[Bioc-devel] PROTECT errors in Bioconductor packages

Aaron Lun alun at wehi.edu.au
Thu Apr 6 11:33:58 CEST 2017

> 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) {
         throw; // break out of this part of the function
     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...



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