sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch

diff --git a/src/Makefile.in b/src/Makefile.in
index 70781f3..b2dcc25 100755
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -760,7 +760,7 @@ chainsawobjs = chainsaw.o
 pdbcur : $(pdbcurobjs)
 	@$(SETFLAGS) ; rm -f pdbcur; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o pdbcur $(pdbcurobjs) $(LDCXXFLAGS)
 ncont : $(ncontobjs)
-	@$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS)
+	@$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS) -lmmdb
 coord_format : $(coord_formatobjs)
 	@$(SETFLAGS) xxx=1 ; \
 	rm -f coord_format; \
diff --git a/src/rapper/LOOP/Makefile.am b/src/rapper/LOOP/Makefile.am
index 85f212e..2608c6d 100755
--- a/src/rapper/LOOP/Makefile.am
+++ b/src/rapper/LOOP/Makefile.am
@@ -15,12 +15,12 @@ params.cpp typed_value.cpp misc.cpp residue.cpp atom.cpp psa.cpp edm_sidechains.
 hash_table.cpp surface.cpp parse.cpp band.cpp edensity.cpp read_map.cpp iterator.cpp \
 residue_range.cpp pop_search_frags.cpp saxs.cpp lib_choral.cpp pdf.cpp WeightedDistribMean.cpp
 
-rapper_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la
+rapper_LDADD = @GC_LIBS@ @LIBXML_LIBS@
 
 pkgdatadir = $(datadir)/rapper
 dist_pkgdata_DATA = params.xml
 
-INCLUDES = -I. -I../gc7.0/include -I../libxml2/include
+INCLUDES = -I. @LIBXML_CFLAGS@ @GC_CFLAGS@
 #SUBDIRS = \
 #@PYTHON_USE_TRUE@ python
 
diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am
index e78b10d..486b931 100755
--- a/src/rapper/Makefile.am
+++ b/src/rapper/Makefile.am
@@ -1,3 +1,3 @@
-SUBDIRS = libxml2 gc7.0 LOOP data
+SUBDIRS = LOOP data
 
 EXTRA_DIST =
diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac
index 5e4ef69..268a579 100755
--- a/src/rapper/configure.ac
+++ b/src/rapper/configure.ac
@@ -48,6 +48,13 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno)
 
 AC_SUBST(rapper_LDFLAGS)
 
-AC_CONFIG_SUBDIRS([gc7.0 libxml2])
+PKG_CHECK_MODULES([LIBXML],[libxml-2.0])
+AC_SUBST([LIBXML_CFLAGS])
+AC_SUBST([LIBXML_LIBS])
+
+PKG_CHECK_MODULES([GC],[bdw-gc])
+AC_SUBST([GC_CFLAGS])
+AC_SUBST([GC_LIBS])
+
 #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile)
 AC_OUTPUT(Makefile LOOP/Makefile data/Makefile)