[gentoo-commits] proj/sci:master commit in: sci-biology/embassy-domsearch/files/, sci-biology/embassy-domsearch/

["Justin Lecher" <jlec@gentoo.org>]

commit:     a23ede41ca8cfe2090e9e202c11cf7e90e679553
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 10 15:18:16 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Mar 10 15:18:16 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a23ede41

Move to new embassy-ng.eclass

(Portage version: 2.2.0_alpha26/git/Linux x86_64, RepoMan options: --force, signed Manifest commit with key 70EB7916)

---
 sci-biology/embassy-domsearch/ChangeLog            |   95 +++++++++++++++++++
 .../embassy-domsearch-0.1.0-r5.ebuild              |   10 ++
 .../files/embassy-domsearch-0.1.0-r5.patch         |   99 ++++++++++++++++++++
 sci-biology/embassy-domsearch/metadata.xml         |    5 +
 4 files changed, 209 insertions(+), 0 deletions(-)

diff --git a/sci-biology/embassy-domsearch/ChangeLog b/sci-biology/embassy-domsearch/ChangeLog
new file mode 100644
index 0000000..9917ea2
--- /dev/null
+++ b/sci-biology/embassy-domsearch/ChangeLog
@@ -0,0 +1,95 @@
+# ChangeLog for sci-biology/embassy-domsearch
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domsearch/ChangeLog,v 1.19 2010/01/01 21:53:24 fauli Exp $
+
+*embassy-domsearch-0.1.0-r5 (10 Mar 2011)
+
+  10 Mar 2011; Justin Lecher <jlec@gentoo.org>
+  +embassy-domsearch-0.1.0-r5.ebuild, +files/embassy-domsearch-0.1.0-r5.patch,
+  +metadata.xml:
+  Move to new embassy-ng.eclass
+
+  01 Jan 2010; Christian Faulhammer <fauli@gentoo.org>
+  embassy-domsearch-0.1.0-r4.ebuild:
+  Transfer Prefix keywords
+
+  01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
+  Giving up maintainership of this package.
+
+*embassy-domsearch-0.1.0-r4 (01 Sep 2009)
+
+  01 Sep 2009; Olivier Fisette <ribosome@gentoo.org>
+  +embassy-domsearch-0.1.0-r4.ebuild:
+  Updated version for EMBASSY 6.1.0.
+
+  01 Sep 2009; Olivier Fisette <ribosome@gentoo.org>
+  embassy-domsearch-0.1.0-r3.ebuild:
+  Stabilised on amd64 and x86.
+
+  27 Aug 2008; Olivier Fisette <ribosome@gentoo.org>
+  -embassy-domsearch-0.1.0-r2.ebuild:
+  Pruning version that will never be stabilised.
+
+*embassy-domsearch-0.1.0-r3 (27 Aug 2008)
+
+  27 Aug 2008; Olivier Fisette <ribosome@gentoo.org>
+  +embassy-domsearch-0.1.0-r3.ebuild:
+  New upstream version/package for EMBASSY 6.0.1.
+
+*embassy-domsearch-0.1.0-r2 (18 Jul 2007)
+
+  18 Jul 2007; Olivier Fisette <ribosome@gentoo.org>
+  +embassy-domsearch-0.1.0-r2.ebuild:
+  New upstream packaging for EMBOSS 5.0.0.
+
+  15 Feb 2007; Jeff Gardner <je_fro@gentoo.org>
+  embassy-domsearch-0.1.0-r1.ebuild:
+  Added ~amd64.
+
+  10 Dec 2006; Olivier Fisette <ribosome@gentoo.org>
+  -embassy-domsearch-0.1.0.ebuild:
+  Pruning old version.
+
+  03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-domsearch-0.1.0-r1.ebuild:
+  Stable on ppc wrt bug 153766
+
+  03 Nov 2006; Fabian Groffen <grobian@gentoo.org>
+  embassy-domsearch-0.1.0.ebuild, embassy-domsearch-0.1.0-r1.ebuild:
+  Dropped ppc-macos, see you in prefix.
+
+  03 Nov 2006; Jeff Gardner <je_fro@gentoo.org>
+  embassy-domsearch-0.1.0-r1.ebuild:
+  Added ~sparc
+
+  02 Nov 2006; Olivier Fisette <ribosome@gentoo.org>
+  embassy-domsearch-0.1.0-r1.ebuild:
+  Added to x86.
+
+*embassy-domsearch-0.1.0-r1 (21 Jul 2006)
+
+  21 Jul 2006; Olivier Fisette <ribosome@gentoo.org>
+  +embassy-domsearch-0.1.0-r1.ebuild:
+  New upstream version building against EMBOSS 4.0.0.
+
+  20 Jul 2006; Olivier Fisette <ribosome@gentoo.org>
+  embassy-domsearch-0.1.0.ebuild:
+  Fixed download URL (silent upstream repackaging).
+
+  03 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
+  embassy-domsearch-0.1.0.ebuild:
+  Stable on ppc-macos (with j4rg0n's permission, bug #102420).
+
+  02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org>
+  embassy-domsearch-0.1.0.ebuild:
+  Stable on ppc.
+
+  21 Sep 2005; Olivier Fisette <ribosome@gentoo.org>
+  embassy-domsearch-0.1.0.ebuild:
+  Added to x86.
+
+*embassy-domsearch-0.1.0 (07 Aug 2005)
+
+  07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +embassy-domsearch-0.1.0.ebuild:
+  Initial import. Part of EMBASSY 3.0.0.
+

diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r5.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r5.ebuild
new file mode 100644
index 0000000..b46bfb2
--- /dev/null
+++ b/sci-biology/embassy-domsearch/embassy-domsearch-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-domsearch/embassy-domsearch-0.1.0-r4.ebuild,v 1.2 2010/01/01 21:53:24 fauli Exp $
+
+EBOV="6.3.1"
+EBO_DESCRIPTION="Protein domain search add-on package"
+
+inherit embassy-ng
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"

diff --git a/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.0-r5.patch b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.0-r5.patch
new file mode 100644
index 0000000..303293c
--- /dev/null
+++ b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.0-r5.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 @@
+ #
+ 
++ACLOCAL_AMFLAGS = -I m4
+ SUBDIRS = src emboss_acd emboss_doc
+ 
+ EXTRA_DIST = depcomp ltmain.sh install-sh config.sub config.guess
+diff --git a/configure.in b/configure.in
+index 8cce01f..7eb5148 100644
+--- a/configure.in
++++ b/configure.in
+@@ -187,15 +187,6 @@ AC_PROG_INSTALL
+ AC_PROG_LN_S
+ AC_PROG_MAKE_SET
+ 
+-dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+-if test "${with_x}" != "no" ; then
+-if test "`uname -a | grep Darwin`"; then
+-OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
+-if test ${OSXX} '>' '10.4'; then
+-CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
+-fi
+-fi
+-fi
+ 
+ dnl Check for header files
+ AC_PATH_XTRA
+@@ -250,8 +241,8 @@ AX_LIB_POSTGRESQL
+ CFLAGS="$CFLAGS $MYSQL_CFLAGS"
+ LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS"
+ 
+-CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS"
+-LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS"
++CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS"
++LDFLAGS="$POSTGRESQL_LDFLAGS $LDFLAGS"
+ 
+ 
+ dnl "Export" these variables for PCRE
+@@ -386,9 +377,30 @@ AC_ARG_ENABLE(systemlibs,
+    AS_HELP_STRING([--enable-systemlibs], [Use system versions of zlib/expat]))
+ if test "${enable_systemlibs}" = "yes" ; then
+     have_systemlibs=yes
++    DEFINE_USE_SYSTEM_PCRE="#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}" != "no" ; then
++    if test "`uname -a | grep Darwin`"; then
++    OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
++    if test ${OSXX} '>' '10.4'; then
++    CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
++    fi
++    fi
++    fi
++    if test "${with_x}" != "no" ; then
++    LF_EMBOSS_PATH_XLIB
++    fi
++     AC_MSG_NOTICE(USING bundled LIBS)
+ fi          
+ AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes")
+ AC_SUBST(ESYSTEMLIBS)
++AC_SUBST(DEFINE_USE_SYSTEM_PCRE)
++AC_SUBST(PLPLOT_CFLAGS)
++AC_SUBST(PLPLOT_LIBS)
+ 
+ 
+ 
+diff --git a/src/Makefile.am b/src/Makefile.am
+index c8c5fd7..9652a64 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -17,9 +17,9 @@ INCLUDES = -I../../../nucleus -I../../../ajax/pcre \
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-INCLUDES = -I${embprefix}/include -I${embprefix}/include/eplplot \
+-	$(NLINCLUDES) \
+-	-I${embprefix}/include/epcre
++INCLUDES = -I${embprefix}/include $(PLPLOT_CFLAGS) \
++	$(NLINCLUDES) -I${embprefix}/include/emboss \
++	-I${embprefix}/include/pcre
+ endif
+ 
+ if ISSHARED
+@@ -61,6 +61,6 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ 	../../../ajax/pcre/libepcre.la \
+ 	../../../plplot/libeplplot.la $(XLIB)
+ else
+-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+-        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
++        -lajax -lpcre $(NLADD) $(PLPLOT_LIBS) $(XLIB)
+ endif

diff --git a/sci-biology/embassy-domsearch/metadata.xml b/sci-biology/embassy-domsearch/metadata.xml
new file mode 100644
index 0000000..d464821
--- /dev/null
+++ b/sci-biology/embassy-domsearch/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+</pkgmetadata>