3.8: Theme-check Issues - file operations should use wp_filesystem

[carlthewebmaster]

WARNING: fwrite was found in the file anno-article-lookup.php File operations should use the WP_Filesystem methods instead of direct PHP filesystem calls.
Line 585: fwrite($file_handler, $xml);
WARNING: fopen was found in the file parsers.php File operations should use the WP_Filesystem methods instead of direct PHP filesystem calls.
Line 686: $fp = $this->fopen( $file, 'r' );
Line 993: function fopen( $filename, $mode = 'r' ) {
Line 996: return fopen( $filename, $mode );
WARNING: fopen was found in the file anno-article-lookup.php File operations should use the WP_Filesystem methods instead of direct PHP filesystem calls.
Line 576: $file_handler = fopen($filename, 'w');
WARNING: file_get_contents was found in the file phpquery.php File operations should use the WP_Filesystem methods instead of direct PHP filesystem calls.
Line 4788: file_get_contents($file), $contentType
Line 4839: return self::newDocumentPHP(file_get_contents($file), $contentType);
WARNING: file_get_contents was found in the file parsers.php File operations should use the WP_Filesystem methods instead of direct PHP filesystem calls.
Line 394: if ( ! xml_parse( $xml, file_get_contents( $file ), true ) ) {
Line 1031: $file_content = file_get_contents($file);
WARNING: file_get_contents was found in the file clone.php File operations should use the WP_Filesystem methods instead of direct PHP filesystem calls.
Line 315: $orig_file = @file_get_contents($orig_file_path);
WARNING: fclose was found in the file parsers.php File operations should use the WP_Filesystem methods instead of direct PHP filesystem calls.
Line 747: $this->fclose($fp);
Line 1011: function fclose( $fp ) {
Line 1014: return fclose( $fp );
WARNING: fclose was found in the file anno-article-lookup.php File operations should use the WP_Filesystem methods instead of direct PHP filesystem calls.
Line 578: fclose($file_handler);
Line 597: fclose($file_handler);