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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.patch149
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