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