Hello Bioconductor team, I am submitting my R package {staRgate} in consideration for Bioconductor release.

Thank you for your time and consideration!

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

Repository: https://github.com/leejasme/staRgate

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Jul 11 '24 20:07 leejasme

Hi @leejasme

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: staRgate
Title: Automated gating pipeline for flow cytometry analysis to characterize 
    the lineage, differentiation, and functional states of T-cells
Version: 0.99.0
Authors@R: 
    person("Jasme", "Lee", email = "[email protected]", role = c("aut", "cre"),
    comment = c(ORCID = "0009-0006-4492-4872"))
Description: An R-based automated gating pipeline for flow cytometry data designed 
    to mimic the manual gating strategy of defining flow biomarker positive populations 
    relative to a unimodal background population to include cells with varying 
    intensities of marker expression. The pipeline’s main feature is a flexible 
    density-based gating strategy capable of capturing varying scenarios based on 
    marker expression patterns to analyze a 29-marker flow panel that characterizes 
    T-cell lineage, differentiation, and functional states.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
biocViews: FlowCytometry, Preprocessing, ImmunoOncology
Imports: 
    dplyr,
    janitor,
    magrittr,
    purrr,
    rlang,
    stringr,
    tidyr, 
    flowCore, 
    flowWorkspace,
    glue, 
    tibble
Suggests: 
    flowAI,
    ggplot2,
    gt,
    knitr,
    openCyto,
    ggcyto,
    rmarkdown,
    data.table,
    here,
    testthat (>= 3.0.0)
VignetteBuilder: knitr
BugReports: https://github.com/leejasme/staRgate/issues
URL: https://leejasme.github.io/staRgate/, https://github.com/leejasme/staRgate
Config/testthat/edition: 3

Jul 11 '24 20:07 bioc-issue-bot

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

Jul 18 '24 13:07 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: "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: staRgate_0.99.0.tar.gz Linux (Ubuntu 22.04.3 LTS): staRgate_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 [email protected]:packages/staRgate to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Jul 18 '24 13:07 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 1dd51d12157d6772b103db28a8cb29bbfbbb97a7

Jul 23 '24 13:07 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: "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: staRgate_0.99.1.tar.gz Linux (Ubuntu 22.04.3 LTS): staRgate_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 [email protected]:packages/staRgate to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Jul 23 '24 13:07 bioc-issue-bot

Hello!

The latest warning that was flagged states: " * WARNING: Package listed as VignetteEngine or VignetteBuilder but not currently Suggested."

I only use knitr for the vignette and have included in the Suggests field. When running the checks on my local machine, I do not get this warning and cannot reproduce.

It looks like this might be a false positive based on a few other packages currently undergoing review (#3379 and #3451)

What is the best course of action for moving this forward?

Thank you!

Jul 24 '24 23:07 leejasme

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

Aug 05 '24 14:08 bioc-issue-bot

@LiNk-NY can you also investigate the reported false positive in the BiocCheck?

Aug 05 '24 14:08 lshep

Hi @lshep The issue was resolved two weeks ago : https://github.com/Bioconductor/BiocCheck/commit/481d8d1fa9c5ac32672d1119a058b8add2a933ed

@leejasme Please bump the version for a more recent run BiocCheck.

Aug 05 '24 14:08 LiNk-NY

Great thank you! Will do

Aug 05 '24 19:08 leejasme

Received a valid push on git.bioconductor.org; starting a build for commit id: 76a09e6aed3247844ae56d9e01d9fb265dfdb0fd

Aug 05 '24 20:08 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: macOS 12.7.1 Monterey: staRgate_0.99.2.tar.gz Linux (Ubuntu 22.04.3 LTS): staRgate_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 [email protected]:packages/staRgate to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Aug 05 '24 20:08 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 336ffa86f92dffc6b0ed2d3bb1a28af6eaefd0a2

Aug 05 '24 21:08 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): staRgate_0.99.3.tar.gz macOS 12.7.1 Monterey: staRgate_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 [email protected]:packages/staRgate to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Aug 05 '24 21:08 bioc-issue-bot

Hi @LiNk-NY, thank you for the initial review!

I wanted to clarify on the first point as I am not familiar with the SummarizedExperiment and stageR class. Do you mean entirely for the pipeline whether it would make sense to change to these classes, or only for the subsequent part where I pull the intensity matrix from the GatingSet?

I will look more closely into each of the comments and update accordingly. Thank you!

Aug 09 '24 18:08 leejasme

Hi @leejasme

Apologies for the confusion. I copied the wrong review.

Please see the review below. Let me know if you have any questions. Best regards, Marcel

staRgate #3485

DESCRIPTION

Looks good.
Consider avoiding the magrittr dependency in favor of the native pipe (|>).

