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-rw-r--r--app-admin/eselect/eselect-1.4.4-r100.ebuild2
-rw-r--r--dev-libs/utf8proc/ChangeLog8
-rw-r--r--dev-libs/utf8proc/Manifest1
-rw-r--r--dev-libs/utf8proc/files/utf8proc-1.2-buildflags.patch14
-rw-r--r--dev-libs/utf8proc/utf8proc-1.2.ebuild31
-rw-r--r--media-gfx/brlcad/ChangeLog4
-rw-r--r--media-gfx/brlcad/brlcad-7.24.2.ebuild4
-rw-r--r--media-gfx/brlcad/brlcad-9999.ebuild4
-rw-r--r--sci-biology/breakdancer/ChangeLog16
-rw-r--r--sci-biology/breakdancer/Manifest1
-rw-r--r--sci-biology/breakdancer/breakdancer-1.1.2.ebuild20
-rw-r--r--sci-biology/breakdancer/breakdancer-9999.ebuild33
-rw-r--r--sci-biology/kallisto/ChangeLog10
-rw-r--r--sci-biology/kallisto/Manifest1
-rw-r--r--sci-biology/kallisto/kallisto-0.42.1.ebuild19
-rw-r--r--sci-biology/kallisto/kallisto-9999.ebuild20
-rw-r--r--sci-biology/kallisto/metadata.xml9
-rw-r--r--sci-libs/amdlibm/amdlibm-3.1.ebuild4
-rw-r--r--sci-libs/arrayfire/ChangeLog9
-rw-r--r--sci-libs/arrayfire/arrayfire-9999.ebuild15
-rw-r--r--sci-libs/arrayfire/files/FindBoostCompute.cmake18
-rw-r--r--sci-libs/arrayfire/files/arrayfire-3.0_beta-FindBoostCompute.patch (renamed from sci-libs/arrayfire/files/FindBoostCompute.patch)0
-rw-r--r--sci-libs/arrayfire/files/arrayfire-3.0_beta-FindCBLAS.patch (renamed from sci-libs/arrayfire/files/FindCBLAS.patch)0
-rw-r--r--sci-libs/arrayfire/files/arrayfire-3.0_beta-opencl_CMakeLists.patch (renamed from sci-libs/arrayfire/files/opencl_CMakeLists.patch)0
-rw-r--r--sci-libs/arrayfire/files/arrayfire-9999-FindCBLAS.patch52
-rw-r--r--sci-libs/calculix-ccx/calculix-ccx-2.7-r1.ebuild4
-rw-r--r--sci-libs/ccif/ChangeLog7
-rw-r--r--sci-libs/ccif/ccif-0.3.20111209.ebuild4
-rw-r--r--sci-libs/geom/ChangeLog6
-rw-r--r--sci-libs/geom/Manifest2
-rw-r--r--sci-libs/geom/geom-5.1.2.7.ebuild10
31 files changed, 274 insertions, 54 deletions
diff --git a/app-admin/eselect/eselect-1.4.4-r100.ebuild b/app-admin/eselect/eselect-1.4.4-r100.ebuild
index 02730fa03..8001cf173 100644
--- a/app-admin/eselect/eselect-1.4.4-r100.ebuild
+++ b/app-admin/eselect/eselect-1.4.4-r100.ebuild
@@ -57,7 +57,7 @@ src_install() {
# band aid for prefix
if use prefix; then
- cd "${ED}"/usr/share/eselect/libs
+ cd "${ED}"/usr/share/eselect/libs || die
sed -i "s:ALTERNATIVESDIR_ROOTLESS=\"${EPREFIX}:ALTERNATIVESDIR_ROOTLESS=\":" alternatives.bash || die
fi
}
diff --git a/dev-libs/utf8proc/ChangeLog b/dev-libs/utf8proc/ChangeLog
index f5afbed53..f822d346b 100644
--- a/dev-libs/utf8proc/ChangeLog
+++ b/dev-libs/utf8proc/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for dev-libs/utf8proc
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*utf8proc-1.2 (21 May 2015)
+
+ 21 May 2015; Marius Brehler <marbre@linux.sungazer.de>
+ +files/utf8proc-1.2-buildflags.patch, +utf8proc-1.2.ebuild:
+ Version bump
+
02 Apr 2014; SĂ©bastien Fabbro <bicatali@gentoo.org> metadata.xml,
utf8proc-1.1.6.ebuild:
dev-libs/utf8proc: Keyworded for amd64-linux x86-linux
diff --git a/dev-libs/utf8proc/Manifest b/dev-libs/utf8proc/Manifest
index 4459cdb6a..7d19b7696 100644
