tidyFlowCore

[keyes-timothy]

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[bioc-issue-bot]

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]

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[bioc-issue-bot]

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]

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]

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

[bioc-issue-bot]

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]

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

• Chunk in vignette generating output should have interpretation afterwards. For example, what does the scatter plot reveal?
• biocViews field of DESCRIPTION file should have Infrastructure like other tidy packages already in Bioconductor do.

[keyes-timothy]

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]

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

[bioc-issue-bot]

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]

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

[bioc-issue-bot]

Your package has been accepted. It will be added to the
Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

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community. If you are interested in becoming a Bioconductor package
reviewer, please see Reviewers Expectations.

[lshep]

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https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

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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

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