Please don't pick things out of context. It does not say .C() is deprecated and it is not talking about R code: it says

There are default variables and rules for this (determined when R is configured and recorded in R_HOME/etcR_ARCH/Makeconf), providing support for C, C++, FORTRAN 77, Fortran 9x, Objective C and Objective C++ with associated extensions .c, .cc or .cpp, .f, .f90 or .f95, .m, and .mm or .M, respectively. We recommend using .h for headers, also for C++ or Fortran 9x include files. (Use of .C for C++ is now deprecated and will be removed in R 2.12.0.)

You missed 'associated extensions', and that the NEWS file says

    o   Use of file extension .C for C++ code in packages is now
        deprecated: it has caused problems for some 'make's on
        case-insensitive file systems (although it currently works
        with the recommended toolkits).


On Wed, 21 Jul 2010, Florian Breitwieser wrote:

Hi,

I am writing a R package and having a bit of trouble to have the C++
code working.

I was planing using the .C interface function, however I found the
comment (Use of ‘.C’ for C++ is now deprecated and will be removed in
R 2.12.0.) in the R-exts manual.

So this interface function should not be used anymore - .Call() or
Rcpp instead? What is the reason for the deprecation?

Thanks,
Florian

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