Merge branch 'master' into librecad

Conflicts:
	media-gfx/librecad/ChangeLog

24 files changed, 195 insertions, 18 deletions

diff --git a/media-gfx/librecad/ChangeLog b/media-gfx/librecad/ChangeLog
index 7b80bf43f..e719749de 100644
--- a/media-gfx/librecad/ChangeLog
+++ b/media-gfx/librecad/ChangeLog
@@ -6,6 +6,9 @@
   librecad-1.0.3.ebuild, librecad-1.0.4.ebuild:
   Move to EAPI=5
 
+  15 Jan 2015; Dongxu Li <dongxuli2011@gmail.com> +librecad-2.0.7.ebuild, -librecad-2.0.3.ebuild:
+  Version bump: 2.0.7
+
   19 Sep 2014; Dongxu Li <dongxuli2011@gmail.com> : librecad-9999.ebuild:
   install appdata.xml
 
diff --git a/media-gfx/librecad/Manifest b/media-gfx/librecad/Manifest
index 8e26254db..2cef675a6 100644
--- a/media-gfx/librecad/Manifest
+++ b/media-gfx/librecad/Manifest
@@ -1,3 +1,3 @@
 DIST librecad-1.0.3.tar.gz 4578450 SHA256 8c2f5a7e55a4ae41a9bd47e2e7981577c740edd526e1f305cd6cbf581d053f30 SHA512 5a8e6e612bc954f3af0dfc26d1fc19938c80e216ac252fb65a38a13651c6e2313d593a3ee834ecc98bbd72a4dfd28ef1c39dd9ed6a6f9140d28b765edb59bee9 WHIRLPOOL d8157af2021bba2cee626d023125045455a2fe5f453ae065c9660be61f4c0d687a1c72957d1af1aa640cfde3815625bb7d0899dc5541fcb82bfe0eea4cfad6c6
 DIST librecad-1.0.4.tar.gz 4578450 SHA256 8c2f5a7e55a4ae41a9bd47e2e7981577c740edd526e1f305cd6cbf581d053f30 SHA512 5a8e6e612bc954f3af0dfc26d1fc19938c80e216ac252fb65a38a13651c6e2313d593a3ee834ecc98bbd72a4dfd28ef1c39dd9ed6a6f9140d28b765edb59bee9 WHIRLPOOL d8157af2021bba2cee626d023125045455a2fe5f453ae065c9660be61f4c0d687a1c72957d1af1aa640cfde3815625bb7d0899dc5541fcb82bfe0eea4cfad6c6
-DIST librecad-2.0.3.zip 16590256 SHA256 4221348541c46c6e9698c1fa3471a14a81376e022a009a164a7f0d0035da4643 SHA512 c40952ae967d83197645bef65dac6e050ddeacf536401b2b99cd18d753462af086ac2a410c6746a92c094ad76fd9177a900c21531ed7b7fcdf1e4b0f7f070e00 WHIRLPOOL c2e1d33b17b7a47ffd9b3795ad292b22cb1225aceacf052494745243630b0537e21701930b9433ea235c462d65581efc2b5ccda3b37712d4ab639ab9bcc6a97d
+DIST librecad-2.0.7.zip 17457197 SHA256 b0e031bca4f00730076606e830d0d559824d0000f8a3e5c1918c4f0b6e507b71 SHA512 432622c9f7d1d006172ec964fc8bb338e5019a70ecd0e6c3d524bf1458febe35a7cb929cc9323df61275247582cb86c6111d4c03e7255da90ffd14a15734abe6 WHIRLPOOL 605937f8028f28d5a94226372f59df2b5975a2c1245303c2fd7b3089babdc4cb230290a96ba283de7230e6c98dccb91b3c9d7f1cdbf6649bef5a8d5cd8f2a140
diff --git a/media-gfx/librecad/librecad-2.0.3.ebuild b/media-gfx/librecad/librecad-2.0.7.ebuild
index 7017bccb8..1700aa8ba 100644
--- a/media-gfx/librecad/librecad-2.0.3.ebuild
+++ b/media-gfx/librecad/librecad-2.0.7.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
diff --git a/sci-biology/bcftools/ChangeLog b/sci-biology/bcftools/ChangeLog
index 4e0a781f2..fc2086f24 100644
--- a/sci-biology/bcftools/ChangeLog
+++ b/sci-biology/bcftools/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  15 Jan 2015; Christoph Junghans <ottxor@gentoo.org> bcftools-1.1.ebuild:
+  fixed license
+
 *bcftools-1.1 (14 Jan 2015)
 
