[Bioc-devel] Register native routines
Martin Morgan
martin.morgan at roswellpark.org
Tue Mar 15 17:37:45 CET 2016
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 <martin.morgan at roswellpark.org
> <mailto: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
>
>
> [[alternative HTML version deleted]]
>
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