Does not pass R CMD check

[fabian-s]

• DESCRIPTION: Your Suggests: should include all packages like fields and evd that are used in your vignettes

• Vignette does not currently include a properly executed example for including covariates:
  https://github.com/meixichen/SpatialGEV/blob/61466b5dde6e5f36965f2244fd8034224076cac3/vignettes/SpatialGEV-vignette.Rmd#L314C1-L340C1 is all just error messages?

• R CMD check --as-cran does not pass:

* checking CRAN incoming feasibility ... [7s/15s] WARNING
Maintainer: ‘Meixi Chen <meixi.chen@uwaterloo.ca>’
Insufficient package version (submitted: 1.0.1, existing: 1.0.1)
Suggests or Enhances not in mainstream repositories:
  INLA
Availability using Additional_repositories specification:
  INLA   yes   https://inla.r-inla-download.org/R/stable/
Package has a VignetteBuilder field but no prebuilt vignette index.
Found the following (possibly) invalid URLs:
  URL: https://codecov.io/github/meixichen/SpatialGEV (moved to https://app.codecov.io/github/meixichen/SpatialGEV)
    From: README.md
    Status: 200
    Message: OK

* checking installed package size ... NOTE
  installed size is 102.1Mb
  sub-directories of 1Mb or more:
    libs  101.5Mb

* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘SpatialGEV.Rproj’

* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘SpatialGEV-vignette.Rmd’ ‘SpatialGEV-vignette.html’ ‘references.bib’
  ‘sim-1plot-y-1.png’ ‘sim1-plot-abs-1.png’
  ‘sim1-plot-num-obs-per-loc-1.png’ ‘sim1-pos-plots-1.png’
  ‘sim2-plot-ab-1.png’ ‘sim2-pred-plot-1.png’
  ‘snow-display-grid-data-1.png’ ‘snow-display-raw-data-1.png’
  ‘snow-return-plots-1.png’ ‘vignette-helper-functions.R’

* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘SpatialGEV-vignette.Rmd’ using rmarkdown
File figure/sim1-plot-abs-1.png not found in resource path
Error: processing vignette 'SpatialGEV-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘SpatialGEV-vignette.Rmd’

linking openjournals/joss-reviews#6878

[meixichen]

Thanks for flagging this! My apologies that I did not check the vignette properly. You are right that a pre-compiled vignette is prone to issues like this. I think I decided to precompile the vignette because it took around 10-20 minutes to build. Do you think it is an acceptable length of time? The old precompiled version (without the covariate section) did pass the CRAN test when I submitted it.

[fabian-s]

I think I decided to precompile the vignette because it took around 10-20 minutes to build. Do you think it is an acceptable length of time?

Not sure -- CRAN policies just say:

Checking the package should take as little CPU time as possible, as the CRAN check farm is a very limited resource and there are thousands of packages. Long-running tests and vignette code can be made optional for checking, but do ensure that the checks that are left do exercise all the features of the package. [...] Examples should run for no more than a few seconds each: they are intended to exemplify to the would-be user how to use the functions in the package.

I think it's fine to use pre-compiled for a CRAN submission, but would not recommend it in your development-version on GH.

[meixichen]

Okay that makes sense. Thanks for this. Will push the changes shortly!

[meixichen]

Have replaced the pre-compiled vignette with the actual rmd for building the vignette. This passed the CRAN check.