fix documentation and linking issues from #306

[mbjones]

Fixes documentation errors in Rd files as reported in issue #306 and doc issues in #307

[mbjones]

The R CMD Check github action was failing because it used old, obsolete Action modules. Updated those to more recent and re-running to see if checks now pass.

[mbjones]

Still seeing documentation errors:

* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dataone-defunct.Rd: getData, getIdentifier, getFormatId,
    setPublicAccess, canRead, addData
  setPublicAccess.Rd: DataObject-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.