[R-pkg-devel] nativeRoutines error when using roxygen2 in RStudio
Joshua Ulrich
jo@h@m@ulrich @ending from gm@il@com
Wed Nov 7 18:02:37 CET 2018
Also note that William's suggestion is documented at the bottom of the
"Generic Functions and Methods" section of Writing R Extensions.
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Generic-functions-and-methods
"... as a package can take over a function in the base package and
make it generic by something like
foo <- function(object, ...) UseMethod("foo")
foo.default <- function(object, ...) base::foo(object)
"Earlier versions of this manual suggested assigning foo.default <-
base::foo. This is not a good idea, as it captures the base function
at the time of installation and it might be changed as R is patched or
updated."
Best,
Josh
On Wed, Nov 7, 2018 at 10:45 AM Rampal S. Etienne
<rampaletienne using gmail.com> wrote:
>
> 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>
> > >>>
> > >>
> > >
> >
> > ______________________________________________
> > 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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>
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--
Joshua Ulrich | about.me/joshuaulrich
FOSS Trading | www.fosstrading.com
R/Finance 2018 | www.rinfinance.com
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