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Deep characterization of cancer drugs mechanism of action #3066

Closed TrinhNguyenP closed 3 months ago

TrinhNguyenP commented 1 year 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]'

I am familiar with the essential aspects of Bioconductor software management, including:

For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.

bioc-issue-bot commented 4 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.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

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): DeepTarget_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/DeepTarget to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

TrinhNguyenP commented 4 months ago

go ahead

Hi @vjcitn, I am not sure why I received an error after pushing the updated version to Bioconductor as below:

"Error: package or namespace load failed for DeepTarget in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called BiocParallel"

Could you please provide me some guidance?

Thanks, Trinh

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: c151b95a6d22e390e02749980f71e4896b488ce1

bioc-issue-bot commented 4 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): DeepTarget_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/DeepTarget to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

TrinhNguyenP commented 4 months ago

Hi @vjcitn and @PeteHaitch,

The new version has been built succesffully. In this new version, I have removed tidyverse package, revised the DeepTarget_Vignette.Rmd to make it clearer, fixed the Big data dump, and replaced all the sapply to vapply.

Please let me know if you have additional comments.

Thanks,

Trinh

TrinhNguyenP commented 3 months ago

go ahead

Hi @vjcitn and @PeteHaitch,

It has been 3 weeks so I would like to check to see whether you have a chance to review the new submission.

Thanks,

Trinh

PeteHaitch commented 3 months ago

Hi Trinh,

@vjcitn has taken over this review, so I'll leave it with him.

vjcitn commented 3 months ago

I will get to it soon.

TrinhNguyenP commented 3 months ago

Hi @vjcitn,

I would love to check to see whether you have an update. :-)

Trinh

vjcitn commented 3 months ago

it would be helpful to introduce line breaks so that the reader can see the entire call without scrolling to the right. This is relevant for a few of the code presentations.

image

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.

TrinhNguyenP commented 3 months ago

it would be helpful to introduce line breaks so that the reader can see the entire call without scrolling to the right. This is relevant for a few of the code presentations.

image

Hi @vjcitn,

Thanks for your suggestions. I will add this useful suggestion to the next update. Thanks for reviewing and accepting the package.

Trinh

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/TrinhNguyenP.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("DeepTarget"). The package 'landing page' will be created at

https://bioconductor.org/packages/DeepTarget

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.