Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/arrayfire: Improve and clean gtest src handling
  sci-libs/arrayfire: Fix DEPEND, unpacker is used instead of unzip
  sci-biology/rnaplex: Fixes according to jlec's advices
  sci-biology/codonw: Drop unnecessary dies
  Drop unnecessary die
  ci-biology/rnaplex: Move to EAPI=5; Update homepage and SRC_URI.
  sci-biology/codonw: Move to EAPI=5

6 files changed, 28 insertions, 25 deletions

diff --git a/sci-biology/codonw/ChangeLog b/sci-biology/codonw/ChangeLog
index d2f9cc3d5..00b6629e0 100644
--- a/sci-biology/codonw/ChangeLog
+++ b/sci-biology/codonw/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/codonw
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  10 Jan 2015; Marius Brehler <marbre@linux.sungazer.de>
+  condow-1.4.4-r1.ebuild:
+  Move to EAPI=5.
+
 *codonw-1.4.4-r1 (08 Nov 2010)
 
   08 Nov 2010; Kacper Kowalik <xarthisius@gentoo.org> -codonw-1.4.4.ebuild,
diff --git a/sci-biology/codonw/codonw-1.4.4-r1.ebuild b/sci-biology/codonw/codonw-1.4.4-r1.ebuild
index f7f48e13b..85c0c5e9e 100644
--- a/sci-biology/codonw/codonw-1.4.4-r1.ebuild
+++ b/sci-biology/codonw/codonw-1.4.4-r1.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=2
+EAPI=5
 
 inherit toolchain-funcs versionator
 
@@ -26,14 +26,14 @@ src_prepare() {
 }
 
 src_compile() {
-	emake CC="$(tc-getCC)" CFLAGS="${CFLAGS}" || die
+	emake CC="$(tc-getCC)" CFLAGS="${CFLAGS}"
 }
 
 src_install() {
-	dobin codonw || die
+	dobin codonw
 	# woohoo watch out for collisions
 	for i in rscu cu aau raau tidy reader cutab cutot transl bases base3s dinuc cai fop gc3s gc cbi enc; do
-		dosym codonw /usr/bin/${i} || die
+		dosym codonw /usr/bin/${i}
 	done
-	dodoc *.txt || die
+	dodoc *.txt
 }
diff --git a/sci-biology/rnaplex/ChangeLog b/sci-biology/rnaplex/ChangeLog
index a960c4ffe..dbdac52b3 100644
--- a/sci-biology/rnaplex/ChangeLog
+++ b/sci-biology/rnaplex/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/rnaplex
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  10 Jan 2015; Marius Brehler <marbre@linux.sungazer.de>
+  rnaplex-0.2.ebuild:
+  Move to EAPI=5; Update homepage and SRC_URI; Cleanup.
+
   29 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
   New package, ebuild written by me
 
diff --git a/sci-biology/rnaplex/Manifest b/sci-biology/rnaplex/Manifest
index 3a17125fb..173cda438 100644
--- a/sci-biology/rnaplex/Manifest
+++ b/sci-biology/rnaplex/Manifest
@@ -1 +1 @@
-DIST RNAplex-0.2.tar.gz 581128 SHA256 7907873009c8fc03b1918400bb82122774bc5df2602adc1426c5686a0b3f37de
+DIST RNAplex-0.2.tar.gz 579904 SHA256 a30ab9128e4b35795f5e6f1e32a8a66b6fe3de1b6395a4326081cc6bec99cebb SHA512 ef91dd869284ad492b627b84288fe3c56a7c8d44dec8d2a48668efa4e476c9e7856380bc1e199604db4fa53f4d9bfe38cf057f2e181bf1b24ad375e5691a0a2e WHIRLPOOL bbba8f625373a5f0ae791c0e3239fb188764607635b79fe41ad364f71e34ed3fb018ba7aa629584cfa995b68e7c3bcf3ea67862e14686fec023de256b65ce423
diff --git a/sci-biology/rnaplex/rnaplex-0.2.ebuild b/sci-biology/rnaplex/rnaplex-0.2.ebuild
index f2a91990c..d9e693b85 100644
--- a/sci-biology/rnaplex/rnaplex-0.2.ebuild
+++ b/sci-biology/rnaplex/rnaplex-0.2.ebuild
@@ -1,24 +1,18 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=2
+EAPI=5
 
 MY_P=RNAplex-${PV}
 
 DESCRIPTION="RNA-RNA interaction search"
-HOMEPAGE="http://www.tbi.univie.ac.at/~htafer/"
-SRC_URI="http://www.tbi.univie.ac.at/~htafer/RNAplex/${MY_P}.tar.gz"
+HOMEPAGE="http://www.bioinf.uni-leipzig.de/Software/RNAplex/"
+SRC_URI="http://www.bioinf.uni-leipzig.de/Software/RNAplex/${MY_P}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
 IUSE=""
 KEYWORDS="~amd64 ~x86"
 
-DEPEND=""
-RDEPEND=""
 S=${WORKDIR}/${MY_P}
-
-src_install() {
-	emake DESTDIR="${D}" install || die "install failed"
-}
diff --git a/sci-libs/arrayfire/arrayfire-9999.ebuild b/sci-libs/arrayfire/arrayfire-9999.ebuild
index a1af26b91..107af240e 100644
--- a/sci-libs/arrayfire/arrayfire-9999.ebuild
+++ b/sci-libs/arrayfire/arrayfire-9999.ebuild
@@ -4,12 +4,14 @@
 
 EAPI=5
 
-inherit cmake-utils git-r3 unpacker
+inherit cmake-utils git-r3
+
+GTEST_PV="1.7.0"
 
 DESCRIPTION="A general purpose GPU library."
 HOMEPAGE="http://www.arrayfire.com/"
 EGIT_REPO_URI="https://github.com/arrayfire/arrayfire.git"
-SRC_URI="test? ( https://googletest.googlecode.com/files/gtest-1.7.0.zip )"
+SRC_URI="test? ( https://googletest.googlecode.com/files/gtest-${GTEST_PV}.zip )"
 KEYWORDS="~amd64"
 
 LICENSE="BSD"
@@ -22,8 +24,7 @@ RDEPEND="
 	virtual/cblas
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-6.0 )
 	sci-libs/fftw:3.0"
-DEPEND="${RDEPEND}
-	test? ( app-arch/unzip )"
+DEPEND="${RDEPEND}"
 
 BUILD_DIR="${S}/build"
 CMAKE_BUILD_TYPE=Release
@@ -52,8 +53,8 @@ src_unpack() {
 	if use test; then
 		mkdir -p "${BUILD_DIR}"/third_party/src/ || die
 		cd "${BUILD_DIR}"/third_party/src/ || die
-		unpack_zip "${DISTDIR}/"gtest-1.7.0.zip
-		mv "${BUILD_DIR}"/third_party/src/gtest-1.7.0 "${BUILD_DIR}"/third_party/src/googletest || die
+		unpack ${A}
+		mv "${BUILD_DIR}"/third_party/src/gtest-"${GTEST_PV}" "${BUILD_DIR}"/third_party/src/googletest || die
 	fi
 }