NAMESPACE

Consider using the native pipe.
Looks good.

vignettes

Consider using BiocStyle::html_document as the output function.
Consider wrapping the lines to a limit of 80 character width. This makes it easier to review and, IMO, maintian.
Remove version specific code from the Installation section. You do not want to update this code at every release.
Remove GitHub installation instructions.
Remove installation instructions for specific packages and only keep the library("package") calls instead. Import'ed and Suggest'ed packages are usually installed with your package.
Use r Biocpkg("flowCore"} etc. for referring to Bioconductor or r CRANpkg("openCyto") for CRAN packages
Consider hiding (echo = FALSE) the theme_set code related to plotting.
Optional. Please encourage good practices and use <- instead of = for assignment.
Avoid using @ to access slots and create an accessor function (e.g. in chk_cm@spillover).
Avoid too much conditional code as it complicates the workflow for the user, e.g., when resolving inconsistencies in naming conventions in the Import FCS section
Consider reducing the amount of repetitive code in the vignette. Please make it easy for the user to use your software (see Extract intensity matrix section).

R

Keep move the roxygen block(s) above the function and not in the body (see getBiexpTransformGS).
Is the standard that all input files be csv? Perhaps the inputs to these functions can be matrices instead. What if names differ, is your code robust enough to handle column name changes?
Consider reducing the cyclomatic complexity in the code by reducing the number of "check inputs" and consider using an S4 class with validity checks.
Avoid nested ifelse and use case_when with mutate.
Minor: Consider using the shorter is.data.frame(), is.numeric() functions instead of inherits(...)

tests

Please increase the package coverage in R/getDensityGates.R:

> covr::package_coverage(type="all")
staRgate Coverage: 81.35%
R/getDensityGates.R: 52.63%
R/getPerc.R: 74.40%
R/getGatedDat.R: 84.38%
R/internal.R: 98.41%
R/getBiexpTransformGS.R: 100.00%
R/getCompGS.R: 100.00%

Aug 13 '24 18:08 LiNk-NY

Thank you!! I will work on updating!

Is there a timeline for when I would need to push updates before this issue would automatically close etc?

Aug 14 '24 01:08 leejasme

Hi @leejasme We usually expect some activity within two weeks of the review. If you need more time, let us know. Best regards, Marcel

Aug 14 '24 16:08 LiNk-NY

This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.

Thank you for your interest in Bioconductor.

Jan 14 '25 19:01 bioc-issue-bot

Hello Bioconductor team, I would like to reopen this issue to submit an updated version of the package for consideration following the helpful first review! Is it sufficent to reopen this issue and bump the version number? Please let me know if I should do anything else to put this back in the queue. Thank you so much!

Dec 09 '25 15:12 leejasme

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

Dec 09 '25 15:12 bioc-issue-bot

Dear @leejasme ,

We have reopened the issue to continue the review process. Please remember to push a version bump to git.bioconductor.org to trigger a new build.

Dec 09 '25 15:12 bioc-issue-bot

yes you should bump the version to trigger a new build report and comment on any of the items previously identified in the review process.

Dec 09 '25 15:12 lshep

Received a valid push on git.bioconductor.org; starting a build for commit id: 77dbdc4d6d7713a811c9346d8fb8ce0538ff1b41

Dec 09 '25 15:12 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 24.04.3 LTS): staRgate_0.99.4.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 [email protected]:packages/staRgate to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Dec 09 '25 15:12 bioc-issue-bot

Thank you! I just pushed a new version bump. Below are comments RE the first review

DESCRIPTION AND NAMESPACE

Updated all to native pipes

vignette

Updated to using BiocStyle::html_document, removed installation instructions,
Whenever possible wrapped code lines to 80 char width except for strings or comments
Use r Biocpkg() and r CRANpkg to reference packages
Avoid using @ to access slots and create an accessor function (to the best of my knowledge the package did not have an accessor function for getting the spillover)
Cleaned up some repetitive and conditional code to make it easier for user to read and use.

R

For inputs, currently the expectation is the input will be csv files instead of matrices but this may be updated in the future to allow both types of inputs for more flexibility.
Updated the method for checking inputs into one wrapping function applied across multiple functions
updated nested ifelse code with case_when when possible
updated to use is.data.frame() etc. functions instead of inherits()

Tests

Updated to include more testing to increase to at least 90% coverage

Dec 09 '25 16:12 leejasme

Hi @leejasme

Thank you for your updates.

After taking a quick look, the package seems to be in good shape. There appears to be some redundancy especially in rlang::* condition signals. For example, instances where "error" and "warning" keywords are in the message of the condition:

rlang::abort("Error: This is an error message")
#' Error:
#' ! Error: This is an error message
#' Run `rlang::last_trace()` to see where the error occurred.

This extra "Error" in the message is redundant since rlang::abort and others already flag the condition in the first line with Error:, as seen above.

Please make sure that you are resolving as many NOTEs as possible in R CMD check and BiocCheck.

-MR

Jan 08 '26 20:01 LiNk-NY

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.

Jan 08 '26 20:01 bioc-issue-bot

Thank you for the review and excited that it is now part of Bioconductor!!

Thanks for pointing out about the messages, will update that!

Jan 08 '26 22:01 leejasme

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/leejasme.keys is not empty), then no further steps are required. Otherwise, do the following:

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("staRgate"). The package 'landing page' will be created at

https://bioconductor.org/packages/staRgate

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.

Jan 12 '26 15:01 lshep