spatialFDA

[mjemons]

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• Repository: https://github.com/mjemons/spatialFDA

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[bioc-issue-bot]

Hi @mjemons

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: spatialFDA
Title: A Tool for Spatial Multi-sample Comparisons
Version: 0.99.0
Authors@R: c(
    person("Martin", "Emons", , "martin.emons@uzh.ch", role = c("aut", "cre"),
 comment = c(ORCID = "0009-0000-5219-5311")),
    person("Samuel", "Gunz", ,role="aut",
 comment = c(ORCID = "0000-0002-8909-0932")),
    person("Mark", "Robinson", , "mark.robinson@mls.uzh.ch", role = c("aut"),
 comment = c(ORCID = "0000-0002-3048-5518")))
Description: spatialFDA is a package to calculate spatial statistics metrics and compare them across samples/conditions using functional additive models. Furthermore, it provides exploratory visualisations using functional principal component analysis.
License: GPL (>= 3) + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Imports: 
    dplyr,
    ggplot2,
    parallel,
    patchwork,
    purrr,
    refund,
    SpatialExperiment,
    spatstat.explore,
    spatstat.geom,
    SummarizedExperiment,
    tidyr
biocViews: Software, Spatial, Transcriptomics
VignetteBuilder: knitr
Suggests: 
    imcdatasets,
    stringr,
    knitr,
    rmarkdown,
    BiocStyle,
    testthat (>= 3.0.0)
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.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

[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): spatialFDA_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/spatialFDA 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: 52f4d7732a102a2c736de7abfef862621fc73cf4

[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): spatialFDA_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/spatialFDA 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]

• No type checking of user inputs. The package consists of a set of simple function definitions. Please use S4 methods which automatically do type checking or alternatively use is(parameter, "className").

• Some functions' return values flood the user's console with text. Need a show method. See Class Design for instructions.

Implement a show() method to effectively convey information to your users without overwhelming them with detail.

• \description section is just copy and paste of \title. Please explain the purpose of each function in a couple of meaningful sentences.

• There are no unit tests. See Chapter 14: Unit Tests. This is a relatively recent requirement for new packages.

• Don't use for loops but vectorise the iterations or otherwise. For example,

for (i in 1:length(colnam)) {data[[colnam[i]]] <- designmat[, i]}

This could be concisely done using cbind(data, designMat).

Also, don't use 1:length(vector) in Bioconductor packages but seq_along. See Code Syntax and Efficiency.

• Inconsistent use of snake_case and camelCase style. camelCase is expected.

• Vignette is well-written and has interpretation sentence after output. Can you put SpatialFDA into the context of existing software (e.g. GraphCompass, spicyR) and perhaps draw a table showing which functionality is shared and unique?