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EpipwR.data #3543

Closed jbarth216 closed 1 month ago

jbarth216 commented 2 months ago

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

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bioc-issue-bot commented 2 months ago

Hi @jbarth216

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: EpipwR.data
Type: Package
Title: EpipwR.data: Reference data for EpipwR
Version: 0.99.0
Authors@R:
  c(person(given="Jackson", family="Barth", role=c("aut","cre"), email="Jackson_Barth@Baylor.edu",
  comment=c(ORCID = "0009-0009-6307-9928")),
    person("Austin", "Reynolds", role="aut"))
Description: This package provides reference data for EpipwR.
    EpipwR is a fast and efficient power analysis for continuous and binary phenotypes
    of epigenomic-wide association studies. This package is only meant to be used in conjunction
    with EpipwR.
License: Artistic-2.0
Encoding: UTF-8
LazyData: false
URL: https://github.com/jbarth216/EpipwR.data
BugReports: https://github.com/jbarth216/EpipwR.data
Imports: 
    ExperimentHub
Suggests:
  knitr,
  rmarkdown,
  sessioninfo
biocViews: ExperimentHub, MethylationArrayData, MicroarrayData, TissueMicroarrayData, Tissue, ExperimentData
VignetteBuilder: knitr
lshep commented 2 months ago

You likely want to show at least an ExperimentHub query to find the dataset in the vignette since there currently is no indication of how one might download the data.

jbarth216 commented 2 months ago

Hi there - so my reasoning for not adding a sample query is because this is meant to be a supplemental package to EpipwR (I will add it to this request once it I get the pre-review tag), which is a power calculator that uses reference data on experiment hub. The data are sets of parameter estimates, so I don't expect it to have much value outside of the EpipwR context (which includes built-in functions that download the datasets). Having said that, I'm more than happy to add in a query for this package if necessary.

lshep commented 2 months ago

Thank you for the clarification. It will be added to git.bioconductor.org and you'll have a build report shortly to begin the in depth review

bioc-issue-bot commented 2 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 2 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): EpipwR.data_0.99.0.tar.gz Linux (Ubuntu 24.04.1 LTS): EpipwR.data_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/EpipwR.data to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

jbarth216 commented 2 months ago

AdditionalPackage: https://github.com/jbarth216/EpipwR

bioc-issue-bot commented 2 months ago

Hi @jbarth216, Thanks for submitting your additional package: https://github.com/jbarth216/EpipwR. We are taking a quick look at it and you will hear back from us soon.

bioc-issue-bot commented 2 months ago

Additional Package has been approved for building.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

bioc-issue-bot commented 2 months ago

Additional Package has been approved for building.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

bioc-issue-bot commented 2 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 24.04.1 LTS): EpipwR_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/EpipwR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 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: "WARNINGS". 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 24.04.1 LTS): EpipwR_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/EpipwR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 months ago

Additional Package has been approved for building.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

bioc-issue-bot commented 2 months ago

Additional Package has been approved for building.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

bioc-issue-bot commented 2 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 24.04.1 LTS): EpipwR_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/EpipwR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 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: "WARNINGS". 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 24.04.1 LTS): EpipwR_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/EpipwR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: ae42b7a8a19e1baf4c5aa4a46456d74ede48739e

bioc-issue-bot commented 2 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: "WARNINGS". 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 24.04.1 LTS): EpipwR_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/EpipwR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 6567aeb730144a23609ff7cda3a9db2cc85398ad

bioc-issue-bot commented 2 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 24.04.1 LTS): EpipwR_0.99.2.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/EpipwR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 months ago

Additional Package has been approved for building.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

bioc-issue-bot commented 2 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 24.04.1 LTS): EpipwR_0.99.2.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/EpipwR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 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 2 months ago

Additional Package has been approved for building.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

bioc-issue-bot commented 2 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 24.04.1 LTS): EpipwR_0.99.2.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/EpipwR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

lshep commented 1 month ago

I apologize for the delay. I am looking at this today and will have a review either later today or latest on monday.

jbarth216 commented 1 month ago

No worries, I know its pretty busy right now. Thanks for the update!

lshep commented 1 month ago

Just a few minor comments for the EpipwR package

man

README

vignette

bioc-issue-bot commented 1 month ago

Received a valid push on git.bioconductor.org; starting a build for commit id: ba3fd1fc0125c967d3cd1322c6aad102f458c754

bioc-issue-bot commented 1 month 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 24.04.1 LTS): EpipwR_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/EpipwR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

jbarth216 commented 1 month ago

Hi @lshep - thanks for the review. All comments have been addressed in the new commit. Please let me know if you have any other feedback.

bioc-issue-bot commented 1 month 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 1 month 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/jbarth216.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("EpipwR.data"). The package 'landing page' will be created at

https://bioconductor.org/packages/EpipwR.data

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.

lshep commented 1 month 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/jbarth216.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("EpipwR"). The package 'landing page' will be created at

https://bioconductor.org/packages/EpipwR

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.