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cfToolsData #3164

Closed RoseHuRan closed 9 months ago

RoseHuRan commented 9 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]'

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 9 months ago

Hi @RoseHuRan

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: cfToolsData
Title: ExperimentHub data for the cfTools package
Version: 0.99.0
Authors@R: c(
    person(given = "Ran",
        family = "Hu",
        role = c("aut", "cre"),
        email = "huran@ucla.edu",
        comment = c(ORCID = "0000-0002-0563-8957")),
    person("Shuo", "Li", 
        role = "aut",
        comment = c(ORCID = "0000-0002-1960-6016")),
    person(c("Xianghong", "Jasmine"), "Zhou", 
        role = "aut", 
        email = "XJZhou@mednet.ucla.edu", 
        comment = c(ORCID = "0000-0002-4522-7490")),
    person("Wenyuan", "Li", 
        role = "aut",
        email = "WenyuanLi@mednet.ucla.edu",
        comment = c(ORCID = "0000-0002-5029-8525")))
Description: The cfToolsData package supplies the data for the cfTools package. 
    It contains two pre-trained deep neural network (DNN) models for the cfSort 
    function. Additionally, it includes the shape parameters of beta 
    distribution characterizing methylation markers associated with four tumor 
    types for the CancerDetector function, as well as the parameters 
    characterizing methylation markers specific to 29 primary human tissue 
    types for the cfDeconvolve function.
License: file LICENSE
LazyData: False
Encoding: UTF-8
Depends: R (>= 4.3.0)
RoxygenNote: 7.2.3
VignetteBuilder: knitr
Imports: 
    utils,
    ExperimentHub
Suggests: 
    knitr,
    rmarkdown,
    ExperimentHubData,
    testthat (>= 3.0.0)
biocViews: 
    ExperimentHub,
    ExperimentData,
    ReproducibleResearch,
    DiseaseModel,
    CancerData,
    Tissue
URL: https://github.com/jasminezhoulab/cfToolsData
BugReports: https://github.com/jasminezhoulab/cfToolsData/issues
bioc-issue-bot commented 9 months ago

Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

bioc-issue-bot commented 9 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): cfToolsData_0.99.0.tar.gz macOS 12.6.5 Monterey: cfToolsData_0.99.0.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/cfToolsData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

RoseHuRan commented 9 months ago

AdditionalPackage: https://github.com/jasminezhoulab/cfTools

bioc-issue-bot commented 9 months ago

Dear @RoseHuRan ,

You (or someone) has already posted that repository to our tracker.

See https://github.com/Bioconductor/Contributions/issues/2963

You cannot post the same repository more than once.

If you would like this repository to be linked to issue number: 3164, Please contact a Bioconductor Core Member.

lshep commented 9 months ago

cfTools is already accepted and on Bioconductor. https://bioconductor.org/packages/release/bioc/html/cfTools.html You can just update your package on git.bioconductor.org

RoseHuRan commented 9 months ago

@lshep Thank you, Lori! I am submitting this data package to supply data for a new feature in my cfTools package. Should I push the updates of cfTools (need to import cfToolsData) to bioconductor after cfToolsData is accepted?

lshep commented 9 months ago

Yes. Wait until your data package is reviewed and accepted and then you can push updates to the software package.

bioc-issue-bot commented 9 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 3b027acd0e12a92e6f8e7990e67959643cdd402a

bioc-issue-bot commented 9 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): cfToolsData_0.99.1.tar.gz macOS 12.6.5 Monterey: cfToolsData_0.99.1.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/cfToolsData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 9 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 925b8e1f6fee0f1a11706dcf714846f6fd8c1920

bioc-issue-bot commented 9 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

On one or more platforms, the build results were: "ERROR, skipped". 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 Bioconductor Build System: ERROR before build products produced.

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

bioc-issue-bot commented 9 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: c3865b6fbb0b8cede0d0e5ad2352d5a16ff7f926

bioc-issue-bot commented 9 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): cfToolsData_0.99.3.tar.gz macOS 12.6.5 Monterey: cfToolsData_0.99.3.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/cfToolsData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 9 months ago

A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.

bioc-issue-bot commented 9 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 9 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/RoseHuRan.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("cfToolsData"). The package 'landing page' will be created at

https://bioconductor.org/packages/cfToolsData

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.