[R-pkg-devel] Package Check "Error" status only for r-release-macos-x86_64 flavor

[FARSHAD TABASINEJAD]

Dear R community experts,

The CRAN package check page shows an “ERROR” status for my “Rmbal” package on 
the r-release-macos-x86_64 flavor. The error seems to be related to a failed 
connection. The following links show the error message.

https://cran.r-project.org/web/checks/check_results_Rmbal.html

https://www.r-project.org/nosvn/R.check/r-release-macos-x86_64/Rmbal-00check.html

There is also one “NOTE” regarding the missing Rdpack and magrittr importFroms 
in the NAMESPACE file which I’ve already fixed it. I don’t know if the “ERROR” 
message I get on r-release-macos-x86_64  is due to this “NOTE” message or not.

The “ERROR” and “NOTE” messages only appeared on CRAN, I didn’t receive any 
message from rhub::check_for_cran(env_vars = c(R_COMPILE_AND_INSTALL_PACKAGES = 
“always”).

Your help is really appreciated!

Regards,
Farshad Tabasinejad


[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] "non-ASCII input" and "--data-compress" ignored

[Ivan Krylov]

On Fri, 17 Jul 2020 18:08:24 -0500
Spencer Graves  wrote:

>    I tried escaping "%" every time it occurred without success,
> but adding "\encoding{UTF-8}" as the 4th line of
> nuclearWeaponStates.Rd eliminated that problem.

Glad it works for you, but you might want to check that the link still
leads to the correct URL in the PDF output. In particular, the
following .Rd file:

\encoding{UTF-8}
\title{title}\name{name}\description{
\href{https://www.americansecurityproject.org/ASP Reports/Ref 0072 -
North Korea’s Nuclear Program .pdf}{Derek Bolton (2012) North Korea's
Nuclear Program}

\href{https://www.americansecurityproject.org/ASP\%20Reports/Ref\%200072\%20-\%20North\%20Korea\%E2\%80\%99s\%20Nuclear\%20Program\%20.pdf}{Derek
Bolton (2012) North Korea's Nuclear Program}
}

...gives two working links when processed with R CMD Rdconv -t html,
but when I process it using R CMD Rd2pdf, the first link gets a
\T1\textquoteright instead of ’ in its URL, which makes it invalid. This
could be a LaTeX problem on my part, of course.

> I also tried loading and resaving all the files in the data
> directory.

You can also try using tools::resaveRdaFiles with various parameters if
you are interested.

> at least the first of the resulting *.rda files was corrupted

This sounds like trying to load a version-3 *.rda file (implemented in
3.5.0, default since 3.6.0) using an older version of R. Or a possible
indicator of a hardware problem.

-- 
Best regards,
Ivan

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Note: information on .o files is not available / Found '_exit', possibly from '_exit' (C)

[Fabio Sigrist]

Many thanks to everybody for the valuable answers.

Several people (Benjamin and Ivan) pointed to the lack of portability due
to the "-Wno-cast-function-type" flag. I have changed this.

Further, as suggested by Benjamin, I also added the " -DNDEBUG" flag.
Consequently, there is no assert call anymore when compiling with gcc under
Linux.

Ivan suggested that the forbidden exit/abort calls might be caused by
linking the R package with -static-libstdc+. I have now removed this but I
am still getting the " Found '_exit'" etc. notes. It is also unclear to me
why these exit / abort symbols are only found under Windows / MinGW and not
under Linux.

I agree with Dirks assessment. It seems that the bottom line is that it is
very difficult to find the exit / abort calls. Very unfortunate...

On Fri, Jul 17, 2020 at 11:25 AM Fabio Sigrist 
wrote:

> Dear all,
>
> I am trying to get an R package with C++ code on CRAN and I have one NOTE
> remaining, for which I can't find a solution:
>
> Note: information on .o files for x64 is not available
>   File
> 'd:/RCompile/CRANincoming/R-devel/lib/gpboost/libs/x64/lib_gpboost.dll':
> Found '_exit', possibly from '_exit' (C)
> Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
> Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
> Found 'printf', possibly from 'printf' (C)
>
> As much as I search through my code, I can't find the place / headers
> where these calls / symbols originate. Also, I have no idea how to add
> information on .o files (apart from the shared library, there are no .o
> files). The .tar.gz file for the package can be found on
> https://github.com/fabsig/GPBoost/blob/master/gpboost_0.2.0.tar.gz. Note
> that the shared library is compiled using install.libs.R (this is a
> deliberate choice) and the flag "GPB_R_BUILD" is set when compiling for the
> R package (I have tried to put "#ifndef GPB_R_BUILD" around all headers
> that could cause the problems with exit / abort calls, but apparently I
> have not been able to find all).
>
> Any help is greatly appreciated.
>
> Best regards,
> Fabio Sigrist
>
>

[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

[R-pkg-devel] import 'as' from another package

[Tim Keitt]

I have

  if (!inherits(x, "RasterLayer")) x <- as(x, "RasterLayer")

in a package and its not finding the coerce definition from the raster
package. I know I need to add an @import roxygen2 directive of some kind,
but I'm not sure the correct syntax. My first try generated a warning that
it was not needed.

