shinyDSP

[kimsjune]

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• Repository: https://github.com/kimsjune/shinyDSP

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[bioc-issue-bot]

Hi @kimsjune

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: shinyDSP
Title: A Shiny App For Visualizing Nanostring GeoMx DSP Data
Version: 0.99.0
Authors@R: 
    c(person("Seung J.", "Kim" , ,"seung.kim@lhsc.on.ca", role = c("aut", "cre"),
 comment = c(ORCID = "0000-0001-5263-0758")),
    person("Angwara", "Nilanont", ,"angwara.nilanont@lhsc.on.ca", role = c("ctb"),
  comment = c(ORCID = "0000-0003-4468-9172")),
    person("Marco", "Mura",  ,"marco.mura@lhsc.on.ca", role = c("fnd"))
    )           
Description: What the package does (one paragraph).
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Imports: 
    AnnotationHub,
    BiocGenerics,
    bsicons,
    bslib,
    circlize,
    ComplexHeatmap,
    cowplot,
    dplyr,
    DT,
    edgeR,
    ExperimentHub,
    ggplot2,
    ggpubr,
    ggrepel,
    grDevices,
    grid,
    htmltools,
    limma,
    magrittr,
    pals,
    readr,
    S4Vectors,
    scales,
    scater,
    shiny,
    shinycssloaders,
    shinyjs,
    shinyvalidate,
    shinyWidgets,
    SingleCellExperiment,
    standR,
    stats,
    stringr,
    SummarizedExperiment,
    svglite,
    tibble,
    tidyr,
    utils,
    withr
biocViews: DifferentialExpression, GeneExpression, ShinyApps, Spatial, Transcriptomics
URL: https://kimsjune.github.com/shinyDSP, http://joonkim.ca/shinyDSP/
BugReports: https://kimsjune.github.com/ShinyDSP/issues
Suggests: 
    BiocStyle,
    knitr,
    rmarkdown,
    shinytest2,
    spelling,
    testthat (>= 3.0.0)
Language: en-US
Depends: 
    R (>= 4.4)
Config/testthat/edition: 3
VignetteBuilder: knitr

[lshep]

You have an incomplete DESCRIPTION. Please fill out description.

We prefer to have a clean upload to Bioconductor. Please remove pkgdown and dev directories from default branch until uploaded to Bioconductor.

Please have a more distinct name for your vignette to avoid load conflicts. We recommend the name of the package ie. shinyDSP.Rmd

I am currently unable to build the package

R CMD build shinyDSP 
* checking for file 'shinyDSP/DESCRIPTION' ... OK
* preparing 'shinyDSP':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘vignette.Rmd’ using rmarkdown
File ui_annotated.png not found in resource path
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

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 complete but when I try to test with covr I am getting an ERROR. I would recommend adding a secondary vignette in addition to the one created that show the underling function calls and explains what they do.

> package_coverage()
Error: Failure in `/tmp/RtmpXPS7uY/R_LIBS1054275bf9fa7/shinyDSP/shinyDSP-tests/testthat.Rout.fail`
.[rR]$", env = env, wrap = FALSE)
  8. │             └─base::lapply(...)
  9. │               └─testthat (local) FUN(X[[i]], ...)
 10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
 11. │                   ├─base::withCallingHandlers(...)
 12. │                   └─base::eval(exprs, env)
 13. │                     └─base::eval(exprs, env)
 14. ├─base::loadNamespace(x) at shinyDSP-tests/testthat/setup-shinytest2.R:2:1
 15. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 16. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
 17. │ │   └─base (local) doWithOneRestart(return(expr), restart)
 18. │ └─base::stop(cond)
 19. └─testthat (local) `<fn>`(`<pckgNtFE>`)
 20.   └─rlang::abort(...)