date:20200110

Re: [R-pkg-devel] Problem with package using reticulate (and Config in DESCRIPTION)

2020-01-10 Thread Mikkel Meyer Andersen

I finally got this to work by removing the Config part of DESCRIPTION
and reverting back to functionality inside .onLoad(). Please see code
that does not trigger any warnings/errors here:

https://github.com/r-cas/caracas/tree/418b3a552de0203c3d2f960f0e4235f7891db71d

Cheers,
Mikkel.

tor, 09 01 2020 kl. 18:20 +0100, skrev Mikkel Meyer Andersen:
> Hello,
> 
> I have submitted a package (source at 
> https://github.com/r-cas/caracas)
> depending on reticulate to CRAN and it failed:
> 
> package caracas_0.0.1.tar.gz does not pass the incoming checks
> automatically, please see the following pre-tests:
> Windows: <
> 
https://win-builder.r-project.org/incoming_pretest/caracas_0.0.1_20200108_193959/Windows/00check.log
> > 
> 
> Status: 6 WARNINGs, 6 NOTEs
> Debian: <
> 
https://win-builder.r-project.org/incoming_pretest/caracas_0.0.1_20200108_193959/Debian/00check.log
> > 
> 
> Status: 1 ERROR, 5 WARNINGs, 6 NOTEs
> 
> More details are given in the directory:
> <
> 
https://win-builder.r-project.org/incoming_pretest/caracas_0.0.1_20200108_193959/
> > 
> 
> As far as I can read, the NOTE's and WARNING's are related to these:
> 
> /usr/bin/python: No module named pip
> 
> error: could not find a Python environment for /usr/bin/python
> 
> Warning: cannot find svn location for rst2pdf===0.93.dev-r0
> You are using pip version 9.0.1, however version 19.3.1 is available.
> You should consider upgrading via the 'python -m pip install --
> upgrade
> pip' command.
> 
> Can anybody see what the error in my package code is?
> 
> Cheers,
> Mikkel.
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[R-pkg-devel] Possible unknown color in r

2020-01-10 Thread Tiago Olivoto

Dear all,

In the last submission of my package the CRAN team has suggested including
some references in the description field of the DESCRIPTION file.
When I submitted it to CRAN it did not pass the incoming checks
automatically and I got the following WARNING.

 

Quitting from lines 108-117 (vignettes_metan.Rmd) 

Error: processing vignette 'vignettes_metan.Rmd' failed with diagnostics:

Unknown colour name: transparent

 

It seems that this warning is related to a function with the argument
'col.segm.gen = "transparent"'.

I don't changed anything in this function and in the last submissions no
warning was related.

For curiosity I ran:

> col2rgb("yellow")

  [,1]

red255

green  255

blue 0

 

> col2rgb("transparent")

  [,1]

red255

green  255

blue   255

 

No warnings or errors were observed while running devtools::check_rhub(),
devtools::check_win_devel(), and devtools::check_win_release()

Any suggestion?

Best,

Tiago

 


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Re: [R-pkg-devel] Checkpoint package failing CRAN checks

2020-01-10 Thread Ivan Krylov

I wonder why does vignettes/checkpoint.Rmd run the following:

> example_project <- tempdir()

Now example_project contains the path of per-session temporary
directory...

> dir.create(example_project, recursive = TRUE, showWarnings = FALSE)

...so there should be no need to create it...

> unlink(example_project, recursive = TRUE)

And deleting it is might be the cause of the problems: rmarkdown
probably uses the same temporary directory to store its own files.

Perhaps example_project should be something like tempfile(project)
instead of just tempdir()? Then dir.create() and unlink() calls start
making sense.

-- 
Best regards,
Ivan

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Re: [R-pkg-devel] Possible unknown color in r

2020-01-10 Thread Joris Meys

Hi Tiago,

Without knowing which package you're talking about or a link to the check 
results, it's impossible to know whether that warning is a proper one or a side 
effect of something else. 

In general though: it is well known that relying on devtools is not enough for 
a good CRAN submission. The guidelines for CRAN clearly state :

"Please ensure that R CMD check --as-cran has been run on the tarball to be 
uploaded before submission. This should be done with the current version of 
R-devel (or if that is not possible and explained in the submission, current 
R-patched or the current release of R.)"

So before submitting a package to CRAN and after running your devtools:: 
check_etc, open a terminal and run the following commands:

R CMD build path_to_pkg_folder
R CMD check --as-cran package_version.tar.gz

The --as-cran is important, as is doing so against a R-devel. I use devtools 
myself extensively, but these checks have to be done outside the RStudio 
ecosystem to be sure.

