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

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

4 files changed, 110 insertions, 3 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/Manifest b/sci-biology/qrna/Manifest
index 475e786f79dd..10e62a0b8784 100644
--- a/sci-biology/qrna/Manifest
+++ b/sci-biology/qrna/Manifest
@@ -1,6 +1,18 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX 26qrna 30 RMD160 c6eb4ba1c559f2cce296915c3d166e134d54b7c4 SHA1 34b74c24f599e5387dd788ec2df1752b043b7b9a SHA256 218d879e5ef893cba33d8be7e0a6cba3f08c0a475781bbbb4c32bde6e79a32b7
 AUX qrna-2.0.3c-glibc-2.10.patch 7571 RMD160 a5e616dfa354361efa117aa8598552d7d81fdf46 SHA1 273aed2a373e9b0f81d977cbb2c54d81be534557 SHA256 17f34c9e3087f2c9d2decd95e07663813087843a778db45c5be793c6b51bb82c
+AUX qrna-2.0.3c-ldflags.patch 1368 RMD160 30d595372093b17fb159213b594bde3d8ed2cf55 SHA1 a684a770cb114b0cc9de3617a830af9fb571904b SHA256 ec99724754ff3f667be139832fd871bd93f7ae0cf7247fb8d15696b0315e01d6
 DIST qrna-2.0.3c.tar.bz2 6423705 RMD160 df0fe89e45d64cf6f205dd3e524a9a27d6c14961 SHA1 1c577a495d538eb50531c4672decae85649ac066 SHA256 fc88b58dddab26f20477a50340453e9d360ea34956ba526f7db6959283399b1c
+EBUILD qrna-2.0.3c-r1.ebuild 1310 RMD160 957caa12dd44753885909ce1cebbfaa18482fcd4 SHA1 c5afbd6f51ec320f4482181e01f6d13c08e671a9 SHA256 ab48a66efd42c85952ccf5d07a406d427abfefa24ccbf86befa297a3bb1b07c2
 EBUILD qrna-2.0.3c.ebuild 1197 RMD160 93543df0a60c501b1abf4cd546e925988f102481 SHA1 53f414307e942d9e627ef646f151f100fda4f003 SHA256 53885ad72d003f6c060b10d5d45e3b3f98499e5108c5e1d7533d3c7172d0f97a
-MISC ChangeLog 3015 RMD160 7a46e7906aa0834f5a690a946f2c930e7b6e50cd SHA1 a186a8b65659975d772b39f74fb78ab00b4fe24f SHA256 0db4bc9af8dd20a3075850800241f1c42319a1327c34952f37f3be3a1115a126
+MISC ChangeLog 3249 RMD160 fbb8c3acd203e17005cb348d5c5ddacc7414fae3 SHA1 fc2bd3ee87c843765b861ac81195a365a3913639 SHA256 01947fc3bcab271d1c84e8780df3e72ec078669eab4d7feff75250b44af3b45a
 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.14 (GNU/Linux)
+
+iEYEARECAAYFAkuYC2gACgkQgAnW8HDreRbsqQCeOmKlBZk1keAgE3cOq5de1BUx
+yt8An0McWpUUm/+zIlRkIWNNTzcHv/cE
+=lTuP
+-----END PGP SIGNATURE-----
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
+}