--- a/dev-libs/utf8proc/Manifest
+++ b/dev-libs/utf8proc/Manifest
@@ -1 +1,2 @@
+DIST utf8proc-1.2.tar.gz 137294 SHA256 9b07ffe12e049974d120f1558459f6ba9b44681c182ac738ca96fb70aa842fd9 SHA512 066b77d599320e0f6d90e52f6ae482c3caf54276920ad4afacaf4d0c4969d94aa33401e63edee14b2887cdf60fdffd07f913d246212aac1a26b480f20cbc24d4 WHIRLPOOL 597f30c1f1b6d413d9ab7b81c203d01386a949bf33a99eb0bf90ffb7b2c560b78b55ad02d074bff57ecaccda46db991d0bbb9dcf113756c87914a488a2e44762
DIST utf8proc-v1.1.6.tar.gz 105825 SHA256 fedc8fa78022eb8f0584fbc85c9f9571bcd7fd510de0ce16955289c42f4199e7 SHA512 3bec2388298c201d9d6992cdd36330f1109d26a37b3411ba633f006f40da9e494ba0565051b763a7d3014e6113cd1e7754e6b95d5cbb2d7b50cee55193f0fdc1 WHIRLPOOL c211419407e80893b66fa7586a8148e9b2e45c89d2d31878658a4ae7f0b1ca72e269cef234ca8b30e27e4bac5a48715520dd546f6605af773d6e165ef76f81b0
diff --git a/dev-libs/utf8proc/files/utf8proc-1.2-buildflags.patch b/dev-libs/utf8proc/files/utf8proc-1.2-buildflags.patch
new file mode 100644
index 000000000..4d583e417
--- /dev/null
+++ b/dev-libs/utf8proc/files/utf8proc-1.2-buildflags.patch
@@ -0,0 +1,14 @@
+Adjust build flags. Proted from 1.1.6.
+
+Patch by Marius Brehler.
+--- Makefile
++++ Makefile
+@@ -6,7 +6,7 @@ AR=ar
+ INSTALL=install
+
+ # compiler settings
+-cflags = -O2 -std=c99 -pedantic -Wall -fpic -DUTF8PROC_EXPORTS $(CFLAGS)
++cflags = -std=c99 -pedantic -fpic -DUTF8PROC_EXPORTS $(CFLAGS)
+ cc = $(CC) $(cflags)
+
+ # shared-library version MAJOR.MINOR.PATCH ... this may be *different*
diff --git a/dev-libs/utf8proc/utf8proc-1.2.ebuild b/dev-libs/utf8proc/utf8proc-1.2.ebuild
new file mode 100644
index 000000000..349806f39
--- /dev/null
+++ b/dev-libs/utf8proc/utf8proc-1.2.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="library for processing UTF-8 encoded Unicode strings"
+HOMEPAGE="http://www.public-software-group.org/utf8proc"
+SRC_URI="https://github.com/JuliaLang/${PN}/archive/v1.2.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="static-libs"
+
+src_prepare() {
+ epatch "${FILESDIR}"/"${P}"-buildflags.patch
+}
+
+src_compile() {
+ emake libutf8proc.so
+ use static-libs & emake libutf8proc.a
+}
+
+src_install() {
+ doheader utf8proc.h
+ dolib.so libutf8proc.so
+ use static-libs && dolib.a libutf8proc.a
+}
diff --git a/media-gfx/brlcad/ChangeLog b/media-gfx/brlcad/ChangeLog
index 98759c562..584b0bb1a 100644
--- a/media-gfx/brlcad/ChangeLog
+++ b/media-gfx/brlcad/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/media-gfx/brlcad/ChangeLog,v 1.3 2011/04/18 22:47:37 dilfridge Exp $
+ 21 May 2015; Dongxu Li <dongxuli2011@gmail.com>
+ brlcad-7.24.2.ebuild, brlcad-9999.ebuild:
+ Fixed deps tcl/tk slots
+
28 April 2015; Dongxu Li <dongxuli2011@gmail.com>
brlcad-7.24.2.ebuild, brlcad-9999.ebuild:
Fixed a deps issue
diff --git a/media-gfx/brlcad/brlcad-7.24.2.ebuild b/media-gfx/brlcad/brlcad-7.24.2.ebuild
index 23ac7c059..86477a34c 100644
--- a/media-gfx/brlcad/brlcad-7.24.2.ebuild
+++ b/media-gfx/brlcad/brlcad-7.24.2.ebuild
@@ -25,8 +25,8 @@ DEPEND="${RDEPEND}
sys-devel/bison
sys-devel/flex
media-libs/libpng:0
- <dev-lang/tcl-8.6:0
