[R-pkg-devel] nativeRoutines error when using roxygen2 in RStudio

[Georgi Boshnakov]

Without code we are guessing.  A bug is possible but I will make another guess suggestion.

Delete all binary files created by devtools during compilation in your package directory.
devtools::load_all() is so fast partly because it recompiles the C/Fortran files only when necessary
but sometimes compilation may be needed even if devtools thinks otherwise.

 Georgi Boshnakov


-----Original Message-----
From: Duncan Murdoch [mailto:murdoch.duncan using gmail.com] 
Sent: 07 November 2018 00:26
To: Rampal Etienne; Georgi Boshnakov; r-package-devel using r-project.org
Subject: Re: [R-pkg-devel] nativeRoutines error when using roxygen2 in RStudio

On 06/11/2018 5:17 PM, Rampal Etienne wrote:
> Dear Duncan,
> 
> I don't get it when using R CMD check.
> 
> I only get it when building/loading using roxygen2 or when I call
> load_all (which roxygen2 does too, I think). load_all calls load_dll
> which then throws this error. I have registered my routines in
> R_init_secsse.c:
> 
> void R_init_secsse(DllInfo *dll)
> {
>     R_registerRoutines(dll, NULL, NULL, FortranEntries, NULL);
>     R_useDynamicSymbols(dll, FALSE);
> }
> 
> Any suggestions?

Nope!  Sounds like a bug in devtools/roxygen2, but I don't know either 
of those packages well.

Duncan Murdoch

> 
> Cheers, Rampal
> 
> 
> On 06-Nov-18 22:50, Duncan Murdoch wrote:
>> On 06/11/2018 3:27 PM, Rampal Etienne wrote:
>>> Dear Georgi,
>>>
>>> Thanks for your suggestions. I have tried to install the development
>>> version of roxygen2, but to no avail.
>>>
>>> I don't have a Collate field in DESCRIPTION.
>>>
>>> devtools::check() gives me:
>>>
>>> Updating secsse documentation Loading secsse Registered S3 method
>>> overwritten by 'dplyr': method from as.data.frame.tbl_df tibble
>>> Registered S3 method overwritten by 'geiger': method from
>>> unique.multiPhylo ape Error in nativeRoutines[[lib]] <- routines :
>>> object 'nativeRoutines' not found
>>
>> Do you get that error if you run "R CMD check" on the tarball of your
>> package?
>>
>> If so, how comfortable are you with debugging R code?  I can tell you
>> how to debug the check process, but it's a little tricky.
>>
>> Duncan Murdoch
>>
>>>
>>>
>>> Any other suggestions?
>>>
>>> Cheers, Rampal
>>>
>>> On 02-Nov-18 08:33, Georgi Boshnakov wrote:
>>>> Try installing the latest development version of roxygen2, if you
>>>> are not using it already.
>>>> There was a bug in the released version preventing installation in
>>>> some cases.
>>>> If you don't want to use development version of roxygen2,
>>>> try putting all filenames in the Collate field in DESCRIPTION on one
>>>> line and make sure that there is a single space
>>>> between them. This should work if your problem is what I think.
>>>>
>>>> By the way, in such cases you will get more informative messages if
>>>> you run devtools::check().
>>>>
>>>> -- 
>>>> Georgi Boshnakov
>>>>
>>>>
>>>> ________________________________________
>>>> From: R-package-devel [r-package-devel-bounces using r-project.org] on
>>>> behalf of Rampal Etienne [rampaletienne using gmail.com]
>>>> Sent: 01 November 2018 22:40
>>>> To: r-package-devel using r-project.org
>>>> Subject: [R-pkg-devel] nativeRoutines error when using roxygen2 in
>>>> RStudio
>>>>
>>>> Since a few weeks (after updating R-devel and Rtools) I get the
>>>> following error when trying to build a package or document it, when
>>>> using roxygen2 in RStudio:
>>>>
>>>> In R CMD INSTALL Error in nativeRoutines[[lib]] <- routines : object
>>>> 'nativeRoutines' not found Calls: suppressPackageStartupMessages ...
>>>> withCallingHandlers -> <Anonymous> -> load_all -> load_dll Execution
>>>> halted
>>>>
>>>> When I disable roxygen2, I do not get this error, but of course the
>>>> documentation is not created.
>>>>
>>>> I have installed the latest versions of RStudio, Rtools, R-devel,
>>>> roxygen2, pkgload, but the problem persists.
>>>>
>>>> Does anybody have a clue what is causing this? I am using Windows 10,
>>>> and the package contains Fortran code.
>>>>
>>>> Kind regards,
>>>> Rampal Etienne
>>>>
>>>>            [[alternative HTML version deleted]]
>>>>
>>>> ______________________________________________
>>>> R-package-devel using r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>
>>>
>>>      [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-package-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>
>>
>