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 1Pxl6o-0001BV-Uy for garchives@archives.gentoo.org; Thu, 10 Mar 2011 19:01:15 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 4E2FBE05A4; Thu, 10 Mar 2011 19:00:23 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id EC6B8E0517 for ; Thu, 10 Mar 2011 19:00:22 +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 681B41B421F for ; Thu, 10 Mar 2011 19:00:22 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id D097780073 for ; Thu, 10 Mar 2011 19:00:21 +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: <931202b27005e0063e76f994f44778f27cf4d861.jlec@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/embassy-structure/files/, sci-biology/embassy-structure/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/embassy-structure/ChangeLog sci-biology/embassy-structure/embassy-structure-0.1.0-r5.ebuild sci-biology/embassy-structure/files/embassy-structure-0.1.0-r5.patch sci-biology/embassy-structure/metadata.xml X-VCS-Directories: sci-biology/embassy-structure/files/ sci-biology/embassy-structure/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 931202b27005e0063e76f994f44778f27cf4d861 Date: Thu, 10 Mar 2011 19:00:21 +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: 0cda836bf984350c6e995bf77d066cc5 commit: 931202b27005e0063e76f994f44778f27cf4d861 Author: Justin Lecher gentoo org> AuthorDate: Thu Mar 10 11:27:03 2011 +0000 Commit: Justin Lecher gentoo org> CommitDate: Thu Mar 10 11:27:03 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3D931202b2 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-structure/ChangeLog | 95 ++++++++++++++= +++++ .../embassy-structure-0.1.0-r5.ebuild | 10 ++ .../files/embassy-structure-0.1.0-r5.patch | 100 ++++++++++++++= ++++++ sci-biology/embassy-structure/metadata.xml | 5 + 4 files changed, 210 insertions(+), 0 deletions(-) diff --git a/sci-biology/embassy-structure/ChangeLog b/sci-biology/embass= y-structure/ChangeLog new file mode 100644 index 0000000..07a6051 --- /dev/null +++ b/sci-biology/embassy-structure/ChangeLog @@ -0,0 +1,95 @@ +# ChangeLog for sci-biology/embassy-structure +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-structure/ChangeL= og,v 1.19 2010/01/01 21:57:51 fauli Exp $ + +*embassy-structure-0.1.0-r5 (10 Mar 2011) + + 10 Mar 2011; Justin Lecher + +embassy-structure-0.1.0-r5.ebuild, +files/embassy-structure-0.1.0-r5.= patch, + +metadata.xml: + Move to new embassy-ng.eclass + + 01 Jan 2010; Christian Faulhammer + embassy-structure-0.1.0-r4.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette metadata.xml: + Giving up maintainership of this package. + +*embassy-structure-0.1.0-r4 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette + +embassy-structure-0.1.0-r4.ebuild: + Updated version for EMBASSY 6.1.0. + + 01 Sep 2009; Olivier Fisette + embassy-structure-0.1.0-r3.ebuild: + Stabilised on amd64 and x86. + + 27 Aug 2008; Olivier Fisette + -embassy-structure-0.1.0-r2.ebuild: + Pruning version that will never be stabilised. + +*embassy-structure-0.1.0-r3 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette + +embassy-structure-0.1.0-r3.ebuild: + New upstream version/package for EMBASSY 6.0.1. + +*embassy-structure-0.1.0-r2 (18 Jul 2007) + + 18 Jul 2007; Olivier Fisette + +embassy-structure-0.1.0-r2.ebuild: + New upstream packaging for EMBOSS 5.0.0. + + 15 Feb 2007; Jeff Gardner + embassy-structure-0.1.0-r1.ebuild: + Added ~amd64. + + 10 Dec 2006; Olivier Fisette + -embassy-structure-0.1.0.ebuild: + Pruning old version. + + 03 Nov 2006; nixnut embassy-structure-0.1.0-r1.ebu= ild: + Stable on ppc wrt bug 153766 + + 03 Nov 2006; Jeff Gardner + embassy-structure-0.1.0-r1.ebuild: + Added ~sparc + + 02 Nov 2006; Fabian Groffen + embassy-structure-0.1.0.ebuild, embassy-structure-0.1.0-r1.ebuild: + Dropped ppc-macos, see you in prefix. + + 02 Nov 2006; Olivier Fisette + embassy-structure-0.1.0-r1.ebuild: + Added to x86. + +*embassy-structure-0.1.0-r1 (21 Jul 2006) + + 21 Jul 2006; Olivier Fisette + +embassy-structure-0.1.0-r1.ebuild: + New upstream version building against EMBOSS 4.0.0. + + 21 Jul 2006; Olivier Fisette + embassy-structure-0.1.0.ebuild: + Fixed download URL (silent upstream repackaging). + + 03 Oct 2005; Olivier Fisette + embassy-structure-0.1.0.ebuild: + Stable on ppc-macos (with j4rg0n's permission, bug #102420). + + 02 Oct 2005; Michael Hanselmann + embassy-structure-0.1.0.ebuild: + Stable on ppc. + + 21 Sep 2005; Olivier Fisette + embassy-structure-0.1.0.ebuild: + Added to x86. + +*embassy-structure-0.1.0 (07 Aug 2005) + + 07 Aug 2005; Olivier Fisette +metadata.xml, + +embassy-structure-0.1.0.ebuild: + New import. This package is part of the EMBASSY 3.0.0 distribution. + diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.0-r5.ebu= ild b/sci-biology/embassy-structure/embassy-structure-0.1.0-r5.ebuild new file mode 100644 index 0000000..a501019 --- /dev/null +++ b/sci-biology/embassy-structure/embassy-structure-0.1.0-r5.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-structure/embassy= -structure-0.1.0-r4.ebuild,v 1.2 2010/01/01 21:57:51 fauli Exp $ + +EBOV=3D"6.3.1" +EBO_DESCRIPTION=3D"Protein structure add-on package" + +inherit embassy-ng + +KEYWORDS=3D"~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-structure/files/embassy-structure-0.1.0-= r5.patch b/sci-biology/embassy-structure/files/embassy-structure-0.1.0-r5= .patch new file mode 100644 index 0000000..10c08d7 --- /dev/null +++ b/sci-biology/embassy-structure/files/embassy-structure-0.1.0-r5.patc= h @@ -0,0 +1,100 @@ +diff --git a/Makefile.am b/Makefile.am +index 6bfb6f0..bb94633 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -1,5 +1,7 @@ + # +=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 2eb3a3f..b9e79d0 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 $LDFLAGS" +=20 +=20 + dnl "Export" these variables for PCRE +@@ -389,9 +380,30 @@ AC_ARG_ENABLE(systemlibs, + AS_HELP_STRING([--enable-systemlibs], [Use system versions of zlib/e= xpat])) + if test "${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 a8c32dc..b60ac0f 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,9 @@ 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 +@@ -65,6 +65,6 @@ 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-structure/metadata.xml b/sci-biology/emb= assy-structure/metadata.xml new file mode 100644 index 0000000..d464821 --- /dev/null +++ b/sci-biology/embassy-structure/metadata.xml @@ -0,0 +1,5 @@ + + + + sci-biology +