diff options
-rw-r--r-- | sci-biology/embassy-memenew/ChangeLog | 61 | ||||
-rw-r--r-- | sci-biology/embassy-memenew/Manifest | 15 | ||||
-rw-r--r-- | sci-biology/embassy-memenew/embassy-memenew-4.0.0-r1.ebuild | 10 | ||||
-rw-r--r-- | sci-biology/embassy-memenew/files/embassy-memenew-4.0.0-r1.patch | 99 | ||||
-rw-r--r-- | sci-biology/embassy-memenew/metadata.xml | 5 |
5 files changed, 190 insertions, 0 deletions
diff --git a/sci-biology/embassy-memenew/ChangeLog b/sci-biology/embassy-memenew/ChangeLog new file mode 100644 index 000000000..4c03c1d6e --- /dev/null +++ b/sci-biology/embassy-memenew/ChangeLog @@ -0,0 +1,61 @@ +# ChangeLog for sci-biology/embassy-memenew +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-memenew/ChangeLog,v 1.11 2010/01/01 22:03:00 fauli Exp $ + +*embassy-memenew-4.0.0-r1 (10 Mar 2011) + + 10 Mar 2011; Justin Lecher <jlec@gentoo.org> + +embassy-memenew-4.0.0-r1.ebuild, +files/embassy-memenew-4.0.0-r1.patch, + +metadata.xml: + Move to new embassy-ng.eclass + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + embassy-memenew-4.0.0.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*embassy-memenew-4.0.0 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + +embassy-memenew-4.0.0.ebuild: + Updated version for EMBASSY 6.1.0. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + embassy-memenew-0.1.0-r1.ebuild: + Stabilised on amd64 and x86. + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + embassy-memenew-0.1.0.ebuild, embassy-memenew-0.1.0-r1.ebuild: + Fixed description. + +*embassy-memenew-0.1.0-r1 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + +embassy-memenew-0.1.0-r1.ebuild: + New upstream version/package for EMBASSY 6.0.1. + + 15 Feb 2007; Jeff Gardner <je_fro@gentoo.org> + embassy-memenew-0.1.0.ebuild: + Added ~amd64. + + 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> + embassy-memenew-0.1.0.ebuild: + Added ~sparc + + 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> + embassy-memenew-0.1.0.ebuild: + Dropped ppc-macos, see you in prefix. + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-memenew-0.1.0.ebuild: + Added to x86. + +*embassy-memenew-0.1.0 (21 Jul 2006) + + 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +embassy-memenew-0.1.0.ebuild: + Initial import. This package will probably replace EMBASSY-MEME in new + EMBASSY releases. + diff --git a/sci-biology/embassy-memenew/Manifest b/sci-biology/embassy-memenew/Manifest new file mode 100644 index 000000000..00c3e1bea --- /dev/null +++ b/sci-biology/embassy-memenew/Manifest @@ -0,0 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +AUX embassy-memenew-4.0.0-r1.patch 3014 RMD160 647aa694e1c8f4bc399173ef8f18f91b19895e69 SHA1 a6a3387a70be970d90f4120dd3999a2dcdd92239 SHA256 14f4c327f69e61e55303b0441ae25fe73aa3b634650068cdccd5d5ab815bda6a +DIST embassy-6.3.1-memenew-4.0.0.tar.gz 513418 RMD160 7072d182479a726e568b0bc2a4c7757ed1c6c087 SHA1 d382f39d1302f1b0799d5b6cb02cd9cfbecee972 SHA256 2192d33b5ee1147742f51416b0504812dfeb13b3b8ec0bfb62fd729e703a19c3 +EBUILD embassy-memenew-4.0.0-r1.ebuild 381 RMD160 82df9d9d812eaaef1caacbba42cc513e5c368bbe SHA1 00918f9f04ba40a606c02465f7164b8163684c42 SHA256 34a921ff0edec8e7e2bbc1c578118a1ca496f8421d7759d8a10c26071822f58a +MISC ChangeLog 1922 RMD160 e2dad93d50b0e5646664095b8bbb605f1811dc62 SHA1 7b3440b830034b5f524f0b46e3309ad1b1628068 SHA256 8e5afd94d3ec66002841f7aee3f6b26871e4cdb0d283f00f887de148e0a1b0bc +MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk14ukoACgkQgAnW8HDreRZ15QCgpquA4cFBqFZdjDcjCPVRCuav +bQsAoJ94O6+vJ5FZPPArqx7b31RVnBlJ +=kLlH +-----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-memenew/embassy-memenew-4.0.0-r1.ebuild b/sci-biology/embassy-memenew/embassy-memenew-4.0.0-r1.ebuild new file mode 100644 index 000000000..18ef903c0 --- /dev/null +++ b/sci-biology/embassy-memenew/embassy-memenew-4.0.0-r1.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-memenew/embassy-memenew-4.0.0.ebuild,v 1.2 2010/01/01 22:03:00 fauli Exp $ + +EBOV="6.3.1" +EBO_DESCRIPTION="MEME - Multiple Em for Motif Elicitation" + +inherit embassy-ng + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-memenew/files/embassy-memenew-4.0.0-r1.patch b/sci-biology/embassy-memenew/files/embassy-memenew-4.0.0-r1.patch new file mode 100644 index 000000000..b90927fa0 --- /dev/null +++ b/sci-biology/embassy-memenew/files/embassy-memenew-4.0.0-r1.patch @@ -0,0 +1,99 @@ +diff --git a/Makefile.am b/Makefile.am +index 9172bb3..349b13b 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 fc16603..1ca9623 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 $LDFLAGS" + + + dnl "Export" these variables for PCRE +@@ -387,9 +378,30 @@ AC_ARG_ENABLE(systemlibs, + AS_HELP_STRING([--enable-systemlibs], [Use system versions of zlib/expat])) + if test "${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 2d0c070..171179d 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 +@@ -59,6 +59,6 @@ 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-memenew/metadata.xml b/sci-biology/embassy-memenew/metadata.xml new file mode 100644 index 000000000..d4648212c --- /dev/null +++ b/sci-biology/embassy-memenew/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> |