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 1RYSxK-0000dt-DY for garchives@archives.gentoo.org; Thu, 08 Dec 2011 01:39:26 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id D195621C06D; Thu, 8 Dec 2011 01:39:18 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 8B2D021C06D for ; Thu, 8 Dec 2011 01:39:18 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id BE8B11B4027 for ; Thu, 8 Dec 2011 01:39:17 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id 3010C80042 for ; Thu, 8 Dec 2011 01:39:17 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <2b33defb28660b66594a4ca772f7a87d6a487089.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/mira/, sci-biology/mira/files/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/mira/ChangeLog sci-biology/mira/files/mira-3.4.0.1-asneeded.patch sci-biology/mira/mira-3.4.0.1.ebuild X-VCS-Directories: sci-biology/mira/ sci-biology/mira/files/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 2b33defb28660b66594a4ca772f7a87d6a487089 Date: Thu, 8 Dec 2011 01:39:17 +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: 66f26544-7d5d-4c94-b7ad-61f355c9113b X-Archives-Hash: a7f88554c0ebc19371c9d19837c1fcff commit: 2b33defb28660b66594a4ca772f7a87d6a487089 Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Thu Dec 8 01:38:57 2011 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Dec 8 01:38:57 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3D2b33defb sci-biology/mira: version bump (Portage version: 2.1.10.38/git/Linux i686, unsigned Manifest commit) --- sci-biology/mira/ChangeLog | 13 +++++ sci-biology/mira/files/mira-3.4.0.1-asneeded.patch | 29 ++++++++++ sci-biology/mira/mira-3.4.0.1.ebuild | 57 ++++++++++++++= ++++++ 3 files changed, 99 insertions(+), 0 deletions(-) diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog new file mode 100644 index 0000000..0982f99 --- /dev/null +++ b/sci-biology/mira/ChangeLog @@ -0,0 +1,13 @@ +# ChangeLog for sci-biology/mira +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*mira-3.4.0.1 (08 Dec 2011) + + 08 Dec 2011; Martin Mokrejs + +mira-3.4.0.1.ebuild, +files/mira-3.4.0.1-asneeded.patch: + version bump and dropped the expat patch for --as-needed CFLAGS as ups= tream + fixed that in a different way, the still applicable part of the patch = is + however provided under files/ but is just a cosmetic change (hence not= really + needed) + diff --git a/sci-biology/mira/files/mira-3.4.0.1-asneeded.patch b/sci-bio= logy/mira/files/mira-3.4.0.1-asneeded.patch new file mode 100644 index 0000000..4184323 --- /dev/null +++ b/sci-biology/mira/files/mira-3.4.0.1-asneeded.patch @@ -0,0 +1,29 @@ +--- config/m4/ax_lib_expat.m4.ori 2011-12-08 01:59:42.000000000 +0100 ++++ config/m4/ax_lib_expat.m4 2011-12-08 02:00:08.000000000 +0100 +@@ -108,7 +108,8 @@ +=20 + if test -n "$expat_prefix"; then + expat_include_dir=3D"$expat_prefix/include" +- expat_lib_flags=3D"-L$expat_prefix/lib -lexpat" ++ expat_lib_flags=3D"-L$expat_prefix/lib" ++ expat_libs=3D"-lexpat" + run_expat_test=3D"yes" + elif test "$expat_requested" =3D "yes"; then + if test -n "$expat_include_dir" -a -n "$expat_lib_flags"; then +@@ -129,6 +130,8 @@ + saved_LDFLAGS=3D"$LDFLAGS" + LIBS=3D"$LDFLAGS $expat_lib_flags" +=20 ++ saved_LIBS=3D"$LIBS" ++ LIBS=3D"$LIBS $expat_libs" + dnl + dnl Check Expat headers + dnl +@@ -188,6 +191,7 @@ +=20 + CPPFLAGS=3D"$saved_CPPFLAGS" + LDFLAGS=3D"$saved_LDFLAGS" ++ LIBS=3D"$saved_LIBS" + fi +=20 + AC_MSG_CHECKING([for Expat XML Parser]) diff --git a/sci-biology/mira/mira-3.4.0.1.ebuild b/sci-biology/mira/mira= -3.4.0.1.ebuild new file mode 100644 index 0000000..78d1cc3 --- /dev/null +++ b/sci-biology/mira/mira-3.4.0.1.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3D3 + +MIRA_3RDPARTY_PV=3D"09-09-2011" + +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 + # 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/$(get_libdir) \ + --with-boost-thread=3Dboost_thread-mt +} + +src_compile() { + base_src_compile + # TODO: resolve docbook incompatibility for building docs + if use doc; then emake -C doc clean docs || die "This will probably die= because upstream did not improve re-generation of the docs yet."; fi +} + +src_install() { + einstall || die + dodoc AUTHORS GETTING_STARTED NEWS README* HELP_WANTED THANKS INSTALL + find doc/docs/man -type f | xargs doman + find doc/docs/texinfo -type f | xargs doinfo + dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} +}