Compilation error on R-devel about qtl HOT 3 CLOSED

Hey Karl,

Seems like some header is not imported in the mqm code, which is imported in the normal R/qtl C code base, since in:

hmm_main.c at line 1014 the function error() is called without any issues of not being defined
discan.c at line at line 249 the function warning() is called without any issues of not being defined

My guess is that it's due to those files being C files, while the mqm files are C++

As far as I can see, the fix would be to:
#include <R_ext/Error.h>

which exports the error() and warning() macros. This is kind of strange, since importing R.h should lead to the R_ext/Error.h being imported (and the MQM code does import R.h)

from qtl.

It's maybe related to the following from the R-exts manual:

Most of these header files, including all those included by R.h, can be used from C++ code.

Note: Because R re-maps many of its external names to avoid clashes with system or user code, it is essential to include the appropriate header files when using these entry points.

This remapping can cause problems, and can be eliminated by defining R_NO_REMAP (before including any R headers) and prepending ‘Rf_’ to all the function names used from Rinternals.h and R_ext/Error.h. These problems can usually be avoided by including other headers (such as system headers and those for external software used by the package) before any R headers.

from qtl.

To reproduce the problem, it seems like, from the NEWS for R-devel, that we want to set an environment variable _R_CXX_USE_NO_REMAP_ to true. This will compile C++ code with -DR_NO_REMAP.

from qtl.