   14 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/bcftools/bcftools-1.1.ebuild b/sci-biology/bcftools/bcftools-1.1.ebuild
index e3f446fe1..73032781c 100644
--- a/sci-biology/bcftools/bcftools-1.1.ebuild
+++ b/sci-biology/bcftools/bcftools-1.1.ebuild
@@ -8,7 +8,7 @@ DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
 HOMEPAGE="http://www.htslib.org/bcftools_release_notes"
 SRC_URI="http://sourceforge.net/projects/samtools/files/samtools/1.1/bcftools-1.1.tar.bz2"
 
-LICENSE="MIT-GRL"
+LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""
diff --git a/sci-biology/edena/ChangeLog b/sci-biology/edena/ChangeLog
new file mode 100644
index 000000000..a3f0909cc
--- /dev/null
+++ b/sci-biology/edena/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/edena
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*edena-3.131028 (15 Jan 2015)
+
+  15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +edena-3.131028.ebuild, +metadata.xml:
+  sci-biology/edena: new package
diff --git a/sci-biology/edena/Manifest b/sci-biology/edena/Manifest
new file mode 100644
index 000000000..cbe128f7c
--- /dev/null
+++ b/sci-biology/edena/Manifest
@@ -0,0 +1 @@
+DIST EdenaV3.131028.tar.gz 497784 SHA256 4037fce486c9725107b1690fbc67731713eef54e3fa53081865904c783533230 SHA512 853a5eb0afe507ba7b967075795593df147ad87c7d45be30eac6b24054ec365d7db39c9cd20bb414478a629c98c82bf0621c007c22a447949ee3f749907cae58 WHIRLPOOL 409bdb1e2f4f344198bff0af50e78afd75fffa10b4c252316a61f0c55e49bb4bdb514ed2414343056d31783e27d8ae800f7e33495cbc8f6c61ec57c5c5d974d8
diff --git a/sci-biology/edena/edena-3.131028.ebuild b/sci-biology/edena/edena-3.131028.ebuild
new file mode 100644
index 000000000..0c4fe10b3
--- /dev/null
+++ b/sci-biology/edena/edena-3.131028.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit toolchain-funcs
+
+DESCRIPTION="De novo short read assembler"
+HOMEPAGE="http://www.genomic.ch/edena.php"
+SRC_URI="http://www.genomic.ch/edena/EdenaV"${PV}".tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/EdenaV"${PV}"
+
+src_prepare(){
+	sed -e "s@^CCC.*@CCC = $(tc-getCXX)@" -e "s@^CFLAGS.*@CFLAGS = ${CFLAGS} -pthread@" -i src/Makefile || die
+}
+
+src_compile(){
+	cd src
+	emake
+}
+
+src_install(){
+	dobin src/edena
+	dodoc referenceManual.pdf
+}
diff --git a/sci-biology/edena/metadata.xml b/sci-biology/edena/metadata.xml
new file mode 100644
index 000000000..2bc893037
--- /dev/null
+++ b/sci-biology/edena/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>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/mosaik/ChangeLog b/sci-biology/mosaik/ChangeLog
