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* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2011-06-10 15:23 Martin Mokrejs
  0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2011-06-10 15:23 UTC (permalink / raw
  To: gentoo-commits

commit:     4d513f25a4f25b460f1d396543851760bbc54bcf
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 23 12:59:22 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 23 12:59:22 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4d513f25

sci-biology/mira: revbump to force inclusion on dev-util/google-perftools deps

(Portage version: 2.1.9.49/git/Linux i686, unsigned Manifest commit)

---
 .../{mira-3.2.1-r1.ebuild => mira-3.2.1-r2.ebuild} |    3 ++-
 sci-biology/mira/mira-3.2.1.17-r1.ebuild           |    5 +++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/sci-biology/mira/mira-3.2.1-r1.ebuild b/sci-biology/mira/mira-3.2.1-r2.ebuild
similarity index 96%
rename from sci-biology/mira/mira-3.2.1-r1.ebuild
rename to sci-biology/mira/mira-3.2.1-r2.ebuild
index 020876c..a4de8cc 100644
--- a/sci-biology/mira/mira-3.2.1-r1.ebuild
+++ b/sci-biology/mira/mira-3.2.1-r2.ebuild
@@ -18,7 +18,8 @@ SLOT="0"
 IUSE=""
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
 
-CDEPEND=">=dev-libs/boost-1.41.0-r3"
+CDEPEND=">=dev-libs/boost-1.41.0-r3
+		dev-util/google-perftools"
 DEPEND="${CDEPEND}
 	dev-libs/expat"
 RDEPEND="${CDEPEND}

diff --git a/sci-biology/mira/mira-3.2.1.17-r1.ebuild b/sci-biology/mira/mira-3.2.1.17-r1.ebuild
index 49e97f6..9fe96ff 100644
--- a/sci-biology/mira/mira-3.2.1.17-r1.ebuild
+++ b/sci-biology/mira/mira-3.2.1.17-r1.ebuild
@@ -20,7 +20,8 @@ KEYWORDS=""
 # masked because of 'libtool: Version mismatch error.  This is libtool 2.4, but the definition of this LT_INIT comes from libtool 2.2.6b. You should recreate aclocal.m4 with macros from libtool 2.4 and run autoconf again.', dyeing at src/examples_programming/
 #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
 
-CDEPEND=">=dev-libs/boost-1.41.0-r3"
+CDEPEND=">=dev-libs/boost-1.41.0-r3
+		dev-util/google-perftools"
 DEPEND="${CDEPEND}
 	dev-libs/expat"
 RDEPEND="${CDEPEND}
@@ -45,7 +46,7 @@ src_configure() {
 src_compile() {
 	base_src_compile
 	# TODO: resolve docbook incompatibility for building docs
-	if use doc; then emake -C doc clean docs || die; fi
+	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() {



^ permalink raw reply related	[flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2014-04-20  0:18 Martin Mokrejs
  0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2014-04-20  0:18 UTC (permalink / raw
  To: gentoo-commits

commit:     b7ea348e4b0d9a92113696cc79860bdec3e5f3ce
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 20 00:16:46 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 20 00:16:46 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b7ea348e

sci-biology/mira-4.0.2: version bump

Package-Manager: portage-2.2.7

---
 sci-biology/mira/{mira-4.0.1.ebuild => mira-4.0.2.ebuild} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/sci-biology/mira/mira-4.0.1.ebuild b/sci-biology/mira/mira-4.0.2.ebuild
similarity index 100%
rename from sci-biology/mira/mira-4.0.1.ebuild
rename to sci-biology/mira/mira-4.0.2.ebuild


