sosta

[sgunz]

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• Repository: https://github.com/sgunz/sosta

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[bioc-issue-bot]

Hi @sgunz

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: sosta
Title: A package for the analysis of anatomical tissue structures in spatial omics data
Version: 0.99.0
Authors@R: c(
    person("Samuel", "Gunz", , "[email protected]", role = c("aut", "cre"),
 comment = c(ORCID = "0000-0002-8909-0932")),
    person("Mark D.", "Robinson", role=c("aut", "fnd"), 
	    email="[email protected]"))
Description: `sosta` (Spatial Omics STructure Analysis) is a package for analyzing
    spatial omics data to explore tissue organization at the anatomical structure level.
    It reconstructs morphologically relevant structures based on molecular features 
    or cell types. It further calculates a range of structural and shape metrics
    to quantitatively describe tissue architecture. The package is designed to integrate 
    with other packages for the analysis of spatial (omics) data.
License: GPL (>= 3) + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
URL: https://github.com/sgunz/sosta, https://sgunz.github.io/sosta/
BugReports: https://github.com/sgunz/sosta/issues
biocViews: Software, Spatial, Transcriptomics, Visualization
Imports: 
    terra,
    sf,
    smoothr,
    spatstat.explore,
    spatstat.geom,
    SpatialExperiment,
    dplyr,
    ggplot2,
    patchwork,
    SummarizedExperiment,
    stats,
    rlang
Suggests:
    knitr,
    rmarkdown,
    ggspavis,
    BiocStyle,
    imcdatasets,
    ggfortify,
    tidyr
VignetteBuilder: knitr

[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: "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 24.04.1 LTS): sosta_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/sosta 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: f5ac7192839afcf34dbe44ef743d5194b78fe9ad

[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 24.04.1 LTS): sosta_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/sosta 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 'sosta' Review

Thank you for submitting your package to Bioconductor. The package passed check and build. However there are several things need to be fixed. 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

• Important: Depends field is not found in DESCRIPTION.
• Important: R version is not clear in DESCRIPTION.

The NAMESPACE file

• Important: Selective imports using importFrom instead of import all with import.
  • in line 20 import(SpatialExperiment)
  • in line 21 import(sf)
  • in line 22 import(spatstat.explore)
  • in line 23 import(spatstat.geom)

General package development

• Important: Consider adding unit tests. We strongly encourage them. See
  http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
• Important: Consider adding input checking. We strongly encourage them. See https://contributions.bioconductor.org/r-code.html#function-arguments

R code

• 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.
  • In file R/reconstructShapePPP.R:
    • at line 118 found ' dplyr::filter(.data$value > max(.data$value) / 250) |>'
    • at line 125 found ' p <- patchwork::wrap_plots(den_im, den_hist, ncol = 2) +'
    • at line 126 found ' patchwork::plot_annotation('
    • at line 309 found ' res <- parallel::mclapply(sample_images, function(x) {'
    • at line 322 found ' res <- dplyr::bind_rows(res)'
    • at line 337 found ' plot(patchwork::wrap_plots(p1, p2, ncol = 2))'
  • In file R/shapeMetricsFromSF.R:
    • at line 63 found ' smooth_poly <- smoothr::smooth(sf::st_boundary(sfPoly),'
    • at line 71 found ' smooth_df <- as.data.frame(sf::st_coordinates(smooth_poly))'
    • at line 126 found ' perimeter <- sf::st_length(sf::st_boundary(sfPoly))'
    • at line 128 found ' radicand <- perimeter^2 - 16 * sf::st_area(sfPoly)'
  • In file R/utils.R:
    • at line 36 found ' terra::ext(r) <- c('
• Important: Fix the TODO list.
  • In file R/reconstructShapePPP.R:
    • at line 29 found ' # TODO: Error when threshold is too small'
    • at line 254 found ' # TODO: do.call(rbind, a)'
  • In file R/utils.R:
    • at line 215 found ' # TODO: this could be improved'
• NOTE: Functional programming: code repetition.
  • repetition in findIntensityThreshold, reconstructShapeDensityImage, and shapeIntensityImage
    • in findIntensityThreshold
      • line 3: if (is.null(bndw))
      • line 4: bndw <- bw.diggle(ppp)
      • line 5: den_df <- as.data.frame(density(ppp, sigma = bndw, dimyx = dimyx,
      • line 6: positive = TRUE))
    • in reconstructShapeDensityImage
      • line 5: pp_sel <- subset(pp, marks %in% mark_select)
      • line 6: dimyx <- getDimXY(pp_sel, dim)
      • line 7: if (is.null(bndw))
      • line 8: bndw <- bw.diggle(pp_sel)
    • in shapeIntensityImage
      • line 5: pp.islet <- subset(pp, marks %in% mark_select)
      • line 6: dimyx <- getDimXY(pp.islet, dim)
      • line 7: if (is.null(bndw))
      • line 8: bndw <- bw.diggle(pp.islet)
      • line 9: im_df <- as.data.frame(density.ppp(pp.islet, sigma = bndw,
      • line 10: dimyx = dimyx, positive = TRUE))

Documentation

• Important: Vignette should have an Installation section.
  • rmd file vignettes/IMC_DiabetesIslets_Vignette.Rmd
• Important: Please include Bioconductor installation instructions using BiocManager.
  • rmd file vignettes/IMC_DiabetesIslets_Vignette.Rmd
• Important: Ensure the news file is updated to the latest version available.