jlec 15/03/28 17:14:17 Added: embassy-mse-3.0.0.650_fix-build-system.patch Log: 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!)
Revision Changes Path 1.1 sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch?rev=1.1&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch?rev=1.1&content-type=text/plain Index: embassy-mse-3.0.0.650_fix-build-system.patch =================================================================== --- MSE-3.0.0.650/configure.ac +++ MSE-3.0.0.650/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${enable_systemlibs}" = "xyes"], +[ +dnl using system libraries + PKG_CHECK_MODULES([PLPLOT], [plplotd]) +]) # Enable the purify tool: --enable-purify, sets CC and LIBTOOL @@ -1000,17 +963,13 @@ -dnl emnu and mse only: uses curses -dnl Test if --with-curses is given -AC_ARG_WITH([curses], - [AS_HELP_STRING([--with-curses], - [curses (or ncurses)])]) -if test "${with_curses}" ; then -AC_MSG_CHECKING([for curses]) -CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses" -LDFLAGS="$LDFLAGS -L${with_curses}/lib" -fi -AC_CHECK_LIB(ncurses, main, LIBS="$LIBS -lncurses", LIBS="$LIBS -lcurses") +dnl Test if --enable-curses is given +AC_ARG_ENABLE([curses], +[AS_HELP_STRING([--enable-curses], [curses])]) + +AS_IF([test "x$enable_curses" = "xyes"], [ + PKG_CHECK_MODULES([NCURSES], [ncurses]) +]) --- MSE-3.0.0.650/src/Makefile.am +++ MSE-3.0.0.650/src/Makefile.am @@ -18,9 +18,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else -AM_CPPFLAGS = -I../h -I${embprefix}/include \ - -I${embprefix}/include/eplplot -I${embprefix}/include/epcre \ - $(NLINCLUDES) +AM_CPPFLAGS = -I$(top_srcdir)/h -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) $(NCURSES_CFLAGS) endif if ISSHARED @@ -60,5 +58,5 @@ $(XLIB) else LDADD = ../ckit/libckit.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ - -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) + -lensembl -lajaxg -lajax $(NLADD) $(NCURSES_LIBS) $(XLIB) endif --- MSE-3.0.0.650/ckit/Makefile.am +++ MSE-3.0.0.650/ckit/Makefile.am @@ -2,7 +2,7 @@ lib_LTLIBRARIES = libckit.la -AM_CPPFLAGS = -I../h +AM_CPPFLAGS = -I$(top_srcdir)/h CKITSRC = datafiles.c next.c seqentry.c strings.c gcg.c pir.c \ seqspec.c ttyinterface.c nextseqentry.c \ --- MSE-3.0.0.650/emboss_acd/Makefile.am +++ MSE-3.0.0.650/emboss_acd/Makefile.am @@ -1,3 +1,3 @@ -pkgdata_DATA = *.acd +pkgdata_DATA = $(srcdir)/*.acd pkgdatadir=$(prefix)/share/EMBOSS/acd