Kind regards
Joris

--
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
--

Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php



From: R-package-devel  on behalf of 
Tiago Olivoto 
Sent: Friday, January 10, 2020 12:43 PM
To: r-package-devel@r-project.org
Subject: [R-pkg-devel] Possible unknown color in r

Dear all,

In the last submission of my package the CRAN team has suggested including
some references in the description field of the DESCRIPTION file.
When I submitted it to CRAN it did not pass the incoming checks
automatically and I got the following WARNING.



Quitting from lines 108-117 (vignettes_metan.Rmd)

Error: processing vignette 'vignettes_metan.Rmd' failed with diagnostics:

Unknown colour name: transparent



It seems that this warning is related to a function with the argument
'col.segm.gen = "transparent"'.

I don't changed anything in this function and in the last submissions no
warning was related.

For curiosity I ran:

> col2rgb("yellow")

  [,1]

red255

green  255

blue 0



> col2rgb("transparent")

  [,1]

red255

green  255

blue   255



No warnings or errors were observed while running devtools::check_rhub(),
devtools::check_win_devel(), and devtools::check_win_release()

Any suggestion?

Best,

Tiago




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[R-pkg-devel] RES: Possible unknown color in r

2020-01-10 Thread Tiago Olivoto

Hi Joris,
Thank you so much for your assistance.
I've built and checked my package with:
R CMD build /d/Desktop/metan
R CMD check --as-cran metan_1.2.1.tar.gz

No WARNINGS were observed. Please, see the log file attached.
Sorry for failing in providing the link to access the check results in the
last email. You can see the link to the test that doesn't pass bellow.

Dear maintainer,
 package metan_1.2.1.tar.gz does not pass the incoming checks automatically,
please see the following pre-tests:
Windows:


Status: 1 WARNING, 1 NOTE
Debian:


It sounds strange because in the last submissions the package passed in the
incoming checks, and the only change I've made from v1.2.0 to 1.2.1 was
adding some references in the description file.
Best regards,
Tiago

-Mensagem original-
De: Joris Meys  
Enviada em: sexta-feira, 10 de janeiro de 2020 09:23
Para: r-package-devel@r-project.org; tiagooliv...@gmail.com
Assunto: Re: [R-pkg-devel] Possible unknown color in r

Hi Tiago,

Without knowing which package you're talking about or a link to the check
results, it's impossible to know whether that warning is a proper one or a
side effect of something else. 

In general though: it is well known that relying on devtools is not enough
for a good CRAN submission. The guidelines for CRAN clearly state :

"Please ensure that R CMD check --as-cran has been run on the tarball to be
uploaded before submission. This should be done with the current version of
R-devel (or if that is not possible and explained in the submission, current
R-patched or the current release of R.)"

So before submitting a package to CRAN and after running your devtools::
check_etc, open a terminal and run the following commands:

R CMD build path_to_pkg_folder
R CMD check --as-cran package_version.tar.gz

The --as-cran is important, as is doing so against a R-devel. I use devtools
myself extensively, but these checks have to be done outside the RStudio
ecosystem to be sure.

Kind regards
Joris

--
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
--

Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php



From: R-package-devel  on behalf of
Tiago Olivoto 
Sent: Friday, January 10, 2020 12:43 PM
To: r-package-devel@r-project.org
Subject: [R-pkg-devel] Possible unknown color in r

Dear all,

In the last submission of my package the CRAN team has suggested including
some references in the description field of the DESCRIPTION file.
When I submitted it to CRAN it did not pass the incoming checks
automatically and I got the following WARNING.



Quitting from lines 108-117 (vignettes_metan.Rmd)

Error: processing vignette 'vignettes_metan.Rmd' failed with diagnostics:

Unknown colour name: transparent



It seems that this warning is related to a function with the argument
'col.segm.gen = "transparent"'.

I don't changed anything in this function and in the last submissions no
warning was related.

For curiosity I ran:

> col2rgb("yellow")

  [,1]

red255

green  255

blue 0



> col2rgb("transparent")

  [,1]

red255

green  255

blue   255



No warnings or errors were observed while running devtools::check_rhub(),
devtools::check_win_devel(), and devtools::check_win_release()

Any suggestion?