^ permalink raw reply	[flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2014-04-12 12:35 Martin Mokrejs
  0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2014-04-12 12:35 UTC (permalink / raw
  To: gentoo-commits

commit:     97b1cf9bacba1cede303203987f487a1290bc60e
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 12 12:28:06 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 12 12:28:06 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=97b1cf9b

sci-biology/mira-4.0.1: bump to current recommended bugfix release

Package-Manager: portage-2.2.7

---
 sci-biology/mira/ChangeLog         |  5 +++
 sci-biology/mira/mira-4.0.1.ebuild | 76 ++++++++++++++++++++++++++++++++++++++
 2 files changed, 81 insertions(+)

diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index 4dd3e5b..b5f200e 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*mira-4.0.1 (12 Apr 2014)
+
+  12 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +mira-4.0.1.ebuild:
+  sci-biology/mira-4.0.1: bump to current recommended bugfix release
+
   06 Jan 2014; Justin Lecher <jlec@gentoo.org> -mira-3.4.0.1.ebuild,
   -mira-3.4.1.1.ebuild, -mira-3.9.9.ebuild, -mira-3.9.15.ebuild,
   -mira-4.0_rc2.ebuild, mira-4.0_rc4.ebuild:

diff --git a/sci-biology/mira/mira-4.0.1.ebuild b/sci-biology/mira/mira-4.0.1.ebuild
new file mode 100644
index 0000000..f9c38fa
--- /dev/null
+++ b/sci-biology/mira/mira-4.0.1.ebuild
@@ -0,0 +1,76 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+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 related	[flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2014-01-06 17:18 Justin Lecher
  0 siblings, 0 replies; 12+ messages in thread
From: Justin Lecher @ 2014-01-06 17:18 UTC (permalink / raw
  To: gentoo-commits

commit:     1be11cbcf6ff6f592b5e652694394899dbe2ae0f
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan  6 15:56:39 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan  6 15:56:39 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1be11cbc

sci-biology/mira: Drop old; punt base.eclass

Package-Manager: portage-2.2.8

---
 sci-biology/mira/ChangeLog           |  7 +++-
 sci-biology/mira/mira-3.4.0.1.ebuild | 62 ----------------------------
 sci-biology/mira/mira-3.4.1.1.ebuild | 61 ---------------------------
 sci-biology/mira/mira-3.9.15.ebuild  | 64 -----------------------------
 sci-biology/mira/mira-3.9.9.ebuild   | 61 ---------------------------
 sci-biology/mira/mira-4.0_rc2.ebuild | 80 ------------------------------------
 sci-biology/mira/mira-4.0_rc4.ebuild |  6 +--
 7 files changed, 9 insertions(+), 332 deletions(-)

diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index 56cb51d..4dd3e5b 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -1,7 +1,12 @@
 # ChangeLog for sci-biology/mira
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  06 Jan 2014; Justin Lecher <jlec@gentoo.org> -mira-3.4.0.1.ebuild,
+  -mira-3.4.1.1.ebuild, -mira-3.9.9.ebuild, -mira-3.9.15.ebuild,
+  -mira-4.0_rc2.ebuild, mira-4.0_rc4.ebuild:
+  Drop old; punt base.eclass
+
   12 Nov 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   mira-3.4.0.1.ebuild, mira-3.4.1.1.ebuild, mira-3.9.9.ebuild,
   mira-3.9.15.ebuild, mira-4.0_rc2.ebuild, +mira-4.0_rc4.ebuild:

diff --git a/sci-biology/mira/mira-3.4.0.1.ebuild b/sci-biology/mira/mira-3.4.0.1.ebuild
deleted file mode 100644
index 88d150a..0000000
--- a/sci-biology/mira/mira-3.4.0.1.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-MIRA_3RDPARTY_PV="09-09-2011"
-
-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/${P}.tar.bz2
-	mirror://sourceforge/mira-assembler/mira_3rdparty_${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
-	# http://sourceforge.net/apps/trac/mira-assembler/ticket/47
-	epatch \
-		"${FILESDIR}"/mira_left_clip.readpool.C.patch \
-		"${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/$(get_libdir) \
-		--with-boost-thread=boost_thread-mt
-}
-
-src_compile() {
-	default
-	# TODO: resolve docbook incompatibility for building docs
-	if use doc; then
-		emake -C doc clean docs || die "This will probably die because upstream did not improve re-generation of the docs yet."
-	fi
-}
-
-src_install() {
-	default
-	dodoc AUTHORS GETTING_STARTED NEWS README* HELP_WANTED THANKS INSTALL
-	find doc/docs/man -type f | xargs doman
-	find doc/docs/texinfo -type f | xargs doinfo
-	dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
-}

diff --git a/sci-biology/mira/mira-3.4.1.1.ebuild b/sci-biology/mira/mira-3.4.1.1.ebuild
deleted file mode 100644
index 5260ee1..0000000
--- a/sci-biology/mira/mira-3.4.1.1.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.4.0.2.ebuild,v 1.1 2012/11/07 22:29:56 jlec Exp $
-
-EAPI=4
-
-MIRA_3RDPARTY_PV="06-07-2012"
-
-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="
-	http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/${P}.tar.gz
-	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE=""
-
-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 )
-
-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
-	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() {
-	base_src_install
-	dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
-}
-
-pkg_postinst() {
-	einfo "Documentation is no longer built, you can find it at:"
-	einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
-}

diff --git a/sci-biology/mira/mira-3.9.15.ebuild b/sci-biology/mira/mira-3.9.15.ebuild
deleted file mode 100644
index 8dbb921..0000000
--- a/sci-biology/mira/mira-3.9.15.ebuild
+++ /dev/null
@@ -1,64 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.4.0.2.ebuild,v 1.1 2012/11/07 22:29:56 jlec Exp $
-
-EAPI=4
-
-MIRA_3RDPARTY_PV="06-07-2012"
-
-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="
-	http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2
-	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-
-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
-	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() {
-	base_src_install
-	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"
-}

diff --git a/sci-biology/mira/mira-3.9.9.ebuild b/sci-biology/mira/mira-3.9.9.ebuild
deleted file mode 100644
index 0deeb87..0000000
--- a/sci-biology/mira/mira-3.9.9.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.4.0.2.ebuild,v 1.1 2012/11/07 22:29:56 jlec Exp $
-
-EAPI=4
-
-MIRA_3RDPARTY_PV="06-07-2012"
-
-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="
-	http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2
-	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE=""
-
-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 )
-
-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
-	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() {
-	base_src_install
-	dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
-}
-
-pkg_postinst() {
-	einfo "Documentation is no longer built, you can find it at:"
-	einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
-}

diff --git a/sci-biology/mira/mira-4.0_rc2.ebuild b/sci-biology/mira/mira-4.0_rc2.ebuild
deleted file mode 100644
index 2c26f0a..0000000
--- a/sci-biology/mira/mira-4.0_rc2.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.9.18.ebuild,v 1.1 2013/07/07 19:41:05 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}"/${PN}-3.4.0.2-boost-1.50.patch
-
-	sed \
-		-e "s:-O[23]::g" \
-		-e "s:-funroll-loops::g" \
-		-i configure.ac || die
-
-	sed \
-		-e 's:m4:config/m4:g' \
-		-i Makefile.am configure.ac || die
-
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		--with-boost="${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"
-}

diff --git a/sci-biology/mira/mira-4.0_rc4.ebuild b/sci-biology/mira/mira-4.0_rc4.ebuild
index 813eee0..682bf23 100644
--- a/sci-biology/mira/mira-4.0_rc4.ebuild
+++ b/sci-biology/mira/mira-4.0_rc4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2013 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/mira/mira-3.9.18.ebuild,v 1.1 2013/07/07 19:41:05 jlec Exp $
 
@@ -7,12 +7,12 @@ 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
+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"


^ permalink raw reply related	[flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2013-11-12 20:20 Martin Mokrejs
  0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2013-11-12 20:20 UTC (permalink / raw
  To: gentoo-commits

commit:     ddb381cc314cdb15f745533a8a0cb379b856a120
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Nov 12 20:19:45 2013 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov 12 20:19:45 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ddb381cc

sci-biology/mira-4.0_rc4: Added 4.0_rc4 release candidate. Removing the sed hack redirecting autoconf to config/m4/ instead of m4/ because upstream accepted that source tree layout change in _rc3 already.

