diff options
4 files changed, 121 insertions, 4 deletions
diff --git a/sci-biology/embassy-vienna/ChangeLog b/sci-biology/embassy-vienna/ChangeLog index 23c45baf17b9..487329567511 100644 --- a/sci-biology/embassy-vienna/ChangeLog +++ b/sci-biology/embassy-vienna/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-biology/embassy-vienna -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/ChangeLog,v 1.10 2011/10/20 08:49:03 xarthisius Exp $ +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/ChangeLog,v 1.11 2015/03/28 17:07:04 jlec Exp $ + +*embassy-vienna-1.7.2.650 (28 Mar 2015) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> +embassy-vienna-1.7.2.650.ebuild, + +files/embassy-vienna-1.7.2.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> embassy-vienna-1.7.2.ebuild, embassy-vienna-1.7.2-r1.ebuild: @@ -46,4 +53,3 @@ 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> +embassy-vienna-1.6.ebuild: Initial import. - diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild new file mode 100644 index 000000000000..9ca6ffa900ea --- /dev/null +++ b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild,v 1.1 2015/03/28 17:07:04 jlec Exp $ + +EAPI=5 + +EBO_DESCRIPTION="Vienna RNA package - RNA folding" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) +AUTOTOOLS_AUTORECONF=1 +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch new file mode 100644 index 000000000000..c9ece691229c --- /dev/null +++ b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch @@ -0,0 +1,98 @@ +--- VIENNA-1.7.2.650/configure.ac ++++ VIENNA-1.7.2.650/configure.ac +@@ -649,33 +649,6 @@ + + + +-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${with_x}" != "xno"], +@@ -751,21 +724,6 @@ + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -888,6 +846,11 @@ + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd]) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +--- VIENNA-1.7.2.650/src/Makefile.am ++++ VIENNA-1.7.2.650/src/Makefile.am +@@ -32,9 +32,7 @@ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I../H -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I$(top_srcdir)/H -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -87,6 +85,7 @@ + endif + + liboviennarna_la_LDFLAGS = $(LINKFLAGS) ++liboviennarna_la_LIBADD = -lajax + + ovrnaalifold_SOURCES = vrnaalifold.c + ovrnaalifoldpf_SOURCES = vrnaalifoldpf.c +@@ -119,5 +118,5 @@ + $(XLIB) + else + LDADD = liboviennarna.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ +- -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lensembl -lajaxg -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-vienna/metadata.xml b/sci-biology/embassy-vienna/metadata.xml index d4648212cbad..f17a827e3101 100644 --- a/sci-biology/embassy-vienna/metadata.xml +++ b/sci-biology/embassy-vienna/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-biology</herd> + <herd>sci-biology</herd> </pkgmetadata> |