[Rd] help with rchk warnings on Rf_eval(Rf_lang2(...))

Martin Maechler m@ech|er @end|ng |rom @t@t@m@th@ethz@ch
Mon Mar 23 22:17:33 CET 2020

>>>>> Ben Bolker 
>>>>>     on Mon, 23 Mar 2020 17:07:36 -0400 writes:

    > Thanks, that's really useful.  One more question for you, or someone
    > else here:

    > const ArrayXd glmLink::linkFun(const ArrayXd& mu) const {
    > return as<ArrayXd>(::Rf_eval(::Rf_lang2(as<SEXP>(d_linkFun),

    > as<SEXP>(Rcpp::NumericVector(mu.data(),

    > mu.data() + mu.size()))
    > ), d_rho);
    > }

    > I guess I need that to read
    > PROTECT(::Rf_eval(PROTECT(::Rf_lang2(...),...) , but as written it
    > doesn't seem I have anywhere to squeeze in an UNPROTECT(2).  Do I need
    > to define a temporary variable so I can UNPROTECT(2) before I return the
    > value?

Ben, as co-author of the package, I could try .. I have lots of
experience with (nice and clean) C API using PROTECT ...
which I could try to apply here.

I'm busy teaching tomorrow (with the extra time of setting up
remote teaching ..)  but could look into it later {and try using
non-Rcpp C code}.

    > Or is there a way I can use Shield() since this an Rcpp-based project
    > anyway?

    > Sorry for all the very basic questions, but I'm flying nearly blind
    > here ...

    > cheers
    > Ben Bolker

    > On 2020-03-23 4:01 p.m., Tomas Kalibera wrote:
    >> On 3/23/20 8:39 PM, Ben Bolker wrote:
    >>> Dear r-devel folks,
    >>>    [if this is more appropriate for r-pkg-devel please let me know and
    >>> I'll repost it over there ...]
    >>> I'm writing to ask for help with some R/C++ integration idioms that are
    >>> used in a package I'm maintaining, that are unfamilar to me, and that
    >>> are now being flagged as problematic by Tomas Kalibera's 'rchk'
    >>> machinery (https://github.com/kalibera/rchk); results are here
    >>> https://raw.githubusercontent.com/kalibera/cran-checks/master/rchk/results/lme4.out
    >>> The problem is with constructions like
    >>> ::Rf_eval(::Rf_lang2(fun, arg), d_rho)
    >>> I *think* this means "construct a two-element pairlist from fun and arg,
    >>> then evaluate it within expression d_rho"
    >>> This leads to warnings like
    >>> "calling allocating function Rf_eval with argument allocated using
    >>> Rf_lang2"
    >>> Is this a false positive or ... ? Can anyone help interpret this?
    >> This is a true error. You need to protect the argument of eval() before
    >> calling eval, otherwise eval() could destroy it before using it. This is
    >> a common rule: whenever passing an argument to a function, that argument
    >> must be protected (directly or indirectly). Rchk tries to be smart and
    >> doesn't report a warning when it can be sure that in that particular
    >> case, for that particular function, it is safe. This is easy to fix,
    >> just protect the result of lang2() before the call and unprotect (some
    >> time) after.
    >>> Not sure why this idiom was used in the first place: speed? (e.g., see
    >>> https://stat.ethz.ch/pipermail/r-devel/2019-June/078020.html ) Should I
    >>> be rewriting to avoid Rf_eval entirely in favor of using a Function?
    >>> (i.e., as commented in
    >>> https://stackoverflow.com/questions/37845012/rcpp-function-slower-than-rf-eval
    >>> : "Also, calling Rf_eval() directly from a C++ context is dangerous as R
    >>> errors (ie, C longjmps) will bypass the destructors of C++ objects and
    >>> leak memory / cause undefined behavior in general. Rcpp::Function tries
    >>> to make sure that doesn't happen.")
    >> Yes, eval (as well as lang2) can throw an error, this error has to be
    >> caught via R API and handled (e.g. by throwing as exception or something
    >> else, indeed that exception then needs to be caught and possibly
    >> converted back when leaving again to C stack frames). An R/C API you can
    >> use here is R_UnwindProtect. This is of course a bit of a pain, and one
    >> does not have to worry when programming in plain C.
    >> I suppose Rcpp provides some wrapper around R_UnwindProtect, that would
    >> be a question for Rcpp experts/maintainers.
    >> Best
    >> Tomas
    >>>   Any tips, corrections, pointers to further documentation, etc. would be
    >>> most welcome ... Web searching for this stuff hasn't gotten me very far,
    >>> and it seems to be deeper than most of the introductory material I can
    >>> find (including the Rcpp vignettes) ...
    >>>    cheers
    >>>     Ben Bolker
    >>> ______________________________________________
    >>> R-devel using r-project.org mailing list
    >>> https://stat.ethz.ch/mailman/listinfo/r-devel

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