Best,

Tiago




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Re: [R-pkg-devel] RES: Possible unknown color in r

2020-01-10 Thread Sebastian Meyer

Hi Tiago,

Then it seems likely that an update of a direct or indirect dependency
of your package causes this failure on CRAN's check system.

ggplot2 currently fails with a similar error message on CRAN

> Error: Unknown colour name: NA

(https://cran.r-project.org/web/checks/check_results_ggplot2.html)

This again seems to come from an update of the "farver" package which is
an indirect dependency of ggplot2 via package "scales"...

So maybe if you update your local installation of "farver" to version
2.0.2 from CRAN, you might be able to reproduce the error.

What I find a bit strange is that the CRAN package website displays
version 2.0.1 while the newer version 2.0.2 can be found in the package
archive.

Best regards,

Sebastian


Am 10.01.20 um 14:17 schrieb Tiago Olivoto:
> Hi Joris,
> Thank you so much for your assistance.
> I've built and checked my package with:
> R CMD build /d/Desktop/metan
> R CMD check --as-cran metan_1.2.1.tar.gz
> 
> No WARNINGS were observed. Please, see the log file attached.
> Sorry for failing in providing the link to access the check results in the
> last email. You can see the link to the test that doesn't pass bellow.
> 
> Dear maintainer,
>  package metan_1.2.1.tar.gz does not pass the incoming checks automatically,
> please see the following pre-tests:
> Windows:
>  153/Windows/00check.log>
> 
> Status: 1 WARNING, 1 NOTE
> Debian:
>  153/Debian/00check.log>
> 
> It sounds strange because in the last submissions the package passed in the
> incoming checks, and the only change I've made from v1.2.0 to 1.2.1 was
> adding some references in the description file.
> Best regards,
> Tiago
> 
> -Mensagem original-
> De: Joris Meys  
> Enviada em: sexta-feira, 10 de janeiro de 2020 09:23
> Para: r-package-devel@r-project.org; tiagooliv...@gmail.com
> Assunto: Re: [R-pkg-devel] Possible unknown color in r
> 
> Hi Tiago,
> 
> Without knowing which package you're talking about or a link to the check
> results, it's impossible to know whether that warning is a proper one or a
> side effect of something else. 
> 
> In general though: it is well known that relying on devtools is not enough
> for a good CRAN submission. The guidelines for CRAN clearly state :
> 
> "Please ensure that R CMD check --as-cran has been run on the tarball to be
> uploaded before submission. This should be done with the current version of
> R-devel (or if that is not possible and explained in the submission, current
> R-patched or the current release of R.)"
> 
> So before submitting a package to CRAN and after running your devtools::
> check_etc, open a terminal and run the following commands:
> 
> R CMD build path_to_pkg_folder
> R CMD check --as-cran package_version.tar.gz
> 
> The --as-cran is important, as is doing so against a R-devel. I use devtools
> myself extensively, but these checks have to be done outside the RStudio
> ecosystem to be sure.
> 
> Kind regards
> Joris
> 
> --
> Joris Meys
> Statistical consultant
> 
> Department of Data Analysis and Mathematical Modelling Ghent University
> Coupure Links 653, B-9000 Gent (Belgium)
> --
> 
> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
> 
> 
> 
> From: R-package-devel  on behalf of
> Tiago Olivoto 
> Sent: Friday, January 10, 2020 12:43 PM
> To: r-package-devel@r-project.org
> Subject: [R-pkg-devel] Possible unknown color in r
> 
> Dear all,
> 
> In the last submission of my package the CRAN team has suggested including
> some references in the description field of the DESCRIPTION file.
> When I submitted it to CRAN it did not pass the incoming checks
> automatically and I got the following WARNING.
> 
> 
> 
> Quitting from lines 108-117 (vignettes_metan.Rmd)
> 
> Error: processing vignette 'vignettes_metan.Rmd' failed with diagnostics:
> 
> Unknown colour name: transparent
> 
> 
> 
> It seems that this warning is related to a function with the argument
> 'col.segm.gen = "transparent"'.
> 
> I don't changed anything in this function and in the last submissions no
> warning was related.
> 
> For curiosity I ran:
> 
>> col2rgb("yellow")
> 
>   [,1]
> 
> red255
> 
> green  255
> 
> blue 0
> 
> 
> 
>> col2rgb("transparent")
> 
>   [,1]
> 
> red255
> 
> green  255
> 
> blue   255
> 
> 
> 
> No warnings or errors were observed while running devtools::check_rhub(),
> devtools::check_win_devel(), and devtools::check_win_release()
> 
> Any suggestion?
> 
> Best,
> 
> Tiago
> 
> 
> 
> 
> [[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

Re: [R-pkg-devel] Possible unknown color in r

2020-01-10 Thread Joris Meys

Hi Tiago,

It's indeed that. For some reason col2rgb() knows the unofficial "transparent". 
Replace this with the correct value from the vector colors(), i.e. "white". 
"transparent" is not mentioned in that vector, so it shouldn't be used in a 
package. See also ?rgb2col and ?colors.

