Open leejasme opened 1 month ago
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
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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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.
Received a valid push on git.bioconductor.org; starting a build for commit id: 1dd51d12157d6772b103db28a8cb29bbfbbb97a7
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.
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!
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
@LiNk-NY can you also investigate the reported false positive in the BiocCheck?
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
.
Great thank you! Will do
Received a valid push on git.bioconductor.org; starting a build for commit id: 76a09e6aed3247844ae56d9e01d9fb265dfdb0fd
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: 336ffa86f92dffc6b0ed2d3bb1a28af6eaefd0a2
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.
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!
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
magrittr
dependency in favor of the native pipe
(|>
).BiocStyle::html_document
as the output function.Installation
section. You do not
want to update this code at every release.library("package")
calls instead. Import
'ed and Suggest
'ed packages are
usually installed with your package.r Biocpkg("flowCore"}
etc. for referring to Bioconductor or r CRANpkg("openCyto")
for CRAN packagesecho = FALSE
) the theme_set
code related to plotting.<-
instead of =
for
assignment.@
to access slots and create an accessor function (e.g. in
chk_cm@spillover
).Import FCS
sectionExtract intensity matrix
section).getBiexpTransformGS
).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?ifelse
and use case_when
with mutate
.is.data.frame()
, is.numeric()
functions instead of inherits(...)
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%
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?
Hi @leejasme We usually expect some activity within two weeks of the review. If you need more time, let us know. Best regards, Marcel
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
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