jlec 15/05/26 06:22:16 Modified: ChangeLog Added: glimmer-3.02b.ebuild glimmer-3.02-r3.ebuild Removed: glimmer-3.02-r1.ebuild Log: Version Bump and patch for file collision, thanks Martin Mokrejs for the fix, bug #247394; Respect CXX, CXXFLAGS and LDFLAGS (Portage version: 2.2.20/cvs/Linux x86_64, signed Manifest commit with key E9402A79B03529A2!)
Revision Changes Path 1.11 sci-biology/glimmer/ChangeLog file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/glimmer/ChangeLog?rev=1.11&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/glimmer/ChangeLog?rev=1.11&content-type=text/plain diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/glimmer/ChangeLog?r1=1.10&r2=1.11 Index: ChangeLog =================================================================== RCS file: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- ChangeLog 11 Mar 2013 15:17:43 -0000 1.10 +++ ChangeLog 26 May 2015 06:22:16 -0000 1.11 @@ -1,6 +1,16 @@ # ChangeLog for sci-biology/glimmer -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.10 2013/03/11 15:17:43 jlec Exp $ +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.11 2015/05/26 06:22:16 jlec Exp $ + +*glimmer-3.02b (26 May 2015) +*glimmer-3.02-r3 (26 May 2015) + + 26 May 2015; Justin Lecher <j...@gentoo.org> + +files/glimmer-3.02b-jobserver-fix.patch, +files/glimmer-3.02b-ldflags.patch, + +files/glimmer-3.02b-rename_extract.patch, +glimmer-3.02-r3.ebuild, + +glimmer-3.02b.ebuild, -glimmer-3.02-r1.ebuild: + Version Bump and patch for file collision, thanks Martin Mokrejs for the fix, + bug #247394; Respect CXX, CXXFLAGS and LDFLAGS 11 Mar 2013; Justin Lecher <j...@gentoo.org> metadata.xml: Drop Andrey as maintainer so that bugs get assigned to sci-biology directly @@ -44,4 +54,3 @@ 07 Sep 2008; weaver <wea...@gentoo.org> +metadata.xml, +glimmer-3.02.ebuild: Import from science overlay - 1.1 sci-biology/glimmer/glimmer-3.02b.ebuild file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/glimmer/glimmer-3.02b.ebuild?rev=1.1&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/glimmer/glimmer-3.02b.ebuild?rev=1.1&content-type=text/plain Index: glimmer-3.02b.ebuild =================================================================== # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/glimmer-3.02b.ebuild,v 1.1 2015/05/26 06:22:16 jlec Exp $ EAPI="5" inherit eutils toolchain-funcs MY_PV=${PV//./} DESCRIPTION="An HMM-based microbial gene finding system from TIGR" HOMEPAGE="http://ccb.jhu.edu/software/glimmer"; SRC_URI="http://ccb.jhu.edu/software/${PN}/${PN}${MY_PV}.tar.gz"; LICENSE="Artistic" SLOT="0" IUSE="" KEYWORDS="~amd64 ~x86" DEPEND="" RDEPEND="app-shells/tcsh sci-biology/elph" #S="${WORKDIR}/${PN}${PV}" S="${WORKDIR}/${PN}3.02" PATCHES=( "${FILESDIR}"/${P}-jobserver-fix.patch "${FILESDIR}"/${P}-ldflags.patch "${FILESDIR}"/${P}-rename_extract.patch ) src_prepare() { sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \ -e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths" # Fix Makefile to die on failure sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die # GCC 4.3 include fix sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh || die # sed -i "s+/fs/szgenefinding/Glimmer3/bin+%${D}/bin/glimmer3+" scripts/g3-* || die sed -i "s+/fs/szgenefinding/Glimmer3/scripts+%${D}/share/glimmer/scripts+" scripts/g3-* || die sed -i "s+/nfshomes/adelcher/bin/elph+%${D}/bin/elph+" scripts/g3-* || die sed -i "s/@ if/if/" src/c_make.gen || die # avoid file collision on /usr/bin/extract #247394 epatch "${PATCHES[@]}" } src_compile() { emake \ -C src \ CC=$(tc-getCC) \ CXX=$(tc-getCXX) \ AR=$(tc-getAR) \ CXXFLAGS="${CXXFLAGS}" \ CFLAGS="${CFLAGS}" \ LDFLAGS="${LDFLAGS}" } src_install() { rm bin/test || die dobin bin/* insinto /usr/share/${PN} doins -r scripts dodoc glim302notes.pdf } 1.1 sci-biology/glimmer/glimmer-3.02-r3.ebuild file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/glimmer/glimmer-3.02-r3.ebuild?rev=1.1&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/glimmer/glimmer-3.02-r3.ebuild?rev=1.1&content-type=text/plain Index: glimmer-3.02-r3.ebuild =================================================================== # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/glimmer-3.02-r3.ebuild,v 1.1 2015/05/26 06:22:16 jlec Exp $ EAPI="5" inherit eutils toolchain-funcs MY_PV=${PV//./} DESCRIPTION="An HMM-based microbial gene finding system from TIGR" HOMEPAGE="http://www.cbcb.umd.edu/software/glimmer/"; SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz"; LICENSE="Artistic" SLOT="0" IUSE="" KEYWORDS="~amd64 ~x86" DEPEND="" RDEPEND="app-shells/tcsh" S="${WORKDIR}/${PN}${PV}" PATCHES=( "${FILESDIR}"/${P}-glibc210.patch "${FILESDIR}"/${P}-jobserver-fix.patch "${FILESDIR}"/${P}-ldflags.patch "${FILESDIR}"/${PN}-3.02b-rename_extract.patch ) src_prepare() { sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \ -e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths" # Fix Makefile to die on failure sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die # GCC 4.3 include fix sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh || die epatch "${PATCHES[@]}" } src_compile() { emake \ -C src \ CC=$(tc-getCC) \ CXX=$(tc-getCXX) \ AR=$(tc-getAR) \ CXXFLAGS="${CXXFLAGS}" \ CFLAGS="${CFLAGS}" \ LDFLAGS="${LDFLAGS}" } src_install() { rm bin/test || die dobin bin/* insinto /usr/share/${PN} doins -r scripts dodoc glim302notes.pdf }
