diff options
Diffstat (limited to 'sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch')
-rw-r--r-- | sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch | 149 |
1 files changed, 149 insertions, 0 deletions
diff --git a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch new file mode 100644 index 000000000000..c1095b266d60 --- /dev/null +++ b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch @@ -0,0 +1,149 @@ + ckit/Makefile.am | 2 +- + configure.ac | 67 +++++++++++--------------------------------------- + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 6 ++--- + 4 files changed, 18 insertions(+), 59 deletions(-) + +diff --git a/ckit/Makefile.am b/ckit/Makefile.am +index f87b131..a670d2b 100644 +--- a/ckit/Makefile.am ++++ b/ckit/Makefile.am +@@ -2,7 +2,7 @@ + + lib_LTLIBRARIES = libckit.la + +-AM_CPPFLAGS = -I../h ++AM_CPPFLAGS = -I$(top_srcdir)/h + + CKITSRC = datafiles.c next.c seqentry.c strings.c gcg.c pir.c \ + seqspec.c ttyinterface.c nextseqentry.c \ +diff --git a/configure.ac b/configure.ac +index a20d488..eb208bf 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-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${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +@@ -1000,17 +965,13 @@ AS_IF([test "x${enable_savestats}" = "xyes"], + + + +-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]) ++]) + + + +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index b44632a..84e89b5 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -18,9 +18,7 @@ AM_CPPFLAGS = -I../h \ + -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 @@ LDADD = ../ckit/libckit.la \ + $(XLIB) + else + LDADD = ../ckit/libckit.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ +- -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lensembl -lajaxg -lajax $(NLADD) $(NCURSES_LIBS) $(XLIB) + endif |