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)

5 files changed, 271 insertions, 0 deletions

diff --git a/sci-biology/embassy-esim4/ChangeLog b/sci-biology/embassy-esim4/ChangeLog
new file mode 100644
index 000000000..b8385d181
--- /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 <jlec@gentoo.org> +embassy-esim4-1.0.0-r7.ebuild,
+  +files/embassy-esim4-1.0.0-r7.patch, +metadata.xml:
+  Move to new embassy-ng.eclass
+
+  01 Jan 2010; Christian Faulhammer <fauli@gentoo.org>
+  embassy-esim4-1.0.0-r6.ebuild:
+  Transfer Prefix keywords
+
+  01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
+  Giving up maintainership of this package.
+
+*embassy-esim4-1.0.0-r6 (01 Sep 2009)
+
+  01 Sep 2009; Olivier Fisette <ribosome@gentoo.org>
+  +embassy-esim4-1.0.0-r6.ebuild:
+  Updated version for EMBASSY 6.1.0.
+
+  01 Sep 2009; Olivier Fisette <ribosome@gentoo.org>
+  embassy-esim4-1.0.0-r5.ebuild:
+  Stabilised on amd64 and x86.
+
+  27 Aug 2008; Olivier Fisette <ribosome@gentoo.org>
+  -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 <ribosome@gentoo.org>
+  +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 <ribosome@gentoo.org>
+  +embassy-esim4-1.0.0-r4.ebuild:
+  New upstream packaging for EMBOSS 5.0.0.
+
+  16 Feb 2007; Jeff Gardner <je_fro@gentoo.org>
+  embassy-esim4-1.0.0-r3.ebuild:
+  Added ~amd64.
+
+  10 Dec 2006; Olivier Fisette <ribosome@gentoo.org>
+  -embassy-esim4-1.0.0-r2.ebuild:
+  Pruning old version.
+
+  03 Nov 2006; Jeff Gardner <je_fro@gentoo.org>
+  embassy-esim4-1.0.0-r3.ebuild:
+  Marked ~sparc
+
+  02 Nov 2006; Fabian Groffen <grobian@gentoo.org>
+  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 <ribosome@gentoo.org>
+  embassy-esim4-1.0.0-r3.ebuild:
+  Added to x86.
+
+*embassy-esim4-1.0.0-r3 (21 Jul 2006)
+
+  21 Jul 2006; Olivier Fisette <ribosome@gentoo.org>
+  +embassy-esim4-1.0.0-r3.ebuild:
+  New upstream version building against EMBOSS 4.0.0.
+
+  20 Jul 2006; Olivier Fisette <ribosome@gentoo.org>
+  embassy-esim4-1.0.0-r2.ebuild:
+  Fixed digest mismatch due to silent upstream repackaging.
+
+  04 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
+  -embassy-esim4-1.0.0-r1.ebuild:
+  Removed obsolete version.
+
+  03 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
+  embassy-esim4-1.0.0-r2.ebuild:
+  Stable on ppc-macos (with j4rg0n's permission, bug #102420).
+
+  02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org>
+  embassy-esim4-1.0.0-r2.ebuild:
+  Stable on ppc.
+
+  21 Sep 2005; Olivier Fisette <ribosome@gentoo.org>
+  embassy-esim4-1.0.0-r2.ebuild:
+  Added to x86.
+
+*embassy-esim4-1.0.0-r2 (07 Aug 2005)
+
+  07 Aug 2005; Olivier Fisette <ribosome@gentoo.org>
+  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 part of
+  EMBASSY 3.0.0.
+
+  28 Jul 2005; Olivier Fisette <ribosome@gentoo.org>
+  -embassy-esim4-1.0.0.ebuild:
+  Removed old version.
+
+  26 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org>
+  embassy-esim4-1.0.0-r1.ebuild:
+  Stable ppc-macos
+
+  24 Jun 2005; Joseph Jezak <josejx@gentoo.org>
+  embassy-esim4-1.0.0-r1.ebuild:
+  Marked ppc stable.
+
+  13 May 2005; Olivier Fisette <ribosome@gentoo.org>
+  embassy-esim4-1.0.0-r1.ebuild:
+  Added to x86.
