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tidyFlowCore #3345

Closed keyes-timothy closed 1 month ago

keyes-timothy commented 3 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 3 months ago

Hi @keyes-timothy

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: tidyFlowCore
Type: Package
Title: tidyFlowCore: Bringing flowCore to the tidyverse
Version: 0.99.0
Authors@R: 
    c(person(given = "Timothy",
   family = "Keyes",
   role = c("cre"),
   email = "tkeyes@stanford.edu", 
   comment = c(ORCID = "0000-0003-0423-9679")),
      person(given = "Kara", 
   family = "Davis", 
   role = c("rth", "own"),
   email = "kldavis@stanford.edu"), 
      person(given = "Garry", 
   family = "Nolan", 
   role = c("rth", "own"), 
   email = "gnolan@stanford.edu"))
Description: tidyFlowCore bridges the gap between flow cytometry analysis using the 
    flowCore Bioconductor package and the tidy data principles advocated by the tidyverse. It provides 
    a suite of dplyr-, ggplot2-, and tidyr-like verbs specifically designed for working with flowFrame 
    and flowSet objects as if they were tibbles; however, your data remain flowCore
    data structures under this layer of abstraction. tidyFlowCore enables 
    intuitive and streamlined analysis workflows that can leverage both the 
    Bioconductor and tidyverse ecosystems for cytometry data. 
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/keyes-timothy/tidyFlowCore, https://keyes-timothy.github.io/tidyFlowCore/
BugReports: https://github.com/keyes-timothy/tidyFlowCore/issues
Depends: 
    R (>= 4.3)
Imports: 
    Biobase,
    dplyr,
    flowCore,
    ggplot2,
    methods,
    purrr,
    rlang,
    stats,
    stringr,
    tibble,
    tidyr
RoxygenNote: 7.3.1
Suggests: 
    BiocStyle,
    HDCytoData,
    knitr,
    RefManageR,
    rmarkdown,
    sessioninfo,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
biocViews: SingleCell, FlowCytometry
VignetteBuilder: knitr
bioc-issue-bot commented 3 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 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.

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

bioc-issue-bot commented 3 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 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0ede10bcc13c669fa02bbdedc851e49add9ed342

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

DarioS commented 2 months ago

The package is well-designed and documentation is clear. It uses many Bioconductor packages. A couple of minor omissions.

keyes-timothy commented 1 month ago

Hi! Thank you for these comments and for your patience while I addressed them.

I added Infrastructure to the biocViews field of the DESCRIPTION file, and I added some additional exposition in the package vignette (particularly in the section you pointed out).

I've incremented the version to 0.99.2 and pushed the changes, but I didn't receive a build report. I suspect this has something to do with my missing the 3.19 release date earlier this week. I'm happy to have the package added to devel (and released with Bioconductor 3.20) - but are there changes on my end for how I should submit to the build system?

Thanks again for your help!

Edit: Also tagging @lshep here, in case I may (very graciously) ask for their guidance as well with my question.

Further edit: I just got the build report, and it looks like it passed. I realized that I hadn't incremented the version number in the DESCRIPTION file (only the NEWS file), so a new build was not triggered. Glad I caught it (and thanks again for your patience!)

bioc-issue-bot commented 1 month ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0c300a8871b371c7f3649262497dc85128c76300

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 22.04.3 LTS): tidyFlowCore_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/tidyFlowCore to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

DarioS commented 1 month ago

Good. Yes, the version number must be incremented for the changes to be considered as an update to rebuild.

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/keyes-timothy.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("tidyFlowCore"). The package 'landing page' will be created at

https://bioconductor.org/packages/tidyFlowCore

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.