[R-pkg-devel] nativeRoutines error when using roxygen2 in RStudio
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 at manchester.ac.uk
<mailto:georgi.boshnakov at 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 at gmail.com
<mailto:murdoch.duncan at gmail.com>]
Sent: 07 November 2018 00:26
To: Rampal Etienne; Georgi Boshnakov;
r-package-devel at r-project.org <mailto:r-package-devel at 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 at r-project.org
<mailto:r-package-devel-bounces at r-project.org>] on
>>>> behalf of Rampal Etienne [rampaletienne at gmail.com
<mailto:rampaletienne at gmail.com>]
>>>> Sent: 01 November 2018 22:40
>>>> To: r-package-devel at r-project.org
<mailto:r-package-devel at 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 at r-project.org
<mailto:R-package-devel at r-project.org> mailing list
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-package-devel at r-project.org
<mailto:R-package-devel at r-project.org> mailing list
>>>
>>
>
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