Fixed compilation w/ glibc-2.10, bug 294876

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

4 files changed, 57 insertions, 15 deletions

diff --git a/sci-biology/arb/ChangeLog b/sci-biology/arb/ChangeLog
index ec2f3bd7ce75..ed39cae6f1ca 100644
--- a/sci-biology/arb/ChangeLog
+++ b/sci-biology/arb/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/arb
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/arb/ChangeLog,v 1.1 2009/10/04 00:25:29 weaver Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/arb/ChangeLog,v 1.2 2010/03/13 12:44:45 jlec Exp $
+
+*arb-5.1-r1 (13 Mar 2010)
+
+  13 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org> +files/5.1-libs.patch,
+  -arb-5.1.ebuild, +arb-5.1-r1.ebuild:
+  Fixed compilation w/ glibc-2.10, #294876
+  Respecting LDFLAGS
 
 *arb-5.1 (03 Oct 2009)
 
diff --git a/sci-biology/arb/Manifest b/sci-biology/arb/Manifest
index 2d5a11d56e4e..33dde826e1c1 100644
--- a/sci-biology/arb/Manifest
+++ b/sci-biology/arb/Manifest
@@ -1,4 +1,17 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 5.1-libs.patch 503 RMD160 a32610db2431b84e9195d7481f50be62dfa6e9da SHA1 37792a725b045bc9948e7bcb3883c29d7cabb0ce SHA256 dfa5f131eafbf163b9a3862360694a7b1f9d6231357247c7f18f696c4c4dd983
+DIST arb-5.1-glibc2.10.patch.bz2 24659 RMD160 b522f6cd0cdcfe327d43e9b237a154e8261f7db9 SHA1 923c298f21100a6b3d3d8c4007031e1601834701 SHA256 1153e3efe73c1027972ee1b2789ee9841749c0bd2cbb2cc3ad8cd53586ff6f2f
+DIST arb-5.1-linker.patch.bz2 4406 RMD160 b1273f0b5c765c257c905f5945039864f4c6194a SHA1 e7d75c7d56112acc6b79ea13617c8e72ed05a7d8 SHA256 62080367ebd11ed3c9991bfb872e083e2d747264a400178ab0ec11a3502f3d43
 DIST arb-5.1.tgz 9727285 RMD160 8757446e7145faf28382c617fc7fe4b57a857baf SHA1 69696e52bf86eea5213ad9d27be30dd74f1255f3 SHA256 7f0a2411e7b95b94f23c51211461047eb74ffd3dd632552a82425cf903f89dbf
-EBUILD arb-5.1.ebuild 1963 RMD160 91c6b1ba1806dda86f15e0f9849f0f9953ad8000 SHA1 bf8c93d7a64303ca1a4323627d413c3190ff5816 SHA256 f3042d09022690e8b73752038853a477523c631f311b50dbc366d220ea74183f
-MISC ChangeLog 359 RMD160 7364433cec0bd934237fa1cac01a010431e6974f SHA1 e3500c10ffb8286fc6eded4497e23b8b586acc65 SHA256 4c6ef7ebc01220146f53fcc2c1988a31be21f653e35ec5b0d7ba5e6c76c2c612
+EBUILD arb-5.1-r1.ebuild 2115 RMD160 6a95b53728da9bdeb58efdfbb3de21e972877f3d SHA1 7e890be6de672d4f10c518640885af656946a98b SHA256 002401662421b1c7d76651e5d336cf8c3f658d03bc0300fb96e6a7fd4b790ea5
+MISC ChangeLog 565 RMD160 cf115640a9a4ba25f68ef4defaba0a05f9369d12 SHA1 5348d3cc742cf66478eb106d6348ec528519c5c5 SHA256 0121f76101902976933bfdbef84d8afc29dec93e36f6d6354ea411189839e694
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.14 (GNU/Linux)
+
+iEYEARECAAYFAkubiMIACgkQgAnW8HDreRa1dACfQmEFBRCV6nnmmaSdcRQmHzm9
+FmQAoMIVfEt+32xobbYNsv1dYaV0I1+O
+=M4JG
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/arb/arb-5.1.ebuild b/sci-biology/arb/arb-5.1-r1.ebuild
index 21a12e1436c8..b8169e6be93e 100644
--- a/sci-biology/arb/arb-5.1.ebuild
+++ b/sci-biology/arb/arb-5.1-r1.ebuild
@@ -1,14 +1,17 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/arb/arb-5.1.ebuild,v 1.1 2009/10/04 00:25:29 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/arb/arb-5.1-r1.ebuild,v 1.1 2010/03/13 12:44:45 jlec Exp $
 
-EAPI=2
+EAPI="2"
 
 inherit eutils toolchain-funcs
 
 DESCRIPTION="Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis"
 HOMEPAGE="http://www.arb-home.de/"
-SRC_URI="http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz"
+SRC_URI="
+	http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz
+	mirror://gentoo/${P}-glibc2.10.patch.bz2
+	mirror://gentoo/${P}-linker.patch.bz2"
 MY_TAG=6213
 
 LICENSE="arb"
@@ -16,7 +19,8 @@ SLOT="0"
 IUSE="+opengl"
 KEYWORDS="~amd64 ~x86"
 
-DEPEND="app-text/sablotron
+DEPEND="
+	app-text/sablotron
 	www-client/lynx
 	x11-libs/openmotif
 	x11-libs/libXpm
@@ -33,7 +37,9 @@ RDEPEND="${DEPEND}
 S="${WORKDIR}/arbsrc_${MY_TAG}"
 
 src_prepare() {
-	sed -i -e 's/getline/arb_getline/' READSEQ/ureadseq.c || die
+	epatch "${WORKDIR}"/${P}-glibc2.10.patch
+	epatch "${WORKDIR}"/${P}-linker.patch
+	epatch "${FILESDIR}"/${PV}-libs.patch
 	sed -i \
 		-e 's/all: checks/all:/' \
 		-e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \
@@ -57,10 +63,10 @@ src_compile() {
 
 src_install() {
 	ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die
-	cat <<EOF > "${S}/99${PN}"
-ARBHOME=/opt/arb
-PATH=/opt/arb/bin
-LD_LIBRARY_PATH=/opt/arb/lib
-EOF
+	cat <<- EOF > "${S}/99${PN}"
+	ARBHOME=/opt/arb
+	PATH=/opt/arb/bin
+	LD_LIBRARY_PATH=/opt/arb/lib
+	EOF
 	doenvd "${S}/99${PN}" || die
 }
diff --git a/sci-biology/arb/files/5.1-libs.patch b/sci-biology/arb/files/5.1-libs.patch
new file mode 100644
index 000000000000..bf0bacad3286
--- /dev/null
+++ b/sci-biology/arb/files/5.1-libs.patch
@@ -0,0 +1,16 @@
+diff --git a/SOURCE_TOOLS/provide_libs.pl b/SOURCE_TOOLS/provide_libs.pl
+index b653a66..b346c96 100644
+--- a/SOURCE_TOOLS/provide_libs.pl
++++ b/SOURCE_TOOLS/provide_libs.pl
+@@ -118,11 +118,6 @@ sub provide_libs($$$) {
+   foreach my $lib (keys %needed_by) {
+     update_lib($lib, $bindir.'/'.$needed_by{$lib}, $addlibsdir);
+   }
+-  if ($opengl==1) {
+-    foreach my $lib (keys %needed_by_opengl) {
+-      update_lib($lib, $bindir.'/'.$needed_by_opengl{$lib}, $addlibsdir);
+-    }
+-  }
+ }
+ 
+ sub main() {