- <dev-lang/tk-8.6:0
+ <dev-lang/tcl-8.6:0/8.5
+ <dev-lang/tk-8.6:0/8.5
dev-tcltk/tktable
sys-libs/zlib
sys-libs/libtermcap-compat
diff --git a/media-gfx/brlcad/brlcad-9999.ebuild b/media-gfx/brlcad/brlcad-9999.ebuild
index 5b5a2a3b3..fb891d8f2 100644
--- a/media-gfx/brlcad/brlcad-9999.ebuild
+++ b/media-gfx/brlcad/brlcad-9999.ebuild
@@ -25,8 +25,8 @@ DEPEND="${RDEPEND}
sys-devel/bison
sys-devel/flex
media-libs/libpng:0
- <dev-lang/tcl-8.6:0
- <dev-lang/tk-8.6:0
+ <dev-lang/tcl-8.6:0/8.5
+ <dev-lang/tk-8.6:0/8.5
dev-tcltk/tktable
sys-libs/zlib
sys-libs/libtermcap-compat
diff --git a/sci-biology/breakdancer/ChangeLog b/sci-biology/breakdancer/ChangeLog
index 2dfc56969..d577653b8 100644
--- a/sci-biology/breakdancer/ChangeLog
+++ b/sci-biology/breakdancer/ChangeLog
@@ -1,7 +1,21 @@
# ChangeLog for sci-biology/breakdancer
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ breakdancer-9999.ebuild:
+ sci-biology/breakdancer: added inherit cmake
+
+ 18 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ breakdancer-9999.ebuild:
+ sci-biology/breakdancer: update homepage
+
+*breakdancer-9999 (18 May 2015)
+
+ 18 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +breakdancer-9999.ebuild, -Manifest, -breakdancer-1.1.2.ebuild:
+ sci-biology/breakdancer: upstream moved to github
+
*breakdancer-1.1.2 (23 Mar 2014)
23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/breakdancer/Manifest b/sci-biology/breakdancer/Manifest
deleted file mode 100644
index 980727e37..000000000
--- a/sci-biology/breakdancer/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST breakdancer-1.1.2_2013_03_08.zip 43732 SHA256 09c66c4d64735e89d893581a10804c66ac43f7bd7b07253bbd10efbe42db9cf2 SHA512 5f5e8ae097217f33a72a8977c5abb1e392800311623e25f126d5d96423f76d03a3fc8afe78b5f13560d125fe4bec7999e81da4b2a1cef5db218b7e40385b1e65 WHIRLPOOL 6b25ea4c63fdcd73707e410ca041731e6caa08fce39115306bc3107d4329e80353d9d5795b47575cd10f11747965193486f54348dc7eea4df7f1393010c4369b
diff --git a/sci-biology/breakdancer/breakdancer-1.1.2.ebuild b/sci-biology/breakdancer/breakdancer-1.1.2.ebuild
deleted file mode 100644
index 6aff8687d..000000000
--- a/sci-biology/breakdancer/breakdancer-1.1.2.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-DESCRIPTION="Genome-wide detection of structural variants from next generation paired-end sequencing reads"
-HOMEPAGE="http://breakdancer.sourceforge.net"
-SRC_URI="http://sourceforge.net/projects/breakdancer/files/breakdancer-1.1.2_2013_03_08.zip"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-lang/perl
- dev-perl/Statistics-Descriptive
- dev-perl/Math-CDF
- sci-biology/samtools"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/breakdancer/breakdancer-9999.ebuild b/sci-biology/breakdancer/breakdancer-9999.ebuild
new file mode 100644
index 000000000..c0599b3bb
--- /dev/null
+++ b/sci-biology/breakdancer/breakdancer-9999.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit cmake-utils
+
+[ "$PV" == "9999" ] && inherit git-r3
+
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module eutils toolchain-funcs
+
