I received the following note this AM. The problem is, I'm not quite
sure how to fix it.
Can one use PROTECT(coxlist(eval(PROTECT.... , do I create an
intermediate variable, or otherwise?
I'm willing to update the code if someone will give me a pointer to the
right documentation. This particular chunk was written when there was a
lot of change going on in the callback mechanism and so there might be a
safer and/or simpler and/or more standard aproach by now. The routine in
question has to do with penalized Cox models, the C code needs to get
the value of the penalty and the penalty is an arbitrary S expression
passed down from top level.
Terry T
----------------------------
In survival_2.36-12 (and earlier), in the function cox_callback() at
cox_Rcallback.c:40:
PROTECT(coxlist=eval(lang2(fexpr,data),rho));
the return value of the call to lang2() is vulnerable if allocations
within eval() give rise to garbage collection.
(Discovered during CXXR development.)
Andrew
On 27/03/2012 14:22, Terry Therneau wrote:> I received the following note this AM. The problem is, I'm not quite > sure how to fix it. > Can one use PROTECT(coxlist(eval(PROTECT.... , do I create an > intermediate variable, or otherwise?You can, but I find it easiest to follow if you create an intermediate variable. Look for example at unique.c: SEXP call, r; PROTECT(call = lang2(install("as.character"), s)); PROTECT(r = eval(call, env)); UNPROTECT(2); return r;> > I'm willing to update the code if someone will give me a pointer to the > right documentation. This particular chunk was written when there was a > lot of change going on in the callback mechanism and so there might be a > safer and/or simpler and/or more standard aproach by now. The routine in > question has to do with penalized Cox models, the C code needs to get > the value of the penalty and the penalty is an arbitrary S expression > passed down from top level. > > Terry T > > ---------------------------- > > In survival_2.36-12 (and earlier), in the function cox_callback() at > cox_Rcallback.c:40: > > PROTECT(coxlist=eval(lang2(fexpr,data),rho)); > > the return value of the call to lang2() is vulnerable if allocations > within eval() give rise to garbage collection. > > (Discovered during CXXR development.) > > Andrew > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
On 12-03-27 9:22 AM, Terry Therneau wrote:> I received the following note this AM. The problem is, I'm not quite > sure how to fix it. > Can one use PROTECT(coxlist(eval(PROTECT.... , do I create an > intermediate variable, or otherwise?I think both would work. The usual style in R sources is to use an intermediate variable, assigned within the PROTECT call, e.g. PROTECT(var = f()); but this would act the same as var = PROTECT(f()); I don't know where the best docs are, but here is my understanding of PROTECT: What PROTECT(x) does is to make a copy of the pointer x in a stack of protected pointers. When garbage collection happens, nothing in that stack will be released. It is safe to protect things that don't need protection, but it is a little inefficient. (You shouldn't call PROTECT() on a pointer that isn't an R object declared as a SEXP, but it will only cause trouble in certain debugging modes.) PROTECT(x) does return the value of x, so f(PROTECT(x)) should evaluate the same as f(x) (but x will be protected from collection). The main thing to watch when you use PROTECT is that you keep track of how many times it is called, because UNPROTECT just pops a number of pointers off the protection stack.> > I'm willing to update the code if someone will give me a pointer to the > right documentation. This particular chunk was written when there was a > lot of change going on in the callback mechanism and so there might be a > safer and/or simpler and/or more standard aproach by now. The routine in > question has to do with penalized Cox models, the C code needs to get > the value of the penalty and the penalty is an arbitrary S expression > passed down from top level. > > Terry T > > ---------------------------- > > In survival_2.36-12 (and earlier), in the function cox_callback() at > cox_Rcallback.c:40: > > PROTECT(coxlist=eval(lang2(fexpr,data),rho)); > > the return value of the call to lang2() is vulnerable if allocations > within eval() give rise to garbage collection. > > (Discovered during CXXR development.) > > Andrew > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel