[R-pkg-devel] Missing R.h file

2020-01-12 Thread Sameh M. Abdulah 
I am getting this error when uploading my package to CRAN,


MLE_misc.h:52:10: fatal error: R.h: No such file or directory
   52 | #include 


On my system I have to export the R include directory to my CPATH  “export 
CPATH=/usr/share/R/include:$CPATH” to avoid this error. Could anyone tell me 
how to do this on my configure file to avoid this error on CRAN?


--Sameh


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

2020-01-12 Thread Uwe Ligges 

Probably some race condition. Simply submit a new versin.

Best,
Uwe Ligges



On 11.01.2020 03:10, Chris Brien wrote:

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

2020-01-12 Thread Uwe Ligges 
Don't worry, this is an issue that trhe CRAN incoimng checks have not 
uncovered with a new farvber version. As we found the breakage later in 
regular checks, the farver package has been rolled back on CRAN, hence 
pls simpy ignore the problem for your own packages.


Best,
Uwe Ligges



On 10.01.2020 20:44, Tiago Olivoto wrote:

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