From d783c334a80d17793bf93f0c344a7b94043f47de Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Wed, 10 Mar 2010 21:13:07 +0000 Subject: Respecting LDFLAGS, rebuilding all libs instead of using upstreams bundled ones, bug 308703 (Portage version: 2.2_rc67/cvs/Linux x86_64) --- sci-biology/qrna/ChangeLog | 11 ++++- sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch | 28 +++++++++++ sci-biology/qrna/qrna-2.0.3c-r1.ebuild | 60 ++++++++++++++++++++++++ 3 files changed, 97 insertions(+), 2 deletions(-) create mode 100644 sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch create mode 100644 sci-biology/qrna/qrna-2.0.3c-r1.ebuild (limited to 'sci-biology') diff --git a/sci-biology/qrna/ChangeLog b/sci-biology/qrna/ChangeLog index 99da71bf8c45..0f5150b086a6 100644 --- a/sci-biology/qrna/ChangeLog +++ b/sci-biology/qrna/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-biology/qrna -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/qrna/ChangeLog,v 1.20 2009/08/05 19:32:12 ssuominen Exp $ +# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/qrna/ChangeLog,v 1.21 2010/03/10 21:13:06 jlec Exp $ + +*qrna-2.0.3c-r1 (10 Mar 2010) + + 10 Mar 2010; Justin Lecher (jlec) + +qrna-2.0.3c-r1.ebuild, +files/qrna-2.0.3c-ldflags.patch: + Respecting LDFLAGS, rebuilding all libs instead of using upstreams bundled + ones, #308703 05 Aug 2009; Samuli Suominen qrna-2.0.3c.ebuild, +files/qrna-2.0.3c-glibc-2.10.patch: diff --git a/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch new file mode 100644 index 000000000000..d03f650dd39e --- /dev/null +++ b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch @@ -0,0 +1,28 @@ +diff --git a/src/Makefile b/src/Makefile +index 1d1631b..4fa3af9 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -131,17 +131,17 @@ DEMOS = + all: $(PROGS) + + main: $(OBJ) main.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) + cfgbuild: $(OBJ) cfgbuild.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + eqrna: $(OBJ) eqrna.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + eqrna_sample: $(OBJ) eqrna_sample.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + shuffle: $(OBJ) shuffle.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + rnamat_main: $(OBJ2) rnamat_main.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS) + + main.o: ../src/main.c + $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? diff --git a/sci-biology/qrna/qrna-2.0.3c-r1.ebuild b/sci-biology/qrna/qrna-2.0.3c-r1.ebuild new file mode 100644 index 000000000000..257bffd7f3e6 --- /dev/null +++ b/sci-biology/qrna/qrna-2.0.3c-r1.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/qrna/qrna-2.0.3c-r1.ebuild,v 1.1 2010/03/10 21:13:06 jlec Exp $ + +inherit eutils toolchain-funcs + +DESCRIPTION="Prototype ncRNA genefinder" +HOMEPAGE="http://selab.janelia.org/software.html" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="" + +RDEPEND="dev-lang/perl + sci-biology/hmmer" +DEPEND="${RDEPEND}" + +src_unpack() { + unpack ${A} + cd "${S}" + epatch "${FILESDIR}"/${P}-glibc-2.10.patch + epatch "${FILESDIR}"/${P}-ldflags.patch + sed -e "s/^CC.*/CC = $(tc-getCC)/" \ + -e "s/CFLAGS = -O/CFLAGS = ${CFLAGS}/" \ + -i src/Makefile squid/Makefile squid02/Makefile || die + rm -v squid*/*.a +} + +src_compile() { + cd "${S}"/squid + emake || die + + cd "${S}"/squid02 + emake || die + + cd "${S}"/src + emake || die +} + +src_install () { + cd "${S}"/src + dobin cfgbuild eqrna eqrna_sample main rnamat_main || die + + cd "${S}" + dobin scripts/* || die + + newdoc 00README README || die + insinto /usr/share/doc/${PF} + doins documentation/* || die + + insinto /usr/share/${PN}/data + doins lib/* || die + insinto /usr/share/${PN}/demos + doins Demos/* || die + + # Sets the path to the QRNA data files. + doenvd "${FILESDIR}"/26qrna || die +} -- cgit v1.2.3-65-gdbad