R CMD Check contains NOTES

[TuomasBorman]

Hi,

currently check contains NOTES. Especially it seems that syntax of list in roxygen has changed.

1. Run devtools::check()
2. List probelmatic things to this issue
3. Let's discuss what we can do about them. (Everything cannot be solved)
4. Fix

[ake123]

Here is the result after running devtools::check()

❯ checking package dependencies ... NOTE
  Imports includes 21 non-default packages.
  Importing from so many packages makes the package vulnerable to any of
  them becoming unavailable.  Move as many as possible to Suggests and
  use conditionally.

❯ checking top-level files ... NOTE
  Non-standard file/directory found at top level:
    ‘CONTRIBUTING.md’

❯ checking Rd cross-references ... NOTE
  Unknown package ‘https’ in Rd xrefs

[TuomasBorman]

Do you have the latest versions? In addition to those NOTEs that you get, I get also NOTEs about roxygen

See the latest workflow run

https://github.com/microbiome/mia/actions/runs/8849563656/job/24301848155

[antagomir]

The status of this issue?