sci-biology/cd-hit-auxtools: new package, needs gcc<=4.6.4 or some CXXFLAG to loosen g++ strictness

Package-Manager: portage-2.2.7

5 files changed, 109 insertions, 0 deletions

diff --git a/sci-biology/cd-hit-auxtools/ChangeLog b/sci-biology/cd-hit-auxtools/ChangeLog
new file mode 100644
index 000000000..6bee54586
--- /dev/null
+++ b/sci-biology/cd-hit-auxtools/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/cd-hit-auxtools
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*cd-hit-auxtools-0.5 (01 Jun 2014)
+
+  01 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +cd-hit-auxtools-0.5.ebuild, +files/0.5-gentoo.patch, +metadata.xml:
+  sci-biology/cd-hit-auxtools: new package, needs gcc<=4.6.4 or some CXXFLAG to
+  loosen g++ strictness
diff --git a/sci-biology/cd-hit-auxtools/Manifest b/sci-biology/cd-hit-auxtools/Manifest
new file mode 100644
index 000000000..60a355a63
--- /dev/null
+++ b/sci-biology/cd-hit-auxtools/Manifest
@@ -0,0 +1 @@
+DIST cd-hit-auxtools-v0.5-2012-03-07.tgz 97230 SHA256 acacb96344eeab2a7cb20613961f0355eba1f5c1f5793f100a252c8c45e4a6ad SHA512 5b00ff4951c9f2b85b23bad7eae484c060f05df8a20c35bf1cff0bae770a6552b7ed19c90bbc36204ea3ba1722490c8ba654c7ec1b1d55f743afbc82be53ef5b WHIRLPOOL d5ff22b2c1fa77089e4543c905e3dacd37769d5e07b2a1ac85651ea8b057d39bf44997590afb12e4757a3482bebc0a63233272c2ae0e95eb88c584dcc0c49084
diff --git a/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild b/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild
new file mode 100644
index 000000000..c40e98b2e
--- /dev/null
+++ b/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/cd-hit-4.6.ebuild,v 1.1 2012/06/20 18:39:24 jlec Exp $
+
+EAPI=4
+
+inherit eutils flag-o-matic toolchain-funcs
+
+RELDATE="2012-03-07"
+RELEASE="${PN}-v${PV}-${RELDATE}"
+
+DESCRIPTION="Additional cd-hit itools: read-linker, cd-hit-lap and cd-hit-dup"
+HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
+SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE="GPL-2"
+IUSE="doc openmp"
+
+S="${WORKDIR}"/${RELEASE}
+
+pkg_setup() {
+	 use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
+}
+
+src_prepare() {
+	tc-export CXX
+	use openmp || append-flags -DNO_OPENMP
+	epatch "${FILESDIR}"/${PV}-gentoo.patch
+}
+
+src_compile() {
+	local myconf=
+	use openmp && myconf="openmp=yes"
+	make ${myconf} || die "If compilation failed try gcc-4.6.4 or older, newer versions are too picky about quality of the source code"
+}
+
+src_install() {
+	dodir /usr/bin
+	dobin read-linker cd-hit-lap cd-hit-dup
+}
diff --git a/sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch b/sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch
new file mode 100644
index 000000000..3977cbee3
--- /dev/null
+++ b/sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch
@@ -0,0 +1,47 @@
+--- Makefile.ori	2014-06-01 20:25:53.000000000 +0200
++++ Makefile	2014-06-01 20:27:15.000000000 +0200
+@@ -1,8 +1,8 @@
+ 
+-CC = g++
++CXX = g++
+ 
+-CFLAGS = -Wall -Wno-unused -I. -Imintlib
+-LFLAGS = -fPIC
++CXXFLAGS = -I. -Imintlib
++LDFLAGS = -fPIC
+ 
+ 
+ UNAME = $(shell uname)
+@@ -16,9 +16,9 @@
+ endif
+ 
+ ifeq ($(debug),yes)
+-CFLAGS += -ggdb
++CiXXFLAGS +=
+ else
+-CFLAGS += -O2
++CXXFLAGS +=
+ endif
+ 
+ 
+@@ -32,16 +32,16 @@
+ .SUFFIXES: .c .obj .cpp .cc .cxx .C
+ 
+ .cxx.o:
+-	$(CC) -c $(CFLAGS) -o $@ $<
++	$(CXX) -c $(CXXFLAGS) -o $@ $<
+ 
+ cd-hit-dup: $(OBJECTS) cdhit-dup.o
+-	$(CC) $(LFLAGS) $(OBJECTS) cdhit-dup.o -o cd-hit-dup
++	$(CXX) $(LDFLAGS) $(OBJECTS) cdhit-dup.o -o cd-hit-dup
+ 
+ cd-hit-lap: $(OBJECTS) cdhit-lap.o
+-	$(CC) $(LFLAGS) $(OBJECTS) cdhit-lap.o -o cd-hit-lap
++	$(CXX) $(LDFLAGS) $(OBJECTS) cdhit-lap.o -o cd-hit-lap
+ 
+ read-linker: $(OBJECTS) read-linker.o
+-	$(CC) $(LFLAGS) $(OBJECTS) read-linker.o -o read-linker
++	$(CXX) $(LDFLAGS) $(OBJECTS) read-linker.o -o read-linker
+ 
+ clean:
+ 	rm $(OBJECTS) cdhit-dup.o cdhit-lap.o read-linker.o
diff --git a/sci-biology/cd-hit-auxtools/metadata.xml b/sci-biology/cd-hit-auxtools/metadata.xml
new file mode 100644
index 000000000..2bc893037
--- /dev/null
+++ b/sci-biology/cd-hit-auxtools/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>