I'm writing a new R function that uses a modified version of the cor function (i.e. cor2), to do this I used the bare bone of the native cor function. In the original code is present a call to a C_cor function in the package stats. I try to run the cor2 function but I get the following error:

Error: object 'C_cor' not found.

I modified the call to the compiled function from

.Call(C_cor, x2, y2, 1L, method == 'kendall')

to

.Call(stats:::C_cor, x2, y2, 1L, method == 'kendall').

After that all works fine.

When I try the R CMD check command to verify the package I'm working to, I get:

* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘stats:::C_cor’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.

and :

* checking foreign function calls ... WARNING
Foreign function call to a base package:
  .Call(stats:::C_cor, ...)
Packages should not make .C/.Call/.External/.Fortran calls to a base
package. They are not part of the API, for use only by R itself and
subject to change without notice.

I read the 'Writing Extension' manual but I've not been able to solve the problem. I also tried to find the C_cor funcion in the stats package (from a fresh R download) as suggested by Uwe Ligge... I found the cov.c function  from within the cor function is called... I think... I tried to copy the cov.c file and compile it but I get several errors:

:$ R CMD SHLIB cov.c
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O2 -pipe -g  -c cov.c -o cov.o
cov.c:31:18: fatal error: Defn.h: No such file or directory
compilation terminated.
make: *** [cov.o] Error 1

I copied the Defn.h file too but the error persist. I'm not expert in c and I have not the idea how to overcome this problem.

Do you have any suggestion? 

Indeed how can I overcome the NOTE and the WARNING from the R CMD check?

All the best

It's more appropriate to ask questions about Bioconductor package development on the Bioc-devel mailing list, but I know you've already asked on StackOverflow, so...

It would help to know a little more about what you are doing. From cor it looks like the code path to the .C call just checks that the arguments are valid, then calls the C function. So shouldn't you be able to just use cor() and put your code before or after it?

mycor <- function(x, y=NULL, ...) {
    ## before things
    ans <- cor(x, y, ..., method="kendall")
    ## after things
    ans
}

I don't think it would be a good idea to copy C code (unnecessary code duplication) or to use the naked .C call (the authors of the stats package have no obligation to maintain compatibility with your invocation.)