Package-Manager: portage-2.2.7

---
 sci-biology/mira/ChangeLog           |  8 ++++
 sci-biology/mira/mira-3.4.0.1.ebuild |  2 +-
 sci-biology/mira/mira-4.0_rc4.ebuild | 76 ++++++++++++++++++++++++++++++++++++
 3 files changed, 85 insertions(+), 1 deletion(-)

diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index 7ea6f3b..56cb51d 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  12 Nov 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  mira-3.4.0.1.ebuild, mira-3.4.1.1.ebuild, mira-3.9.9.ebuild,
+  mira-3.9.15.ebuild, mira-4.0_rc2.ebuild, +mira-4.0_rc4.ebuild:
+  Added 4.0_rc4 release candidate. Removing the sed hack redirecting autoconf
+  to config/m4/ instead of m4/ because upstream accepted that source tree
+  layout change in _rc3 already.
+
+
   01 Oct 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   mira-4.0_rc2.ebuild:
   Improve ebuild to use MY_PV.

diff --git a/sci-biology/mira/mira-3.4.0.1.ebuild b/sci-biology/mira/mira-3.4.0.1.ebuild
index 45d9911..88d150a 100644
--- a/sci-biology/mira/mira-3.4.0.1.ebuild
+++ b/sci-biology/mira/mira-3.4.0.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 

diff --git a/sci-biology/mira/mira-4.0_rc4.ebuild b/sci-biology/mira/mira-4.0_rc4.ebuild
new file mode 100644
index 0000000..813eee0
--- /dev/null
+++ b/sci-biology/mira/mira-4.0_rc4.ebuild
@@ -0,0 +1,76 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.9.18.ebuild,v 1.1 2013/07/07 19:41:05 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 related	[flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2013-10-01 13:03 Martin Mokrejs
  0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2013-10-01 13:03 UTC (permalink / raw
  To: gentoo-commits

commit:     bda8fb1dc8bcbe8b80ec358e178a3c66ac7547a0
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Oct  1 13:02:40 2013 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Oct  1 13:02:40 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bda8fb1d

Improve ebuild to use MY_PV

Package-Manager: portage-2.1.12.2

---
 sci-biology/mira/ChangeLog           | 4 ++++
 sci-biology/mira/mira-4.0_rc2.ebuild | 6 ++++--
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index bd72985..7ea6f3b 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  01 Oct 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  mira-4.0_rc2.ebuild:
+  Improve ebuild to use MY_PV.
+
   25 Sep 2013; Justin Lecher <jlec@gentoo.org> mira-4.0_rc2.ebuild,
   metadata.xml:
   Fix m4 macrodir location

diff --git a/sci-biology/mira/mira-4.0_rc2.ebuild b/sci-biology/mira/mira-4.0_rc2.ebuild
index 48a135a..2c26f0a 100644
--- a/sci-biology/mira/mira-4.0_rc2.ebuild
+++ b/sci-biology/mira/mira-4.0_rc2.ebuild
@@ -5,17 +5,19 @@
 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/mira-4.0rc2.tar.bz2
+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="${WORKDIR}/mira-4.0rc2"
+S="${WORKDIR}"/"${PN}"-"${MY_PV}"
 
 SLOT="0"
 LICENSE="GPL-2"


^ permalink raw reply related	[flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2013-09-25 14:33 Justin Lecher
  0 siblings, 0 replies; 12+ messages in thread
From: Justin Lecher @ 2013-09-25 14:33 UTC (permalink / raw
  To: gentoo-commits

commit:     f27a3ee1061d4a2aa0d81db7863700d6a49cd507
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 25 14:32:27 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep 25 14:32:27 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f27a3ee1

sci-biology/mira: Fix m4 macrodir location

Package-Manager: portage-2.2.7

---
 sci-biology/mira/ChangeLog           |  4 ++++
 sci-biology/mira/metadata.xml        | 10 +++++-----
 sci-biology/mira/mira-4.0_rc2.ebuild |  8 +++++---
 3 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index afda6bd..bd72985 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  25 Sep 2013; Justin Lecher <jlec@gentoo.org> mira-4.0_rc2.ebuild,
+  metadata.xml:
+  Fix m4 macrodir location
+
 *mira-3.9.15 (30 Apr 2013)
 
   30 Apr 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml
index 07b5255..2bc8930 100644
--- a/sci-biology/mira/metadata.xml
+++ b/sci-biology/mira/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
-	<maintainer>
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
 </pkgmetadata>

diff --git a/sci-biology/mira/mira-4.0_rc2.ebuild b/sci-biology/mira/mira-4.0_rc2.ebuild
index 13df7b7..48a135a 100644
--- a/sci-biology/mira/mira-4.0_rc2.ebuild
+++ b/sci-biology/mira/mira-4.0_rc2.ebuild
@@ -44,9 +44,11 @@ src_prepare() {
 		-e "s:-funroll-loops::g" \
 		-i configure.ac || die
 
-	ln -s config/m4 .
-	AT_M4DIR="config/m4" eaclocal
-	AT_M4DIR="config/m4" eautoreconf
+	sed \
+		-e 's:m4:config/m4:g' \
+		-i Makefile.am configure.ac || die
+
+	eautoreconf
 }
 
 src_configure() {


^ permalink raw reply related	[flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2013-09-25 13:35 Martin Mokrejs
  0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2013-09-25 13:35 UTC (permalink / raw
  To: gentoo-commits

commit:     bc1bf424a20c10b9a2ae6e2bfd337d47173e3810
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Sep 25 13:36:49 2013 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Sep 25 13:36:49 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bc1bf424

version bump

---
 sci-biology/mira/mira-4.0_rc2.ebuild | 76 ++++++++++++++++++++++++++++++++++++
 1 file changed, 76 insertions(+)

diff --git a/sci-biology/mira/mira-4.0_rc2.ebuild b/sci-biology/mira/mira-4.0_rc2.ebuild
new file mode 100644
index 0000000..13df7b7
--- /dev/null
+++ b/sci-biology/mira/mira-4.0_rc2.ebuild
@@ -0,0 +1,76 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.9.18.ebuild,v 1.1 2013/07/07 19:41:05 jlec Exp $
+
+EAPI=5
+
+MIRA_3RDPARTY_PV="06-07-2012"
+
+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/mira-4.0rc2.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}/mira-4.0rc2"
+
+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
+
+	ln -s config/m4 .
+	AT_M4DIR="config/m4" eaclocal
+	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() {
+	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 related	[flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2013-04-30  9:42 Martin Mokrejs
  0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2013-04-30  9:42 UTC (permalink / raw
  To: gentoo-commits

commit:     00bb77fe4833272c18c448942d8e19b99d729e77
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Apr 30 09:42:18 2013 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Apr 30 09:42:18 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=00bb77fe

sci-biology/mira-3.9.15: bump to current besta version

Package-Manager: portage-2.1.11.62

---
 sci-biology/mira/ChangeLog          |    6 +++
 sci-biology/mira/mira-3.9.15.ebuild |   64 +++++++++++++++++++++++++++++++++++
 2 files changed, 70 insertions(+), 0 deletions(-)

diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index 68b66f6..afda6bd 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*mira-3.9.15 (30 Apr 2013)
+
+  30 Apr 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +mira-3.9.15.ebuild:
+  sci-biology/mira-3.9.15: bump to current besta version mira-3.9.15.ebuild
+
 *mira-3.4.1.1 (22 Feb 2013)
 *mira-3.9.9 (22 Feb 2013)
 

