Fix some issues near recent chomp changes.

Reviewed-by: Richard Levitte <levitte@openssl.org>

apps/CA.pl.in

@@ -120,9 +120,9 @@ if ($WHAT eq '-newcert' ) {
     close OUT;
     # ask user for existing CA certificate
     print "CA certificate filename (or enter to create)\n";
-    $FILE = <STDIN>;
-    $FILE = s|\R$|| if $FILE;
-    if ($FILE) {
+    $FILE = "" unless defined($FILE = <STDIN>);
+    $FILE =~ s{\R$}{};
+    if ($FILE ne "") {
         copy_pemfile($FILE,"${CATOP}/private/$CAKEY", "PRIVATE");
         copy_pemfile($FILE,"${CATOP}/$CACERT", "CERTIFICATE");
     } else {