Bioc developers,
Tomas Kalibera has developed an offline bug-finding tool written
specifically to detect C PROTECT errors. The tool detects errors in the
following Bioconductor packages:
affyio affyPLM Biostrings BufferedMatrix chopsticks CNEr crlmm csaw
DECIPHER DiffBind diffHic DirichletMultinomial EBImage edgeR fabia graph
GraphAlignment HIBAG immunoClust InteractionSet IRanges metahdep mgsa
MotIV mzR ncdfFlow PICS PING qpgraph QuasR R453Plus1Toolbox rqubic
Rsamtools rSFFreader rtracklayer S4Vectors SANTA scran SeqArray SIMLR
SNPRelate snpStats STAN TargetSearch ternarynet TitanCNA vsn xcms XVector
Additional information and the reports are available at
https://github.com/kalibera/rprotect
Each package has its own subdirectory with textual reports and with
DESCRIPTION file with the version of the package the tool has been run on.
Please have a look at reports for your package(s) and fix if necessary.
If you wish to re-run the bug-finding tool on your package after fixing,
please refer to
https://github.com/kalibera/rchk
where installation instructions are available, including a script to
automatically install the tool into a virtual machine. Still, please be
advised that the automated installation may take long (about 1 hour on a
decent machine).
The tool is not perfect, so assess each report carefully. '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!
Have fun, and safe coding!
Martin
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