 +0000
+@@ -149,7 +149,7 @@ double opts[LM_OPTS_SZ], info[LM_INFO_SZ
+ // if (coeffs[i+2]>-1E-16){
+ /* invoke the optimisation function with box boundaries*/
+ ret=dlevmar_bc_dif(dim_screening, coeffs, yvals, c_ncoeffs, c_nvals, \
+- lower_bounds, upper_bounds, 3000, opts, info, NULL, NULL, \
++ lower_bounds, upper_bounds, NULL, 3000, opts, info, NULL, NULL, \
+ (void *)&adata); // Box boundary conditions without Jacobian
+ //}
+ //}
+@@ -219,7 +219,7 @@ double opts[LM_OPTS_SZ], info[LM_INFO_SZ
+ // if (coeffs[i+2]>-1E-16){
+ /* invoke the optimisation function with box boundaries*/
+ ret=dlevmar_bc_dif(dre_and_im_screening, coeffs, yvals, c_ncoeffs, c_nvals, \
+- lower_bounds, upper_bounds, 1000, opts, info, NULL, NULL, \
++ lower_bounds, upper_bounds, NULL, 1000, opts, info, NULL, NULL, \
+ (void *)&adata); // Box boundary conditions without Jacobian
+ //}
+ //}
diff --git a/sci-physics/abinit/files/7.4.2-syntax.patch b/sci-physics/abinit/files/7.4.2-syntax.patch
new file mode 100644
index 000000000..87026d926
--- /dev/null
+++ b/sci-physics/abinit/files/7.4.2-syntax.patch
@@ -0,0 +1,21 @@
+diff -Naurp abinit-7.4.2.orig/src/98_main/mrgscr.F90 abinit-7.4.2/src/98_main/mrgscr.F90
+--- abinit-7.4.2.orig/src/98_main/mrgscr.F90 2013-09-08 07:24:13.000000000 +0000
++++ abinit-7.4.2/src/98_main/mrgscr.F90 2013-09-17 10:32:55.212877871 +0000
+@@ -2309,7 +2309,7 @@ program mrgscr
+
+ case(2) ! Fit everything
+
+- if (is_scr/=.true.) then
++ if (is_scr.neqv..true.) then
+ write(std_out,'(2(a))') ch10,&
+ & ' Complete fits can only be done for _SCR file for now. Exiting ...'
+ goto 100
+@@ -2387,7 +2387,7 @@ program mrgscr
+
+ !!OMP *** OPENMP SECTION *** Added by MS
+ !$OMP PARALLEL SHARED(Hscr_file,epsm1,nfreqre,epsm1_pole, &
+-!$OMP is_scr,npoles,std_out,iqibz,one) &
++!$OMP is_scr,npoles,std_out,iqibz) &
+ !$OMP PRIVATE(ig1,ig2,refval,imfval,phase)
+ !!OMP write(std_out,'(a,i0)') ' Entering openmp loop. Number of threads: ',omp_get_num_threads()
+ ABI_MALLOC(refval,(Hscr_file(1)%nomega))
diff --git a/sci-physics/abinit/metadata.xml b/sci-physics/abinit/metadata.xml
index e8b3b1d6a..192c6f3cb 100644
--- a/sci-physics/abinit/metadata.xml
+++ b/sci-physics/abinit/metadata.xml
@@ -15,6 +15,12 @@ Many-Body Perturbation Theory (the GW approximation). In addition to the main
ABINIT code, different utility programs are provided.
</longdescription>
<use>
+ <flag name="atompaw">Enable support for atompaw, a Projector Augmented Waves atomic data generator</flag>
+ </use>
+ <use>
+ <flag name="bigdft">Enable support for BigDFT, DFT package using wavelet basis set</flag>
+ </use>
+ <use>
<flag name="cuda">Enable support for nVidia CUDA</flag>
</use>
<use>
@@ -23,7 +29,10 @@ ABINIT code, different utility programs are provided.
</flag>
</use>
<use>
- <flag name="etsf_io">This USE needs documentation</flag>
+ <flag name="etsf_io">
+ Enable support for reading and writing the European Theoretical
+ Spectroscopy facility (ETSF) file format.
+ </flag>
</use>
<use>
<flag name="fftw-threads">
@@ -34,7 +43,16 @@ ABINIT code, different utility programs are provided.
<flag name="fox">Enable support for FoX Fortran XML library</flag>
</use>
<use>
- <flag name="gui">Build the abinit GUI (requires java)</flag>
+ <flag name="gui">
+ Build the abinit GUI (requires java);
+ since 7.4.x a separate package
+ </flag>
+ </use>
+ <use>
+ <flag name="levmar">
+ Enable support for <pkg>sci-libs/levmar</pkg>,
+ the Levenberg-Marquardt least-squares optimisation
+ </flag>
</use>
<use>
<flag name="libabinit">
@@ -43,6 +61,18 @@ ABINIT code, different utility programs are provided.
</flag>
</use>
<use>
- <flag name="vdwxc">Activate van der Waals exchange-correlation</flag>
+ <flag name="libxc">Enable support for libxc, an exchange-correlation potentials library</flag>
+ </use>
+ <use>
+ <flag name="lotf">Activate the Learn on The Fly method (LOTF) for Molecular Dynamics</flag>
+ </use>
+ <use>
+ <flag name="scripts">Install helper scripts, mostly Python</flag>
+ </use>
+ <use>
+ <flag name="vdwxc">Activate van der Waals exchange-correlation correction</flag>
+ </use>
+ <use>
+ <flag name="wannier">Enable support for wannier90, a maximally localized Wannier functions (MLWFs) calculator</flag>
</use>
</pkgmetadata>
diff --git a/sci-physics/openmx/ChangeLog b/sci-physics/openmx/ChangeLog
index b38e7280f..e0852b2c5 100644
--- a/sci-physics/openmx/ChangeLog
+++ b/sci-physics/openmx/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*openmx-3.7.6 (19 Sep 2013)
+
+ 19 Sep 2013; Honza Macháček <Hloupy.Honza@centrum.cz> -openmx-3.7.4.ebuild,
+ +openmx-3.7.6.ebuild:
+ Updated to 3.7.6, corrected linking with fortran code using gcc.
