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biocroxytest #3274

Closed xec-cm closed 4 months ago

xec-cm 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]'

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 5 months ago

Hi @xec-cm

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: biocroxytest
Title: Handle Long Tests in Bioconductor Packages
Version: 0.99.0
Authors@R: 
    c(person(given = "Francesc",
   family = "Catala-Moll",
   role = c("aut", "cre"),
   email = "fcatala@irsicaixa.es",
   comment = c(ORCID = "0000-0002-2354-8648"))
    )
Description: This package provides a roclet for roxygen2 that identifies and 
    processes code blocks in your documentation marked with `@longtests`. These
    blocks should contain tests that take a long time to run and thus cannot be 
    included in the regular test suite of the package. When you run 
    `roxygen2::roxygenise` with the `longtests_roclet`, it will extract these 
    long tests from your documentation and save them in a separate directory.
    This allows you to run these long tests separately from the rest of your 
    tests, for example, on a continuous integration server that is set up to 
    run long tests.
License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE, roclets = c("rd", "collate", "namespace"))
RoxygenNote: 7.3.0
URL: https://github.com/xec-cm/biocroxytest
BugReports: https://github.com/xec-cm/biocroxytest/issues
biocViews: Software, Infrastructure
Imports: 
    cli,
    glue,
    roxygen2,
    stringr
Suggests: 
    BiocStyle,
    here,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
Depends: R (>= 4.4.0)
Config/testthat/edition: 3
Config/testthat/parallel: false
VignetteBuilder: knitr
bioc-issue-bot commented 5 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 5 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: macOS 12.7.1 Monterey: biocroxytest_0.99.0.tar.gz Linux (Ubuntu 22.04.2 LTS): biocroxytest_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/biocroxytest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 67b2f99a7844beba5e9afe4900ea95b03ba4dbd5

bioc-issue-bot commented 5 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: macOS 12.7.1 Monterey: biocroxytest_0.99.1.tar.gz Linux (Ubuntu 22.04.2 LTS): biocroxytest_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/biocroxytest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d04127ec01a65b79837899cae533f5fc1c893802

bioc-issue-bot commented 5 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: macOS 12.7.1 Monterey: biocroxytest_0.99.2.tar.gz Linux (Ubuntu 22.04.2 LTS): biocroxytest_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/biocroxytest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 8e864cee7a403946d87b2b98ba82b1a66c0d9118

bioc-issue-bot commented 5 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: macOS 12.7.1 Monterey: biocroxytest_0.99.3.tar.gz Linux (Ubuntu 22.04.2 LTS): biocroxytest_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/biocroxytest to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

xec-cm commented 5 months ago

Hello,

In response to the warning received, I would like to clarify that although the submitted package does not have any direct dependencies on Bioconductor, it is specifically designed to facilitate the development of R packages for Bioconductor. One of its key features is the ability to write and manage long tests directly within the function documentation.

Thank you

lshep commented 5 months ago

Thank you for the clarification. We will take another quick glance at the package and assign a reviewer in the next few days. Thank you

bioc-issue-bot commented 5 months ago

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

hpages commented 4 months ago

Thanks for the submission. Package looks good and is accepted.

Cheers, H.

bioc-issue-bot commented 4 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 4 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/xec-cm.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("biocroxytest"). The package 'landing page' will be created at

https://bioconductor.org/packages/biocroxytest

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.