On 04/06/2017 05:33 AM, Aaron Lun wrote:
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...
yes, tag needs protection.
I attributed the bug to R_alloc because I failed to reason that R_alloc
(obviously) allocates and hence can trigger a garbage collection.
Somehow it reflects my approach to PROTECTion, probably not shared by
everyone. I like to PROTECT only when necessary, rather than
indiscriminately. Probably this has no practical consequence in terms of
performance, making the code a little easier to read at the expense of
exposing me to bugs like this.
Martin
Cheers,
Aaron
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or...{{dropped:2}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
