http://code.google.com/p/bioapi-linux/issues/detail?id=4

--- a/addins/pwbsp/Makefile.in
+++ b/addins/pwbsp/Makefile.in
@@ -87,7 +87,7 @@ CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CFLAGS = @CFLAGS@
 CPP = @CPP@
-CPPFLAGS = -I${top_srcdir}/include/ \
+AM_CPPFLAGS = -I${top_srcdir}/include/ \
 		-I${top_srcdir}/imports/cdsa/v2_0/inc/
 
 CXX = @CXX@
@@ -111,7 +111,7 @@ INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
 INSTALL_SCRIPT = @INSTALL_SCRIPT@
 INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-LDFLAGS = -Wl,--version-script=${srcdir}/libpwbsp.ver
+AM_LDFLAGS = -Wl,--version-script=${srcdir}/libpwbsp.ver
 LEX = @LEX@
 LEXLIB = @LEXLIB@
 LEX_OUTPUT_ROOT = @LEX_OUTPUT_ROOT@
--- a/addins/qtpwbsp/Makefile.in
+++ b/addins/qtpwbsp/Makefile.in
@@ -96,7 +96,7 @@ CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CFLAGS = @CFLAGS@
 CPP = @CPP@
-CPPFLAGS = -I${top_srcdir}/include \
+AM_CPPFLAGS = -I${top_srcdir}/include \
 		-I${top_srcdir}/imports/cdsa/v2_0/inc \
 		${QT_CXXFLAGS}
 
@@ -121,7 +121,7 @@ INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
 INSTALL_SCRIPT = @INSTALL_SCRIPT@
 INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-LDFLAGS = -Wl,--version-script=${srcdir}/libqtpwbsp.ver \
+AM_LDFLAGS = -Wl,--version-script=${srcdir}/libqtpwbsp.ver \
 		${QT_LIBS}
 
 LEX = @LEX@