[Bioc-devel] Register native routines

[Aaron Taudt]

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?



*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 <martin.morgan at roswellpark.org>:

> 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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>>
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>>
>>
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