[Bioc-devel] PROTECT errors in Bioconductor packages

The tool is not perfect, so assess each report carefully.

I also get a warning on almost every C++ function I've written, because
I use the following code to handle exceptions:

     SEXP output=PROTECT(allocVector(...));
     try {
         // do something that might raise an exception
     } catch (std::exception& e) {
         UNPROTECT(1);
         throw; // break out of this part of the function
     }
     UNPROTECT(1);
     return output;

Presumably the check doesn't account for transfer of control to the
catch block. I find that R itself is pretty good at complaining about
stack imbalances during execution of tests, examples, etc.

'My' packages
(Rsamtools, DirichletMultinomial) had several false positives (all
associated with use of an attribute of a protected SEXP), one subtle
problem (a symbol from a PROTECT'ed package name space; the symbol could
in theory be an active binding and the value obtained not PROTECTed by
the name space), and a genuine bug

                tag = NEW_CHARACTER(n);
                for (int j = 0; j < n; ++j)
                    SET_STRING_ELT(tag, j, NA_STRING);
                if ('A' == aux[0]) {
                    buf_A = R_alloc(2, sizeof(char));  # <<- bug
                    buf_A[1] = '\0';
                }
                ...
                SET_VECTOR_ELT(tags, i, tag); # PROTECT tag, too late!

I assume the bug refers to the un-PROTECT'd NEW_CHARACTER here - the
R_alloc call looks okay to me...

Cheers,

Aaron