+DESCRIPTION="Genome-wide detection of structural variants from next generation paired-end sequencing reads"
+HOMEPAGE="http://gmt.genome.wustl.edu/packages/breakdancer"
+if [ "$PV" == "9999" ]; then
+ EGIT_REPO_URI="https://github.com/genome/breakdancer.git"
+ KEYWORDS=""
+else
+ # TODO: fish out 1.3.6 version from github
+ SRC_URI="http://sourceforge.net/projects/breakdancer/files/breakdancer-1.1.2_2013_03_08.zip"
+ KEYWORDS=""
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+# http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm
+DEPEND="dev-lang/perl
+ dev-perl/Statistics-Descriptive
+ sci-biology/samtools"
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/kallisto/ChangeLog b/sci-biology/kallisto/ChangeLog
new file mode 100644
index 000000000..6b15b362c
--- /dev/null
+++ b/sci-biology/kallisto/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/kallisto
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*kallisto-0.42.1 (21 May 2015)
+*kallisto-9999 (21 May 2015)
+
+ 21 May 2015; Michael Schubert <mschu.dev@gmail.com> +kallisto-0.42.1.ebuild,
+ +kallisto-9999.ebuild, +metadata.xml:
+ sci-biology/kallisto: add kallisto
diff --git a/sci-biology/kallisto/Manifest b/sci-biology/kallisto/Manifest
new file mode 100644
index 000000000..9994a955e
--- /dev/null
+++ b/sci-biology/kallisto/Manifest
@@ -0,0 +1 @@
+DIST kallisto-0.42.1.tar.gz 1047963 SHA256 e620623fe36ee183cf7e1245aba8e0b7490f530c2b68c81d6e8f0c21e2c97381 SHA512 bcfec13ac9c281610486f128a72b112616823d007cccf170f1e5846f1bd206759d5b3e94c5bc26f66e458f20b04fc4ed68d0bda6a46a23636bd61483e28c21e7 WHIRLPOOL 6b2b3cc50b24534ce4e6845447f619a2b06f0d5da608f202092ef9463c6be7e7f2f812a131e6475cd5918af96034cce1613b8b74151abebb411cab0e84543cfd
diff --git a/sci-biology/kallisto/kallisto-0.42.1.ebuild b/sci-biology/kallisto/kallisto-0.42.1.ebuild
new file mode 100644
index 000000000..dfc4eafb5
--- /dev/null
+++ b/sci-biology/kallisto/kallisto-0.42.1.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit cmake-utils
+
+DESCRIPTION="Near-optimal RNA-Seq quantification"
+HOMEPAGE="http://pachterlab.github.io/kallisto/"
+SRC_URI="https://github.com/pachterlab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="all-rights-reserved"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND="sci-libs/hdf5"
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/kallisto/kallisto-9999.ebuild b/sci-biology/kallisto/kallisto-9999.ebuild
new file mode 100644
index 000000000..cc5b26957
--- /dev/null
+++ b/sci-biology/kallisto/kallisto-9999.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit git-r3 cmake-utils
+
+DESCRIPTION="Near-optimal RNA-Seq quantification"
+HOMEPAGE="http://pachterlab.github.io/kallisto/"
+SRC_URI=""
+EGIT_REPO_URI="https://github.com/pachterlab/kallisto.git"
+
+LICENSE="all-rights-reserved"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND="sci-libs/hdf5"
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/kallisto/metadata.xml b/sci-biology/kallisto/metadata.xml
new file mode 100644
index 000000000..b7551a6aa
--- /dev/null
+++ b/sci-biology/kallisto/metadata.xml