diff --git a/sci-biology/mira/mira-3.9.15.ebuild b/sci-biology/mira/mira-3.9.15.ebuild
new file mode 100644
index 0000000..8dbb921
--- /dev/null
+++ b/sci-biology/mira/mira-3.9.15.ebuild
@@ -0,0 +1,64 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.4.0.2.ebuild,v 1.1 2012/11/07 22:29:56 jlec Exp $
+
+EAPI=4
+
+MIRA_3RDPARTY_PV="06-07-2012"
+
+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="
+	http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2
+	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
+
+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
+	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() {
+	base_src_install
+	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 related	[flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2012-05-22 19:43 Justin Lecher
  0 siblings, 0 replies; 12+ messages in thread
From: Justin Lecher @ 2012-05-22 19:43 UTC (permalink / raw
  To: gentoo-commits

commit:     5d074abd7b1d4ea82db2fd5ea860ac8f9afd80cb
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue May 22 19:07:51 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue May 22 19:07:51 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5d074abd

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)

---
 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: $
 
+  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/mira-3.2.1-r2.ebuild b/sci-biology/mira/mira-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=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 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=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 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=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 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: $
 
-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



^ permalink raw reply related	[flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2011-07-05  8:22 Martin Mokrejs
  0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2011-07-05  8:22 UTC (permalink / raw
  To: gentoo-commits

commit:     e8d6087005fecd88056d173b940a2cd39a9e0e2c
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jul  5 08:22:32 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jul  5 08:22:32 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e8d60870

sci-biology/mira-3.2.1.20: version bump

(Portage version: 2.1.10.3/git/Linux i686, unsigned Manifest commit)

---
 .../{mira-3.2.1.18.ebuild => mira-3.2.1.20.ebuild} |    0
 1 files changed, 0 insertions(+), 0 deletions(-)

diff --git a/sci-biology/mira/mira-3.2.1.18.ebuild b/sci-biology/mira/mira-3.2.1.20.ebuild
similarity index 100%
rename from sci-biology/mira/mira-3.2.1.18.ebuild
rename to sci-biology/mira/mira-3.2.1.20.ebuild



^ permalink raw reply	[flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2011-05-18 16:18 Martin Mokrejs
  0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2011-05-18 16:18 UTC (permalink / raw
  To: gentoo-commits

commit:     3751e59f2601bea758e63a00485a64d3edeec1a1
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed May 18 16:17:52 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed May 18 16:17:52 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3751e59f

sci-biology/mira-3.2.1.17-r1: maks the devel. version until it can be compiled (due autoreconf issues)

(Portage version: 2.1.9.43/git/Linux i686, unsigned Manifest commit)

---
 sci-biology/mira/mira-3.2.1.17-r1.ebuild |    4 +++-
 1 files changed, 3 insertions(+), 1 deletions(-)

diff --git a/sci-biology/mira/mira-3.2.1.17-r1.ebuild b/sci-biology/mira/mira-3.2.1.17-r1.ebuild
index 020876c..49e97f6 100644
--- a/sci-biology/mira/mira-3.2.1.17-r1.ebuild
+++ b/sci-biology/mira/mira-3.2.1.17-r1.ebuild
@@ -16,7 +16,9 @@ SRC_URI="mirror://sourceforge/mira-assembler/${P}.tar.bz2
 LICENSE="GPL-2"
 SLOT="0"
 IUSE=""
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+KEYWORDS=""
+# masked because of 'libtool: Version mismatch error.  This is libtool 2.4, but the definition of this LT_INIT comes from libtool 2.2.6b. You should recreate aclocal.m4 with macros from libtool 2.4 and run autoconf again.', dyeing at src/examples_programming/
+#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
 
 CDEPEND=">=dev-libs/boost-1.41.0-r3"
 DEPEND="${CDEPEND}



^ permalink raw reply related	[flat|nested] 12+ messages in thread
end of thread, other threads:[~2014-04-20  0:19 UTC | newest]

Thread overview: 12+ messages (download: mbox.gz follow: Atom feed
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