Cleaned ebuild

(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)

5 files changed, 103 insertions, 42 deletions

diff --git a/sci-biology/nrcl/ChangeLog b/sci-biology/nrcl/ChangeLog
new file mode 100644
index 000000000..b0231c2a8
--- /dev/null
+++ b/sci-biology/nrcl/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/nrcl
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*nrcl-110625 (25 Jun 2011)
+
+  25 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/0.1-build.patch,
+  -nrcl-0.1.ebuild, +nrcl-110625.ebuild:
+  Cleaned ebuild
+
diff --git a/sci-biology/nrcl/Manifest b/sci-biology/nrcl/Manifest
index 41cd6ca97..12109829b 100644
--- a/sci-biology/nrcl/Manifest
+++ b/sci-biology/nrcl/Manifest
@@ -1,4 +1,16 @@
-DIST cdbfasta.tar.gz 59735 RMD160 c90e0ede03a01bf2da77f9beaa3c97fa7e46ff2a SHA1 2419421ab1d753d3bb8778c92236da74fee30526 SHA256 68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c
-DIST nrcl.tar.gz 14782 RMD160 c3e122ccd1d30e25c278e9f0a7928ab6d1a1e451 SHA1 8650388bbf27640f5b2c261e1eafe286e34adcb4 SHA256 8795728d60416d1329a352479335b084d3627af8e6ba5e4ba043041970886f46
-EBUILD nrcl-0.1.ebuild 1223 RMD160 163f2e14872074fb445b8941038e417d22d1193a SHA1 c842fdc757a6b984a724981155d122ce5d178cb7 SHA256 cbb0f36d07ede9150b1b8b37558f83a7c4a3692fcaf0344f58db61ef85c7efda
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA256
+
+AUX 0.1-build.patch 1184 RMD160 adbdf53d27d41f8095492ed28a437d6b64191886 SHA1 09bbb5e77185ecc7cde825d395a908600bda794d SHA256 eee62d137ca6359c2a2f614054d55afb711291dffc239c62a5cc07f01b9f293e
+DIST gclib.tar.gz 82727 RMD160 f12395354b47980577e9d83cc100a6bf6568bd33 SHA1 4c433e6a87663211dc00e2d855a11a058e5b6b48 SHA256 0c7f21fc92b033cd442b672e9014e3ffb9f2de97769ca525715692ed9359439b
+DIST nrcl-110625.tar.gz 14782 RMD160 c3e122ccd1d30e25c278e9f0a7928ab6d1a1e451 SHA1 8650388bbf27640f5b2c261e1eafe286e34adcb4 SHA256 8795728d60416d1329a352479335b084d3627af8e6ba5e4ba043041970886f46
+EBUILD nrcl-110625.ebuild 695 RMD160 0fc3eaa7b2e44a6f75a02338c0cdb46c40e746f4 SHA1 9abbc7a63ee83d05d6b4a0beda87a5d49a2805dd SHA256 c26a2521b93facdb258ddafd778cff41e77dfe7fcc8807c36e678ba01ee13846
+MISC ChangeLog 275 RMD160 fd93c1ba69b602e4763cb3170657ffec4b9aba0f SHA1 0dab452c803d665afb16503211b4f234ff33a13a SHA256 e97975abefb4db768e4b1d7918fceb29e56fbb255f54fe228e8a49a87fa4d3ac
 MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.17 (GNU/Linux)
+
+iEYEAREIAAYFAk4F+AYACgkQgAnW8HDreRa+RwCfeLpiieJ7dbg03JinaG+VCAsj
+EPYAnjZ4j3SkPQTcidQo9D1km0Car2AU
+=M3Nc
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/nrcl/files/0.1-build.patch b/sci-biology/nrcl/files/0.1-build.patch
new file mode 100644
index 000000000..64fa893a4
--- /dev/null
+++ b/sci-biology/nrcl/files/0.1-build.patch
@@ -0,0 +1,48 @@
+ Makefile |   18 +++++++++---------
+ 1 files changed, 9 insertions(+), 9 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 6d5d68f..30a1019 100644
+--- a/Makefile
++++ b/Makefile
+@@ -11,23 +11,23 @@ SYSTYPE :=     $(shell uname)
+ 
+ # C compiler
+ 
+-CC      := g++
+-CFLAGS  = -O2 -Wall ${SEARCHDIRS} -fno-exceptions -fno-rtti -fno-strict-aliasing -D_REENTRANT
++CXX      ?= g++
++CXXFLAGS  += -Wall ${SEARCHDIRS} -fno-exceptions -fno-rtti -fno-strict-aliasing -D_REENTRANT
+ 
+ %.o : %.c
+-	${CC} ${CFLAGS} -c $< -o $@
++	${CXX} ${CXXFLAGS} -c $< -o $@
+ 
+-%.o : %.cc
+-	${CC} ${CFLAGS} -c $< -o $@
++%.o : %.CXX
++	${CXX} ${CXXFLAGS} -c $< -o $@
+ 
+ %.o : %.C
+-	${CC} ${CFLAGS} -c $< -o $@
++	${CXX} ${CXXFLAGS} -c $< -o $@
+ 
+ %.o : %.cpp
+-	${CC} ${CFLAGS} -c $< -o $@
++	${CXX} ${CXXFLAGS} -c $< -o $@
+ 
+ %.o : %.cxx
+-	${CC} ${CFLAGS} -c $< -o $@
++	${CXX} ${CXXFLAGS} -c $< -o $@
+ 
+ # C/C++ linker
+ 
+@@ -39,7 +39,7 @@ LOADLIBES :=
+ all:    nrcl
+ 
+ nrcl:  ./nrcl.o ${GCLDIR}/GBase.o ${GCLDIR}/GStr.o ${GCLDIR}/GArgs.o
+-	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
++	${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
+ 
+ # target for removing all object files
+ 
diff --git a/sci-biology/nrcl/nrcl-0.1.ebuild b/sci-biology/nrcl/nrcl-0.1.ebuild
deleted file mode 100644
index 6f44a0b17..000000000
--- a/sci-biology/nrcl/nrcl-0.1.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-DESCRIPTION="Containment clustering and layout utility for processing pairwise alignments from TIGR Gene Indices project tools"
-HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
-SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz
-		ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}
-
-src_prepare() {
-	# we need gclib from cdbfasta.tar.gz bundle which has fewer files than tgi_cpp_library.tar.gz wbut has e.g. GStr.h
-	sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' "${S}"/${PN}/Makefile || die "Failed to run sed"
-	sed -i 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' "${S}"/"${PN}"/Makefile || die
-	cd ${PN} || die
-	ln -s ../cdbfasta/gcl . || die "Cannot make a softlink"
-}
-
-src_compile() {
-	cd ${PN} || die
-	emake || die "emake failed in "${S}"/${PN}"
-}
-
-src_install() {
-	cd ${PN} || die
-	dobin ${PN} || die "Failed to install ${PN} binary"
-	newdoc README README.${PN}
-}
diff --git a/sci-biology/nrcl/nrcl-110625.ebuild b/sci-biology/nrcl/nrcl-110625.ebuild
new file mode 100644
index 000000000..1a599dd4c
--- /dev/null
+++ b/sci-biology/nrcl/nrcl-110625.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Containment clustering and layout utility for processing pairwise alignments"
+HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
+SRC_URI="
+	ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz -> ${P}.tar.gz
+	ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/gclib.tar.gz -> gclib.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+S="${WORKDIR}"/${PN}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-build.patch
+	tc-export CXX
+}
+
+src_install() {
+	dobin ${PN}
+	dodoc README
+}