LiNk-NY
commented
5 months ago @LiNk-NY - Sorry for the delay. The review of the packages are below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the packages are ready for a re-review.
Thank you Kayla @Kayla-Morrell for your review. I have updated the packages. Please see below.
AnVILBase
- [x] REQUIRED: The
R CMD checkdid not finish because of the other AnVIL packages suggests. Any issues should be corrected once this is resolved and can complete.
Both AnVILAz and AnVILGCP packages should be installed first. I am not sure why there is an error in the SPB since both packages should be installed before AnVILBase gets run. Any insights Lori? @lshep
https://bioconductor.org/spb_reports/AnVILBase_buildreport_20240603105555.html
- [x] SUGGESTION: No Bioconductor dependencies detected.
AnVILBase is an infrastructure package and does not use Bioconductor dependencies. The downstream packages AnVIL, AnVILAz, and AnVILGCP do.
AnVILAz
- [x] SUGGESTION: All declared Imports should be used.
- [x] SUGGESTION: Import utils in NAMESPACE as well as DESCRIPTION.
- [x] SUGGESTION: Empty or missing \value sections found in man pages.
I don't see this when running BiocCheck
AnVILGCP
- [x] SUGGESTION: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
- [x] SUGGESTION: Import parallel in DESCRIPTION as well as NAMESPACE
- [x] REQUIRED: 'sessionInfo' not found in vignette(s).
- [x] SUGGESTION: Avoid using '=' for assignment and use '<-' instead.
- [x] SUGGESTION: Avoid the use of 'paste' in condition signals.
- [x] SUGGESTION: Avoid redundant 'stop' and 'warn*' in signal conditions.
Some are false positives, e.g., "first error" in the error message, "function returned an error" in the converted warning
- [x] REQUIRED: There should be runnable examples in man pages that document exported objects.
- [x] REQUIRED: Use 'donttest{}' instead of 'dontrun{}' where possible.
- [x] SUGGESTION: Consider adding a NEWS file.
Kayla-Morrell
bioc-issue-bot
lshep
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