staRgate

[leejasme]

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

Thank you for your time and consideration!

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

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[bioc-issue-bot]

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 = "leej22@mskcc.org", 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

[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.

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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: "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
git@git.bioconductor.org:packages/staRgate to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

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

[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
git@git.bioconductor.org:packages/staRgate to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[leejasme]

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!

[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.

[lshep]

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

[LiNk-NY]

Hi @lshep
The issue was resolved two weeks ago : Bioconductor/BiocCheck@481d8d1

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

[leejasme]

Great thank you! Will do

[bioc-issue-bot]

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

[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
git@git.bioconductor.org:packages/staRgate to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

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

[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
git@git.bioconductor.org:packages/staRgate to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[leejasme]

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!

[LiNk-NY]

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%

[leejasme]

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?

[LiNk-NY]

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