diff --git a/avrdude/bootstrap b/avrdude/bootstrap
index 9a5ef9d4..fa38ff33 100755
--- a/avrdude/bootstrap
+++ b/avrdude/bootstrap
@@ -2,6 +2,11 @@
 
 # autoconf-2.57 is preferred, but >= 2.53 should be ok
 
+AUTOHEADER=autoheader
+AUTOCONF=autoconf
+ACLOCAL=aclocal
+AUTOMAKE=automake
+
 if [ "x${AUTOHEADER}" = "x" ]; then
 	AUTOHEADER="autoheader-2.57"
 fi
diff --git a/avrdude/lexer.l b/avrdude/lexer.l
index cd67d912..a09cd234 100644
--- a/avrdude/lexer.l
+++ b/avrdude/lexer.l
@@ -184,7 +184,7 @@ yes              { yylval=new_token(K_YES); return K_YES; }
 ";"       { yylval = NULL; pyytext(); return TKN_SEMI; }
 
 "\n"      { lineno++; }
-[ \t]+  /* ignore whitespace */
+[ \r\t]+  /* ignore whitespace */
 
 c: { fprintf(stderr, "error at %s:%d: possible old-style config file entry\n",
              infile, lineno);