What is the correct way to do this? Or does raster need to export this
definition?

THK

[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] import 'as' from another package

[Ben Bolker]

   @importFrom methods as

?

On 7/20/20 12:06 PM, Tim Keitt wrote:

I have

   if (!inherits(x, "RasterLayer")) x <- as(x, "RasterLayer")

in a package and its not finding the coerce definition from the raster
package. I know I need to add an @import roxygen2 directive of some kind,
but I'm not sure the correct syntax. My first try generated a warning that
it was not needed.

What is the correct way to do this? Or does raster need to export this
definition?

THK

[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel


__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] import 'as' from another package

[Tim Keitt]

It works but "check" gives

> checking package dependencies ... ERROR
  Namespace dependency not required: ‘methods’

THK

On Mon, Jul 20, 2020 at 11:24 AM Ben Bolker  wrote:

> @importFrom methods as
>
> ?
>
> On 7/20/20 12:06 PM, Tim Keitt wrote:
> > I have
> >
> >if (!inherits(x, "RasterLayer")) x <- as(x, "RasterLayer")
> >
> > in a package and its not finding the coerce definition from the raster
> > package. I know I need to add an @import roxygen2 directive of some kind,
> > but I'm not sure the correct syntax. My first try generated a warning
> that
> > it was not needed.
> >
> > What is the correct way to do this? Or does raster need to export this
> > definition?
> >
> > THK
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] import 'as' from another package

[Ben Bolker]

    I think this is a classic confusing R message.  Try adding methods 
to the Imports: statement in your DESCRIPTION file and see if that 
helps. (Maybe I should file a bug report about that error message - it 
confuses me every time.)

On 7/20/20 12:34 PM, Tim Keitt wrote:
> It works but "check" gives
>
> > checking package dependencies ... ERROR
>   Namespace dependency not required: ‘methods’
>
> THK
>
> On Mon, Jul 20, 2020 at 11:24 AM Ben Bolker  > wrote:
>
> @importFrom methods as
>
> ?
>
> On 7/20/20 12:06 PM, Tim Keitt wrote:
> > I have
> >
> >    if (!inherits(x, "RasterLayer")) x <- as(x, "RasterLayer")
> >
> > in a package and its not finding the coerce definition from the
> raster
> > package. I know I need to add an @import roxygen2 directive of
> some kind,
> > but I'm not sure the correct syntax. My first try generated a
> warning that
> > it was not needed.
> >
> > What is the correct way to do this? Or does raster need to
> export this
> > definition?
> >
> > THK
> >
> >       [[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org
>  mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
> __
> R-package-devel@r-project.org
>  mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] import 'as' from another package

[Tim Keitt]

That did it. Thanks Ben.

THK

On Mon, Jul 20, 2020 at 11:36 AM Ben Bolker  wrote:

>I think this is a classic confusing R message.  Try adding methods to
> the Imports: statement in your DESCRIPTION file and see if that helps.
> (Maybe I should file a bug report about that error message - it confuses me
> every time.)
> On 7/20/20 12:34 PM, Tim Keitt wrote:
>
> It works but "check" gives
>
> > checking package dependencies ... ERROR
>   Namespace dependency not required: ‘methods’
>
> THK
>
> On Mon, Jul 20, 2020 at 11:24 AM Ben Bolker  wrote:
>
>> @importFrom methods as
>>
>> ?
>>
>> On 7/20/20 12:06 PM, Tim Keitt wrote:
>> > I have
>> >
>> >if (!inherits(x, "RasterLayer")) x <- as(x, "RasterLayer")
>> >
>> > in a package and its not finding the coerce definition from the raster
>> > package. I know I need to add an @import roxygen2 directive of some
>> kind,
>> > but I'm not sure the correct syntax. My first try generated a warning
>> that
>> > it was not needed.
>> >
>> > What is the correct way to do this? Or does raster need to export this
>> > definition?
>> >
>> > THK
>> >
>> >   [[alternative HTML version deleted]]
>> >
>> > __
>> > R-package-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>

[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] import 'as' from another package

