Respect LDFLAGS wrt bug 336533. Thanks to Diego for the report. Fix implicit function declarations.

Package-Manager: portage-2.2_rc77/cvs/Linux x86_64

4 files changed, 73 insertions, 12 deletions

diff --git a/sci-biology/dialign-tx/ChangeLog b/sci-biology/dialign-tx/ChangeLog
index cb8d1df0bba9..7cc5b6fc2eef 100644
--- a/sci-biology/dialign-tx/ChangeLog
+++ b/sci-biology/dialign-tx/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/dialign-tx
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/dialign-tx/ChangeLog,v 1.3 2010/02/09 11:20:45 pacho Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/dialign-tx/ChangeLog,v 1.4 2010/09/09 09:36:17 xarthisius Exp $
+
+*dialign-tx-1.0.2-r1 (09 Sep 2010)
+
+  09 Sep 2010; Kacper Kowalik <xarthisius@gentoo.org>
+  +dialign-tx-1.0.2-r1.ebuild, +files/dialign-tx-1.0.2-implicits.patch:
+  Respect LDFLAGS wrt bug 336533. Thanks to Diego for the report. Fix
+  implicit function declarations.
 
   09 Feb 2010; Pacho Ramos <pacho@gentoo.org> dialign-tx-1.0.2.ebuild:
   amd64 stable, bug 298774
diff --git a/sci-biology/dialign-tx/Manifest b/sci-biology/dialign-tx/Manifest
index f20965061531..59bf3b7d0330 100644
--- a/sci-biology/dialign-tx/Manifest
+++ b/sci-biology/dialign-tx/Manifest
@@ -1,14 +1,6 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
+AUX dialign-tx-1.0.2-implicits.patch 776 RMD160 18a539cba2653cb6fb1a0777a0296f03b10d5002 SHA1 8e815982a637c2633991ef974296a9070761ed9e SHA256 c13bfae6c2ffa4a676fc92a1dbe7f82d08578e5f36add057d0ad84a955aa7ca5
 DIST DIALIGN-TX_1.0.2.tar.gz 1765296 RMD160 0bd076c5efe50b037a08554fdb565d8d9364e599 SHA1 4d4e50070f019b88078105ec21f22b1005a010af SHA256 fb3940a48a12875332752a298f619f0da62593189cd257d28932463c7cebcb8f
+EBUILD dialign-tx-1.0.2-r1.ebuild 1126 RMD160 808eddc61bf70b3a76902e66740d44b7b4bcfbfa SHA1 2756ba5b513eb5c5cd9a7f1815409831440ce908 SHA256 2b005337b85ccb7337470299f3182b37a1d83469d864454208ee866b4312173d
 EBUILD dialign-tx-1.0.2.ebuild 988 RMD160 209000d7fd01fb2e6f93ade92b98db11cd1617db SHA1 e68d2f85ab6b027727093340e232ba10a9618c4a SHA256 c9988b388b6acfbd18302b95d6597822a6b4dd762bdee9b5521e9de0043d0d39
-MISC ChangeLog 1709 RMD160 32937a194e81c55e2ec53f02ec809801c0dd12a4 SHA1 331c479bd540c93d19922dfc975afee7bc554dd6 SHA256 c01ea365f8317232fb330655601cc4ddea9bcdf07bce81aee475dd12657b79a1
+MISC ChangeLog 1981 RMD160 4232d653fcf5197ec38e36531b59b450dcc507cf SHA1 857852eaa50d7bc101d852dc3d356193a1eeeaf7 SHA256 1a7bc993cefd2aeb39e97607fd22c6ae58828b87fbe59c78f1dbee1bb64fcd74
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.14 (GNU/Linux)
-
-iEYEARECAAYFAktxRRMACgkQCaWpQKGI+9QzRgCfXAc5SDY2yUtBf0tcyBOgbM3Y
-aukAmgJm8W+3IKgQYynz0i79uOyRIvNH
-=UaAJ
------END PGP SIGNATURE-----
diff --git a/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild b/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild
new file mode 100644
index 000000000000..bcc252eb42f7
--- /dev/null
+++ b/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild,v 1.1 2010/09/09 09:36:17 xarthisius Exp $
+
+EAPI=2
+
+inherit eutils multilib toolchain-funcs
+
+MY_P=DIALIGN-TX_${PV}
+
+DESCRIPTION="Greedy and progressive approaches for segment-based multiple sequence alignment"
+HOMEPAGE="http://dialign-tx.gobics.de/"
+SRC_URI="http://dialign-tx.gobics.de/${MY_P}.tar.gz"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+S=${WORKDIR}/${MY_P}
+
+src_prepare() {
+	sed -e "s/\$(CC) -o/\$(CC) \$(LDFLAGS) -o/" \
+		-i source/Makefile || die #336533
+	epatch "${FILESDIR}"/${P}-implicits.patch
+}
+
+src_compile() {
+	emake -C source clean
+	emake -C source CC="$(tc-getCC)" \
+		CPPFLAGS=""	|| die "make failed"
+}
+
+src_install() {
+	DESTTREE="/usr" dobin "${S}"/source/dialign-tx
+	insinto /usr/$(get_libdir)/${PN}/conf
+	doins "${S}"/conf/*
+}
+
+pkg_postinst() {
+	einfo "The configuration directory is"
+	einfo "${ROOT}usr/$(get_libdir)/${PN}/conf"
+	einfo "You will need to pass this to ${PN} on every run."
+}
diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch
new file mode 100644
index 000000000000..a8388d03232f
--- /dev/null
+++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch
@@ -0,0 +1,18 @@
+--- source/museq.c
++++ source/museq.c
+@@ -38,6 +38,7 @@
+ //extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
+ //		 struct prob_dist *pdist);
+ //extern struct diag_col *create_diag_col(int seq_amount);
++extern void free_diag(struct diag* dg);
+ extern void free_diag_col(struct diag_col* dcol);
+ extern struct diag_col *find_all_diags(struct scr_matrix *smatrix, 
+ 				struct prob_dist *pdist, 
+@@ -52,6 +53,7 @@
+ 
+ // alig.c
+ extern struct alignment* create_empty_alignment(struct seq_col *scol);
++extern void free_alignment(struct alignment *algn);
+ //extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
+ extern int  simple_aligner(struct seq_col *scol, struct diag_col *dcol, 
+ 			    struct scr_matrix* smatrix,