date:20191128

Re: [R-pkg-devel] vignette error in debian

2019-11-28 Thread Sebastian Meyer

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  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@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
> 
>

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Re: [R-pkg-devel] R CMD check: Titles in README

2019-11-28 Thread Uwe Ligges

We had to install the most recent pandoc release as the old failed for
the recent texlive release with rmarkdown.

Apparently pandoc gives a different error message for empty titles now.
The simplest solution would be to provide a proper title anyway.

Best,
Uwe Ligges

On 27.11.2019 22:33, Ben Bolker wrote:

Maybe already obvious to you, but this seems to be coming from pandoc,
not from R machinery. There are a few extra lines in the log that seem
to be relevant ...

[WARNING] This document format requires a nonempty element.
Defaulting to ‘README’ as the title.
To specify a title, use ‘title’ in metadata or --metadata title="...".
pandoc: Stack space overflow: current size 33624 bytes.
pandoc: Use `+RTS -Ksize -RTS' to increase it.

I think you'd have to figure out what's happened to the pandoc
version/configuration in the most recent Debian setup on CRAN ... I
don't know if there's a canonical place (or anywhere, for that matter)
where one can find a complete list of library/tool versions for the
various platforms on CRAN ...

cheers
Ben Bolker

On 2019-11-27 4:19 p.m., Sam Albers wrote:

HI all,

Submission of a new version of the tidyhydat package to CRAN, I get
this warning on the pre-test checks for Debian:

* checking top-level files ... WARNING
Conversion of ‘README.md’ failed:
[WARNING] This document format requires a nonempty element.
Defaulting to ‘README’ as the title.
To specify a title, use ‘title’ in metadata or --metadata title="...".

Here is the actual log:
https://win-builder.r-project.org/incoming_pretest/tidyhydat_0.5.0_20191127_215625/Debian/00check.log

The .yaml header for the README has not changed since the last
successful submission. Looking at the changes to R 3.6.1 patched,
nothing has changed in README requirement AFAIK.

Is this a false positive? If not, any thoughts on how to make it go away?

Best,

Sam

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Re: [R-pkg-devel] Compiler warning using C versions of base R integrate function

2019-11-28 Thread Tomas Kalibera


On 11/21/19 7:25 PM, Devin Incerti wrote:

Hi,

I'm attempting to submit a very minor update to my package where I replaced
a deprecated C++ function with an alternative. However, I'm receiving an
unrelated warning "*array subscript -1 is outside array bounds of ‘double
[52]’ [-Warray-bounds] *" on Debian during the CRAN pre-tests. I do not
receive this warning on my local OS X, Ubuntu 16.04 (on Travis-CI), with
Win-builder, or with R-hub builder. I also did not receive this warning on
previous submissions to CRAN, but it does now show up on the most recent CRAN
checks

.

The warning is related to the header file integrate.h
,
which is just integrate.c

from
R source with function pointers replaced by C++ functors. These integration
functions are needed so that the package can integrate at the C++ level.

I don't know how to avoid this warning. Is it perhaps related to the
particular version of GCC used during the CRAN checks. Any thoughts or
suggestions would be much appreciated.

Thank you!


The warning is generated by GCC when inlining the function rdqelg(), I 
can reproduce it with the integrate.c we have in R, but only if I add 
"inline" to rdqelg() definition (GCC 6 and newer - on Ubuntu but that 
should not matter). The inliner knows the callsite, so it knows that 
what is being passed is an array (and not an arbitrary pointer), and 
hence it emits the warning. It is not smart enough to know that the 
first element of the new "array" will (unless there is a bug) never be 
used. When not inlining and the function is compiled independently from 
its callsites, it assumes it is a pointer, and hence there is no warning.


The code is automatically converted from Fortran, maybe these pointer 
decrements in function prologues are to adjust to Fortran 1-based array 
indexing. If you must use this modified copy of integrate.c from R, 
perhaps a quick hack to get rid of the warning would be to avoid the 
"inline" keywords in declarations of functions like rdqelg(). In a 
perfect world, the code would be rewritten to more idiomatic C (not just 
to avoid these decrements). Or perhaps the Fortran original could be used.


Tomas


()

Devin

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Re: [R-pkg-devel] vignette error in debian

2019-11-28 Thread 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  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  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@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@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>


-- 
Fernando Roa

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Re: [R-pkg-devel] vignette error in debian

2019-11-28 Thread Sebastian Meyer

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 :
>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 
>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 
>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@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
>> > vigne

Re: [R-pkg-devel] vignette error in debian

2019-11-28 Thread Sebastian Meyer

I forgot to mention: the code that you pasted in the email does not reproduce 
the error. The vignette actually runs different code. You need to run the code 
from the vignette to see the error (with the environment variable set).

Cheers, Sebastian

Am 28. November 2019 18:16:12 MEZ schrieb Sebastian Meyer :
>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
>:
>>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 
>>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 
>>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@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 t

Re: [R-pkg-devel] vignette error in debian

2019-11-28 Thread Fernando Roa

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  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  >:
> >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 
> >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 
> >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@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

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