[Sebastian Meyer]

Yes, indeed, it is confusing. You don't need to file a new bug report, though. 
There is one already:

https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17179

Please feel free to comment there. This thread could serve as another 
confirmation. :-)

Best regards,
Sebastian

Am 20. Juli 2020 18:36:21 MESZ schrieb Ben Bolker :
>    I think this is a classic confusing R message.  Try adding methods 
>to the Imports: statement in your DESCRIPTION file and see if that 
>helps. (Maybe I should file a bug report about that error message - it 
>confuses me every time.)
>
>On 7/20/20 12:34 PM, Tim Keitt wrote:
>> It works but "check" gives
>>
>> > checking package dependencies ... ERROR
>>   Namespace dependency not required: ‘methods’
>>
>> THK
>>
>> On Mon, Jul 20, 2020 at 11:24 AM Ben Bolker > > wrote:
>>
>> @importFrom methods as
>>
>> ?
>>
>> On 7/20/20 12:06 PM, Tim Keitt wrote:
>> > I have
>> >
>> >    if (!inherits(x, "RasterLayer")) x <- as(x, "RasterLayer")
>> >
>> > in a package and its not finding the coerce definition from the
>> raster
>> > package. I know I need to add an @import roxygen2 directive of
>> some kind,
>> > but I'm not sure the correct syntax. My first try generated a
>> warning that
>> > it was not needed.
>> >
>> > What is the correct way to do this? Or does raster need to
>> export this
>> > definition?
>> >
>> > THK
>> >
>> >       [[alternative HTML version deleted]]
>> >
>> > __
>> > R-package-devel@r-project.org
>>  mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>> __
>> R-package-devel@r-project.org
>>  mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>
>   [[alternative HTML version deleted]]
>
>__
>R-package-devel@r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-package-devel

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] import 'as' from another package

[Tim Keitt]

Thanks for pointing to the bug.

Now I am finding I cannot use the 'as' definitions from 'raster' without
loading the package. Do I need an @import directive that specifies the
definitions in the 'raster' package? My understanding is that the 'setAs'
function generates a 'coerce,...' signature but I'm not sure how to import
it to my package.

Thanks again.

THK

On Mon, Jul 20, 2020 at 2:25 PM Sebastian Meyer  wrote:

> Yes, indeed, it is confusing. You don't need to file a new bug report,
> though. There is one already:
>
> https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17179
>
> Please feel free to comment there. This thread could serve as another
> confirmation. :-)
>
> Best regards,
> Sebastian
>
> Am 20. Juli 2020 18:36:21 MESZ schrieb Ben Bolker :
> >I think this is a classic confusing R message.  Try adding methods
> >to the Imports: statement in your DESCRIPTION file and see if that
> >helps. (Maybe I should file a bug report about that error message - it
> >confuses me every time.)
> >
> >On 7/20/20 12:34 PM, Tim Keitt wrote:
> >> It works but "check" gives
> >>
> >> > checking package dependencies ... ERROR
> >>   Namespace dependency not required: ‘methods’
> >>
> >> THK
> >>
> >> On Mon, Jul 20, 2020 at 11:24 AM Ben Bolker  >> > wrote:
> >>
> >> @importFrom methods as
> >>
> >> ?
> >>
> >> On 7/20/20 12:06 PM, Tim Keitt wrote:
> >> > I have
> >> >
> >> >if (!inherits(x, "RasterLayer")) x <- as(x, "RasterLayer")
> >> >
> >> > in a package and its not finding the coerce definition from the
> >> raster
> >> > package. I know I need to add an @import roxygen2 directive of
> >> some kind,
> >> > but I'm not sure the correct syntax. My first try generated a
> >> warning that
> >> > it was not needed.
> >> >
> >> > What is the correct way to do this? Or does raster need to
> >> export this
> >> > definition?
> >> >
> >> > THK
> >> >
> >> >   [[alternative HTML version deleted]]
> >> >
> >> > __
> >> > R-package-devel@r-project.org
> >>  mailing list
> >> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>
> >> __
> >> R-package-devel@r-project.org
> >>  mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>
> >
> >   [[alternative HTML version deleted]]
> >
> >__
> >R-package-devel@r-project.org mailing list
> >https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

[R-pkg-devel] Cartograflow package

[cartograf...@gmail.com]

HelloYesterday a new version of cartograflow v1.0.3 was updated on the crank.  
Everything seems to be OK.
However, when I write in help cartograflow I don't see the thumbnail with the 
different possibilities of visualization: pdf, HTML ...
Is this normal?
Thank you in advance for your answer
Sylvain
[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel