[R-pkg-devel] Debian note: non-standard things in the check directory

[Vihtakari, Mikko]

Dear R developers,

I submitted my package (https://github.com/MikkoVihtakari/ggOceanMaps) to CRAN 
and got a note I have not seen before in this context. R CMD check --as-cran on 
the source version, rhub::check_for_cran(), and devtools::check() all run 
without problems. So did CRAN checks on every platform except Debian. Here is 
the log I received from CRAN:



Flavor: r-devel-windows-ix86+x86_64
Check: CRAN incoming feasibility, Result: NOTE
  Maintainer: 'Mikko Vihtakari '

  New submission

  Package was archived on CRAN

  Possibly misspelled words in DESCRIPTION:
GitHub (26:13)
bathymetric (18:38)
geospatial (24:3)
shapefiles (23:24, 25:17, 25:45)

  CRAN repository db overrides:
X-CRAN-Comment: Archived on 2021-06-04 as check problems were not
  corrected in time.

  Suggests or Enhances not in mainstream repositories:
ggOceanMapsData
  Availability using Additional_repositories specification:
ggOceanMapsData   yes   https://mikkovihtakari.github.io/drat

Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
Check: package dependencies, Result: NOTE
  Package suggested but not available for checking: 'ggOceanMapsData'

Flavor: r-devel-linux-x86_64-debian-gcc
Check: CRAN incoming feasibility, Result: NOTE
  Maintainer: 'Mikko Vihtakari '

  New submission

  Package was archived on CRAN

  Possibly misspelled words in DESCRIPTION:
bathymetric (18:38)
geospatial (24:3)
shapefiles (23:24, 25:17, 25:45)

  CRAN repository db overrides:
X-CRAN-Comment: Archived on 2021-06-04 as check problems were not
  corrected in time.

  Suggests or Enhances not in mainstream repositories:
ggOceanMapsData
  Availability using Additional_repositories specification:
ggOceanMapsData   yes   https://mikkovihtakari.github.io/drat

Flavor: r-devel-linux-x86_64-debian-gcc
Check: for non-standard things in the check directory, Result: NOTE
  Found the following files/directories:
'ggOceanMapsData'



I am lost with what they mean by "Check: for non-standard things in the check 
directory, Result: NOTE  Found the following files/directories:  
'ggOceanMapsData'".

The package requires ggOceanMapsData package to function. That package is too 
large for CRAN and has been placed in a drat repository on Github. I have used 
install.packages() in the vignette ( 
https://github.com/MikkoVihtakari/ggOceanMaps/blob/3c3d4daa5a26b262db569a3465208face0fca731/vignettes/ggOceanMaps.Rmd#L17)
 to make it possible to compile the vignette. Could it be that the check on 
Debian has begun to pick on this line for some reason? As said, I have not 
encountered this issue before, and the package was on CRAN before being pulled 
by another problem.

Any insight would be appreciated.

All the best,

__

Mikko Vihtakari
PhD in Natural Science
Researcher
Deep sea species and cartilaginous fish
Institute of Marine Research
Fram Centre, 9296 Tromsø, Norway
Email: mikko.vihtak...@hi.no
Tel: +47-91891316
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[R-pkg-devel] Additional CRAN Checks

[Colin Gillespie]

Dear All,

Sorry if this is the wrong mailing address.

I was doing a little investigation of R versions in packages and
discovered a number of errors:

https://cran.r-project.org/web/packages/bartCause/index.html  - R (≥ 3.1-0)
https://cran.r-project.org/web/packages/activityGCMM/index.html  - R (3.00)
https://cran.r-project.org/web/packages/deTestSet/index.html - R (≥ 2.01)

and also

https://cran.r-project.org/web/packages/NGSSEML/ - R (≥ 1.9.0), R (≥
3.5.0), R (≥ 3.5.0), R (≥ 3.5.0), R (≥ 3.5.0), R (≥ 3.5.0), R (≥
3.5.0)

Overall I detected ~40 packages with issues:

c("activityGCMM", "behavr", "bioassays", "bvpSolve", "celestial",
"chest", "CRTSize", "csppData", "damr", "deTestSet", "diagram",
"directPA", "DiscreteFDR", "ecolMod", "ecp", "epibasix", "europepmc",
"fabisearch", "FDX", "ggetho", "hyper.fit", "MedSurvey", "NBPSeq",
"NetIndices", "NFWdist", "OmegaG", "primer", "RATest", "refund",
"RmarineHeatWaves", "rmcfs", "rootSolve", "RPPASPACE", "scopr",
"scoringRules", "seqDesign", "shape", "sleepr", "SMPracticals",
"text", "tggd", "zeitgebr")

It seems like this would be a useful check to implement on the R CMD check.

