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cypress #3272

Closed renlyly closed 3 months ago

renlyly commented 5 months ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Confirm the following by editing each check box to '[x]'

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bioc-issue-bot commented 3 months ago

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_0.99.18.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.

renlyly commented 3 months ago

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

HelenaLC commented 3 months ago

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.

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d9a7503412fb84458bc1feb85b3a3144fc2114e4

bioc-issue-bot commented 3 months ago

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.

renlyly commented 3 months ago

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.

bioc-issue-bot commented 3 months ago

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

lshep commented 3 months ago

The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/renlyly.keys is not empty), then no further steps are required. Otherwise, do the following:

  1. Add an SSH key to your github account
  2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("cypress"). The package 'landing page' will be created at

https://bioconductor.org/packages/cypress

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.