pinkbyte 14/10/17 08:07:31 Modified: ChangeLog tophat-1.0.12.ebuild Log: Non-maintainer commit: fix building, approved by Justin Lecher (Portage version: 2.2.12/cvs/Linux x86_64, signed Manifest commit with key 0x1F357D42)
Revision Changes Path 1.13 sci-biology/tophat/ChangeLog file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/tophat/ChangeLog?rev=1.13&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/tophat/ChangeLog?rev=1.13&content-type=text/plain diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/tophat/ChangeLog?r1=1.12&r2=1.13 Index: ChangeLog =================================================================== RCS file: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- ChangeLog 6 Mar 2014 09:46:50 -0000 1.12 +++ ChangeLog 17 Oct 2014 08:07:31 -0000 1.13 @@ -1,6 +1,9 @@ # ChangeLog for sci-biology/tophat # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v 1.12 2014/03/06 09:46:50 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v 1.13 2014/10/17 08:07:31 pinkbyte Exp $ + + 17 Oct 2014; Sergey Popov <[email protected]> tophat-1.0.12.ebuild: + Non-maintainer commit: fix building, approved by Justin Lecher *tophat-2.0.9 (06 Mar 2014) 1.6 sci-biology/tophat/tophat-1.0.12.ebuild file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/tophat/tophat-1.0.12.ebuild?rev=1.6&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/tophat/tophat-1.0.12.ebuild?rev=1.6&content-type=text/plain diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/tophat/tophat-1.0.12.ebuild?r1=1.5&r2=1.6 Index: tophat-1.0.12.ebuild =================================================================== RCS file: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-1.0.12.ebuild,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- tophat-1.0.12.ebuild 25 Apr 2012 16:39:53 -0000 1.5 +++ tophat-1.0.12.ebuild 17 Oct 2014 08:07:31 -0000 1.6 @@ -1,6 +1,6 @@ -# Copyright 1999-2012 Gentoo Foundation +# Copyright 1999-2014 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-1.0.12.ebuild,v 1.5 2012/04/25 16:39:53 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-1.0.12.ebuild,v 1.6 2014/10/17 08:07:31 pinkbyte Exp $ EAPI="2" @@ -19,8 +19,12 @@ RDEPEND="sci-biology/bowtie" src_prepare() { - # fix gcc-4.4 missing include + # fix missing includes sed -i '/#include <string>/ a #include <stdio.h>' "${S}/src/gff_juncs.cpp" || die + sed -i \ + -e '/#include <stdio.h>/ a #include <unistd.h>' \ + "${S}/src/prep_reads.cpp" \ + "${S}/src/extract_reads.cpp" || die # fix parallel make race sed -i -e 's/\$(top_builddir)\/src\///g' src/Makefile.am || die # remove broken arch-dependent CFLAGS setting
