Respecting LDFLAGS, 337856

Package-Manager: portage-2.2_rc83/cvs/Linux x86_64

4 files changed, 92 insertions, 3 deletions

diff --git a/sci-biology/poa/ChangeLog b/sci-biology/poa/ChangeLog
index 8ef0bf72d20d..fcc3307104e7 100644
--- a/sci-biology/poa/ChangeLog
+++ b/sci-biology/poa/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/poa
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/poa/ChangeLog,v 1.2 2008/09/07 11:36:01 markusle Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/poa/ChangeLog,v 1.3 2010/09/18 16:04:00 jlec Exp $
+
+*poa-2-r1 (18 Sep 2010)
+
+  18 Sep 2010; Justin Lecher <jlec@gentoo.org> +files/2-respect-flags.patch,
+  +poa-2-r1.ebuild:
+  Respecting LDFLAGS, 337856
 
   07 Sep 2008; Markus Dittrich <markusle@gentoo.org> poa-2.ebuild:
   Fix outdated HOMEPAGE and keyword amd64.
diff --git a/sci-biology/poa/Manifest b/sci-biology/poa/Manifest
index f4b3db4adef0..4bbaa4026f65 100644
--- a/sci-biology/poa/Manifest
+++ b/sci-biology/poa/Manifest
@@ -1,5 +1,17 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 2-respect-flags.patch 743 RMD160 480671401e4378a6cc98e9785d61210ba78f57cb SHA1 d27f8d6806b0997b9df4429efc60076d63375dec SHA256 12178e90b6ed7a70e6d436f0ad391e151b2b0a5b36d31133016acc6a6bbded6c
 AUX respect-cflags.patch 464 RMD160 c5323a4944cc953336b70f924ced36aca1533301 SHA1 e6ed80baa01ed807778411760b69e51e969b9601 SHA256 851c738b9ecfa567b21f3b551e6819b8ae05db02a3f5a42ae4aa93d55577ed0e
 DIST poaV2.tar.gz 62612 RMD160 31fdc50527a826fb7fdab4256f51e4f0f03c5492 SHA1 57f863956736498dd76afb57967036bf92c6d599 SHA256 d98d8251af558f442d909a6527694825ef6f79881b7636cad4925792559092c2
+EBUILD poa-2-r1.ebuild 1057 RMD160 0d21805327e981ee5e3e14096b59307c65bb1937 SHA1 191a4ea9d3ba2c925872989f954bbc85898ada4d SHA256 36cf20f7e95dc7fe76656afe7a30531442b3359f6d7b2ff8fc699f1de36ec852
 EBUILD poa-2.ebuild 1055 RMD160 958fe3aa71bd824314e440265649f138ab69d78f SHA1 c3aa1f77552143600108e7f35a630fc30c8bf5d3 SHA256 6375292a369ae117d5a4b029efc8c63a2fe2e0a8269dc86e95586b267c6c351f
-MISC ChangeLog 532 RMD160 fea277ac5a752400c1ed9df75b4d089d381d0316 SHA1 d7fb55a441e9ef0315e053d55b4993e43b06ad09 SHA256 eb43f949188736e2dda9c3604d654c2e7e73d622fbbe9486f772dde90a86845f
+MISC ChangeLog 680 RMD160 256d10e0b75accac07ae65ff2e0a1f474c588956 SHA1 e780884d5aafcc9d1b7ed693d0328a966d9f0ab1 SHA256 70a39cd2dd75191cf547c43bcfe2d07e82fbdd0dc5c5588fe9dfd6d3af92fad9
 MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.16 (GNU/Linux)
+
+iEYEARECAAYFAkyU4vUACgkQgAnW8HDreRavGQCfahzdj1M85q4RyNm7VrykxbO9
+0KwAoIdxGIglJ5Ry606nHV9XOQW/ltCx
+=9qA2
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/poa/files/2-respect-flags.patch b/sci-biology/poa/files/2-respect-flags.patch
new file mode 100644
index 000000000000..bdd638cf64b7
--- /dev/null
+++ b/sci-biology/poa/files/2-respect-flags.patch
@@ -0,0 +1,26 @@
+diff --git a/Makefile b/Makefile
+index a65bed0..713a7ab 100644
+--- a/Makefile
++++ b/Makefile
+@@ -26,9 +26,10 @@ LIBOBJECTS= \
+ 	stringptr.o
+ 
+ 
+-CC = gcc
++CC ?= gcc
+ #CFLAGS= -g -ansi-strict -W -Wall -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
+-CFLAGS= -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
++OPT_CFLAGS = -g
++CFLAGS= $(OPT_CFLAGS) -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
+ # -I$(HOME)/lib/include
+ # -DREPORT_MAX_ALLOC
+ 
+@@ -44,7 +45,7 @@ liblpo.a: $(LIBOBJECTS)
+ 
+ # NB: LIBRARY MUST FOLLOW OBJECTS OR LINK FAILS WITH UNRESOLVED REFERENCES!!
+ poa: $(OBJECTS) liblpo.a
+-	$(CC) -o $@ $(OBJECTS) -lm liblpo.a
++	$(CC) $(LDFLAGS) -o $@ $(OBJECTS) -lm liblpo.a
+ 
+ what:
+ 	@echo poa: partial-order based sequence alignment program
diff --git a/sci-biology/poa/poa-2-r1.ebuild b/sci-biology/poa/poa-2-r1.ebuild
new file mode 100644
index 000000000000..a44fe8e66a71
--- /dev/null
+++ b/sci-biology/poa/poa-2-r1.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/poa/poa-2-r1.ebuild,v 1.1 2010/09/18 16:04:00 jlec Exp $
+
+EAPI="3"
+
+inherit eutils
+
+MY_P="${PN}V${PV}"
+
+DESCRIPTION="Fast multiple sequence alignments using partial-order graphs"
+HOMEPAGE="http://bioinfo.mbi.ucla.edu/poa/"
+SRC_URI="mirror://sourceforge/poamsa/${MY_P}.tar.gz"
+
+# According to SF project page
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE=""
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-respect-flags.patch
+}
+
+src_compile() {
+	emake \
+		CC="$(tc-getCC)" \
+		OPT_CFLAGS="${CFLAGS}" \
+		poa || die "make failed"
+}
+
+src_install() {
+	dobin "${S}"/poa "${S}"/make_pscores.pl || die
+	dolib.a "${S}"/liblpo.a || die
+	dodoc "${S}"/README "${S}"/multidom.* || die
+	insinto /usr/share/poa
+	doins "${S}"/*.mat || die
+}
+
+pkg_postinst() {
+	elog "poa requires a score matrix as the first argument."
+	elog "This package installs two examples to ${EROOT}usr/share/poa/."
+}