$content = file( 'yourfile' );
array_splice( $content, $lineNumber );
$fd = fopen( 'yourfile', 'w+' );
fwrite( $fd, implode( '', $content ) );
fclose( $fd );
Note: Array_splice is sometimes hard to understand when your read the code, using unset on your array index will do the same job...
unset( $content[ $lineNumber ] );