scDotPlot

[ben-laufer]

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• Repository: https://github.com/ben-laufer/scDotPlot

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[bioc-issue-bot]

Hi @ben-laufer

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: scDotPlot
Title: Cluster a Single-cell RNA-seq Dot Plot
Version: 0.99.0
Authors@R: c(
    person(given = c("Benjamin", "I"),
 family = "Laufer",
 role = c("aut", "cre"),
 email = "blaufer@gmail.com"),
    person(given = c("Brad", "A"),
 family = "Friedman",
 role = c("aut")))
Description: Dot plots of single-cell RNA-seq data allow for an examination of the relationships between cell groupings (e.g. clusters) and marker gene expression. The scDotPlot package offers a unified approach to perform a hierarchical clustering analysis and add annotations to the columns and/or rows of a scRNA-seq dot plot. It works with SingleCellExperiment and Seurat objects as well as data frames.
License: Artistic-2.0
URL: https://github.com/ben-laufer/scDotPlot
BugReports: https://github.com/ben-laufer/scDotPlot/issues
biocViews: 
    Software,
    Visualization,
    DifferentialExpression,
    GeneExpression,
    Transcription,
    RNASeq,
    SingleCell,
    Sequencing,
    Clustering
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Depends:
    R (>= 4.4.0)
Imports: 
    aplot,
    BiocGenerics,
    cli,
    dplyr,
    ggplot2,
    ggsci,
    ggtree,
    grDevices,
    magrittr,
    purrr,
    rlang,
    scales,
    scater,
    Seurat,
    SingleCellExperiment,
    stats,
    stringr,
    tibble,
    tidyr
Suggests: 
    AnnotationDbi,
    knitr,
    rmarkdown,
    scQC,
    scran,
    scRNAseq,
    scuttle,
    SeuratObject
VignetteBuilder: knitr
LazyData: false

[lshep]

All package dependencies must be on CRAN or Bioconductor. It does not appear that scQC is. You will need to ask the maintainers to submit to CRAN/Bioconductor or not reference/utilize this as a package dependency.

[ben-laufer]

I've removed that package suggestion, since it was no longer needed.

[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:
Linux (Ubuntu 22.04.3 LTS): scDotPlot_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/scDotPlot 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.

[jianhong]

Package 'scDotPlot' Review

Thank you for submitting your package to Bioconductor. The package passed check and build. It is in pretty good shape. Please try to answer the comments line by line when you are ready for a second review.
Code: Note: please consider; Important: must be addressed.

The DESCRIPTION file

• NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
  'comment=c(ORCID="...")'

The NAMESPACE file

• Important: Selective imports using importFrom instead of import all with import.
  • in line 7 import(aplot)
  • in line 8 import(ggplot2)
  • in line 9 import(ggtree)

General package development

• Important: Please fix the package size issue.
• Note: Consider adding unit tests. We strongly encourage them. See
  http://bioconductor.org/developers/how-to/unitTesting-guidelines/.

R code

• Important: no direct slot access with @ or slot() - accessors implemented and used. You may want to check function [[.
  • In file R/scDotPlot.R:
    • at line 236 found ' object@meta.data %>%'
• NOTE: :: is not suggested in source code unless you can make sure all the packages are imported. Some people think it is better to keep ::. However, please be aware that you will need to manually double-check the imported items if you make any changes to the DESCRIPTION file during development. My suggestion is to remove one or two repetitions to trigger the dependency check.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 361aa6c984e0792875f1d7588ae2407863dc81ff

[ben-laufer]

Hi @jianhong, thank you for reviewing scDotPlot. All important comments have been addressed in the line by line response.

The DESCRIPTION file

• NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
  'comment=c(ORCID="...")'

The NAMESPACE file

• Important: Selective imports using importFrom instead of import all with import.

  • in line 7 import(aplot)
  • in line 8 import(ggplot2)
  • in line 9 import(ggtree)

These have been replaced by selective imports.

General package development

• Important: Please fix the package size issue.

The package size should no longer result in a warning.

• Note: Consider adding unit tests. We strongly encourage them. See
  http://bioconductor.org/developers/how-to/unitTesting-guidelines/.

Unit tests have been added.

R code

• Important: no direct slot access with @ or slot() - accessors implemented and used. You may want to check function [[.

  • In file R/scDotPlot.R:

    • at line 236 found ' object@meta.data %>%'

The code has been changed to remove this.

• NOTE: :: is not suggested in source code unless you can make sure all the packages are imported. Some people think it is better to keep ::. However, please be aware that you will need to manually double-check the imported items if you make any changes to the DESCRIPTION file during development. My suggestion is to remove one or two repetitions to trigger the dependency check.

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