Closed renlyly closed 3 months ago
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Dear @HelenaLC , Thank you again for your constructive feedback. Below are the modifications I've implemented in response to your input:
•I believe the simFromParam.Rd and quickPower.Rd man pages have some syntax issues that result in faulty formatting (see NOTES in the build report and, e.g., ?quickPower)
A: Thank you for your suggestion. We have revised the syntax issues for Rd. files
•There are still some @s left in inst/unitTests/test_cypress.R (fyi, you can use shift+command+F to search the entire package)
A: Thank you for your suggestion. We have corrected the @s in unitTests.
•The DESCRIPTION contains a couple syntax (missing/too many spaces), phrasing and grammar mistakes; please revise (e.g., A cell type on AN, input of A SE object not THE, to identify differentialLY expressed genes -> common abbreviation for that is DEGs/never seen csDE)
A: We have re-examined the syntax issues in the DESCRIPTION. Regarding the use of the abbreviation csDE, csDE is our research focus, not the DEG. We would like to retain it.
•The generics defined in cypress-methods.R should go under AllGenerics.R
A: Thanks for the suggestion. We have rectified this issue.
•I noticed an instance of bplapply in cypress_wrapper(); it'd make sense to expose an argument to the user that would enable controlling how to perform parallelizatio, e.g., an argument BPPARAM in the function definition that is passed to the bplapply call; otherwise users need to be familiar with how to registed a backend with bpparam(), which is rather less obvious than passing a parameter imo. (also: still some commented out code here.)
A: Thank you for your suggestion. We've removed unnecessary code. Regarding bpparam(), we have added related functions.
Shilin
Alright, thanks for these modifications - that's all clear now. I noticed one last thing I'd like to be resolved before acceptance, and apologies for missing this earlier as I am more used to roxygen
-based documentation...
Looking at the NAMESPACE, you should use importFrom()
in all but rare cases (see here for details) - for 2/3 dependencies, the entire package is currently being imported.
Received a valid push on git.bioconductor.org; starting a build for commit id: d9a7503412fb84458bc1feb85b3a3144fc2114e4
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): cypress_0.99.19.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/cypress
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear @HelenaLC,
Thank you very much for your guidance and patience. In the recent update, I made the necessary adjustments for the dependencies as advised and ensured it aligns better with practices.
Thank you again for your valuable feedback.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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