Matthew Turland came across an interesting bug when working with the Cares Document Checker he's developing related to linting (running a syntax check) on a given PHP file.

While doing a lint check on a code block, a parse error was occurring on a line that contained a comment in the original source file. [...] Presumably what was happening was, even though the var_dump() call showed that actual newlines were being interpreted correctly, the r was also being interpreted rather than taken literally. This caused the comma following it to generate the error I was receiving.

An alternative to the method he was using, shell_exec, is proc_open, a function that opens a resource to handle a command execution and allows for more than just the "point and shoot" execution that things like shell_exec, or system.