CRAN preparations

[keller-mark]

Resources:

• https://cran.r-project.org/web/packages/policies.html
• https://kbroman.org/pkg_primer/pages/cran.html
• https://cran.r-project.org/web/packages/submission_checklist.html

Things to do/check

• [x] R CMD check --as-cran
• [x] Please ensure that R CMD check --as-cran has been run on the tarball to be uploaded before submission
• [x] Add DOI to Zarr publication(s) in package Description
• [x] As a general rule, neither data nor documentation should exceed 5MB (see #87 )
• [x] If running a package uses multiple threads/cores it must never use more than two simultaneously (may need to modify recent tests added in #91 )
• [x] Packages which use Internet resources should fail gracefully with an informative message if the resource is not available or has changed (and not give a check warning nor error). (may require changes in HttpStore)
• [x] Update GH Actions to run on Ubuntu, Mac, and Windows using an os strategy matrix

[dblodgett-usgs]

Working on a bit of no internet grace. Probably some more to do yet.

[dblodgett-usgs]

With #93, we are pretty close to ready to go. I want to do a bit more testing without internet and we'll need to reduce the size of the demo data. There are two ways to do that -- either make it a download or reduce its size. Will comment on that issue about that.

[dblodgett-usgs]

With what I just pushed, I think we should call the http error issues resolved. There is now only one NOTE:

❯ checking installed package size ... NOTE
    installed size is  7.5Mb
    sub-directories of 1Mb or more:
      extdata   6.3Mb

I'll kick off a few more checks here and see if anything surfaces.

[dblodgett-usgs]

Looks like a few things are picked up by the cran winbuilder.

(note that I changed the description temporarily so it had me as maintainer so I could get the emails about the test)

https://win-builder.r-project.org/7zmyrXTli9Cp/00check.log

Nothing crazy in there.

Possibly misspelled words in DESCRIPTION:
  Zarr (3:19, 20:31)

Found the following (possibly) invalid URLs:
  URL: https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  The canonical URL of the CRAN page for a package is 
    https://CRAN.R-project.org/package=pkgname

The Title field should be in title case. Current version is:
'Slice into Zarr arrays in R'
In title case that is:
'Slice into Zarr Arrays in R'

Found the following \keyword or \concept entries
which likely give several index terms:
  File 'ZarrArray.Rd':
    \keyword{(default),}
    \keyword{False,}
    \keyword{Object,}
    \keyword{String,}
    \keyword{True,}
    \keyword{provided,}
    \keyword{stored,}
    \keyword{value,}

* checking HTML version of manual ... [12s] NOTE
Found the following HTML validation problems:
ZarrArray.html:203:9 (ZarrArray.Rd:163): Warning: <a> illegal characters found in URI
ZarrArray.html:206:9 (ZarrArray.Rd:164): Warning: <a> illegal characters found in URI

[dblodgett-usgs]

[dblodgett-usgs]

Two notes from the winbuilder still.

New submission

Possibly misspelled words in DESCRIPTION:
  Zarr (3:19, 12:31)

Found the following (possibly) invalid URLs:
  URL: https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://github.com/traversc/qs (moved to https://github.com/qsbase/qs)
    From: README.md
    Status: 301
    Message: Moved Permanently
  URL: https://numcodecs.readthedocs.io/en/stable/vlen.html#vlenutf8
    From: README.md
    Status: 404
    Message: Not Found
The canonical URL of the CRAN page for a package is 
  https://CRAN.R-project.org/package=pkgname
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.

The Title field should be in title case. Current version is:
  'Slice into Zarr arrays in R'
In title case that is:
  'Slice into Zarr Arrays in R'

Found the following \keyword or \concept entries
which likely give several index terms:
  File 'ZarrArray.Rd':
    \keyword{(default),}
    \keyword{False,}
    \keyword{Object,}
    \keyword{String,}
    \keyword{True,}
    \keyword{provided,}
    \keyword{stored,}
    \keyword{value,}
    ```
    
    ```
    * checking HTML version of manual ... [13s] NOTE
Found the following HTML validation problems:
ZarrArray.html:203:9 (ZarrArray.Rd:185): Warning: <a> illegal characters found in URI
ZarrArray.html:206:9 (ZarrArray.Rd:186): Warning: <a> illegal characters found in URI

[dblodgett-usgs]

With what I just pushed to #124 -- I only see two notes.

One is related to urls with illegal "[" characters in them -- I don't see how we can change them without just removing documentation for those methods.

The other is related to the word "Zarr" not being recognized.

I think we are probably basically ready to submit to CRAN but a high level review of introductory documentation and caveats about how the package is new / in development would be good still.

[pepijn-devries]

@dblodgett-usgs: you can probably replace "[" with "%5b" in your URL. Warning about the 'Zarr' is because it's not in the dictionary. You can ignore it and explain it when you submit to CRAN... Really hoping to see this package on CRAN.