Cheers
Joris

--
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
--

Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php



From: Tiago Olivoto 
Sent: Friday, January 10, 2020 2:17 PM
To: Joris Meys; r-package-devel@r-project.org
Subject: RES: [R-pkg-devel] Possible unknown color in r

Hi Joris,
Thank you so much for your assistance.
I've built and checked my package with:
R CMD build /d/Desktop/metan
R CMD check --as-cran metan_1.2.1.tar.gz

No WARNINGS were observed. Please, see the log file attached.
Sorry for failing in providing the link to access the check results in the
last email. You can see the link to the test that doesn't pass bellow.

Dear maintainer,
 package metan_1.2.1.tar.gz does not pass the incoming checks automatically,
please see the following pre-tests:
Windows:


Status: 1 WARNING, 1 NOTE
Debian:


It sounds strange because in the last submissions the package passed in the
incoming checks, and the only change I've made from v1.2.0 to 1.2.1 was
adding some references in the description file.
Best regards,
Tiago

-Mensagem original-
De: Joris Meys 
Enviada em: sexta-feira, 10 de janeiro de 2020 09:23
Para: r-package-devel@r-project.org; tiagooliv...@gmail.com
Assunto: Re: [R-pkg-devel] Possible unknown color in r

Hi Tiago,

Without knowing which package you're talking about or a link to the check
results, it's impossible to know whether that warning is a proper one or a
side effect of something else.

In general though: it is well known that relying on devtools is not enough
for a good CRAN submission. The guidelines for CRAN clearly state :

"Please ensure that R CMD check --as-cran has been run on the tarball to be
uploaded before submission. This should be done with the current version of
R-devel (or if that is not possible and explained in the submission, current
R-patched or the current release of R.)"

So before submitting a package to CRAN and after running your devtools::
check_etc, open a terminal and run the following commands:

R CMD build path_to_pkg_folder
R CMD check --as-cran package_version.tar.gz

The --as-cran is important, as is doing so against a R-devel. I use devtools
myself extensively, but these checks have to be done outside the RStudio
ecosystem to be sure.

Kind regards
Joris

--
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
--

Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php



From: R-package-devel  on behalf of
Tiago Olivoto 
Sent: Friday, January 10, 2020 12:43 PM
To: r-package-devel@r-project.org
Subject: [R-pkg-devel] Possible unknown color in r

Dear all,

In the last submission of my package the CRAN team has suggested including
some references in the description field of the DESCRIPTION file.
When I submitted it to CRAN it did not pass the incoming checks
automatically and I got the following WARNING.



Quitting from lines 108-117 (vignettes_metan.Rmd)

Error: processing vignette 'vignettes_metan.Rmd' failed with diagnostics:

Unknown colour name: transparent



It seems that this warning is related to a function with the argument
'col.segm.gen = "transparent"'.

I don't changed anything in this function and in the last submissions no
warning was related.

For curiosity I ran:

> col2rgb("yellow")

  [,1]

red255

green  255

blue 0



> col2rgb("transparent")

  [,1]

red255

green  255

blue   255



No warnings or errors were observed while running devtools::check_rhub(),
devtools::check_win_devel(), and devtools::check_win_release()

Any suggestion?

Best,

Tiago




[[alternative HTML version deleted]]

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[R-pkg-devel] RES: Possible unknown color in r

2020-01-10 Thread Tiago Olivoto

Hi Joris,
Thank you for your suggestions.
After installing the version v 2.0.2 of "farver" I was able to reproduce the
WARNING.
To fix this issue, I created a simple helper function:
transparent_color <- function() {
  return("#00FF")
}
And changed "transparent" with "transparent_color()" in my R scripts.
After, I built and check again with 'R CMD check --as-cran
metan_1.2.1.tar.gz' and no longer WARNINGS were observed.
Thanks again,
Tiago

-Mensagem original-
De: Joris Meys  
Enviada em: sexta-feira, 10 de janeiro de 2020 10:57
Para: r-package-devel@r-project.org; tiagooliv...@gmail.com
Assunto: Re: [R-pkg-devel] Possible unknown color in r

Hi Tiago,

It's indeed that. For some reason col2rgb() knows the unofficial
"transparent". Replace this with the correct value from the vector colors(),
i.e. "white". "transparent" is not mentioned in that vector, so it shouldn't
be used in a package. See also ?rgb2col and ?colors.

