[R-pkg-devel] Calling registered C methods with a "variable name"

Ulrich Bodenhofer bodenhofer at bioinf.jku.at
Mon Jul 3 18:14:19 CEST 2017


As R CMD check is more pedantic about the registration of native 
routines since version 3.4, I wanted to update my CRAN packages 
accordingly. While this worked nicely for my 'apcluster' packages (and, 
some time ago, for my  Bioconductor packages), I am having problems with 
my 'rococo' package. The problem is that I use string variables for some 
of the .NAME arguments of the calls to the .Call() function. In other 
word, the R function calling .Call() uses paste() to put together the 
function name into a string and then calls .Call() with the .NAME 
argument being this string variable. This is the simplest and most 
efficient approach under the given circumstances (I omit a detailed 
justification at this point, but I can provide it if wanted). Any other 
approach would require a lot more coding. It is also safe, since the 
variable part of the name is secured against invalid names using 
match.arg() with a fixed list of options.

In more detail, here is a (slightly simplified) example: suppose there 
are three C functions rcor_matrix_min, rcor_matrix_prod, and 
rcor_matrix_lukasiewicz ...

     dummy <- function(x, y, sim=c("min", "prod", "lukasiewicz"))
         sim <- match.arg(sim)


         funcName <- paste0("rcor_matrix_", sim)
         result <- .Call(funcName, x, y)


The approach described above worked perfectly before I registered the 
native routines rcor_matrix_min, rcor_matrix_prod, and 
rcor_matrix_lukasiewicz. And it still works now with registered native 
routines. The whole package also passes 'R CMD check' without errors, 
warnings, or notes. However, if I add the option '--as-cran', I get a 
bunch of notes saying that the symbol 'funcName' that I use as .NAME 
argument is not registered. Can anybody comment on that please? Can I 
simply ignore this? Is it imperative to fix this? Or is it an issue in 
the 'R CMD check *** --as-cran' that this special case is simply overlooked?

Thanks in advance and best regards,

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