@@ -0,0 +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>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-libs/amdlibm/amdlibm-3.1.ebuild b/sci-libs/amdlibm/amdlibm-3.1.ebuild
index 4b8d041c4..5d62ae37b 100644
--- a/sci-libs/amdlibm/amdlibm-3.1.ebuild
+++ b/sci-libs/amdlibm/amdlibm-3.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -48,7 +48,7 @@ src_prepare() {
}
src_test() {
- cd examples
+ cd examples || die
sh build_and_run.sh || die
}
diff --git a/sci-libs/arrayfire/ChangeLog b/sci-libs/arrayfire/ChangeLog
index 0ba626039..61231847c 100644
--- a/sci-libs/arrayfire/ChangeLog
+++ b/sci-libs/arrayfire/ChangeLog
@@ -1,6 +1,15 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 23 May 2015; Marius Brehler <marbre@linux.sungazer.de>
+ +files/FindBoostCompute.cmake,
+ +files/arrayfire-3.0_beta-FindBoostCompute.patch,
+ +files/arrayfire-3.0_beta-FindCBLAS.patch,
+ +files/arrayfire-3.0_beta-opencl_CMakeLists.patch,
+ +files/arrayfire-9999-FindCBLAS.patch, -files/FindBoostCompute.patch,
+ -files/FindCBLAS.patch, -files/opencl_CMakeLists.patch, arrayfire-9999.ebuild:
+ Split up ebuilds to fix 9999
+
24 Mar 2015; Marius Brehler <marbre@linux.sungazer.de>
-files/arrayfire-0.9999-build_gtest.patch:
Drop patch, fixed upstream
diff --git a/sci-libs/arrayfire/arrayfire-9999.ebuild b/sci-libs/arrayfire/arrayfire-9999.ebuild
index dda442eb6..b976a150b 100644
--- a/sci-libs/arrayfire/arrayfire-9999.ebuild
+++ b/sci-libs/arrayfire/arrayfire-9999.ebuild
@@ -13,13 +13,6 @@ HOMEPAGE="http://www.arrayfire.com/"
EGIT_REPO_URI="https://github.com/${PN}/${PN}.git git://github.com/${PN}/${PN}.git"
SRC_URI="test? ( https://googletest.googlecode.com/files/gtest-${GTEST_PV}.zip )"
KEYWORDS=""
-if [[ ${PV} == "0.9999" ]] ; then
- # the remote HEAD points to devel, but we want to pull the master instead
- EGIT_BRANCH="master"
-elif [[ ${PV} == "3.0_beta" ]] ; then
- EGIT_COMMIT="v3.0beta"
- KEYWORDS="~amd64"
-fi
LICENSE="BSD"
SLOT="0"
@@ -34,6 +27,7 @@ RDEPEND="
cpu? (
virtual/blas
virtual/cblas
+ virtual/lapacke
sci-libs/fftw:3.0
)
opencl? (
@@ -48,9 +42,7 @@ BUILD_DIR="${S}/build"
CMAKE_BUILD_TYPE=Release
PATCHES=(
- "${FILESDIR}"/FindCBLAS.patch
- "${FILESDIR}"/FindBoostCompute.patch
- "${FILESDIR}"/opencl_CMakeLists.patch
+ "${FILESDIR}"/${P}-FindCBLAS.patch
)
# We need write acccess /dev/nvidiactl, /dev/nvidia0 and /dev/nvidia-uvm and the portage
@@ -74,6 +66,9 @@ src_unpack() {
unpack ${A}
mv "${BUILD_DIR}"/third_party/src/gtest-"${GTEST_PV}" "${BUILD_DIR}"/third_party/src/googletest || die
fi
+
+ rm "${S}"/CMakeModules/build_boost_compute.cmake || die
+ cp "${FILESDIR}"/FindBoostCompute.cmake "${S}"/CMakeModules/ || die
}
src_configure() {
diff --git a/sci-libs/arrayfire/files/FindBoostCompute.cmake b/sci-libs/arrayfire/files/FindBoostCompute.cmake
new file mode 100644
index 000000000..d98ea4b67
--- /dev/null
+++ b/sci-libs/arrayfire/files/FindBoostCompute.cmake
@@ -0,0 +1,18 @@
+# Downloads and builds the Boost Compute library from github.com
+# Defines the following variables
+# * BoostCompute_FOUND Flag for Boost Compute
+# * BoostCompute_INCLUDE_DIR Location of the Boost Compute headers
+
+
+set(BoostCompute_INCLUDE_DIR "/usr/include/compute")
+SET( BoostCompute_FOUND ON CACHE BOOL "BoostCompute Found" )
+
+
+IF(NOT BoostCompute_FOUND)
+ MESSAGE(FATAL_ERROR, "Boost.Compute not found! Clone Boost.Compute from https://github.com/kylelutz/compute.git")
+ENDIF(NOT BoostCompute_FOUND)
+
+MARK_AS_ADVANCED(
+ BoostCompute_FOUND
+ BoostCompute_INCLUDE_DIR
+ )
diff --git a/sci-libs/arrayfire/files/FindBoostCompute.patch b/sci-libs/arrayfire/files/arrayfire-3.0_beta-FindBoostCompute.patch
index 3052df20d..3052df20d 100644
--- a/sci-libs/arrayfire/files/FindBoostCompute.patch
+++ b/sci-libs/arrayfire/files/arrayfire-3.0_beta-FindBoostCompute.patch
diff --git a/sci-libs/arrayfire/files/FindCBLAS.patch b/sci-libs/arrayfire/files/arrayfire-3.0_beta-FindCBLAS.patch
index 263c62aaf..263c62aaf 100644
--- a/sci-libs/arrayfire/files/FindCBLAS.patch
+++ b/sci-libs/arrayfire/files/arrayfire-3.0_beta-FindCBLAS.patch
diff --git a/sci-libs/arrayfire/files/opencl_CMakeLists.patch b/sci-libs/arrayfire/files/arrayfire-3.0_beta-opencl_CMakeLists.patch
index 7279afaa6..7279afaa6 100644
--- a/sci-libs/arrayfire/files/opencl_CMakeLists.patch
+++ b/sci-libs/arrayfire/files/arrayfire-3.0_beta-opencl_CMakeLists.patch
diff --git a/sci-libs/arrayfire/files/arrayfire-9999-FindCBLAS.patch b/sci-libs/arrayfire/files/arrayfire-9999-FindCBLAS.patch
new file mode 100644
index 000000000..7f757e8a2
--- /dev/null
+++ b/sci-libs/arrayfire/files/arrayfire-9999-FindCBLAS.patch
@@ -0,0 +1,52 @@
+Use pkg-config to find cblas.
+
+Patch by Marius Brehler.
+
+--- CMakeModules/FindCBLAS.cmake 2015-05-23 17:12:41.000000000 +0200
++++ CMakeModules/FindCBLAS.cmake.new 2015-05-23 17:13:51.000000000 +0200
+@@ -1,3 +1,9 @@
++#
++# Version modified for Gentoo Linux
++# If a valid PkgConfig configuration for cblas is found, this overrides and cancels
++# all further checks.
++#
++
+ # Using FindCBLAS.cmake from the following repo
+ # https://github.com/clementfarabet/THC/blob/master/COPYRIGHT.txt
+
+@@ -21,6 +27,29 @@ SET(CBLAS_INCLUDE_DIR CACHE STRING
+ SET(CBLAS_INCLUDE_FILE CACHE STRING
+ "CBLAS header name")
+
++
++#
++# first, try PkgConfig
++#
++find_package(PkgConfig REQUIRED)
++pkg_check_modules(PC_CBLAS cblas)
++if(PC_CBLAS_FOUND)
++ foreach(PC_LIB ${PC_CBLAS_LIBRARIES})
++ find_library(${PC_LIB}_LIBRARY NAMES ${PC_LIB} HINTS ${PC_CBLAS_LIBRARY_DIRS} )
++ if (NOT ${PC_LIB}_LIBRARY)
++ message(FATAL_ERROR "Something is wrong in your pkg-config file - lib ${PC_LIB} not found in ${PC_CBLAS_LIBRARY_DIRS}")
++ endif (NOT ${PC_LIB}_LIBRARY)
++ list(APPEND CBLAS_LIBRARIES ${${PC_LIB}_LIBRARY})
++ endforeach(PC_LIB)
++ find_package_handle_standard_args(CBLAS DEFAULT_MSG CBLAS_LIBRARIES)
++ mark_as_advanced(CBLAS_LIBRARIES)
++else(PC_CBLAS_FOUND)
++message(STATUS "No PkgConfig configuration for CBLAS found; starting more extensive search.")
++
++
++
++
++
+ SET(INTEL_MKL_ROOT_DIR CACHE STRING
+ "Root directory of the Intel MKL")
+
+@@ -277,3 +306,5 @@ IF(NOT CBLAS_FIND_QUIETLY)
+ MESSAGE(STATUS "CBLAS library not found.")