Cheers
Joris

--
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
--

Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php



From: Tiago Olivoto 
Sent: Friday, January 10, 2020 2:17 PM
To: Joris Meys; r-package-devel@r-project.org
Subject: RES: [R-pkg-devel] Possible unknown color in r

Hi Joris,
Thank you so much for your assistance.
I've built and checked my package with:
R CMD build /d/Desktop/metan
R CMD check --as-cran metan_1.2.1.tar.gz

No WARNINGS were observed. Please, see the log file attached.
Sorry for failing in providing the link to access the check results in the
last email. You can see the link to the test that doesn't pass bellow.

Dear maintainer,
 package metan_1.2.1.tar.gz does not pass the incoming checks automatically,
please see the following pre-tests:
Windows:


Status: 1 WARNING, 1 NOTE
Debian:


It sounds strange because in the last submissions the package passed in the
incoming checks, and the only change I've made from v1.2.0 to 1.2.1 was
adding some references in the description file.
Best regards,
Tiago

-Mensagem original-
De: Joris Meys 
Enviada em: sexta-feira, 10 de janeiro de 2020 09:23
Para: r-package-devel@r-project.org; tiagooliv...@gmail.com
Assunto: Re: [R-pkg-devel] Possible unknown color in r

Hi Tiago,

Without knowing which package you're talking about or a link to the check
results, it's impossible to know whether that warning is a proper one or a
side effect of something else.

In general though: it is well known that relying on devtools is not enough
for a good CRAN submission. The guidelines for CRAN clearly state :

"Please ensure that R CMD check --as-cran has been run on the tarball to be
uploaded before submission. This should be done with the current version of
R-devel (or if that is not possible and explained in the submission, current
R-patched or the current release of R.)"

So before submitting a package to CRAN and after running your devtools::
check_etc, open a terminal and run the following commands:

R CMD build path_to_pkg_folder
R CMD check --as-cran package_version.tar.gz

The --as-cran is important, as is doing so against a R-devel. I use devtools
myself extensively, but these checks have to be done outside the RStudio
ecosystem to be sure.

Kind regards
Joris

--
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
--

Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php



From: R-package-devel  on behalf of
Tiago Olivoto 
Sent: Friday, January 10, 2020 12:43 PM
To: r-package-devel@r-project.org
Subject: [R-pkg-devel] Possible unknown color in r

Dear all,

In the last submission of my package the CRAN team has suggested including
some references in the description field of the DESCRIPTION file.
When I submitted it to CRAN it did not pass the incoming checks
automatically and I got the following WARNING.



Quitting from lines 108-117 (vignettes_metan.Rmd)

Error: processing vignette 'vignettes_metan.Rmd' failed with diagnostics:

Unknown colour name: transparent



It seems that this warning is related to a function with the argument
'col.segm.gen = "transparent"'.

I don't changed anything in this function and in the last submissions no
warning was related.

For curiosity I ran:

> col2rgb("yellow")

  [,1]

red255

green  255

blue 0



> col2rgb("transparent")

  [,1]

red255

green  255

blue   255



No warnings or errors were observed while running devtools::check_rhub(),
devtools::check_win_devel(), and devtools::check_win_release()

Any sugg

Re: [R-pkg-devel] RES: Possible unknown color in r

2020-01-10 Thread Berry Boessenkool



Side Note:

plot(1, col="#00FF", cex=4, pch=16)

is black on my machine.
The last two values are alpha (I think) and should be 00 for transparency.

Instead of writing an extra function, you could also use col=NA.

