Fixed test, #318641; multilib, LDFLAGS, PREFIX awareness

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

4 files changed, 92 insertions, 3 deletions

diff --git a/sci-biology/trnascan-se/ChangeLog b/sci-biology/trnascan-se/ChangeLog
index dabe53f87bf2..6b1c6bb13f18 100644
--- a/sci-biology/trnascan-se/ChangeLog
+++ b/sci-biology/trnascan-se/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/trnascan-se
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/trnascan-se/ChangeLog,v 1.10 2009/08/05 18:45:47 ssuominen Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/trnascan-se/ChangeLog,v 1.11 2010/06/25 09:40:04 jlec Exp $
+
+*trnascan-se-1.23-r2 (25 Jun 2010)
+
+  25 Jun 2010; Justin Lecher <jlec@gentoo.org> +trnascan-se-1.23-r2.ebuild,
+  +files/trnascan-se-1.23-ldflags.patch:
+  Fixed test, #318641; multilib, LDFLAGS, PREFIX awareness
 
   05 Aug 2009; Samuli Suominen <ssuominen@gentoo.org>
   trnascan-se-1.23-r1.ebuild, +files/trnascan-se-1.23-glibc-2.10.patch:
diff --git a/sci-biology/trnascan-se/Manifest b/sci-biology/trnascan-se/Manifest
index 612052394ecc..09e24dc0caa0 100644
--- a/sci-biology/trnascan-se/Manifest
+++ b/sci-biology/trnascan-se/Manifest
@@ -1,5 +1,17 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX trnascan-se-1.23-glibc-2.10.patch 6702 RMD160 1ac6cf0d4630ae7c9f7cd55c209d3b7d7391b18e SHA1 a2a7017c37e8db122026a2066ae107428b05ac95 SHA256 16c6083f8a2991d22252a23184a45c74e0fd75b5a45085c3dcea7d1cd503cf42
+AUX trnascan-se-1.23-ldflags.patch 971 RMD160 93382a13c9b14e687a884fff06a926abd6ea634c SHA1 0561f26cea27f2ec6268b54383be6aeb07367c1f SHA256 6013162268bc78f6752ce8703d9fd1810f634a9176b55dac67155b8decb8e6e9
 DIST trnascan-se-1.23.tar.bz2 482202 RMD160 41180bc008e64258470a241418467b9b97220669 SHA1 2b35e9b63854bb8ceb9fb602582f7de47d15d095 SHA256 a1d18a0b9decf4a93fa6cf02fb5867367729449fc8e47e3749c91678fc1f344a
 EBUILD trnascan-se-1.23-r1.ebuild 1320 RMD160 dda2944e1d7e44bd5f4f3e0038eed1a923dbc9bb SHA1 4856f02e96e8c06164537f4ef926539bc9923ec7 SHA256 7900c0bdef3751c8552cd67ae04147b2c8679fbce3badbc88ad5fd7e5d6d0290
-MISC ChangeLog 1482 RMD160 993c9ff098d4c8bccaa23f23684d25ba10565411 SHA1 ed654390d9918706170c1501d58777f7e5686b36 SHA256 3190720392b9fa69deb53e948bf836ce6247358a5dfa44b08e4ab0be85464bb2
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+MISC ChangeLog 1690 RMD160 6d593d6650fea275d32134da2b10a7c93f51dc5a SHA1 194b9e13dbb515707c33b7c95bceb211ed4995bd SHA256 ea7c6688fb61238ae9677e8bd04bb2f7bcd80074cd06036d8fdf3e1eb4947d12
 MISC metadata.xml 505 RMD160 f2fa2c8de86e9ade0dc4f877b1d196ac68b92e5c SHA1 0f12c05690d0dfcb666e902d7993b7ef0775a74e SHA256 dbc8cc4c1391bf4846f2aa70d6598bc4b40a28568d3cb36e0a8ff8941eee9b23
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diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.23-ldflags.patch b/sci-biology/trnascan-se/files/trnascan-se-1.23-ldflags.patch
new file mode 100644
index 000000000000..783e4340823d
--- /dev/null
+++ b/sci-biology/trnascan-se/files/trnascan-se-1.23-ldflags.patch
@@ -0,0 +1,26 @@
+diff --git a/Makefile b/Makefile
+index 53e5c5b..a2d3feb 100644
+--- a/Makefile
++++ b/Makefile
+@@ -109,17 +109,17 @@ MPOBJ = mpviterbi.o mp-dbviterbi.o
+ all: 	$(PROGS) tRNAscanSE setpaths
+ 
+ covels-SE:  $(OBJ) scan_main.o
+-	$(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
++	$(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
+ 
+ coves-SE: $(OBJ) score_main.o
+-	$(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
++	$(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
+ 
+ eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o
+-	$(CC) $(CFLAGS)  -o eufindtRNA eufind_main.o \
++	$(CC) $(CFLAGS)  $(LDFLAGS) -o eufindtRNA eufind_main.o \
+ 	pavesi.o $(SQUIDOBJ) $(LIBS)
+ 
+ trnascan-1.4: trnascan.o
+-	$(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c
++	$(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" $(LDFLAGS) -o trnascan-1.4 trnascan.c
+ 
+ tRNAscanSE:
+ 	$(PERLDIR)/$(PERLBIN) checkversion.pl
diff --git a/sci-biology/trnascan-se/trnascan-se-1.23-r2.ebuild b/sci-biology/trnascan-se/trnascan-se-1.23-r2.ebuild
new file mode 100644
index 000000000000..e4d182fcc95f
--- /dev/null
+++ b/sci-biology/trnascan-se/trnascan-se-1.23-r2.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/trnascan-se/trnascan-se-1.23-r2.ebuild,v 1.1 2010/06/25 09:40:04 jlec Exp $
+
+EAPI="3"
+
+inherit eutils multilib toolchain-funcs
+
+DESCRIPTION="tRNA detection in large-scale genome sequences"
+HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="dev-lang/perl"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-glibc-2.10.patch
+	epatch "${FILESDIR}"/${P}-ldflags.patch
+	sed -e "s%BINDIR  = \$(HOME)/bin%BINDIR = ${EPREFIX}/usr/bin%" \
+		-e "s%LIBDIR  = \$(HOME)/lib/tRNAscan-SE%LIBDIR = ${EPRFIX}/usr/$(get_libdir)/${PN}%" \
+		-e "s%MANDIR  = \$(HOME)/man%MANDIR = ${EPREFIX}/usr/share/man%" \
+		-e "s%CC = gcc%CC = $(tc-getCC)%" \
+		-e "s%CFLAGS = -O%CFLAGS = ${CFLAGS}%" \
+		-i Makefile || die
+}
+
+src_install() {
+	mv tRNAscan-SE.man tRNAscan-SE.man.1 || die
+	dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4 || die
+	doman tRNAscan-SE.man.1 || die
+	dodoc MANUAL README Release.history || die
+	insinto /usr/$(get_libdir)/${PN}/
+	doins *.cm gcode.* Dsignal TPCsignal || die
+	insinto /usr/share/doc/${PF}
+	doins Manual.ps || die
+}
+
+src_test() {
+	make PATH="${S}:${PATH}" testrun || die
+}