On 03/15/2016 12:30 PM, Aaron Taudt wrote:
I know they were not registered because BiocCheck told me so. In
addition, getDLLRegisteredRoutines('AneuFinder') returned an empty
data.frame.
But wrapping the R_init_<pkg> in an extern "C" block solved the problem:
extern "C" {
void R_init_AneuFinder(DllInfo *dll)
{
R_registerRoutines(dll, CEntries, NULL, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
// R_forceSymbols(dll, TRUE);
}
}
Thanks!
I am not sure what causes the nan_detected problem and I cannot
reproduce it ... Any advice?
This requires that the optimization flag be set to level 0, which can be
done by editing R.home("etc/Makeconf") to have a line like
CXXFLAGS = -O0
I *think* this reproduces across g++ and clang...
The problem is I think with the 'extern' keyword. With optimizations,
the pre-processor inlines the definition, so there is never a symbol
nan_detected. Without optimization the 'extern' keyword is taken
literally to mean that the symbol is defined elsewhere; since there is
no actual definition, it remains undefined. [probably playing a little
loose with what is actually going on...]. One solution is to provide an
actual (non-extern) definition, e.g., in a .cpp file. The high-scoring
answer here
http://stackoverflow.com/questions/11055802/static-and-extern-global-variables-in-c-and-c
might provide a starting point for more rigorous understanding / solution.
Martin
/Dipl. Biol. (t.o.) Aaron Taudt | PhD Student | University Medical
Center Groningen
European Research Institute for the Biology of Ageing (ERIBA)|
Quantitative Epigenetics
///
/A. Deusinglaan 1, gebouw 3226 | 9700 AD Groningen. |
//_www.ERIBA.umcg.nl_/
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2016-03-15 14:09 GMT+01:00 Martin Morgan <[email protected]
<mailto:[email protected]>>:
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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