[R-pkg-devel] vignette error in debian

[Fernando Roa]

Thx Sebastian
I set _R_CLASS_MATRIX_ARRAY_ to true in console and also in onLoad, but
could not replicate the error in console.
In addition, setting _R_CLASS_MATRIX_ARRAY_ to "" in onLoad did not
solve the problem while checking as cran.

I do not understand how the values I got from the debug print when checking
as cran could result in the error.

Any ideas?

On Thu, Nov 28, 2019 at 3:00 AM Sebastian Meyer <seb.meyer using fau.de> wrote:

> This is most likely related to the recently changed class of matrices.
>
> R> class(matrix(1))
>
> returned "matrix" but will return c("matrix", "array") in future
> versions of R. See the corresponding item in the R-devel NEWS
>
> https://stat.ethz.ch/R-manual/R-devel/doc/html/NEWS.html
>
> To reproduce the error, you need a fairly recent R-devel and set the
> environment variable
>
> _R_CLASS_MATRIX_ARRAY_=true
>
> On CRAN, this configuration is currently only used in the two R-devel
> flavors which give warnings for your package.
>
> Happy debugging!
>
>         Sebastian
>
>
> Am 27.11.19 um 23:16 schrieb Fernando Roa:
> > After Ege answer, I could replicate the error(s): list' object cannot be
> > coerced to type 'double'
> > with CMD check: bash R-devel.sh CMD check --as-cran
> > idiogramFISH_1.9.1.tar.gz  in a vmware
> > debian guest with the r-devel (4.0) version of R installed after:
> > http://singmann.org/installing-r-devel-on-linux/
> >
> > Error does not occur in a R-devel console session installed
> > in /usr/local/lib/R-devel/bin
> >
> > After adding debug prints to the code, problem points to a mapply
> >
> > Here are the values I got with debug printing
> >
> > labelytoplot<-list(c(0.654545454545455, 0.654545454545455,
> > 0.763636363636364, 0.763636363636364), c(0.872727272727273,
> > 0.872727272727273, 0.981818181818182, 0.981818181818182),
> > c(1.09090909090909, 1.09090909090909, 1.2, 1.2), c(1.30909090909091,
> > 1.30909090909091, 1.41818181818182, 1.41818181818182))
> > labelxtoplot<-list(c(42.5, 44.75, 44.75, 42.5), c(42.5, 44.75, 44.75,
> > 42.5), c(42.5, 44.75, 44.75, 42.5), c(42.5, 44.75, 44.75, 42.5))
> > borders<-marks<-c("green","blue","yellow","black")
> >
> > CODE producing the error in R CMD check only:
> > # plot(1:50)
> > mapply(function(x,y,z,w) graphics::polygon(x=x,
> >                                            y=y,
> >                                            col=z,
> >                                            lwd=rep(.5,length(marks) )
> >                                            ,border=w
> > ),
> > x = labelxtoplot,
> > y = labelytoplot
> > ,z = marks
> > ,w = borders
> > )
> >
> > Grateful for any guidance ,
> >
> >
> >
> >
> >
> >
> > On Wed, Nov 27, 2019 at 8:34 AM Ege Rubak <rubak using math.aau.dk> wrote:
> >
> >> On 27/11/2019 00.22, Fernando Roa wrote:
> >>> - I used a guest debian 10 in vmware in my system, and couldn't
> replicate
> >>> the error installing with R CMD INSTALL ....
> >>
> >> I guess you should rather run "R CMD check ..." on the tar.gz file to
> >> reproduce the error.
> >>
> >> Hope that helps.
> >>
> >> /Ege
> >>
> >> ______________________________________________
> >> R-package-devel using r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
> >
> > Original message:
> > I got a warning only in debian after submitting package to CRAN.
> > I want to replicate the vignette warning of debian in the following link
> to
> > solve it:
> >
> > Debian:
> >
> https://win-builder.r-project.org/incoming_pretest/idiogramFISH_1.9.1_20191126_012524/Debian/00check.log
> > 1 WARNING
> >
> > Warning summary:
> > "checking re-building of vignette outputs ... [15s/17s] WARNING
> > Error(s) in re-building vignettes:
> > 'list' object cannot be coerced to type 'double'" several times
> > --
> >
> > - I used a guest debian 10 in vmware in my system, and couldn't replicate
> > the error installing with R CMD INSTALL ....
> >
> > - In R of host, I installed rhub and run
> > rhub::check_with_sanitizers() # success
> > rhub::check_on_debian() # does not work because of vignette dependencies
> > not installed
> > rhub::check(platform = "debian-gcc-devel") # does not work because of
> > vignette dependencies not installed
> >
> > https://pastebin.com/wwhbqcSw
> >
> > Grateful for any guidance
> >
> >
>
> ______________________________________________
> R-package-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>


-- 
Fernando Roa

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