Fixed ignored LDFLAGS issues and bogus detection of GD support. Also enabled the tests that come with the package.

(Portage version: 2.2_rc11/cvs/Linux 2.6.26-SENTINEL-2 i686)

4 files changed, 62 insertions, 4 deletions

diff --git a/sci-biology/vienna-rna/ChangeLog b/sci-biology/vienna-rna/ChangeLog
index 7b5d6edd2c62..d0dd201a2b7a 100644
--- a/sci-biology/vienna-rna/ChangeLog
+++ b/sci-biology/vienna-rna/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/vienna-rna
 # Copyright 2000-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.17 2008/08/29 01:21:38 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.18 2008/10/06 22:34:27 markusle Exp $
+
+  06 Oct 2008; Markus Dittrich <markusle@gentoo.org>
+  +files/vienna-rna-1.7.2-LDFLAGS.patch,
+  +files/vienna-rna-1.7.2-disable-gd.patch, vienna-rna-1.7.2.ebuild:
+  Fixed ignored LDFLAGS issues and bogus detection of GD support. Also
+  enabled the tests that come with the package.
 
 *vienna-rna-1.7.2 (28 Aug 2008)
 
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.7.2-LDFLAGS.patch b/sci-biology/vienna-rna/files/vienna-rna-1.7.2-LDFLAGS.patch
new file mode 100644
index 000000000000..37e2f8c6a880
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.7.2-LDFLAGS.patch
@@ -0,0 +1,24 @@
+diff -Naur ViennaRNA-1.7.2/Perl/Makefile.am ViennaRNA-1.7.2.new/Perl/Makefile.am
+--- ViennaRNA-1.7.2/Perl/Makefile.am	2007-12-19 05:33:14.000000000 -0500
++++ ViennaRNA-1.7.2.new/Perl/Makefile.am	2008-10-06 14:20:54.000000000 -0400
+@@ -4,7 +4,7 @@
+ 	     RNA.i tmaps.i
+ 
+ Makefile.perl: Makefile.PL Makefile
+-	@PerlCmd@ Makefile.PL
++	@PerlCmd@ Makefile.PL LDDLFLAGS="${LDFLAGS} -shared"
+ 
+ # the perl command repairs some errors in the SWIG CVS version
+ RNA_wrap.c: RNA.i tmaps.i
+diff -Naur ViennaRNA-1.7.2/Readseq/Makefile ViennaRNA-1.7.2.new/Readseq/Makefile
+--- ViennaRNA-1.7.2/Readseq/Makefile	2008-01-23 05:32:00.000000000 -0500
++++ ViennaRNA-1.7.2.new/Readseq/Makefile	2008-10-06 14:21:13.000000000 -0400
+@@ -40,7 +40,7 @@
+ 
+ build: $(SOURCES)
+ 	@echo "Compiling readseq..."
+-	$(CC) $(CFLAGS) -o readseq readseq.c ureadseq.c
++	$(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c
+ 
+ # if using NCBI, uncomment these lines in place of build: above
+ #build: $(SOURCES)
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.7.2-disable-gd.patch b/sci-biology/vienna-rna/files/vienna-rna-1.7.2-disable-gd.patch
new file mode 100644
index 000000000000..6b3bdefa6875
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.7.2-disable-gd.patch
@@ -0,0 +1,16 @@
+# unfortunately, vienna-rna's build system is a little broken and sometimes detects
+# gd in RNAforested but then realizes in g2 that it can't actually build it 
+# resulting in unresolved symbols.
+
+diff -Naur ViennaRNA-1.7.2/RNAforester/configure.in ViennaRNA-1.7.2.new/RNAforester/configure.in
+--- ViennaRNA-1.7.2/RNAforester/configure.in	2006-01-19 10:26:09.000000000 -0500
++++ ViennaRNA-1.7.2.new/RNAforester/configure.in	2008-10-06 14:08:56.000000000 -0400
+@@ -31,7 +31,7 @@
+ CPPFLAGS=["-Ig2-0.70/src/ -Lg2-0.70/ ${CPPFLAGS}"]	
+ 
+ 			    
+-AC_CHECK_LIB(gd,gdImageLine,,)
++dnl AC_CHECK_LIB(gd,gdImageLine,,)
+ 		  
+ dnl Checks for header files.
+ AC_HEADER_STDC
diff --git a/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild b/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild
index 6e40c88002a0..575ee269d3ef 100644
--- a/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild
+++ b/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild
@@ -1,8 +1,8 @@
 # Copyright 1999-2008 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild,v 1.1 2008/08/29 01:21:38 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild,v 1.2 2008/10/06 22:34:27 markusle Exp $
 
-inherit toolchain-funcs multilib eutils versionator
+inherit toolchain-funcs multilib eutils versionator autotools
 
 DESCRIPTION="The Vienna RNA Package - RNA secondary structure prediction and comparison"
 LICENSE="vienna-rna"
@@ -23,6 +23,13 @@ src_unpack() {
 	cd "${S}"
 	epatch "${FILESDIR}"/${PN}-1.6.5-c-fixes.patch
 	epatch "${FILESDIR}"/${P}-gcc4.3.patch
+	epatch "${FILESDIR}"/${P}-LDFLAGS.patch
+	epatch "${FILESDIR}"/${P}-disable-gd.patch
+	eautoreconf
+
+	# we need a separate eautoreconf in RNAforester
+	cd RNAforester
+	eautoreconf
 }
 
 src_compile() {
@@ -36,10 +43,15 @@ src_compile() {
 	cd "${S}"/Readseq
 	sed -e "s:CC=cc:CC=$(tc-getCC):" -e "s:CFLAGS=:CFLAGS=${CFLAGS}:" \
 		-i Makefile || die "Failed patching readseq Makefile."
-	make || die "Failed to compile readseq."
+	emake || die "Failed to compile readseq."
 	# TODO: Add (optional?) support for the NCBI toolkit.
 }
 
+src_test() {
+	cd "${S}"/Perl && emake check || die "Perl tests failed"
+	cd "${S}"/Readseq && emake test || die "Readseq tests failed"
+}
+
 src_install() {
 	make install DESTDIR="${D}" || die "Installation failed."
 	dodoc AUTHORS ChangeLog NEWS README THANKS \