Berry



From: R-package-devel  on behalf of 
Tiago Olivoto 
Sent: Friday, January 10, 2020 18:05
To: 'Joris Meys' ; r-package-devel@r-project.org 

Subject: [R-pkg-devel] RES: Possible unknown color in r

Hi Joris,
Thank you for your suggestions.
After installing the version v 2.0.2 of "farver" I was able to reproduce the
WARNING.
To fix this issue, I created a simple helper function:
transparent_color <- function() {
  return("#00FF")
}
And changed "transparent" with "transparent_color()" in my R scripts.
After, I built and check again with 'R CMD check --as-cran
metan_1.2.1.tar.gz' and no longer WARNINGS were observed.
Thanks again,
Tiago

-Mensagem original-
De: Joris Meys 
Enviada em: sexta-feira, 10 de janeiro de 2020 10:57
Para: r-package-devel@r-project.org; tiagooliv...@gmail.com
Assunto: Re: [R-pkg-devel] Possible unknown color in r

Hi Tiago,

It's indeed that. For some reason col2rgb() knows the unofficial
"transparent". Replace this with the correct value from the vector colors(),
i.e. "white". "transparent" is not mentioned in that vector, so it shouldn't
be used in a package. See also ?rgb2col and ?colors.

Cheers
Joris

--
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
--

Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php



From: Tiago Olivoto 
Sent: Friday, January 10, 2020 2:17 PM
To: Joris Meys; r-package-devel@r-project.org
Subject: RES: [R-pkg-devel] Possible unknown color in r

Hi Joris,
Thank you so much for your assistance.
I've built and checked my package with:
R CMD build /d/Desktop/metan
R CMD check --as-cran metan_1.2.1.tar.gz

No WARNINGS were observed. Please, see the log file attached.
Sorry for failing in providing the link to access the check results in the
last email. You can see the link to the test that doesn't pass bellow.

Dear maintainer,
 package metan_1.2.1.tar.gz does not pass the incoming checks automatically,
please see the following pre-tests:



It sounds strange because in the last submissions the package passed in the
incoming checks, and the only change I've made from v1.2.0 to 1.2.1 was
adding some references in the description file.
Best regards,
Tiago

-Mensagem original-
De: Joris Meys 
Enviada em: sexta-feira, 10 de janeiro de 2020 09:23
Para: r-package-devel@r-project.org; tiagooliv...@gmail.com
Assunto: Re: [R-pkg-devel] Possible unknown color in r

Hi Tiago,

Without knowing which package you're talking about or a link to the check
results, it's impossible to know whether that warning is a proper one or a
side effect of something else.

In general though: it is well known that relying on devtools is not enough
for a good CRAN submission. The guidelines for CRAN clearly state :

"Please ensure that R CMD check --as-cran has been run on the tarball to be
uploaded before submission. This should be done with the current version of
R-devel (or if that is not possible and explained in the submission, current
R-patched or the current release of R.)"

So before submitting a package to CRAN and after running your devtools::
check_etc, open a terminal and run the following commands:

R CMD build path_to_pkg_folder
R CMD check --as-cran package_version.tar.gz

The --as-cran is important, as is doing so against a R-devel. I use devtools
myself extensively, but these checks have to be done outside the RStudio
ecosystem to be sure.

Kind regards
Joris

--
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
--

Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php



From: R-package-devel  on behalf of
Tiago Olivoto 
Sent: Friday, January 10, 2020 12:43 PM
To: r-package-devel@r-project.org
Subject: [R-pkg-devel] Possible unknown color in r

Dear all,

In the last submission of my package the CRAN team has suggested including
some references in the description field of the DESCRIPTION file.
When I submitted it to CRAN it did not pass the incoming checks
automatically and I got the following WARNING.



Quitting from lines 108-117 (vignettes_metan.Rmd)

Error: processing vignette 'vignettes_metan.Rmd' failed with diagnostics:

Unknown colour name: transparent



It seems that this warning is related to a function with the argument
'col.segm.gen = "

[R-pkg-devel] RES: RES: Possible unknown color in r

2020-01-10 Thread Tiago Olivoto

Hi Berry, 

Thank you for the note.

When I run my example code with transparent_color() all was working (the
color was transparent).

Now, reproducing the code again it becomes black. Could be this be changed
after package "farver" be updated to v. 2.0.2?

You is right regarding the use of col = NA. I have some functions that uses
ggplot2 and col = NA works with lines

 

library(ggplot2)

ggplot(mpg, aes(displ, hwy)) + 

  geom_smooth(color = NA, method = "lm")

 

but return a warning message with points

ggplot(mpg, aes(displ, hwy)) + 

  geom_point(color = NA)

# Warning message:

# Removed 234 rows containing missing values (geom_point).

 

It seems that the correct "transparent" color I was looking for can be set
without a warning with "#FF00"

ggplot(mpg, aes(displ, hwy)) + 

  geom_point(color = "#FF00")

Thanks for the tips.

