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

Package-Manager: portage-2.2_rc11/cvs/Linux 2.6.26-SENTINEL-2 i686

5 files changed, 66 insertions, 6 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/Manifest b/sci-biology/vienna-rna/Manifest
index 5a4ff0ca75e5..0962e686c95c 100644
--- a/sci-biology/vienna-rna/Manifest
+++ b/sci-biology/vienna-rna/Manifest
@@ -1,10 +1,12 @@
 AUX vienna-rna-1.6.5-c-fixes.patch 728 RMD160 5f427bb976200f58599b1878ca7273844b21aac0 SHA1 7089237c787d780d53b92c4c38ba73ec60b81218 SHA256 49955a6244eb3be73f8d2472f3a4f9b8d1f8f92ba11327961b901a2c1f1e24d8
+AUX vienna-rna-1.7.2-LDFLAGS.patch 978 RMD160 ab19413ba9c5468e7d755c0eb979462d00112cb0 SHA1 5f29863572d3c16fa7616ee7aa0d2e140d94c497 SHA256 0c7db17c7a1a8a075e26f6b98b19c84a3f98f9ecdaa06755e4e426fcb1b8ce8c
+AUX vienna-rna-1.7.2-disable-gd.patch 662 RMD160 3a4017911729aec9dca467242ac5570c05dc1b71 SHA1 5795bdc2ee5e14242f122f590239d77acd8ff3b2 SHA256 48e90848aa061c7339eea4966cb5e47831213af447272c20628d3b43c1fe0d6f
 AUX vienna-rna-1.7.2-gcc4.3.patch 2738 RMD160 c559c768b8c4e9b92f9bdbd66f5e3ff12ba5e5df SHA1 d1c1f8b9fa8109ad58613db53c72d8ae921990ce SHA256 234374db06aacef6cf7856fcb61642c501d8b03cd5bd579c167e1455774f5610
 DIST ViennaRNA-1.4.tar.gz 483047 RMD160 31ce5f6e3f1adbd0c8e4759c243764523828a258 SHA1 fde493bfeeb443cb427bbe58b0d4daa446771ccf SHA256 8021ebe40d4fdf609fc9ad9aa7525736f69146666b6222d78d1016c20707522f
 DIST ViennaRNA-1.7.2.tar.gz 1298982 RMD160 768f53ba9e0f784b066ae485451eb0abd6f6631c SHA1 36a4bfcf88599afc479be14bc324ef4ce9d629a3 SHA256 202887653033de9e50644acd5c3d8607f215d6c84eef9d68a936837edf71a00e
 DIST ViennaRNA-1.7.tar.gz 1249073 RMD160 7f07ae00f0efbd992f7d7dfdb3c215dde7835355 SHA1 3856b4d18e09bc640e7e0aa344346efbe31b2421 SHA256 b1df6ec6c68ecaf5256cb0a3fbb3cbee4dc84138254499f3c471ca5afbb82c58
 EBUILD vienna-rna-1.4.ebuild 2411 RMD160 df875d116e09cb23ae6fbda5d59bf12202584aa2 SHA1 7cbe01e26e40d1fb92d6bece04f1ceba543c42b8 SHA256 db9071a8513e921026a11fcb1a57751dfdece8448e42f07d4b702af1736bf7d6
 EBUILD vienna-rna-1.7.0.ebuild 1795 RMD160 35771c487766583375c59d513bd3bac59e2aaaa6 SHA1 01da384c1830df80f232c4e361b96a28b77acc81 SHA256 4a2044beeb9070f2c415c491b94eadb74972db2987806e524da1c7927686c499
-EBUILD vienna-rna-1.7.2.ebuild 1787 RMD160 937574695e34e7a5b2dcaab38d14fd5801b21221 SHA1 97227df81bdd9eeba6cf5ae3dce88732f6f084c3 SHA256 8b6bb15d35bf5158251524dcfd6a0dca6d5ce06c02b04d8fc5067ec14b2eab14
-MISC ChangeLog 2892 RMD160 d6e093f408bb070b73f78ede64ccb162070b72b1 SHA1 75730c01f9c00cb04111b67af53880dc23a7c617 SHA256 27830b5fe43e4e696249963efaa0e9893cf7c6d7a7ea49821409e8d485d8edf0
+EBUILD vienna-rna-1.7.2.ebuild 2112 RMD160 8e83a49c3171c3bc1e5759fdde7e2f8ebe499383 SHA1 c2e3ce8b5252b859dfde1cb6ebfece65aadb1f59 SHA256 6a2ef3e0285e6d174461fa5f07152cdfdfa409abd998ff3eefd61962013163f4
+MISC ChangeLog 3175 RMD160 af584ddae8a718afc811efc6f8452f6c59a86872 SHA1 d3e9d9e0c07e33b81fd7d7ccd7f6a19666a0a70b SHA256 1c39b4623a83bf832fe4535f04f48d59a832fbe289cf53ccbdab7dfbe6d9ac21
 MISC metadata.xml 1435 RMD160 539ba60c7a5ca6656e5716b61e2bbf44bb5b9c27 SHA1 77777cd6e84bb6e799e0bfb357580c6a3edfbb91 SHA256 93f911332c6232466324a14891ee9ede4fb23633b12b8ea42ed8cfa2c32b294b
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 \