From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1SWv0s-0005dc-3O for garchives@archives.gentoo.org; Tue, 22 May 2012 19:44:58 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id C5643E0769; Tue, 22 May 2012 19:43:24 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 85B32E0769 for ; Tue, 22 May 2012 19:43:24 +0000 (UTC) Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id E5C9A1B4019 for ; Tue, 22 May 2012 19:43:17 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id 39799E542A for ; Tue, 22 May 2012 19:43:15 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1337713671.5d074abd7b1d4ea82db2fd5ea860ac8f9afd80cb.jlec@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/mira/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/mira/ChangeLog sci-biology/mira/mira-3.2.1-r2.ebuild sci-biology/mira/mira-3.2.1.17-r1.ebuild sci-biology/mira/mira-3.2.1.20.ebuild sci-biology/mira/mira-3.4.0.1.ebuild X-VCS-Directories: sci-biology/mira/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 5d074abd7b1d4ea82db2fd5ea860ac8f9afd80cb X-VCS-Branch: master Date: Tue, 22 May 2012 19:43:15 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: 1f25195f-f700-456b-b647-21a1ea41b39d X-Archives-Hash: f86e1c3026c0ff72d74abd8eea7ca2d6 commit: 5d074abd7b1d4ea82db2fd5ea860ac8f9afd80cb Author: Justin Lecher gentoo org> AuthorDate: Tue May 22 19:07:51 2012 +0000 Commit: Justin Lecher gentoo org> CommitDate: Tue May 22 19:07:51 2012 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3D5d074abd sci-biology/mira: Add missing eutils.eclass, bump to EAPI=3D4, remove usa= ge of base.eclass; drop old (Portage version: 2.2.0_alpha107/git/Linux x86_64, unsigned Manifest comm= it) --- sci-biology/mira/ChangeLog | 7 +++- sci-biology/mira/mira-3.2.1-r2.ebuild | 57 ------------------------= ----- sci-biology/mira/mira-3.2.1.17-r1.ebuild | 57 ------------------------= ----- sci-biology/mira/mira-3.2.1.20.ebuild | 58 ------------------------= ------ sci-biology/mira/mira-3.4.0.1.ebuild | 27 ++++++++------ 5 files changed, 22 insertions(+), 184 deletions(-) diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog index 0982f99..4cd234f 100644 --- a/sci-biology/mira/ChangeLog +++ b/sci-biology/mira/ChangeLog @@ -1,7 +1,12 @@ # ChangeLog for sci-biology/mira -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ =20 + 22 May 2012; Justin Lecher -mira-3.2.1-r2.ebuild, + -mira-3.2.1.17-r1.ebuild, -mira-3.2.1.20.ebuild, mira-3.4.0.1.ebuild: + Add missing eutils.eclass, bump to EAPI=3D4, remove usage of base.ecla= ss; drop + old + *mira-3.4.0.1 (08 Dec 2011) =20 08 Dec 2011; Martin Mokrejs diff --git a/sci-biology/mira/mira-3.2.1-r2.ebuild b/sci-biology/mira/mir= a-3.2.1-r2.ebuild deleted file mode 100644 index c110959..0000000 --- a/sci-biology/mira/mira-3.2.1-r2.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3D3 - -MIRA_3RDPARTY_PV=3D"17-04-2010" - -inherit autotools base multilib - -DESCRIPTION=3D"Whole Genome Shotgun and EST Sequence Assembler for Sange= r, 454 and Solexa / Illumina" -HOMEPAGE=3D"http://www.chevreux.org/projects_mira.html" -SRC_URI=3D"mirror://sourceforge/mira-assembler/${P}.tar.bz2 - mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.t= ar.bz2" - -LICENSE=3D"GPL-2" -SLOT=3D"0" -IUSE=3D"" -KEYWORDS=3D"~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" - -CDEPEND=3D">=3Ddev-libs/boost-1.41.0-r3 - dev-util/google-perftools" -DEPEND=3D"${CDEPEND} - dev-libs/expat" -RDEPEND=3D"${CDEPEND} - sci-biology/smalt-bin - sci-biology/ssaha2-bin" - -src_prepare() { - find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/= flex -+/' || die - epatch "${FILESDIR}"/${PN}-3.0.0-asneeded.patch - # http://sourceforge.net/apps/trac/mira-assembler/ticket/47 - epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch - epatch "${FILESDIR}"/libtool.m4.patch - AT_M4DIR=3D"config/m4" eautoreconf -} - -src_configure() { - econf \ - --with-boost=3D"${EPREFIX}"/usr/$(get_libdir) \ - --with-boost-libdir=3D"${EPREFIX}"/usr/$(get_libdir) \ - --with-boost-thread=3Dboost_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() { - einstall || die - dodoc AUTHORS GETTING_STARTED NEWS README* HELP_WANTED THANKS INSTALL - find doc/docs/man -type f | xargs doman - find doc/docs/texinfo -type f | xargs doinfo - dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} -} diff --git a/sci-biology/mira/mira-3.2.1.17-r1.ebuild b/sci-biology/mira/= mira-3.2.1.17-r1.ebuild deleted file mode 100644 index 04b3767..0000000 --- a/sci-biology/mira/mira-3.2.1.17-r1.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3D3 - -MIRA_3RDPARTY_PV=3D"17-04-2010" - -inherit autotools base multilib - -DESCRIPTION=3D"Whole Genome Shotgun and EST Sequence Assembler for Sange= r, 454 and Solexa / Illumina" -HOMEPAGE=3D"http://www.chevreux.org/projects_mira.html" -SRC_URI=3D"mirror://sourceforge/mira-assembler/${P}.tar.bz2 - mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.t= ar.bz2" - -LICENSE=3D"GPL-2" -SLOT=3D"0" -IUSE=3D"" -KEYWORDS=3D"~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" - -CDEPEND=3D">=3Ddev-libs/boost-1.41.0-r3 - dev-util/google-perftools" -DEPEND=3D"${CDEPEND} - dev-libs/expat" -RDEPEND=3D"${CDEPEND} - sci-biology/smalt-bin - sci-biology/ssaha2-bin" - -src_prepare() { - find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/= flex -+/' || die - epatch "${FILESDIR}"/${PN}-3.0.0-asneeded.patch - # http://sourceforge.net/apps/trac/mira-assembler/ticket/47 - epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch - epatch "${FILESDIR}"/libtool.m4.patch - AT_M4DIR=3D"config/m4" eautoreconf -} - -src_configure() { - econf \ - --with-boost=3D"${EPREFIX}"/usr/$(get_libdir) \ - --with-boost-libdir=3D"${EPREFIX}"/usr/$(get_libdir) \ - --with-boost-thread=3Dboost_thread-mt -} - -src_compile() { - base_src_compile - # TODO: resolve docbook incompatibility for building docs - if use doc; then emake -C doc clean docs || die "This will probably die= because upstream did not imrove re-genartion of the docs yet."; fi -} - -src_install() { - einstall || die - dodoc AUTHORS GETTING_STARTED NEWS README* HELP_WANTED THANKS INSTALL - find doc/docs/man -type f | xargs doman - find doc/docs/texinfo -type f | xargs doinfo - dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} -} diff --git a/sci-biology/mira/mira-3.2.1.20.ebuild b/sci-biology/mira/mir= a-3.2.1.20.ebuild deleted file mode 100644 index 3ea8ce1..0000000 --- a/sci-biology/mira/mira-3.2.1.20.ebuild +++ /dev/null @@ -1,58 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3D3 - -MIRA_3RDPARTY_PV=3D"17-04-2010" - -inherit autotools base multilib - -DESCRIPTION=3D"Whole Genome Shotgun and EST Sequence Assembler for Sange= r, 454 and Solexa / Illumina" -HOMEPAGE=3D"http://www.chevreux.org/projects_mira.html" -SRC_URI=3D"mirror://sourceforge/mira-assembler/${P}.tar.bz2 - mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.t= ar.bz2" - -LICENSE=3D"GPL-2" -SLOT=3D"0" -IUSE=3D"" -KEYWORDS=3D"~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" - -CDEPEND=3D">=3Ddev-libs/boost-1.41.0-r3 - dev-util/google-perftools" -DEPEND=3D"${CDEPEND} - dev-libs/expat" -RDEPEND=3D"${CDEPEND} - sci-biology/smalt-bin - sci-biology/ssaha2-bin" - -src_prepare() { - find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/= flex -+/' || die - epatch "${FILESDIR}"/${PN}-3.0.0-asneeded.patch - # http://sourceforge.net/apps/trac/mira-assembler/ticket/47 - epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch - epatch "${FILESDIR}"/libtool.m4.patch - AT_M4DIR=3D"config/m4" eautoreconf - #epatch "${FILESDIR}"/libtool.patch -} - -src_configure() { - econf \ - --with-boost=3D"${EPREFIX}"/usr/$(get_libdir) \ - --with-boost-libdir=3D"${EPREFIX}"/usr/$(get_libdir) \ - --with-boost-thread=3Dboost_thread-mt -} - -src_compile() { - base_src_compile - # TODO: resolve docbook incompatibility for building docs - if use doc; then emake -C doc clean docs || die "This will probably die= because upstream did not imrove re-genartion of the docs yet."; fi -} - -src_install() { - einstall || die - dodoc AUTHORS GETTING_STARTED NEWS README* HELP_WANTED THANKS INSTALL - find doc/docs/man -type f | xargs doman - find doc/docs/texinfo -type f | xargs doinfo - dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} -} diff --git a/sci-biology/mira/mira-3.4.0.1.ebuild b/sci-biology/mira/mira= -3.4.0.1.ebuild index 78d1cc3..45d9911 100644 --- a/sci-biology/mira/mira-3.4.0.1.ebuild +++ b/sci-biology/mira/mira-3.4.0.1.ebuild @@ -1,16 +1,17 @@ -# Copyright 1999-2011 Gentoo Foundation +# Copyright 1999-2012 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ =20 -EAPI=3D3 +EAPI=3D4 =20 MIRA_3RDPARTY_PV=3D"09-09-2011" =20 -inherit autotools base multilib +inherit autotools eutils multilib =20 DESCRIPTION=3D"Whole Genome Shotgun and EST Sequence Assembler for Sange= r, 454 and Solexa / Illumina" HOMEPAGE=3D"http://www.chevreux.org/projects_mira.html" -SRC_URI=3D"mirror://sourceforge/mira-assembler/${P}.tar.bz2 +SRC_URI=3D" + mirror://sourceforge/mira-assembler/${P}.tar.bz2 mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.t= ar.bz2" =20 LICENSE=3D"GPL-2" @@ -18,8 +19,9 @@ SLOT=3D"0" IUSE=3D"" KEYWORDS=3D"~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" =20 -CDEPEND=3D">=3Ddev-libs/boost-1.41.0-r3 - dev-util/google-perftools" +CDEPEND=3D" + >=3Ddev-libs/boost-1.41.0-r3 + dev-util/google-perftools" DEPEND=3D"${CDEPEND} dev-libs/expat" RDEPEND=3D"${CDEPEND} @@ -29,8 +31,9 @@ RDEPEND=3D"${CDEPEND} src_prepare() { find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/= flex -+/' || die # http://sourceforge.net/apps/trac/mira-assembler/ticket/47 - epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch - epatch "${FILESDIR}"/libtool.m4.patch + epatch \ + "${FILESDIR}"/mira_left_clip.readpool.C.patch \ + "${FILESDIR}"/libtool.m4.patch AT_M4DIR=3D"config/m4" eautoreconf #epatch "${FILESDIR}"/libtool.patch } @@ -43,13 +46,15 @@ src_configure() { } =20 src_compile() { - base_src_compile + default # TODO: resolve docbook incompatibility for building docs - if use doc; then emake -C doc clean docs || die "This will probably die= because upstream did not improve re-generation of the docs yet."; fi + if use doc; then + emake -C doc clean docs || die "This will probably die because upstrea= m did not improve re-generation of the docs yet." + fi } =20 src_install() { - einstall || die + default dodoc AUTHORS GETTING_STARTED NEWS README* HELP_WANTED THANKS INSTALL find doc/docs/man -type f | xargs doman find doc/docs/texinfo -type f | xargs doinfo