Tiago.

 

De: Berry Boessenkool  
Enviada em: sexta-feira, 10 de janeiro de 2020 15:42
Para: 'Joris Meys' ; r-package-devel@r-project.org;
tiagooliv...@gmail.com
Assunto: Re: [R-pkg-devel] RES: Possible unknown color in r

 

 

Side Note: 

plot(1, col="#00FF", cex=4, pch=16)

is black on my machine.

The last two values are alpha (I think) and should be 00 for transparency.

 

Instead of writing an extra function, you could also use col=NA.

 

Berry

 

  _  

From: R-package-devel mailto:r-package-devel-boun...@r-project.org> > on behalf of Tiago Olivoto
mailto:tiagooliv...@gmail.com> >
Sent: Friday, January 10, 2020 18:05
To: 'Joris Meys' mailto:joris.m...@ugent.be> >;
r-package-devel@r-project.org 
mailto:r-package-devel@r-project.org> >
Subject: [R-pkg-devel] RES: Possible unknown color in r 

 

Hi Joris,
Thank you for your suggestions.
After installing the version v 2.0.2 of "farver" I was able to reproduce the
WARNING.
To fix this issue, I created a simple helper function:
transparent_color <- function() {
  return("#00FF")
}
And changed "transparent" with "transparent_color()" in my R scripts.
After, I built and check again with 'R CMD check --as-cran
metan_1.2.1.tar.gz' and no longer WARNINGS were observed.
Thanks again,
Tiago

-Mensagem original-
De: Joris Meys mailto:joris.m...@ugent.be> > 
Enviada em: sexta-feira, 10 de janeiro de 2020 10:57
Para: r-package-devel@r-project.org  ;
tiagooliv...@gmail.com  
Assunto: Re: [R-pkg-devel] Possible unknown color in r

Hi Tiago,

It's indeed that. For some reason col2rgb() knows the unofficial
"transparent". Replace this with the correct value from the vector colors(),
i.e. "white". "transparent" is not mentioned in that vector, so it shouldn't
be used in a package. See also ?rgb2col and ?colors.

Cheers
Joris

--
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
--

Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php



From: Tiago Olivoto mailto:tiagooliv...@gmail.com>
>
Sent: Friday, January 10, 2020 2:17 PM
To: Joris Meys; r-package-devel@r-project.org
 
Subject: RES: [R-pkg-devel] Possible unknown color in r

Hi Joris,
Thank you so much for your assistance.
I've built and checked my package with:
R CMD build /d/Desktop/metan
R CMD check --as-cran metan_1.2.1.tar.gz

No WARNINGS were observed. Please, see the log file attached.
Sorry for failing in providing the link to access the check results in the
last email. You can see the link to the test that doesn't pass bellow.

Dear maintainer,
 package metan_1.2.1.tar.gz does not pass the incoming checks automatically,
please see the following pre-tests:
Windows:
 
153/Windows/00check.log>

Status: 1 WARNING, 1 NOTE
Debian:
 
153/Debian/00check.log>

It sounds strange because in the last submissions the package passed in the
incoming checks, and the only change I've made from v1.2.0 to 1.2.1 was
adding some references in the description file.
Best regards,
Tiago

-Mensagem original-
De: Joris Meys mailto:joris.m...@ugent.be> >
Enviada em: sexta-feira, 10 de janeiro de 2020 09:23
Para: r-package-devel@r-project.org  ;
tiagooliv...@gmail.com  
Assunto: Re: [R-pkg-devel] Possible unknown color in r

Hi Tiago,

Without knowing which package you're talking about or a link to the check
results, it's impossible to know whether that warning is a proper one or a
side effect of something else.

In general tho

[R-pkg-devel] CRAN Package Check ERROR involving stringi

2020-01-10 Thread Chris Brien

Hi list members,

On checking the CRAN Package Check Results for my package growthPheno I find 
that there is the error below for r-devel-windows-ix86+x86_64, but not for 
r-devel-windows-ix86+x86_64-gcc8. Further, I do not get this error when I run R 
CMD check --as-cran on the tarball for a new version of growthPheno using 
r-devel build 77631.

* installing *source* package 'growthPheno' ...
** package 'growthPheno' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called 'stringi'
Calls:  ... loadNamespace -> withRestarts -> withOneRestart -> 
doWithOneRestart
Execution halted
ERROR: lazy loading failed for package 'growthPheno'
* removing 'd:/Rcompile/CRANpkg/lib/4.0/growthPheno'
* restoring previous 'd:/Rcompile/CRANpkg/lib/4.0/growthPheno'

 My understanding is that the error arises in connection with ggplot2, which is 
imported by growthPheno.