Thanks

Colin


Dr Colin Gillespie
https://twitter.com/csgillespie

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Re: [R-pkg-devel] Checking package dependencies before loading namespace

[Tiago Olivoto]

Thanks to all for the suggestions!
Best,
Tiago

Em sáb., 4 de set. de 2021 às 23:45, Martin Morgan 
escreveu:

> Actually, I think the right thing to do is to tell the user what to do
> ("To use this feature, install EBImage following the directions at
> https://bioconductor.org/packages/EBImage') instead of doing it for them.
>
> Martin
>
> From: Tiago Olivoto 
> Date: Friday, September 3, 2021 at 2:14 PM
> To: Martin Morgan 
> Cc: Uwe Ligges , R Package Devel <
> r-package-devel@r-project.org>
> Subject: Re: [R-pkg-devel] Checking package dependencies before loading
> namespace
> Thanks for your response Martin,
> I'm definitely thinking to use BiocManager::install("EBImage") since it is
> the official suggestion of the Bioconductor community. Anyway, I've been
> learning a lot from this discussion. Thanks all!!
> Best,
> Tiago
>
> Em sex., 3 de set. de 2021 às 12:58, Martin Morgan  mtmorgan.b...@gmail.com> escreveu:
> The specific repository you've chosen is not what you want to do. This
> will always install EBImage from Bioconductor version 3.13, but
> Bioconductor version 3.13 is only relevant for R-4.1 (see
> https://bioconductor.org/about/release-announcements/)
>
> Personally, I would encourage you to follow the Bioconductor community
> best practice of BiocManager::install("EBImage"). In that way you will get
> the version of EBImage that has been tested with other Bioconductor
> packages in the same release, and on the version of R in use by your user.
>
> If you were to use a specific repository, it should the one that is as
> good as base R can do (this can be different from the version that
> BiocManager would choose because R's release cycle is different from
> Bioconductor's). I think this is most easily accomplished by
> utils::chooseBioCmirror(), and then selecting the 0-Bioconductor
> repository. That's a lot to tell your users... Maybe others in the R
> community have a better way (the key information is in
> tools:::.BioC_version_associated_with_R_version(), but that is not an
> exported function so not recommended for CRAN packages...)
>
> Martin Morgan
>
> On 9/1/21, 8:13 AM, "R-package-devel on behalf of Tiago Olivoto"  r-package-devel-boun...@r-project.org on behalf of mailto:
> tiagooliv...@gmail.com> wrote:
>
> Thank you, Duncan and Uwe for the suggestions.
>  I followed your instructions and created a function to check for
> EBImage
> that is only called in an interactive section and, if necessary, ask
> the
> user to install the package with install.packages("EBImage", repos="
> https://bioconductor.org/packages/3.13/bioc;)
>
> Best,
> Tiago
>
> Em qua., 1 de set. de 2021 às 03:53, Uwe Ligges <
> mailto:lig...@statistik.tu-dortmund.de> escreveu:
>
> > Two more comments.
> >
> > 1. Note that your code only works in interactice mode, not when
> checking
> > your package as it waits infinitely for the user's choice.
> >
> > 2. I do not see an advantage of installing BiocManager if EBImage is
> > needed, the essential part is simply to select BioC as a repository
> to
> > install packages from.
> >
> > Best,
> > Uwe Ligges
> >
> >
> > On 31.08.2021 23:33, Duncan Murdoch wrote:
> > > People shouldn't be able to install your package unless the "hard"
> > > dependencies are available.
> > >
> > > If EBImage isn't essential to your package, you should make it a
> "soft"
> > > dependency by listing it in Suggests and checking for it every
> time you
> > > use it.
> > >
> > > Duncan Murdoch
> > >
> > > On 31/08/2021 3:20 p.m., Tiago Olivoto wrote:
> > >> Dear all,
> > >> I have a package called pliman
> > >> 
> > >> which depends on the Bioconductor package EBImage.
> > >>
> > >> When running install.packages("pliman") I get the following
> warning
> > >>
> > >> Warning in install.packages :  dependency ‘EBImage’ is not
> available
> > >>
> > >> and thus when loading the package with library(pliman), the
> following
> > >> error
> > >> occurs
> > >>
> > >> Erro: package or namespace load failed for ‘pliman’ in
> loadNamespace(i,
> > >> c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
> > >>   there is no package called ‘EBImage’
> > >>
> > >> I created a check function to check if EBImage is available and if
> > >> not, ask
> > >> users if they want to install it
> > >>
> > >> ---
> > >> check_ebi <- function(){
> > >>if(!requireNamespace("EBImage", quietly = TRUE)) {
> > >>  inst <-
> > >>  switch(menu(c("Yes", "No"), title = "Package {EBImage}
> required
> > >> but not
> > >> available.\nDo you want to install it now?"),
> > >> "yes", "no")
> > >>  if(inst == "yes"){
> > >>if (!requireNamespace("BiocManager", quietly = TRUE)){
> > >>