[R-pkg-devel] EHRtemporalVariability package check warning, cannot fix

2020-10-05 Thread Carlos Sáez 
Hi,

 

Some weeks ago we received the CRAN notification to update our
EHRtemporalVariability package in light of some Warnings found on the
vignette compilation.

 

We managed to solve most by including the �webshot� package in the Suggests
list in DESCRIPTION, since the Vignette is rendered in .html including
dynamic Plotly plots.

 

However, we cannot manage to solve the last one, and thus we cannot update
the package in CRAN. Local checks show no Warnings (only a Note due to
having 5.1MB file). Even updated R to the latest ver 4.0.2 and R tools to
the latest 4, and all checks ok. But submitting on winbuilder the Warning is
still there.

 

The logs are here:

 
https://win-builder.r-project.org/9IvFwBBcgDlI

 

This is the error:

 

Error(s) in re-building vignettes:

--- re-building 'EHRtemporalVariability.Rmd' using rmarkdown

Quitting from lines 35-36 (EHRtemporalVariability.Rmd) 

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

argument is of length zero

--- failed re-building 'EHRtemporalVariability.Rmd'

 

The package is exactly that found in
https://github.com/hms-dbmi/EHRtemporalVariability

 

Those lines 35-36 are the first chunk in the .Rmd vignette file:

```{r setup, include=FALSE}

knitr::opts_chunk$set(echo = TRUE, warning=FALSE)

```

Surprisingly, if removing this chunk and resubmitting, the same �argument is
of length zero� error is present but in the following (now first) chunk of
code.

 

Any help would be really appreciated. We would kindly provide any additional
info that could help.

Best regards!

Carlos


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[R-pkg-devel] is R CMD build --compact-vignettes working as expected?

2020-10-05 Thread Ben Bolker 

  Am I confused, or doing something wrong, or ... ?

  I have qpdf installed, and am running R CMD build with 
--compact-vignettes, but the PDF in the tarball doesn't seem to be 
compressed despite the fact that the output messages say "compacting 
vignettes ..."



  $ R CMD build --compact-vignettes lme4
* checking for file ‘lme4/DESCRIPTION’ ... OK
* preparing ‘lme4’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... OK
Warning: ‘inst/doc’ files
‘lmerperf.html’, ‘lmer.pdf’, ‘PLSvGLS.pdf’, ‘Theory.pdf’
  ignored as vignettes have been rebuilt.
  Run R CMD build with --no-build-vignettes to prevent rebuilding.
* compacting vignettes and other PDF files
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘lme4_1.1-24.tar.gz’

  The copy of lmer.pdf in the resulting tarball is 900K or so:

$ tar ztvf lme4_1.1-24.tar.gz lme4/inst/doc/lmer.pdf
-rw-r--r-- bolker/bolker 907022 2020-10-05 12:59 lme4/inst/doc/lmer.pdf

  The previously built (and manually compacted) version of lmer.pdf in 
the tarball is 500K:


$ ls -l lme4/inst/doc/lmer.pdf
-rw-r--r-- 1 bolker bolker 495199 Oct  3 22:15 lme4/inst/doc/lmer.pdf

   Is 'R CMD build' confused by the presence of a pre-built PDF in the 
inst/doc directory? Or am I somehow mistaken about how this is supposed 
to work?


   I would just use --no-build-vignettes and submit the tarball with 
the previously built/compressed PDF, but I'm trying to avoid a
"Package has a VignetteBuilder field but no prebuilt vignette index" 
NOTE, which I assume is missing because I built without building 
vignettes ... ?


  As always, enlightenment is welcome.

  cheers
Ben Bolker

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Re: [R-pkg-devel] EHRtemporalVariability package check warning, cannot fix

2020-10-05 Thread Ayala Hernandez, Rafael 
Hi Carlos,

Your package seems to use BiocStyle to output the vignette. I have encountered 
a similar error with my NutrienTrackeR package. The issue was triggered by the 
latest update to the knitr package, which caused knitting of vignettes in 
BiocStyle output to fail.

The issue was resolved by the Bioconductor team by pushing a new version of 
BiocStyle. This fixed all packages dependent on BiocStyle on Bioconductor, and 
seems to also have fixed the build reports for NutrienTrackeR for all linux and 
MacOS builds.

However, it has not fixed the error for the windows builds 
(https://cran.r-project.org/web/checks/check_results_NutrienTrackeR.html) . The 
error seems very similar to what you are getting, also being triggered by the 
first line of code in the vignette. If the issue is the same as what I was 
having, it will be triggered no matter how many chunks you remove, since it is 
the underlying combination of updated knitr and possibly not latest BiocStyle 
which triggers it.

Perhaps winbuilder and the machine building CRAN packages under windows are 
still not using the latest BiocStyle version for some reason?

Best wishes,

Rafa

De: R-package-devel  en nombre de Carlos 
Sáez 
Enviado: lunes, 5 de octubre de 2020 18:43
Para: r-package-devel@r-project.org 
Asunto: [R-pkg-devel] EHRtemporalVariability package check warning, cannot fix


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Hi,



Some weeks ago we received the CRAN notification to update our
EHRtemporalVariability package in light of some Warnings found on the
vignette compilation.



We managed to solve most by including the �webshot� package in the Suggests
list in DESCRIPTION, since the Vignette is rendered in .html including
dynamic Plotly plots.



However, we cannot manage to solve the last one, and thus we cannot update
the package in CRAN. Local checks show no Warnings (only a Note due to
having 5.1MB file). Even updated R to the latest ver 4.0.2 and R tools to
the latest 4, and all checks ok. But submitting on winbuilder the Warning is
still there.



The logs are here:

 
https://win-builder.r-project.org/9IvFwBBcgDlI



This is the error:



Error(s) in re-building vignettes:

--- re-building 'EHRtemporalVariability.Rmd' using rmarkdown

Quitting from lines 35-36 (EHRtemporalVariability.Rmd)

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

argument is of length zero

--- failed re-building 'EHRtemporalVariability.Rmd'



The package is exactly that found in
https://github.com/hms-dbmi/EHRtemporalVariability



Those lines 35-36 are the first chunk in the .Rmd vignette file:

```{r setup, include=FALSE}

knitr::opts_chunk$set(echo = TRUE, warning=FALSE)

```

Surprisingly, if removing this chunk and resubmitting, the same �argument is
of length zero� error is present but in the following (now first) chunk of
code.



Any help would be really appreciated. We would kindly provide any additional
info that could help.

Best regards!

Carlos


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