sci-biology/mira: Add missing eutils.eclass, bump to EAPI=4, remove usage of base.eclass; drop old

(Portage version: 2.2.0_alpha107/git/Linux x86_64, unsigned Manifest commit)

6 files changed, 22 insertions, 188 deletions

diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index 0982f998f..4cd234f7e 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: $
 
+  22 May 2012; Justin Lecher <jlec@gentoo.org> -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=4, remove usage of base.eclass; drop
+  old
+
 *mira-3.4.0.1 (08 Dec 2011)
 
   08 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest
index 4ae708ab5..2bebb9aa7 100644
--- a/sci-biology/mira/Manifest
+++ b/sci-biology/mira/Manifest
@@ -1,6 +1,2 @@
-DIST mira-3.2.1.17.tar.bz2 9611305 RMD160 b9a124c572763fa8923c1b1ee5b12e54b881b67c SHA1 a2731ba4da5af9f0c575ff355a481ea0190dd898 SHA256 2d79ebbbfc6801ff500cabd79cd63358e50296fbdcd1aed4028ea52503d76f8c
-DIST mira-3.2.1.20.tar.bz2 9619538 RMD160 9838827d50b7ee2a726be4ee3badec25bd5c5799 SHA1 73fd04dffb3e3a7bb5425b16e565f5e85584e215 SHA256 38eb701b6585696a70b7ad8aae7285059415c7b335c9138c014002d2a8289a83
-DIST mira-3.2.1.tar.bz2 9626154 RMD160 b998226fe4ea0efbe6023dac8b073af1782167b9 SHA1 432d1ecd2acb62a8584f29a10b55943165cd0586 SHA256 86a2c00d182573008ef41f7725aec72ea69756ea9f3dc7e798a7d253a47f8bd7
 DIST mira-3.4.0.1.tar.bz2 10262667 RMD160 dc008eeb8dd291f9255f7b50ec5e0f888004cddd SHA1 a993c4e30d85b063768d3c5c1af7c3a5d5ff2aa4 SHA256 cafe45601b3c143ac142c022e1fc0a21544e880bb226897824de5dbf6d516d7e
 DIST mira_3rdparty_09-09-2011.tar.bz2 31285 RMD160 9c890ed445b75c2caf46c91adfb7040e7e9309c1 SHA1 c650b903861218854b8976bf3ebe977ec06afe99 SHA256 0e00cd0efff5601d559ee8d40d29b8d3b87db3f4cd5b7bfa5970501ea43f840b
-DIST mira_3rdparty_17-04-2010.tar.bz2 31296 RMD160 888a38f865963b3109d3a331604e079010b55d81 SHA1 5f2fbe3e2e1bb5c5de44d414963e57b8dbcf760c SHA256 ec2c77508d75b7c28d3d26137ab69648b1ed653af93d486245ad0e4624e332b2
diff --git a/sci-biology/mira/mira-3.2.1-r2.ebuild b/sci-biology/mira/mira-3.2.1-r2.ebuild
deleted file mode 100644
index c110959eb..000000000
--- 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=3
-
-MIRA_3RDPARTY_PV="17-04-2010"
-
-inherit autotools base 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="mirror://sourceforge/mira-assembler/${P}.tar.bz2
-	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-
-CDEPEND=">=dev-libs/boost-1.41.0-r3
-		dev-util/google-perftools"
-DEPEND="${CDEPEND}
-	dev-libs/expat"
-RDEPEND="${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="config/m4" 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() {
-	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 04b37674c..000000000
--- 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=3
-
-MIRA_3RDPARTY_PV="17-04-2010"
-
-inherit autotools base 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="mirror://sourceforge/mira-assembler/${P}.tar.bz2
-	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-
-CDEPEND=">=dev-libs/boost-1.41.0-r3
-		dev-util/google-perftools"
-DEPEND="${CDEPEND}
-	dev-libs/expat"
-RDEPEND="${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="config/m4" 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 "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/mira-3.2.1.20.ebuild
deleted file mode 100644
index 3ea8ce177..000000000
--- 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=3
-
-MIRA_3RDPARTY_PV="17-04-2010"
-
-inherit autotools base 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="mirror://sourceforge/mira-assembler/${P}.tar.bz2
-	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-
-CDEPEND=">=dev-libs/boost-1.41.0-r3
-		dev-util/google-perftools"
-DEPEND="${CDEPEND}
-	dev-libs/expat"
-RDEPEND="${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="config/m4" eautoreconf
-	#epatch "${FILESDIR}"/libtool.patch
-}
-
-src_configure() {
-	econf \
-		--with-boost="${EPREFIX}"/usr/$(get_libdir) \
-		--with-boost-libdir="${EPREFIX}"/usr/$(get_libdir) \
-		--with-boost-thread=boost_thread-mt
-}
-
-src_compile() {
-	base_src_compile
-	# TODO: resolve docbook incompatibility for building docs
-	if use doc; then emake -C doc clean docs || die "This will probably die because upstream did not imrove re-genartion of the docs yet."; fi
-}
-
-src_install() {
-	einstall || die
-	dodoc AUTHORS GETTING_STARTED NEWS README* HELP_WANTED THANKS INSTALL
-	find doc/docs/man -type f | xargs doman
-	find doc/docs/texinfo -type f | xargs doinfo
-	dobin "${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 78d1cc367..45d9911fb 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: $
 
-EAPI=3
+EAPI=4
 
 MIRA_3RDPARTY_PV="09-09-2011"
 
-inherit autotools base multilib
+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="mirror://sourceforge/mira-assembler/${P}.tar.bz2
+SRC_URI="
+	mirror://sourceforge/mira-assembler/${P}.tar.bz2
 	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
 
 LICENSE="GPL-2"
@@ -18,8 +19,9 @@ SLOT="0"
 IUSE=""
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
 
-CDEPEND=">=dev-libs/boost-1.41.0-r3
-		dev-util/google-perftools"
+CDEPEND="
+	>=dev-libs/boost-1.41.0-r3
+	dev-util/google-perftools"
 DEPEND="${CDEPEND}
 	dev-libs/expat"
 RDEPEND="${CDEPEND}
@@ -29,8 +31,9 @@ RDEPEND="${CDEPEND}
 src_prepare() {
 	find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
 	# http://sourceforge.net/apps/trac/mira-assembler/ticket/47
-	epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch
-	epatch "${FILESDIR}"/libtool.m4.patch
+	epatch \
+		"${FILESDIR}"/mira_left_clip.readpool.C.patch \
+		"${FILESDIR}"/libtool.m4.patch
 	AT_M4DIR="config/m4" eautoreconf
 	#epatch "${FILESDIR}"/libtool.patch
 }
@@ -43,13 +46,15 @@ src_configure() {
 }
 
 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 upstream did not improve re-generation of the docs yet."
+	fi
 }
 
 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