index 87f4c4bbb..51160219f 100644
--- a/sci-biology/mosaik/ChangeLog
+++ b/sci-biology/mosaik/ChangeLog
@@ -1,7 +1,15 @@
 # ChangeLog for sci-biology/mosaik
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*mosaik-2.2.3 (15 Jan 2015)
+
+  15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +mosaik-2.2.3.ebuild, -mosaik-2.1.33.ebuild:
+   version bump, masking a crappy package until at least the Makefile's
+  propagate an error code back to upstream caller, https://code.google.com/p
+  /mosaik-aligner/issues/detail?id=135
+
   07 Jan 2014; Justin Lecher <jlec@gentoo.org> mosaik-2.1.33.ebuild,
   mosaik-9999.ebuild, metadata.xml:
   Readd ebuild
@@ -33,4 +41,3 @@
   Fastq.cpp:224, Fastq.cpp:226, Fasta.cpp:258, Fasta.cpp:260, Fasta.cpp:266,
   Fasta.cpp:268, but the package itself installs and executes at least
   mosaik-1.1.0021.ebuild
-
diff --git a/sci-biology/mosaik/Manifest b/sci-biology/mosaik/Manifest
index e7f7074d3..c378492e7 100644
--- a/sci-biology/mosaik/Manifest
+++ b/sci-biology/mosaik/Manifest
@@ -1,2 +1,2 @@
-DIST MOSAIK-2.1.33-source.tar 3911680 SHA256 210764cddbd8a3866976f065b912eb30fcd94d681901be93b42724708b86e2aa SHA512 9eeda8698bc929f95ff16b4e611174f631a5affb8712d582eda7e02a45f27ea8a50ffc56c6595f837af342f266a5bfe44ca1eb006d301caef671e01ed794ba20 WHIRLPOOL 89b65f5ff47dbce615f37e4ae2d3d207cde1482f3e9d4cb280cca55c399784eeb272d3af490327b3c1ac348f7d6bdc1305df67a726acea7b9e2502df02848136
+DIST MOSAIK-2.2.3-source.tar 3819520 SHA256 b2b291603949f179d5f0686045aaf48ab34ea47001bc1e0c573adf517e8b3b28 SHA512 d60a0559dced935f736ca105569593165474134985b1d32405c8f4537dc5da7a05d89ce3a10e4536e2b4f62f622055c327abddb3783c9331465061c5f866129f WHIRLPOOL a66221037900f64c15dc6f444ff19be5bb3496625d426515b5fb33c8b181d35ab69d6f383ce92912d4354c8b9acc1d23d68c544e38db056c0ef1314875dfadcf
 DIST Mosaik-1.0-Documentation.pdf 10589 SHA256 470e2a534668a2a8744df7b00b9b8af5a6966d2df70f0ab1a4b271bdddadae9c SHA512 b2febce1e85eea89e5ff5d9f1aae351c59574314f361b66503ec473da7641adc083e52ee739c04abfe5b074fd57271f2ca20bea215982ee3ecfce073bbfd7b38 WHIRLPOOL 764a984408590417345daf624cda3dfb5df4255f18efc8f8cfbfc61885ed14be9863eef886dacfe90562469cd6af50220c0a776653a429b888eedac86270dc06
diff --git a/sci-biology/mosaik/mosaik-2.1.33.ebuild b/sci-biology/mosaik/mosaik-2.2.3.ebuild
index bc26a056b..6bd994ba8 100644
--- a/sci-biology/mosaik/mosaik-2.1.33.ebuild
+++ b/sci-biology/mosaik/mosaik-2.2.3.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: $
 
