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 1Pxl7l-0001MK-IS for garchives@archives.gentoo.org; Thu, 10 Mar 2011 19:02:14 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 9F8A6E0656; Thu, 10 Mar 2011 19:00:26 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 5E14BE0656 for ; Thu, 10 Mar 2011 19:00:26 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher ADH-CAMELLIA256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id BBD391BC019 for ; Thu, 10 Mar 2011 19:00:25 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id 2E4F880075 for ; Thu, 10 Mar 2011 19:00:25 +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: <6c0a8a44499d0f1604528a41c386647198930f49.jlec@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/embassy-esim4/, sci-biology/embassy-esim4/files/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/embassy-esim4/ChangeLog sci-biology/embassy-esim4/embassy-esim4-1.0.0-r7.ebuild sci-biology/embassy-esim4/files/embassy-esim4-1.0.0-r7.patch sci-biology/embassy-esim4/metadata.xml X-VCS-Directories: sci-biology/embassy-esim4/ sci-biology/embassy-esim4/files/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 6c0a8a44499d0f1604528a41c386647198930f49 Date: Thu, 10 Mar 2011 19:00:25 +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: X-Archives-Hash: 4cf075eec8e91b78bb5ef2fb2e68dd91 commit: 6c0a8a44499d0f1604528a41c386647198930f49 Author: Justin Lecher gentoo org> AuthorDate: Thu Mar 10 14:36:34 2011 +0000 Commit: Justin Lecher gentoo org> CommitDate: Thu Mar 10 14:36:34 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3D6c0a8a44 Move to new embassy-ng.eclass (Portage version: 2.2.0_alpha26/git/Linux x86_64, RepoMan options: --forc= e, signed Manifest commit with key 70EB7916) --- sci-biology/embassy-esim4/ChangeLog | 142 ++++++++++++++= ++++++ .../embassy-esim4/embassy-esim4-1.0.0-r7.ebuild | 10 ++ .../files/embassy-esim4-1.0.0-r7.patch | 99 ++++++++++++++ sci-biology/embassy-esim4/metadata.xml | 5 + 4 files changed, 256 insertions(+), 0 deletions(-) diff --git a/sci-biology/embassy-esim4/ChangeLog b/sci-biology/embassy-es= im4/ChangeLog new file mode 100644 index 0000000..b8385d1 --- /dev/null +++ b/sci-biology/embassy-esim4/ChangeLog @@ -0,0 +1,142 @@ +# ChangeLog for sci-biology/embassy-esim4 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/ChangeLog,v= 1.28 2010/01/01 21:58:14 fauli Exp $ + +*embassy-esim4-1.0.0-r7 (10 Mar 2011) + + 10 Mar 2011; Justin Lecher +embassy-esim4-1.0.0-r7.e= build, + +files/embassy-esim4-1.0.0-r7.patch, +metadata.xml: + Move to new embassy-ng.eclass + + 01 Jan 2010; Christian Faulhammer + embassy-esim4-1.0.0-r6.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette metadata.xml: + Giving up maintainership of this package. + +*embassy-esim4-1.0.0-r6 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette + +embassy-esim4-1.0.0-r6.ebuild: + Updated version for EMBASSY 6.1.0. + + 01 Sep 2009; Olivier Fisette + embassy-esim4-1.0.0-r5.ebuild: + Stabilised on amd64 and x86. + + 27 Aug 2008; Olivier Fisette + -embassy-esim4-1.0.0-r4.ebuild: + Pruning version that will never be stabilised. + +*embassy-esim4-1.0.0-r5 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette + +embassy-esim4-1.0.0-r5.ebuild: + New upstream version/package for EMBASSY 6.0.1. + +*embassy-esim4-1.0.0-r4 (18 Jul 2007) + + 18 Jul 2007; Olivier Fisette + +embassy-esim4-1.0.0-r4.ebuild: + New upstream packaging for EMBOSS 5.0.0. + + 16 Feb 2007; Jeff Gardner + embassy-esim4-1.0.0-r3.ebuild: + Added ~amd64. + + 10 Dec 2006; Olivier Fisette + -embassy-esim4-1.0.0-r2.ebuild: + Pruning old version. + + 03 Nov 2006; Jeff Gardner + embassy-esim4-1.0.0-r3.ebuild: + Marked ~sparc + + 02 Nov 2006; Fabian Groffen + embassy-esim4-1.0.0-r2.ebuild, embassy-esim4-1.0.0-r3.ebuild: + Dropped ppc-macos, see you in prefix. + + 02 Nov 2006; Olivier Fisette + embassy-esim4-1.0.0-r3.ebuild: + Added to x86. + +*embassy-esim4-1.0.0-r3 (21 Jul 2006) + + 21 Jul 2006; Olivier Fisette + +embassy-esim4-1.0.0-r3.ebuild: + New upstream version building against EMBOSS 4.0.0. + + 20 Jul 2006; Olivier Fisette + embassy-esim4-1.0.0-r2.ebuild: + Fixed digest mismatch due to silent upstream repackaging. + + 04 Oct 2005; Olivier Fisette + -embassy-esim4-1.0.0-r1.ebuild: + Removed obsolete version. + + 03 Oct 2005; Olivier Fisette + embassy-esim4-1.0.0-r2.ebuild: + Stable on ppc-macos (with j4rg0n's permission, bug #102420). + + 02 Oct 2005; Michael Hanselmann + embassy-esim4-1.0.0-r2.ebuild: + Stable on ppc. + + 21 Sep 2005; Olivier Fisette + embassy-esim4-1.0.0-r2.ebuild: + Added to x86. + +*embassy-esim4-1.0.0-r2 (07 Aug 2005) + + 07 Aug 2005; Olivier Fisette + embassy-esim4-1.0.0-r1.ebuild, +embassy-esim4-1.0.0-r2.ebuild: + Ported 1.0.0-r1 to the improved embassy.eclass. The new version is par= t of + EMBASSY 3.0.0. + + 28 Jul 2005; Olivier Fisette + -embassy-esim4-1.0.0.ebuild: + Removed old version. + + 26 Jun 2005; Lina Pezzella + embassy-esim4-1.0.0-r1.ebuild: + Stable ppc-macos + + 24 Jun 2005; Joseph Jezak + embassy-esim4-1.0.0-r1.ebuild: + Marked ppc stable. + + 13 May 2005; Olivier Fisette + embassy-esim4-1.0.0-r1.ebuild: + Added to x86. + +*embassy-esim4-1.0.0-r1 (25 Mar 2005) + + 25 Mar 2005; Olivier Fisette + +embassy-esim4-1.0.0-r1.ebuild: + Build against the EMBOSS 2.10 source tree. + + 02 Mar 2005; Lina Pezzella embassy-esim4-1.0.0.ebu= ild: + Stable ppc-macos + + 25 Jan 2005; Lina Pezzella embassy-esim4-1.0.0.ebu= ild: + Unstable ppc-macos. + +*embassy-esim4-1.0.0 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette +metadata.xml, + +embassy-esim4-1.0.0.ebuild: + Moved from app-sci/embassy-esim4 to sci-biology/embassy-esim4. + + 31 Oct 2004; Olivier Fisette + embassy-esim4-1.0.0.ebuild: + Added to x86. + + 21 Jul 2004; David Holm embassy-esim4-1.0.0.ebuild: + Added to ~ppc. + +* embassy-esim4-1.0.0 (19 Jul 2004) + + 19 Jul 2004; Olivier Fisette + embassy-esim4-1.0.0.ebuild, metadata.xml, ChangeLog + Initial import. diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r7.ebuild b/sc= i-biology/embassy-esim4/embassy-esim4-1.0.0-r7.ebuild new file mode 100644 index 0000000..6e77128 --- /dev/null +++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r7.ebuild @@ -0,0 +1,10 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/embassy-esi= m4-1.0.0-r6.ebuild,v 1.2 2010/01/01 21:58:14 fauli Exp $ + +EBOV=3D"6.3.1" +EBO_DESCRIPTION=3D"sim4 - Alignment of cDNA and genomic DNA" + +inherit embassy-ng + +KEYWORDS=3D"~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0-r7.patch= b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0-r7.patch new file mode 100644 index 0000000..f74823d --- /dev/null +++ b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0-r7.patch @@ -0,0 +1,99 @@ +diff --git a/Makefile.am b/Makefile.am +index 6bfb6f0..d547b12 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -1,5 +1,6 @@ + # +=20 ++ACLOCAL_AMFLAGS =3D -I m4 + SUBDIRS =3D src emboss_acd emboss_doc +=20 + EXTRA_DIST =3D depcomp ltmain.sh install-sh config.sub config.guess +diff --git a/configure.in b/configure.in +index 077c81b..7ba7af1 100644 +--- a/configure.in ++++ b/configure.in +@@ -187,15 +187,6 @@ AC_PROG_INSTALL + AC_PROG_LN_S + AC_PROG_MAKE_SET +=20 +-dnl Intel MacOSX 10.6 puts X11 in a non-standard place +-if test "${with_x}" !=3D "no" ; then +-if test "`uname -a | grep Darwin`"; then +-OSXX=3D`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'` +-if test ${OSXX} '>' '10.4'; then +-CFLAGS=3D"$CFLAGS -I/usr/X11/include -L/usr/X11/lib" +-fi +-fi +-fi +=20 + dnl Check for header files + AC_PATH_XTRA +@@ -250,8 +241,8 @@ AX_LIB_POSTGRESQL + CFLAGS=3D"$CFLAGS $MYSQL_CFLAGS" + LDFLAGS=3D"$LDFLAGS $MYSQL_LDFLAGS" +=20 +-CFLAGS=3D"$CFLAGS $POSTGRESQL_CFLAGS" +-LDFLAGS=3D"$LDFLAGS $POSTGRESQL_LDFLAGS" ++CFLAGS=3D"$POSTGRESQL_CFLAGS $CFLAGS" ++LDFLAGS=3D"$POSTGRESQL_LDFLAGS $LDFLAGS" +=20 +=20 + dnl "Export" these variables for PCRE +@@ -388,9 +379,30 @@ AC_ARG_ENABLE(systemlibs, + AS_HELP_STRING([--enable-systemlibs], [Use system versions of zlib/e= xpat])) + if test "${enable_systemlibs}" =3D "yes" ; then + have_systemlibs=3Dyes ++ DEFINE_USE_SYSTEM_PCRE=3D"#define" ++ PKG_CHECK_MODULES([PLPLOT], [plplotd]) ++ PKG_CHECK_MODULES([ZLIB], [zlib]) ++else ++ dnl X11 is only used by plplot ++ dnl Intel MacOSX 10.6 puts X11 in a non-standard place ++ if test "${with_x}" !=3D "no" ; then ++ if test "`uname -a | grep Darwin`"; then ++ OSXX=3D`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'` ++ if test ${OSXX} '>' '10.4'; then ++ CFLAGS=3D"$CFLAGS -I/usr/X11/include -L/usr/X11/lib" ++ fi ++ fi ++ fi ++ if test "${with_x}" !=3D "no" ; then ++ LF_EMBOSS_PATH_XLIB ++ fi ++ AC_MSG_NOTICE(USING bundled LIBS) + fi =20 + AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" =3D "yes") + AC_SUBST(ESYSTEMLIBS) ++AC_SUBST(DEFINE_USE_SYSTEM_PCRE) ++AC_SUBST(PLPLOT_CFLAGS) ++AC_SUBST(PLPLOT_LIBS) +=20 +=20 +=20 +diff --git a/src/Makefile.am b/src/Makefile.am +index e593a9c..6132408 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -18,9 +18,9 @@ INCLUDES =3D -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-INCLUDES =3D -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++INCLUDES =3D -I${embprefix}/include $(PLPLOT_CFLAGS) \ ++ $(NLINCLUDES) -I${embprefix}/include/emboss \ ++ -I${embprefix}/include/pcre + endif +=20 + if ISSHARED +@@ -63,6 +63,6 @@ LDADD =3D ../../../nucleus/libnucleus.la ../../../ajax= /acd/libacd.la \ + ../../../plplot/libeplplot.la \ + $(XLIB) + else +-LDADD =3D -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg= \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD =3D -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ ++ -lajax -lpcre $(NLADD) $(PLPLOT_LIBS) $(XLIB) + endif diff --git a/sci-biology/embassy-esim4/metadata.xml b/sci-biology/embassy= -esim4/metadata.xml new file mode 100644 index 0000000..d464821 --- /dev/null +++ b/sci-biology/embassy-esim4/metadata.xml @@ -0,0 +1,5 @@ + + + + sci-biology +