miaDash

[RiboRings]

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[bioc-issue-bot]

Hi @RiboRings

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: miaDash
Version: 0.99.0
Authors@R: 
    c(person(given = "Giulio", family = "Benedetti", role = c("aut", "cre"),
 email = "[email protected]",
 comment = c(ORCID = "0000-0002-8732-7692")),
    person(given = "Akewak", family = "Jeba", role = c("ctb"),
   email = "[email protected]",
   comment = c(ORCID = "0009-0007-1347-7552")),
    person(given = "Leo", family = "Lahti", role = c("aut"),
   email = "[email protected]",
   comment = c(ORCID = "0000-0001-5537-637X")))
Title: Shiny app for interactive analysis and exploration of microbiome data
Description:
    miaDash provides a Graphical User Interface for the exploration of
    microbiome data. This way, no knowledge of programming is required to
    perform analyses. Datasets can be imported, manipulated, analysed and
    visualised with a user-friendly interface.
biocViews: Microbiome, Software, Visualization, GUI, ShinyApps, DataImport
License: Artistic-2.0
Encoding: UTF-8
Depends:
    R (>= 4.4.0),
    iSEE
Imports:
    biomformat,
    iSEEtree,
    methods,
    mia,
    rintrojs,
    scater,
    shiny,
    shinyjs,
    S4Vectors,
    SingleCellExperiment,
    SummarizedExperiment,
    TreeSummarizedExperiment,
    utils,
    vegan
Suggests:
    BiocStyle,
    knitr,
    RefManageR,
    remotes,
    rmarkdown,
    testthat (>= 3.0.0)
URL: https://github.com/microbiome/miaDash
BugReports: https://github.com/microbiome/miaDash/issues
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Config/testthat/edition: 3

[lshep]

Currently the vignette does not meet Bioconductor standards as there is no
executed R code. We might make an exception for a shiny app if testing coverage
is close to complete.I would recommend adding a secondary vignette in addition
to the one created that show the underling function calls and explains what they
do or increase or justify the missing coverage.

> covr::package_coverage()
miaDash Coverage: 60.61%
R/landing_page.R: 0.00%
R/miaDash.R: 0.00%
R/utils.R: 61.11%
R/observers.R: 87.50%
R/outputs.R: 100.00%

I'll move this forward but may require discussion during review.

[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, skipped".
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:
ERROR before build products produced.

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Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/miaDash 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: 87bfa23ba892d4f73384f35b275daebb4388fc9d

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

[RiboRings]

Hi @lshep! Thanks for the useful remarks.

We might make an exception for a shiny app if testing coverage is close to complete.

I improved the coverage. However, many parts of the package are strictly interactive, so I had to exclude them from coverage tracking. I am open for suggestions if there is any way to test interactive code recommended by Bioconductor.

I would recommend adding a secondary vignette in addition
to the one created that show the underling function calls and explains what they
do

Just to understand better. Would you suggest to write a vignette that explains how the app works under the hood? For example, describing how the server and ui components interact and how other utility functions support them?

Thank you in advance!

[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.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 744818a5442f7dd040bcaa786958453381e50d53

[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): miaDash_0.99.4.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/miaDash to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.