[R-pkg-devel] vignette error in debian

Thu Nov 28 19:48:25 CET 2019

This was exactly what needed to be done. (inherits in conditional)
Thank you ,

Issue Closed.
Best,

On Thu, Nov 28, 2019 at 12:16 PM Sebastian Meyer <seb.meyer using fau.de> wrote:

> I was able to reproduce the vignette error in an R-devel session with this
> environment variable set. It came from a strange polygon() call with x and
> y arguments being matrices with list elements.
>
> I cannot test at the moment. Maybe you condition on
> class(something) == "matrix"
> somewhere in your code? This should be replaced by
> inherits(something, "matrix")
> since in future R, matrix objects also formally belong to the array class,
> so the class vector has length two. See the corresponding blog post by
> Martin Mächler for further details:
>
> https://developer.r-project.org/Blog/public/2019/11/09/when-you-think-class.-think-again/index.html
>
> Cheers, Sebastian
>
> Am 28. November 2019 14:56:37 MEZ schrieb Fernando Roa <froao using unal.edu.co
> >:
> >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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