sci-biology/seqan: Version BUmp

Package-Manager: portage-2.2.14_rc1/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

5 files changed, 122 insertions, 17 deletions

diff --git a/sci-biology/seqan/ChangeLog b/sci-biology/seqan/ChangeLog
index 02a4845e6eca..eaf19ac1f317 100644
--- a/sci-biology/seqan/ChangeLog
+++ b/sci-biology/seqan/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/seqan
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/seqan/ChangeLog,v 1.4 2013/07/17 07:09:45 jlec Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/seqan/ChangeLog,v 1.5 2014/10/17 13:51:56 jlec Exp $
+
+*seqan-1.4.2 (17 Oct 2014)
+
+  17 Oct 2014; Justin Lecher <jlec@gentoo.org> +seqan-1.4.2.ebuild,
+  +files/seqan-1.4.2-include.patch, +files/seqan-1.4.2-shared.patch:
+  Version BUmp
 
   17 Jul 2013; Justin Lecher <jlec@gentoo.org> seqan-1.3.1-r1.ebuild:
   Add missing dep
diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest
index 1844d03671b4..565a8620e44c 100644
--- a/sci-biology/seqan/Manifest
+++ b/sci-biology/seqan/Manifest
@@ -1,24 +1,30 @@
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 Hash: SHA512
 
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 DIST seqan-1.3.1.zip 8787521 SHA256 87eebe73ace9ada2f4664a768ae212d4acc5fb3ce87702709c3d15bf2d153aeb SHA512 dafacccb4647fd0fc5a055d33390cb85f1c00ca74132e9b3839a739916acf9a2990db7db4f09e34f899b283cad8ccf6553a60cc7693164f250f08260c8ce8ae4 WHIRLPOOL 5a0a80d09e80285a4fc9fb9fb71adbea6b0b324a6a219cd7c9ef3d30e88133f5b25b3cf792b2b89e4ed07ff612f4aa347dc6f94e06974f947fe980c2e0a5d26b
+DIST seqan-src-1.4.2.tar.gz 120601994 SHA256 2b2c48572ea82fc2ac6a6e46bbd4204b6f8200fde717612797426af5ff6b82c3 SHA512 dbb56167c507b70111619a414054d9e70f1db42507bbfdf9e40c5dcbbe9489ad4187d882e638a675e96551c860c08f8203c929c4c9a558b19ea7d6059f50492a WHIRLPOOL 3c7f38e35d826adad94d53d359df8b5f1fb51746f3103457b12b41bd0bf161dc463d4a1932b0b23f2274d723c796116af0940260e1922ce806bb2466445788f0
 EBUILD seqan-1.3.1-r1.ebuild 979 SHA256 9feff642a58a7beec934130f8bfd0fa39ea614c22883bf7c832b6904d0f62b4b SHA512 cbf66445a3a3d862b8eb15c4bea8d3890c7a62f5aa6f295180d7899a2e7e9221fab726ac2e666faff78cb1fbf26d974505f1e41295aad80d247243d1a9b72114 WHIRLPOOL 0d303318d83105d64c22179b665a7235a3dcbf9ef8ef3362cdfcfdb32d74d011f5b751977d4f45a298ac0f79263f19385261a3649f9bab23b7e0e8cee5e7c729
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+EBUILD seqan-1.4.2.ebuild 1243 SHA256 89214e908cf6c10b7330ae3e58362e5e325326680657adfcc99ddadbab11a176 SHA512 4ee8a719685204f14a83dd311d62dbc8703136bedd143ccadc19fd3e415b3dfdd32c6b8e1f2c9acd0e67f7d52a74bf865f6dd46ef1f2f5cda453eee8b491ef55 WHIRLPOOL ab8442f926206236424aa53c0dd1152b2956884a077213ea83ac31465a0b0d406eb22d7e06ca633ab6d634f41a2896af0082419fe0116e40e9f8dfaef064da20
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diff --git a/sci-biology/seqan/files/seqan-1.4.2-include.patch b/sci-biology/seqan/files/seqan-1.4.2-include.patch
new file mode 100644
index 000000000000..5baee4d8ebc0
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-1.4.2-include.patch
@@ -0,0 +1,16 @@
+ core/include/seqan/index/index_qgram_openaddressing.h | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/core/include/seqan/index/index_qgram_openaddressing.h b/core/include/seqan/index/index_qgram_openaddressing.h
+index 4a6c2e6..8cc9a42 100644
+--- a/core/include/seqan/index/index_qgram_openaddressing.h
++++ b/core/include/seqan/index/index_qgram_openaddressing.h
+@@ -35,6 +35,8 @@
+ #ifndef SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H
+ #define SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H
+ 
++#include <smmintrin.h>
++
+ namespace SEQAN_NAMESPACE_MAIN
+ {
+ 
diff --git a/sci-biology/seqan/files/seqan-1.4.2-shared.patch b/sci-biology/seqan/files/seqan-1.4.2-shared.patch
new file mode 100644
index 000000000000..0f438ff07bce
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-1.4.2-shared.patch
@@ -0,0 +1,22 @@
+ util/cmake/SeqAnBuildSystem.cmake | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/util/cmake/SeqAnBuildSystem.cmake b/util/cmake/SeqAnBuildSystem.cmake
+index bcba2c0..d53cd01 100644
+--- a/util/cmake/SeqAnBuildSystem.cmake
++++ b/util/cmake/SeqAnBuildSystem.cmake
+@@ -144,10 +144,10 @@ macro (seqan_register_apps)
+     set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DSEQAN_ENABLE_DEBUG=1")
+ 
+     # enable static linkage for seqan apps
+-    if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
+-      set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+-      set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
+-    endif ()
++#    if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
++#      set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
++#      set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
++#    endif ()
+ 
+     # Get all direct entries of the current source directory into ENTRIES.
+     file (GLOB ENTRIES
diff --git a/sci-biology/seqan/seqan-1.4.2.ebuild b/sci-biology/seqan/seqan-1.4.2.ebuild
new file mode 100644
index 000000000000..f1e36479061b
--- /dev/null
+++ b/sci-biology/seqan/seqan-1.4.2.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/seqan/seqan-1.4.2.ebuild,v 1.1 2014/10/17 13:51:56 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils flag-o-matic python-single-r1
+
+DESCRIPTION="C++ Sequence Analysis Library"
+HOMEPAGE="http://www.seqan.de/"
+SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}
+	sci-biology/samtools"
+DEPEND="${RDEPEND}"
+
+#S="${WORKDIR}"/${P}/cmake
+
+PATCHES=(
+	"${FILESDIR}"/${P}-shared.patch
+	"${FILESDIR}"/${P}-include.patch
+)
+
+src_prepare() {
+	rm -f \
+		util/cmake/FindZLIB.cmake \
+		|| die
+	touch extras/apps/seqan_flexbar/README || die
+	sed \
+		-e "s:share/doc:share/doc/${PF}:g" \
+		-i docs/CMakeLists.txt util/cmake/SeqAnBuildSystem.cmake || die
+	cmake-utils_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DZLIB_INCLUDE_DIRS="${EPREFIX}"/usr/include
+	)
+	cmake-utils_src_configure
+}
+
+src_install() {
+	mkdir -p "${BUILD_DIR}"/docs/html || die
+	cmake-utils_src_install
+	chmod 755 "${ED}"/usr/bin/*sh || die
+}