Import latest changes from science overlay, thanks Ted Tanberry for the work; fixes #335603

(Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

5 files changed, 125 insertions, 0 deletions

diff --git a/sci-biology/embassy-meme/ChangeLog b/sci-biology/embassy-meme/ChangeLog
new file mode 100644
index 000000000000..d4133ff2be74
--- /dev/null
+++ b/sci-biology/embassy-meme/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/embassy-meme
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-meme/ChangeLog,v 1.22 2015/03/28 17:17:41 jlec Exp $
+
+*embassy-meme-4.7.650 (28 Mar 2015)
+
+  28 Mar 2015; Justin Lecher <jlec@gentoo.org> +embassy-meme-4.7.650.ebuild,
+  +files/embassy-meme-4.7.650_fix-build-system.patch, +metadata.xml:
+  Import latest changes from science overlay, thanks Ted Tanberry for the work;
+  fixes #335603
diff --git a/sci-biology/embassy-meme/Manifest b/sci-biology/embassy-meme/Manifest
new file mode 100644
index 000000000000..4c5f81081608
--- /dev/null
+++ b/sci-biology/embassy-meme/Manifest
@@ -0,0 +1,5 @@
+AUX embassy-meme-4.7.650_fix-build-system.patch 2359 SHA256 d28fa6f227a8131d0f582c61c75679410712d696c81735903bae4f49e78ca897 SHA512 3669c1d9a19d531d63f45f0ca5ab81e50a714158d62304ef115bb3c3a19032856049eb16857f07ccec72150c5d6a50efdf8beafceb29b99fc96c2e3c554b7125 WHIRLPOOL b1f18556c06f4eede7ab731e34607b50348512153ac931626891fa02e4d8023d289817556491e33c36a333c446fbabfd8066dd670c13ad182f84e256cef0d5f7
+DIST embassy-meme-4.7.650.tar.gz 622448 SHA256 a9ce0af5f8e05d82cf7678c9781041520bb9889a5706e38480940003ef2a9e8f SHA512 0536531b198aac09a9fe6c17cf1c60c766789c94a7f83f743a90aaa65061c95534bf398c53611a34549b7ec1a4928fdc45fe0d2553f25f85eeda41f90c2e8c6f WHIRLPOOL 041fec3789c86375edb64b34a0190484cda6a59aab564c5deee19930a8cec0455ed9689d726cb647cca30e7c3c59f728aff5546ab8ad491aed4f331e76497b51
+EBUILD embassy-meme-4.7.650.ebuild 386 SHA256 88f501bbfc8a98722f1f5a15872268a0e74b56017e36ea379cedfd2f649ff5e3 SHA512 05993f00077d92dcf10d0badcd76fb1eda89d4f96ec74026f3ecd7166275f629574cbd92bf235c92216ad16b824adce8e01636c719c6b969495efb4f85826796 WHIRLPOOL b6c00c95ca3580ffbeac20aeda36cb75c8f150ef177271476f95c452ab6ed32a6a83eaa16e44cf078f89b7ede6edf53a7ba56413a7ffdbffc24dfaf3012d1f4b
+MISC ChangeLog 404 SHA256 c8d9d0bc2705dbe3b957c8676d32ecf57a4e8c3919984410ec5d772f9dfeeaec SHA512 8cfd2c8b64d8fee714c095192806ee4adbadc512710553386de915535c56a057acee8a5e3ba5c229fb7bb1371b794f7fb7fe052c2dba45f393dc6f2e79ac4d27 WHIRLPOOL de87b1cdf3846b6885a3b3dfb72504720cc9da994afbc31110ba4d3167658097a7148e70589f58eadd57e9b11b99b0051b1275bdd87ae7ccef42bce3678e9841
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
diff --git a/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild b/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild
new file mode 100644
index 000000000000..26a4aa2042a2
--- /dev/null
+++ b/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild
@@ -0,0 +1,15 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild,v 1.1 2015/03/28 17:17:41 jlec Exp $
+
+EAPI=5
+
+EBO_DESCRIPTION="wrappers for MEME - Multiple Em for Motif Elicitation"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+
+RDEPEND+=" sci-biology/meme"
diff --git a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch
new file mode 100644
index 000000000000..03c42460455e
--- /dev/null
+++ b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch
@@ -0,0 +1,90 @@
+--- MEME-4.7.650/configure.ac
++++ MEME-4.7.650/configure.ac
+@@ -635,33 +635,6 @@
+ 
+ 
+ 
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
+-
+-dnl Default values for miscellaneous macros
+-
+-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
+-
+-dnl Provide versioning information for libtool shared libraries that
+-dnl are built by default on Unix systems.
+-
+-PCRE_LIB_VERSION="0:1:0"
+-PCRE_POSIXLIB_VERSION="0:0:0"
+-
+-
+-
+-
+ dnl FIXME: This does no longer seem required with Autoconf 2.67?
+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+ dnl AS_IF([test "x${with_x}" != "xno"],
+@@ -737,21 +710,6 @@
+ 
+ 
+ 
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -874,6 +832,11 @@
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+ 
+ 
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd])
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+--- MEME-4.7.650/src/Makefile.am
++++ MEME-4.7.650/src/Makefile.am
+@@ -17,9 +17,7 @@
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+-	$(NLINCLUDES) \
+-	-I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+ 
+ if ISSHARED
+@@ -60,5 +58,5 @@
+ 	$(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+-        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++        -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-meme/metadata.xml b/sci-biology/embassy-meme/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/embassy-meme/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>