+ ENDIF()
+ ENDIF(NOT CBLAS_FIND_QUIETLY)
++
++endif(PC_CBLAS_FOUND)
diff --git a/sci-libs/calculix-ccx/calculix-ccx-2.7-r1.ebuild b/sci-libs/calculix-ccx/calculix-ccx-2.7-r1.ebuild
index a511dc9a0..5dc1f0073 100644
--- a/sci-libs/calculix-ccx/calculix-ccx-2.7-r1.ebuild
+++ b/sci-libs/calculix-ccx/calculix-ccx-2.7-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -59,7 +59,7 @@ src_install () {
dosym ${MY_P} /usr/bin/ccx
if use doc; then
- cd "${S}/../doc"
+ cd "${S}/../doc" || die
ps2pdf ${MY_P}.ps ${MY_P}.pdf
dodoc ${MY_P}.pdf
fi
diff --git a/sci-libs/ccif/ChangeLog b/sci-libs/ccif/ChangeLog
index 09ecdb00d..15efc4d8f 100644
--- a/sci-libs/ccif/ChangeLog
+++ b/sci-libs/ccif/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-libs/ccif
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 23 May 2015; Marius Brehler <marbre@linux.sungazer.de>
+ ccif-0.3.20111209.ebuild:
+ Bump to EAPI=5
+
24 Jan 2012; Justin Lecher <jlec@gentoo.org> ccif-0.3.20111209.ebuild:
Dropped DOCS as it is handled by default
@@ -13,4 +17,3 @@
04 Jan 2012; Justin Lecher <jlec@gentoo.org> +ccif-0.3.20111209.ebuild,
+metadata.xml:
Initial commit
-
diff --git a/sci-libs/ccif/ccif-0.3.20111209.ebuild b/sci-libs/ccif/ccif-0.3.20111209.ebuild
index 792067ee8..b4e066a34 100644
--- a/sci-libs/ccif/ccif-0.3.20111209.ebuild
+++ b/sci-libs/ccif/ccif-0.3.20111209.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
inherit autotools-utils fortran-2
diff --git a/sci-libs/geom/ChangeLog b/sci-libs/geom/ChangeLog
index bef4c80d9..d488d7f8e 100644
--- a/sci-libs/geom/ChangeLog
+++ b/sci-libs/geom/ChangeLog
@@ -1,10 +1,12 @@
# ChangeLog for sci-libs/geom
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 23 May 2015; Marius Brehler <marbre@linux.sungazer.de> geom-5.1.2.7.ebuild:
+ Bump to EAPI=5
+
*geom-5.1.2.7 (09 Mar 2011)
09 Mar 2011; Oliver Borm (boroli) <oli.borm@web.de> +geom-5.1.2.7.ebuild,
+metadata.xml:
sci-libs/geom: New ebuild from bug 358061
-
diff --git a/sci-libs/geom/Manifest b/sci-libs/geom/Manifest
index ed41324cf..557594be2 100644
--- a/sci-libs/geom/Manifest
+++ b/sci-libs/geom/Manifest
@@ -1 +1 @@
-DIST geom-5.1.2.7.tar.gz 612914 SHA256 c0685d82535db3899d9321d72237b5d1be2dbafd1c85f990f767d5cd88571055
+DIST geom-5.1.2.7.tar.gz 612914 SHA256 c0685d82535db3899d9321d72237b5d1be2dbafd1c85f990f767d5cd88571055 SHA512 06454a4a92959fa08f2e81d8e5fcfdb957a49cdf51bd5e7efd6895ab2d1aedbd99dfb30ddc4b278b10d125f9d2d66260eff584e670716c96e2d0ec10b169fb08 WHIRLPOOL 0d9d11efe518c98788e921336552435639eb3bd8f53e39381babc1baaa3c609c37c9aa21e320a3342fbe03472f557e32f94e8fd8658e8b1017d99672ee618fc3
diff --git a/sci-libs/geom/geom-5.1.2.7.ebuild b/sci-libs/geom/geom-5.1.2.7.ebuild
index 5ad13c7a9..98331d566 100644
--- a/sci-libs/geom/geom-5.1.2.7.ebuild
+++ b/sci-libs/geom/geom-5.1.2.7.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=3
+EAPI=5
inherit autotools eutils
@@ -27,14 +27,14 @@ src_prepare() {
}
src_compile() {
- emake || die 'emake failed'
+ default
if use doc ; then
- cd ../../doc/src
+ cd ../../doc/src || die
doxygen || die 'doxygen failed'
fi
}
src_install() {
- emake DESTDIR="${D}" install || die "emake install failed!"
+ default
use doc && dohtml -r ../../doc/html/*
}