Can I assume that this error is due to some transitory  peculiarity with 
r-devel-windows-ix86+x86_64 and submit anyway?

Thanks in advance for any help,

Cheers, 

  Chris Brien

Adjunct Associate Professor in Statistics
-
School of Information Technology &  Mathematical Sciences
University of South Australia
GPO Box 2471
ADELAIDE  5001  South Australia
Phone:  +61 8 8302 5535   Fax:  +61 8 8302 5785
Email:   chris.br...@unisa.edu.au 
WEB page:   
CRICOS No 00121B 

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R-package-devel@r-project.org mailing list
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Re: [R-pkg-devel] Problem with package using reticulate (and Config in DESCRIPTION)

2020-01-10 Thread Kevin Ushey

Note that by calling py_module_available() in your .onLoad(), as done here:

https://github.com/r-cas/caracas/blob/418b3a552de0203c3d2f960f0e4235f7891db71d/R/init.R#L51

you are forcing reticulate to initialize the Python session eagerly
when your package is loaded (so before the user might've had a chance
to configure which version of Python should be loaded as well).

Please see:

https://rstudio.github.io/reticulate/articles/package.html

and be very careful that loading your package does not inadvertently
force reticulate to initialize Python before the user has requested
it.

Re: Config/reticulate, I plan to submit a patch to reticulate soon to
ensure that environment configuration does not happen
non-interactively in this way.

Thanks,
Kevin

On Fri, Jan 10, 2020 at 2:55 AM Mikkel Meyer Andersen  wrote:
>
> I finally got this to work by removing the Config part of DESCRIPTION
> and reverting back to functionality inside .onLoad(). Please see code
> that does not trigger any warnings/errors here:
>
> https://github.com/r-cas/caracas/tree/418b3a552de0203c3d2f960f0e4235f7891db71d
>
> Cheers,
> Mikkel.
>
> tor, 09 01 2020 kl. 18:20 +0100, skrev Mikkel Meyer Andersen:
> > Hello,
> >
> > I have submitted a package (source at
> > https://github.com/r-cas/caracas)
> > depending on reticulate to CRAN and it failed:
> >
> > package caracas_0.0.1.tar.gz does not pass the incoming checks
> > automatically, please see the following pre-tests:
> > Windows: <
> >
> https://win-builder.r-project.org/incoming_pretest/caracas_0.0.1_20200108_193959/Windows/00check.log
> > >
> >
> > Status: 6 WARNINGs, 6 NOTEs
> > Debian: <
> >
> https://win-builder.r-project.org/incoming_pretest/caracas_0.0.1_20200108_193959/Debian/00check.log
> > >
> >
> > Status: 1 ERROR, 5 WARNINGs, 6 NOTEs
> >
> > More details are given in the directory:
> > <
> >
> https://win-builder.r-project.org/incoming_pretest/caracas_0.0.1_20200108_193959/
> > >
> >
> > As far as I can read, the NOTE's and WARNING's are related to these:
> >
> > /usr/bin/python: No module named pip
> >
> > error: could not find a Python environment for /usr/bin/python
> >
> > Warning: cannot find svn location for rst2pdf===0.93.dev-r0
> > You are using pip version 9.0.1, however version 19.3.1 is available.
> > You should consider upgrading via the 'python -m pip install --
> > upgrade
> > pip' command.
> >
> > Can anybody see what the error in my package code is?
> >
> > Cheers,
> > Mikkel.
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

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Re: [R-pkg-devel] Problem with package using reticulate (and Config in DESCRIPTION)

[R-pkg-devel] Possible unknown color in r

Re: [R-pkg-devel] Checkpoint package failing CRAN checks

Re: [R-pkg-devel] Possible unknown color in r

[R-pkg-devel] RES: Possible unknown color in r

Re: [R-pkg-devel] RES: Possible unknown color in r

Re: [R-pkg-devel] Possible unknown color in r

[R-pkg-devel] RES: Possible unknown color in r

Re: [R-pkg-devel] RES: Possible unknown color in r

[R-pkg-devel] RES: RES: Possible unknown color in r

[R-pkg-devel] CRAN Package Check ERROR involving stringi

Re: [R-pkg-devel] Problem with package using reticulate (and Config in DESCRIPTION)

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