@@ -13,10 +13,16 @@ SRC_URI="
 LICENSE="GPL-2 || ( MIT )"
 SLOT="0"
 IUSE=""
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
+
+# https://code.google.com/p/mosaik-aligner/issues/detail?id=135
 
 S="${WORKDIR}"/MOSAIK-${PV}-source
 
+src_prepare(){
+	sed -e "s@export LDFLAGS = -Wl@#export LDFLAGS = -Wl@" -i Makefile
+}
+
 src_install() {
 	dobin "${WORKDIR}"/bin/*
 
diff --git a/sci-biology/ncbi-blast+/ChangeLog b/sci-biology/ncbi-blast+/ChangeLog
index 819f1f40c..0e7a67d54 100644
--- a/sci-biology/ncbi-blast+/ChangeLog
+++ b/sci-biology/ncbi-blast+/ChangeLog
@@ -2,10 +2,12 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  15 Jan 2015; Christoph Junghans <ottxor@gentoo.org> metadata.xml:
+  added use flags to metadata.xml
+
 *ncbi-blast+-2.2.30 (14 Jan 2015)
 
   14 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   +ncbi-blast+-2.2.30.ebuild, +files/disable-testsuite-compilation.txt,
   +files/fix_lib_deps.patch, +metadata.xml:
   ebuild derived from ncbi-tools++-12.0.0.ebuild with a Debian patch
-
diff --git a/sci-biology/ncbi-blast+/metadata.xml b/sci-biology/ncbi-blast+/metadata.xml
index 2bc893037..feff0f132 100644
--- a/sci-biology/ncbi-blast+/metadata.xml
+++ b/sci-biology/ncbi-blast+/metadata.xml
@@ -6,4 +6,31 @@
     <email>mmokrejs@fold.natur.cuni.cz</email>
     <name>Martin Mokrejs</name>
   </maintainer>
+  <use>
+    <flag name="boost">Undocumented USE</flag>
+  </use>
+  <use>
+    <flag name="cppunit">Undocumented USE</flag>
+  </use>
+  <use>
+    <flag name="freetype">Undocumented USE</flag>
+  </use>
+  <use>
+    <flag name="mesa">Undocumented USE</flag>
+  </use>
+  <use>
+    <flag name="muparser">Undocumented USE</flag>
+  </use>
+  <use>
+    <flag name="sablotron">Undocumented USE</flag>
+  </use>
+  <use>
+    <flag name="xerces">Undocumented USE</flag>
+  </use>
+  <use>
+    <flag name="xalan">Undocumented USE</flag>
+  </use>
+  <use>
+    <flag name="xslt">Undocumented USE</flag>
+  </use>
 </pkgmetadata>
diff --git a/sci-biology/quast/ChangeLog b/sci-biology/quast/ChangeLog
index ccf3a0e68..e29320d4a 100644
--- a/sci-biology/quast/ChangeLog
+++ b/sci-biology/quast/ChangeLog
@@ -1,7 +1,16 @@
 # ChangeLog for sci-biology/quast
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> quast-2.3.ebuild:
+  added a note about additional bundled package licenses
+
+*quast-2.3 (15 Jan 2015)
+
+  15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +quast-2.3.ebuild,
+  -quast-2.2.ebuild:
+  version bump
+
   13 Nov 2014; Justin Lecher <jlec@gentoo.org> quast-2.2.ebuild, metadata.xml:
   Bump to new python eclasses
 
diff --git a/sci-biology/quast/Manifest b/sci-biology/quast/Manifest
index 9ddb43cb2..f89b3dc4e 100644
--- a/sci-biology/quast/Manifest
+++ b/sci-biology/quast/Manifest
@@ -1 +1 @@
-DIST quast-2.2.tar.gz 19814517 SHA256 c66cb9b063d82962bceb11762794fb2e5a57846c8a3aa93ca5f83951cf669d85 SHA512 e979b63f53c3909f804d733ae2cbfd0963fca3dc9194b2a04c8d7be53d253d087853520198a8261a5eba186369486f6e2f4d469814a2d8632072bd73d0e5b8bb WHIRLPOOL 76078a45e24a961acd6fafadf26d08daa79d0b65f224d1bfb87fd404532161c4b667a2873fcf1023e7156bc1c5273de48adb7bfcc5eee68bd3218d03db3aaaa2
+DIST quast-2.3.tar.gz 17631110 SHA256 efad099097e4d148b02e98892c5e93a2407c4debecb12860629142192be62b0d SHA512 eddece31d2ba51548f3e395f77a382d019ef282fb97c5ecfa18cf124c6a619bee760f238b046517a67b7ccbc5354ff36666d0f01cc75b098e9baee2dd3652f40 WHIRLPOOL 82520b21ba791918f05d75e7cc098e54628af1f73bb3735efcd86c2eb669029a28ef40756b7c4aa23e0cd6a547032428cfcb718bbcd9aa970e43e1aa89d4667c
diff --git a/sci-biology/quast/quast-2.2.ebuild b/sci-biology/quast/quast-2.3.ebuild
index 383914717..701f274f4 100644
--- a/sci-biology/quast/quast-2.2.ebuild
+++ b/sci-biology/quast/quast-2.3.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: $
 
@@ -12,7 +12,7 @@ DESCRIPTION="Compare quality of multiple genome assemblies to each other"
 HOMEPAGE="http://bioinf.spbau.ru/QUAST"
 SRC_URI="http://sourceforge.net/projects/quast/files/${P}.tar.gz"
 
-LICENSE="GPL-2"
+LICENSE="GPL-2" # and some other for the bundled copies, see http://quast.bioinf.spbau.ru/LICENSE
 SLOT="0"
 KEYWORDS=""
 IUSE=""
diff --git a/sci-biology/sabre/ChangeLog b/sci-biology/sabre/ChangeLog
new file mode 100644
index 000000000..f7f747fa1
--- /dev/null
+++ b/sci-biology/sabre/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/sabre
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*sabre-9999 (15 Jan 2015)
+
+  15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
+  +sabre-9999.ebuild:
+  sci-biology/sabre: new package
diff --git a/sci-biology/sabre/metadata.xml b/sci-biology/sabre/metadata.xml
new file mode 100644
index 000000000..2bc893037
--- /dev/null
+++ b/sci-biology/sabre/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>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/sabre/sabre-9999.ebuild b/sci-biology/sabre/sabre-9999.ebuild
new file mode 100644
index 000000000..2aee70121
--- /dev/null
+++ b/sci-biology/sabre/sabre-9999.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+[ "$PV" == "9999" ] && inherit git-2
+
+inherit toolchain-funcs
+
+DESCRIPTION="Barcode demultiplexing and trimming tool for Illumina FastQ files"
+HOMEPAGE="https://github.com/najoshi/sabre"
+if [ "$PV" == "9999" ]; then
+	EGIT_REPO_URI="https://github.com/najoshi/sabre.git"
+	KEYWORDS=""
+else
+	SRC_URI=""
+	KEYWORDS=""
+fi
+
+
+LICENSE="MIT" # almost verbatim
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sys-libs/zlib"
+RDEPEND="${DEPEND}"
+
+S="${S}"/src
+
+src_prepare(){
+	sed -e "s#OPT = -O3#OPT = ${CFLAGS}#" \
+		-e "s#CC = gcc#CC = $(tc-getCC)#" -i Makefile || die
+}
+
+src_install(){
+	dobin sabre
+}
diff --git a/sci-biology/sickle/ChangeLog b/sci-biology/sickle/ChangeLog
index bdbc7e730..443ff95fa 100644
--- a/sci-biology/sickle/ChangeLog
+++ b/sci-biology/sickle/ChangeLog
@@ -1,11 +1,13 @@
 # ChangeLog for sci-biology/sickle
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> sickle-9999.ebuild:
+  correct package description
+
 *sickle-9999 (24 Mar 2014)
 
   24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   +sickle-9999.ebuild, +metadata.xml:
   simple ebuild, bundled Makefile forces compile flags, program version, but
   works
-
diff --git a/sci-biology/sickle/sickle-9999.ebuild b/sci-biology/sickle/sickle-9999.ebuild
index d256d7313..022474e57 100644
--- a/sci-biology/sickle/sickle-9999.ebuild
+++ b/sci-biology/sickle/sickle-9999.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: $
 
@@ -6,7 +6,7 @@ EAPI=5
 
 inherit eutils git-r3
 
-DESCRIPTION="Windowed adaptive adaptor trimming tool for FASTQ data from Illumina/Solexa"
+DESCRIPTION="Windowed adaptive quality-based trimming tool for FASTQ data from Illumina/Solexa"
 HOMEPAGE="https://github.com/najoshi/sickle"
 EGIT_REPO_URI="https://github.com/najoshi/sickle"
 
diff --git a/sci-chemistry/nwchem/ChangeLog b/sci-chemistry/nwchem/ChangeLog
index 21a81b95b..153b2dc79 100644
--- a/sci-chemistry/nwchem/ChangeLog
+++ b/sci-chemistry/nwchem/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*nwchem-6.5_p26243-r5 (15 Jan 2015)
+
+  15 Jan 2015; Honza Macháček <Hloupy.Honza@centrum.cz>
+  -nwchem-6.5_p26243-r4.ebuild, +nwchem-6.5_p26243-r5.ebuild:
+  Added -lstdc++ to CUDA libraries, now CUDA support (used in TCE only)
+  compiles
+
 *nwchem-6.5_p26243-r4 (05 Jan 2015)
 
   05 Jan 2015; Honza Macháček <Hloupy.Honza@centrum.cz>
diff --git a/sci-chemistry/nwchem/nwchem-6.5_p26243-r4.ebuild b/sci-chemistry/nwchem/nwchem-6.5_p26243-r5.ebuild
index f740f4ae7..efbae8f65 100644
--- a/sci-chemistry/nwchem/nwchem-6.5_p26243-r4.ebuild
+++ b/sci-chemistry/nwchem/nwchem-6.5_p26243-r5.ebuild
@@ -196,7 +196,7 @@ src_compile() {
 		export CUDA=${CUDA_PATH}/bin/nvcc
 		export CUDA_FLAGS="-arch=compute_20 -code=sm_20,compute_20"
 		export CUDA_INCLUDE="-I${CUDA_PATH}/include"
-		export CUDA_LIBS="-L${CUDA_PATH}/$(get_libdir) -lcublas -lcufft -lcudart -lcuda"
+		export CUDA_LIBS="-L${CUDA_PATH}/$(get_libdir) -lcublas -lcufft -lcudart -lcuda -lstdc++"
 	fi
 	export LARGE_FILES="TRUE"