+
+*embassy-esim4-1.0.0-r1 (25 Mar 2005)
+
+  25 Mar 2005; Olivier Fisette <ribosome@gentoo.org>
+  +embassy-esim4-1.0.0-r1.ebuild:
+  Build against the EMBOSS 2.10 source tree.
+
+  02 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-esim4-1.0.0.ebuild:
+  Stable ppc-macos
+
+  25 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-esim4-1.0.0.ebuild:
+  Unstable ppc-macos.
+
+*embassy-esim4-1.0.0 (23 Dec 2004)
+
+  23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +embassy-esim4-1.0.0.ebuild:
+  Moved from app-sci/embassy-esim4 to sci-biology/embassy-esim4.
+
+  31 Oct 2004; Olivier Fisette <ribosome@gentoo.org>
+  embassy-esim4-1.0.0.ebuild:
+  Added to x86.
+
+  21 Jul 2004; David Holm <dholm@gentoo.org> embassy-esim4-1.0.0.ebuild:
+  Added to ~ppc.
+
+* embassy-esim4-1.0.0 (19 Jul 2004)
+
+  19 Jul 2004; Olivier Fisette <ribosome@gentoo.org>
+  embassy-esim4-1.0.0.ebuild, metadata.xml, ChangeLog
+  Initial import.
diff --git a/sci-biology/embassy-esim4/Manifest b/sci-biology/embassy-esim4/Manifest
new file mode 100644
index 000000000..153df191b
--- /dev/null
+++ b/sci-biology/embassy-esim4/Manifest
@@ -0,0 +1,15 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX embassy-esim4-1.0.0-r7.patch 3014 RMD160 7d476277588a9aa081c81b3a532b7fd0294dc2cf SHA1 35b3d7686a6fe09aa7d28554e98c60c3336b74ad SHA256 be6f784667ebae5509a08daf785490fae19eec8101bc2e5a34d6a41b0eefac72
+DIST embassy-6.3.1-esim4-1.0.0.tar.gz 415096 RMD160 9043eaaed74aab481b1a2e690a06932211421003 SHA1 76a2ea556a23241d94e17fdfdcc05bfa17dd8bfb SHA256 7abd69516d6e12ae58f568662db3bfa19bb3a15c03413db61ecda3f013b144f5
+EBUILD embassy-esim4-1.0.0-r7.ebuild 380 RMD160 5e379d38e12aa940f7ce4fa3b20e72a08ee6106b SHA1 05e463f4cebdb6d21c5620b1cb90090e1522ef55 SHA256 a8588476af70c89c8cf0d2832fde4b38d980c86d2719e844bb156ea352b721b6
+MISC ChangeLog 4381 RMD160 16bdb5f7f6901d50372983a3d86fd9ceae4be72d SHA1 42f281ca8694736bc0e8d07bf6c37e5842c76895 SHA256 e35b2898a37fb4b63709a7e9c025896c687f2d2e42952bbcc8904bd32ca24aaa
+MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.17 (GNU/Linux)
+
+iEYEARECAAYFAk144fIACgkQgAnW8HDreRYzfACfdFQWvijH1O1qrpKT+2YYI5Ap
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diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r7.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r7.ebuild
new file mode 100644
index 000000000..6e7712849
--- /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-esim4-1.0.0-r6.ebuild,v 1.2 2010/01/01 21:58:14 fauli Exp $
+
+EBOV="6.3.1"
+EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA"
+
+inherit embassy-ng
+
+KEYWORDS="~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 000000000..f74823dee
--- /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 @@
+ #
+ 
++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 077c81b..7ba7af1 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 $LDFLAGS"
+ 
+ 
+ dnl "Export" these variables for PCRE
+@@ -388,9 +379,30 @@ AC_ARG_ENABLE(systemlibs,
+    AS_HELP_STRING([--enable-systemlibs], [Use system versions of zlib/expat]))
+ if test "${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 e593a9c..6132408 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -18,9 +18,9 @@ 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
+@@ -63,6 +63,6 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.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-esim4/metadata.xml b/sci-biology/embassy-esim4/metadata.xml
new file mode 100644
index 000000000..d4648212c
--- /dev/null
+++ b/sci-biology/embassy-esim4/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>