[R-pkg-devel] nativeRoutines error when using roxygen2 in RStudio
Rampal S. Etienne
r@mp@letienne @ending from gm@il@com
Wed Nov 7 17:44:52 CET 2018
The problem was resolved by installing again a new version of devtools.
However, this new version gives other problems: devtools::check() says
the DESCRIPTION file is missing a License field, but there IS a license
field in this file.
On 7-11-2018 16:59, William Dunlap wrote:
> After installing a new version of R the OP may have to rebuild (and
> retest) packages like pkgload that define functions by grabbing
> functions from the base package and modifying them, as in
> pkgload/R/namespace-env.r:
>
> onload_assign("makeNamespace",
> eval(
> modify_lang(
> extract_lang(body(loadNamespace),
>
> # Find makeNamespace definition
> comp_lang, y = quote(makeNamespace <- NULL), idx = 1:2)[[3]],
>
> # Replace call to .Internal(registerNamespace()) is replaced by
> a call to
> # register_namespace
> function(x) {
> if (comp_lang(x, quote(.Internal(registerNamespace(name,
> env))))) {
> quote(register_namespace(name, env))
> } else {
> x
> }
> }))
> )
>
>
>
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com <http://tibco.com>
>
> On Wed, Nov 7, 2018 at 3:45 AM, Georgi Boshnakov
> <georgi.boshnakov using manchester.ac.uk
> <mailto:georgi.boshnakov using manchester.ac.uk>> wrote:
>
> 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
> <mailto:murdoch.duncan using gmail.com>]
> Sent: 07 November 2018 00:26
> To: Rampal Etienne; Georgi Boshnakov;
> r-package-devel using r-project.org <mailto: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
> <mailto:r-package-devel-bounces using r-project.org>] on
> >>>> behalf of Rampal Etienne [rampaletienne using gmail.com
> <mailto:rampaletienne using gmail.com>]
> >>>> Sent: 01 November 2018 22:40
> >>>> To: r-package-devel using r-project.org
> <mailto: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
> <mailto:R-package-devel using r-project.org> mailing list
> >>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> <https://stat.ethz.ch/mailman/listinfo/r-package-devel>
> >>>
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> ______________________________________________
> >>> R-package-devel using r-project.org
> <mailto:R-package-devel using r-project.org> mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> <https://stat.ethz.ch/mailman/listinfo/r-package-devel>
> >>>
> >>
> >
>
> ______________________________________________
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> <mailto:R-package-devel using r-project.org> mailing list
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