* [gentoo-commits] gentoo-x86 commit in sci-biology/mira: ChangeLog mira-4.0.2.ebuild
@ 2015-01-23 11:48 Justin Lecher (jlec)
0 siblings, 0 replies; 2+ messages in thread
From: Justin Lecher (jlec) @ 2015-01-23 11:48 UTC (permalink / raw
To: gentoo-commits
jlec 15/01/23 11:48:13
Modified: ChangeLog
Added: mira-4.0.2.ebuild
Log:
sci-biology/mira: Version BUmp, thanks Martin Mokrejš for the work
(Portage version: 2.2.15/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)
Revision Changes Path
1.29 sci-biology/mira/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mira/ChangeLog?rev=1.29&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mira/ChangeLog?rev=1.29&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mira/ChangeLog?r1=1.28&r2=1.29
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v
retrieving revision 1.28
retrieving revision 1.29
diff -u -r1.28 -r1.29
--- ChangeLog 23 Jan 2015 11:25:31 -0000 1.28
+++ ChangeLog 23 Jan 2015 11:48:13 -0000 1.29
@@ -1,6 +1,11 @@
# ChangeLog for sci-biology/mira
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v 1.28 2015/01/23 11:25:31 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v 1.29 2015/01/23 11:48:13 jlec Exp $
+
+*mira-4.0.2 (23 Jan 2015)
+
+ 23 Jan 2015; Justin Lecher <jlec@gentoo.org> +mira-4.0.2.ebuild:
+ Version BUmp, thanks Martin Mokrejš for the work
23 Jan 2015; Justin Lecher <jlec@gentoo.org> mira-3.9.18.ebuild:
Add workaroung for m4 dir location, #536172
1.1 sci-biology/mira/mira-4.0.2.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mira/mira-4.0.2.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mira/mira-4.0.2.ebuild?rev=1.1&content-type=text/plain
Index: mira-4.0.2.ebuild
===================================================================
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-4.0.2.ebuild,v 1.1 2015/01/23 11:48:13 jlec Exp $
EAPI=5
MIRA_3RDPARTY_PV="06-07-2012"
MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat)
inherit autotools eutils multilib
DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina"
HOMEPAGE="http://www.chevreux.org/projects_mira.html"
SRC_URI="
http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2
mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
# http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2
# mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
S="${WORKDIR}"/"${PN}"-"${MY_PV}"
SLOT="0"
LICENSE="GPL-2"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
IUSE="doc"
CDEPEND="
dev-libs/boost
dev-util/google-perftools"
DEPEND="${CDEPEND}
app-editors/vim-core
dev-libs/expat"
RDEPEND="${CDEPEND}"
#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED
# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf )
DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS )
src_prepare() {
find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
epatch \
"${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch
sed \
-e "s:-O[23]::g" \
-e "s:-funroll-loops::g" \
-i configure.ac || die
eautoreconf
}
src_configure() {
econf \
--with-boost="${EPREFIX}/usr/$(get_libdir)" \
--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \
--with-boost-thread=boost_thread-mt
}
#src_compile() {
# base_src_compile
# # TODO: resolve docbook incompatibility for building docs
# if use doc; then emake -C doc clean docs || die; fi
#}
src_install() {
default
dodoc ${DOCS[@]}
dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta}
}
pkg_postinst() {
einfo "Documentation is no longer built, you can find it at:"
einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
}
^ permalink raw reply [flat|nested] 2+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-biology/mira: ChangeLog mira-4.0.2.ebuild
@ 2015-01-25 17:04 Justin Lecher (jlec)
0 siblings, 0 replies; 2+ messages in thread
From: Justin Lecher (jlec) @ 2015-01-25 17:04 UTC (permalink / raw
To: gentoo-commits
jlec 15/01/25 17:04:35
Modified: ChangeLog mira-4.0.2.ebuild
Log:
sci-biology/mira: Build fix for newer gcc, #537564
(Portage version: 2.2.15/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)
Revision Changes Path
1.30 sci-biology/mira/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mira/ChangeLog?rev=1.30&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mira/ChangeLog?rev=1.30&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mira/ChangeLog?r1=1.29&r2=1.30
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v
retrieving revision 1.29
retrieving revision 1.30
diff -u -r1.29 -r1.30
--- ChangeLog 23 Jan 2015 11:48:13 -0000 1.29
+++ ChangeLog 25 Jan 2015 17:04:35 -0000 1.30
@@ -1,6 +1,10 @@
# ChangeLog for sci-biology/mira
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v 1.29 2015/01/23 11:48:13 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v 1.30 2015/01/25 17:04:35 jlec Exp $
+
+ 25 Jan 2015; Justin Lecher <jlec@gentoo.org> mira-4.0.2.ebuild,
+ +files/mira-4.0.2-cout.patch:
+ Build fix for newer gcc, #537564
*mira-4.0.2 (23 Jan 2015)
1.2 sci-biology/mira/mira-4.0.2.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mira/mira-4.0.2.ebuild?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mira/mira-4.0.2.ebuild?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mira/mira-4.0.2.ebuild?r1=1.1&r2=1.2
Index: mira-4.0.2.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-4.0.2.ebuild,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- mira-4.0.2.ebuild 23 Jan 2015 11:48:13 -0000 1.1
+++ mira-4.0.2.ebuild 25 Jan 2015 17:04:35 -0000 1.2
@@ -1,6 +1,6 @@
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-4.0.2.ebuild,v 1.1 2015/01/23 11:48:13 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-4.0.2.ebuild,v 1.2 2015/01/25 17:04:35 jlec Exp $
EAPI=5
@@ -39,7 +39,8 @@
src_prepare() {
find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
epatch \
- "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch
+ "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \
+ "${FILESDIR}"/${P}-cout.patch
sed \
-e "s:-O[23]::g" \
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2015-01-23 11:48 Justin Lecher (jlec)
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