update data.table syntax to avoid triggering CRAN check NOTE

[alkaZeltser]

• small tweaks to data.table syntax to avoid triggering false positive NOTE re unassigned global vars
• a statement declaring global variables "ID", ".", "new.ID" whose syntax cannot be changed to avoid the NOTE.

• I have read the code review guidelines and the code review best practice on GitHub check-list.

• The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)-[brief_description_of_branch].

• I have set up or verified the branch protection rule following the github standards before opening this pull request.

• I have added the changes included in this pull request to NEWS under the next release version or unreleased, and updated the date.

• I have updated the version number in metadata.yaml and DESCRIPTION.

• Both R CMD build and R CMD check run successfully.

Testing Results

Case 1

All unit tests pass

[alkaZeltser]

@dan-knight so I think I've resolved the data.table syntax NOTE... but the GitHub checker spawned a new NOTE which wasn't in the previous release. It flagged the package size and specifically the /doc directory for exceeding 1 Mb. This is... weird because /doc is not part of the repo. I know it's created when the package is built to store the vignettes, but I haven't edited the vignette since the last release so I don't understand why this is a problem now and not before?

* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb

[alkaZeltser]

@dan-knight so I think I've resolved the data.table syntax NOTE... but the GitHub checker spawned a new NOTE which wasn't in the previous release. It flagged the package size and specifically the /doc directory for exceeding 1 Mb. This is... weird because /doc is not part of the repo. I know it's created when the package is built to store the vignettes, but I haven't edited the vignette since the last release so I don't understand why this is a problem now and not before?

* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb

Looks like this NOTE can be resolved by compressing vignettes upon building the package:
R CMD build package-ApplyPolygenicScore/ --compact-vignettes="both"

[rachelmadang]

LGTM.

[dan-knight]

Looks like this NOTE can be resolved by compressing vignettes upon building the package: R CMD build package-ApplyPolygenicScore/ --compact-vignettes="both"

Yep. If that's the case, then it's fine to submit as long as you use the compressed build. I should check the CI/CD action to make sure it's using the same setting so we're consistent.