Respecting LDFLAGS, rebuilding all libs instead of using upstreams bundled ones, bug 308703

(Portage version: 2.2_rc67/cvs/Linux x86_64)

3 files changed, 97 insertions, 2 deletions

diff --git a/sci-biology/qrna/ChangeLog b/sci-biology/qrna/ChangeLog
index 99da71bf8c45..0f5150b086a6 100644
--- a/sci-biology/qrna/ChangeLog
+++ b/sci-biology/qrna/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/qrna
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/qrna/ChangeLog,v 1.20 2009/08/05 19:32:12 ssuominen Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/qrna/ChangeLog,v 1.21 2010/03/10 21:13:06 jlec Exp $
+
+*qrna-2.0.3c-r1 (10 Mar 2010)
+
+  10 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +qrna-2.0.3c-r1.ebuild, +files/qrna-2.0.3c-ldflags.patch:
+  Respecting LDFLAGS, rebuilding all libs instead of using upstreams bundled
+  ones, #308703
 
   05 Aug 2009; Samuli Suominen <ssuominen@gentoo.org> qrna-2.0.3c.ebuild,
   +files/qrna-2.0.3c-glibc-2.10.patch:
diff --git a/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch
new file mode 100644
index 000000000000..d03f650dd39e
--- /dev/null
+++ b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch
@@ -0,0 +1,28 @@
+diff --git a/src/Makefile b/src/Makefile
+index 1d1631b..4fa3af9 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -131,17 +131,17 @@ DEMOS =
+ all: 	$(PROGS)
+ 
+ main:              $(OBJ) main.o
+-	           $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o  $(LIBS)
++	           $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o  $(LIBS)
+ cfgbuild:          $(OBJ) cfgbuild.o
+-	           $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
++	           $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ eqrna:             $(OBJ) eqrna.o
+-	           $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
++	           $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ eqrna_sample:      $(OBJ) eqrna_sample.o
+-	           $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
++	           $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ shuffle:           $(OBJ) shuffle.o
+-	           $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
++	           $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ rnamat_main:       $(OBJ2) rnamat_main.o
+-	           $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS)
++	           $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS)
+ 
+ main.o:            ../src/main.c
+ 	           $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
diff --git a/sci-biology/qrna/qrna-2.0.3c-r1.ebuild b/sci-biology/qrna/qrna-2.0.3c-r1.ebuild
new file mode 100644
index 000000000000..257bffd7f3e6
--- /dev/null
+++ b/sci-biology/qrna/qrna-2.0.3c-r1.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/qrna/qrna-2.0.3c-r1.ebuild,v 1.1 2010/03/10 21:13:06 jlec Exp $
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Prototype ncRNA genefinder"
+HOMEPAGE="http://selab.janelia.org/software.html"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE=""
+
+RDEPEND="dev-lang/perl
+	sci-biology/hmmer"
+DEPEND="${RDEPEND}"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}"/${P}-glibc-2.10.patch
+	epatch "${FILESDIR}"/${P}-ldflags.patch
+	sed -e "s/^CC.*/CC = $(tc-getCC)/" \
+		-e "s/CFLAGS = -O/CFLAGS = ${CFLAGS}/" \
+		-i src/Makefile squid/Makefile squid02/Makefile || die
+	rm -v squid*/*.a
+}
+
+src_compile() {
+	cd "${S}"/squid
+	emake || die
+
+	cd "${S}"/squid02
+	emake || die
+
+	cd "${S}"/src
+	emake || die
+}
+
+src_install () {
+	cd "${S}"/src
+	dobin cfgbuild eqrna eqrna_sample main rnamat_main || die
+
+	cd "${S}"
+	dobin scripts/* || die
+
+	newdoc 00README README || die
+	insinto /usr/share/doc/${PF}
+	doins documentation/* || die
+
+	insinto /usr/share/${PN}/data
+	doins lib/* || die
+	insinto /usr/share/${PN}/demos
+	doins Demos/* || die
+
+	# Sets the path to the QRNA data files.
+	doenvd "${FILESDIR}"/26qrna || die
+}