Added a warning for when users do not supply custom pathways, but count_pathways_by = gene is declared. (Doing so may be biologically incorrect.)
If there is an GitHub issue associated with this pull request, please provide link.
This would close #167 (though I haven't looked at the associated testing)
Reviewer Checklist (if item does not apply, mark is as complete)
[ ] PR branch has pulled the most recent updates from main branch. Ensure the pull request branch and your local version match and both have the latest updates from the main branch.
[ ] If a new function was added, function included in _pkgdown.yml
[ ] If a bug was fixed, a unit test was added for the bug check
[ ] Run pkgdown::build_site(). Check the R console for errors, and review the rendered website.
[ ] Code coverage is suitable for any new functions/features. Review coverage with withr::with_envvar(new = c("NOT_CRAN" = "true"), covr::report()). Begin in a fresh R session without any packages loaded.
[ ] R CMD Check runs without errors, warnings, and notes
[ ] usethis::use_spell_check() runs with no spelling errors in documentation
When the branch is ready to be merged into master:
[ ] Update NEWS.md with the changes from this pull request under the heading "# cbioportalR (development version)". If there is an issue associated with the pull request, reference it in parentheses at the end update (see NEWS.md for examples).
karissawhiting
commented
1 year ago
What changes are proposed in this pull request?
count_pathways_by = geneis declared. (Doing so may be biologically incorrect.)If there is an GitHub issue associated with this pull request, please provide link. This would close #167 (though I haven't looked at the associated testing)
Reviewer Checklist (if item does not apply, mark is as complete)
_pkgdown.ymlpkgdown::build_site(). Check the R console for errors, and review the rendered website.withr::with_envvar(new = c("NOT_CRAN" = "true"), covr::report()). Begin in a fresh R session without any packages loaded.usethis::use_spell_check()runs with no spelling errors in documentationWhen the branch is ready to be merged into master:
NEWS.mdwith the changes from this pull request under the heading "# cbioportalR (development version)". If there is an issue associated with the pull request, reference it in parentheses at the end update (seeNEWS.mdfor examples).codemetar::write_codemeta()usethis::use_spell_check()again