SpatialExperimentIO

[estellad]

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[bioc-issue-bot]

Hi @estellad

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: SpatialExperimentIO
Title: Read in Xenium, CosMx, MERSCOPE or STARmapPLUS data as SpatialExperiment object
Version: 0.99.0
Authors@R: c(
    person("Yixing E.", "Dong", 
        email = "estelladong729@gmail.com", 
        role = c("aut", "cre"), 
        comment = c(ORCID = "0009-0003-5115-5686")))
URL: https://github.com/estellad/SpatialExperimentIO
BugReports: https://github.com/estellad/SpatialExperimentIO/issues
Description: Read in imaging-based spatial transcriptomics technology data. Current available modules are for Xenium by 10X Genomics, CosMx by Nanostring, MERSCOPE by Vizgen, or STARmapPLUS from Broad Institute. You can choose to read the data in as a SpatialExperiment or a SingleCellExperiment object. 
License: Artistic-2.0
Encoding: UTF-8
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
Imports: 
  DropletUtils,
  SpatialExperiment,
  SingleCellExperiment,
  methods,
  utils
Suggests: 
  knitr, 
  rmarkdown, 
  testthat (>= 3.0.0), 
  BiocStyle
biocViews:
  DataRepresentation, 
  DataImport, 
  Infrastructure, 
  Transcriptomics, 
  SingleCell, 
  Spatial,
  GeneExpression
RoxygenNote: 7.3.1
Config/testthat/edition: 3

[bioc-issue-bot]

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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 22.04.3 LTS): SpatialExperimentIO_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/SpatialExperimentIO to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[lshep]

Please resolve ERRORs before a formal reviewer is assigned

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 2d1220850e111a3c4c503cdfbe37dcbc1eb14bba

[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 22.04.3 LTS): SpatialExperimentIO_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/SpatialExperimentIO 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: 2ef6f5895339fa736c1397755fab419ec28e702a

[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): SpatialExperimentIO_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/SpatialExperimentIO 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.

[DarioS]

Good work. Some minor issues.

• News file seems mistaken. Hopefully, you are not simulatenously submitting to CRAN, which is against Bioconductor policy.

SpatialExperimentIO 0.0.99
Initial CRAN submission.

Also, version number is not one which is associated to the package.

• Note sure why \dontRun wraps a URL. It should be fine to have without it. Did you intend to write \url instead?

#' \dontrun{
#' https://nanostring.com/resources/smi-ffpe-dataset-lung9-rep1-data/
#' }

• For limiting output to a set of valid values, please use match.arg and see tutorial.

readCosmxSXE <- function(dirname = dirname, return_type = "SPE", ...
if(!return_type %in% c("SPE", "SCE")){

• camelCase versus snake_case e.g. coord_names. Please see Variable Names in developer's guide and be consistent.
• The data files in inst/extdata need to each be documented in an Rd file. See Raw Data Directory instructions.