$NetBSD$

--- src/Makefile.in.orig	Tue Jul 27 14:15:13 2004
+++ src/Makefile.in	Tue Jul 27 14:17:37 2004
@@ -53,7 +53,7 @@
 	$(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
-mkinstalldirs = $(mkdir_p)
+mkinstalldirs = $(SHELL) ../mkinstalldirs
 CONFIG_CLEAN_FILES =
 am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(bindir)"
 libLTLIBRARIES_INSTALL = $(INSTALL)
@@ -172,8 +172,8 @@
 @LOCALLINK_TRUE@	../../../ajax/libajax.la \
 @LOCALLINK_TRUE@	../../../plplot/libplplot.la \
 @LOCALLINK_TRUE@	$(am__DEPENDENCIES_1)
-DEFAULT_INCLUDES = -I. -I$(srcdir)
-depcomp = $(SHELL) $(top_srcdir)/depcomp
+DEFAULT_INCLUDES = -I.
+depcomp = $(SHELL) ../depcomp
 am__depfiles_maybe = depfiles
 @AMDEP_TRUE@DEP_FILES = ./$(DEPDIR)/aligneval.Plo \
 @AMDEP_TRUE@	./$(DEPDIR)/alignio.Plo ./$(DEPDIR)/alphabet.Plo \
@@ -356,7 +356,7 @@
 target_alias = @target_alias@
 lib_LTLIBRARIES = libhmmer.la
-@LOCALLINK_FALSE@INCLUDES = -IINCLUDE -I${embprefix}/include
-@LOCALLINK_TRUE@INCLUDES = -IINCLUDE -I../../../ajax
+@LOCALLINK_FALSE@INCLUDES = -IINCLUDE -I@INCLUDE@
+@LOCALLINK_TRUE@INCLUDES = -IINCLUDE -I@INCLUDE@
 @ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS = 
 @ISAIXIA64_TRUE@@ISSHARED_TRUE@@LOCALLINK_FALSE@AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lajax
 @ISAIXIA64_TRUE@@ISSHARED_TRUE@@LOCALLINK_TRUE@AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L../../../ajax/.libs -lajax
