Hi Aaron --
On 03/15/2016 08:40 AM, Aaron Taudt wrote:
I am trying to register my native routines as recommended by BiocCheck. I
followed the instructions in "Writing R Extensions" and have implemented
the following code in "init.cpp". However, the routines are still not
registered.
#include <Rinternals.h>
#include <R_ext/Rdynload.h>
#include "R_interface.h" // contains univariate_hmm, multivariate_hmm, etc.
static const R_CMethodDef CEntries[] = {
{"univariate_hmm", (DL_FUNC) &univariate_hmm, 24,
(R_NativePrimitiveArgType[24]) {INTSXP, INTSXP, INTSXP, INTSXP, REALSXP,
REALSXP, INTSXP, INTSXP, REALSXP, INTSXP, REALSXP, REALSXP, REALSXP,
REALSXP, INTSXP, REALSXP, REALSXP, REALSXP, REALSXP, LGLSXP, INTSXP,
INTSXP, INTSXP, INTSXP}},
{"multivariate_hmm", (DL_FUNC) &multivariate_hmm, 18,
(R_NativePrimitiveArgType[18]) {REALSXP, INTSXP, INTSXP, INTSXP, INTSXP,
INTSXP, INTSXP, REALSXP, INTSXP, REALSXP, REALSXP, REALSXP, REALSXP,
REALSXP, LGLSXP, INTSXP, INTSXP, INTSXP}},
{"univariate_cleanup", (DL_FUNC) &univariate_cleanup, 0, NULL},
{"multivariate_cleanup", (DL_FUNC) &multivariate_cleanup, 1,
(R_NativePrimitiveArgType[1]) {INTSXP}},
{NULL, NULL, 0, NULL}
};
void R_init_AneuFinder(DllInfo *dll)
{
R_registerRoutines(dll, CEntries, NULL, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
}
My NAMESPACE contains
useDynLib(AneuFinder, .registration = TRUE)
I don't see what's missing here, because the routines are still not
registered. I appreciate any help.
How do you know that they are not registered?
This is C code, but init.cpp is compiled by the C++ compiler; do you
need extern "C" {} around the this code?
When I try to install the most recent version of your package on the
tracker, my default setting has compiler option -O0 (in
R.home("etc/Makeconf")) and the nan_expected symbol is missing from the
shared object
** testing if installed package can be loaded
Bioconductor version 3.3 (BiocInstaller 1.21.3), ?biocLite for help
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
'/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.3/AneuFinder/libs/AneuFinder.so':
/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.3/AneuFinder/libs/AneuFinder.so:
undefined symbol: nan_detected
Error: loading failed
Execution halted
ERROR: loading failed
Martin
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