+
16 Jul 2013; Honza Macháček <Hloupy.Honza@centrum.cz> openmx-3.7.4.ebuild:
Another quick fix, the version number of the PDF manual.
diff --git a/sci-physics/openmx/Manifest b/sci-physics/openmx/Manifest
index 6493a09d8..4f59a085b 100644
--- a/sci-physics/openmx/Manifest
+++ b/sci-physics/openmx/Manifest
@@ -1,4 +1,4 @@
DIST openmx3.6.tar.gz 83023744 SHA256 e344914a615d4179e724877207335e44f9d629cd3931b70e135011877355ab71 SHA512 f4d59e839bbd216893149c83d1059aa4dc4fb011d113cb40efbd99db96d558501b371628f0ea064d3091d8ef0d2c8664412b0c3541fa2a7135811e3536cb0018 WHIRLPOOL 54c72309133dbb010218ce138992362e98eb4c345eb3b2897e1d86f3f2469cc95a2024c8547cc3dc0db78befaf620e624640b6a64522c0937bf7158658a28109
DIST openmx3.7.tar.gz 117784869 SHA256 24329cd1fbad98d6cb99b04e4d988b0715e2ce3156f79e4855c46f93a0c981f9 SHA512 e05e2839776be17d0df71818444ff7234b75f00177111ff4003eacbe3663a025965990c293cd1dfa078c3960fe89385cbe16393c9cfaf5953e1c683e7964423a WHIRLPOOL 68694dd0ea3899a79c2c299377671725ad5e971af2d0a842501a422fc30483d43373dcc7d2f1e5dc62f6298dbf8f87cc5806a0d2eab3add80a3adca0a3f5a327
DIST patch3.6.1.tar.gz 202531 SHA256 56cba052a84c73bf332ff3a65787001376f8d50ec50e7e363a67dfb5b417febd SHA512 1f1c2c156c80a21649826cfaeb79a9b2b7d81b46920e713fb0e4489eeceb8cc6a9193c49efb0d4c1a1a69313e21186e10ed4fd97d27e63b555ce1092425c641d WHIRLPOOL 006cb7ec822ef485c03a371b9c3a99c426fc5e6e1249fd17d9f5527f0220f09df1acc049e31a59d6834a3ce44431ae385268954898613a9fe31ff892262a5503
-DIST patch3.7.4.tar.gz 73191 SHA256 1c57ed3e473eb036f96ad626c6c7ce1fec8ccda6f1a4fade360bdf6265935d61 SHA512 91c7ee6d6fd3bc4394d06b41bbd62d003695061d026f1f1f17e0e0adea17482a2fcb67a29425a74d8b4a9c81fd170de54814a782972b919709fb3e7171c43d5f WHIRLPOOL e65c4cb6e2699c659150c4eff9af77a690cd94a2772edeadea303d83b9d5b2d4dc3daf5497505e79ef9d31a7a4e89ec745bd9a5f55d74e57b5be774e0d25b9cf
+DIST patch3.7.6.tar.gz 73220 SHA256 fc24dcf3ee22854def1b4c012cd1d459f406f7a785732fa478478be2f0c00dc9 SHA512 bafe4d0da12e4aab619720266f43e3f554360f292fb9a9cba26d772d7fe37146c2f7ec0a50f5967c1e473f6cf91602e6d283fc907cd413d0ba0300517d79dc69 WHIRLPOOL 60d15cf474bd471c27c905d37eb0ef3ae094ae1f3a0b89a8a97ad09881323540afd97f190910d175fb7f38d0d8c0c39fc64853cf98c5d97e1ae9aeb4f544b283
diff --git a/sci-physics/openmx/openmx-3.7.4.ebuild b/sci-physics/openmx/openmx-3.7.6.ebuild
index e4fff03b6..bb44f1648 100644
--- a/sci-physics/openmx/openmx-3.7.4.ebuild
+++ b/sci-physics/openmx/openmx-3.7.6.ebuild
@@ -6,7 +6,7 @@ EAPI=5
inherit eutils multilib toolchain-funcs fortran-2
-PATCHDATE="13July03"
+PATCHDATE="13Sep01"
DESCRIPTION="Material eXplorer using DFT, NC pseudopotentials, and pseudo-atomic localized basis functions"
HOMEPAGE="http://www.openmx-square.org/"
@@ -34,6 +34,14 @@ MAKEOPTS+=" -j1"
FORTRAN_STANDARD=90
pkg_setup() {
+ # Link in the GNU Fortran library for Fortran code.
+ # Other compilers may need other hacks.
+ FC_LIB=""
+ if [[ $(tc-getCC)$ == *gcc* ]]; then
+ FC_LIB="-lgfortran"
+ fi
+ export FC_LIB
+
if use mpi; then
export CC="mpicc"
export FC="mpif90"
@@ -136,7 +144,7 @@ src_configure() {
sed \
-e "s%^CC *=.*$%CC = ${CC} ${CFLAGS}%" \
-e "s%^FC *=.*$%FC = ${FC} ${FCFLAGS}%" \
- -e "s%^LIB *=.*$%LIB = ${MX_LIB}%" \
+ -e "s%^LIB *=.*$%LIB = ${MX_LIB} ${FC_LIB}%" \
-i source/makefile || die
}