(inactive) vitessceR

[keller-mark]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/vitessce/vitessceR

Confirm the following by editing each check box to '[x]'

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[bioc-issue-bot]

Hi @keller-mark

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: vitessceR
Type: Package
Title: Create Interactive Single-cell Visualizations with the 'Vitessce' JavaScript Library
Version: 0.99.0
Authors@R: c(
    person(
      given = "Mark",
      family = "Keller",
      email = "mark_keller@g.harvard.edu",
      role = c("cre", "aut"),
      comment = c(ORCID = "0000-0003-3003-874X")
    )
  )
Description:
  R API and htmlwidget facilitating interactive visualization
  of spatial single-cell data with Vitessce. The R API contains
  classes and functions for loading single-cell data stored as
  SingleCellExperiment, SpatialExperiment, and Seurat objects.
  The htmlwidget is a wrapper around the Vitessce JavaScript
  library and can be used in the Viewer tab of RStudio or Shiny
  apps.
biocViews: SingleCell, Spatial, Visualization, ShinyApps
License: MIT + file LICENSE
BugReports: https://github.com/vitessce/vitessceR/issues
URL: https://github.com/vitessce/vitessceR
Encoding: UTF-8
Language: en-US
StagedInstall: no
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
VignetteBuilder: knitr
Imports:
    Matrix,
    DelayedArray,
    htmlwidgets,
    jsonlite,
    R6,
    plumber,
    future,
    httpuv,
    stringr,
    reticulate,
    varhandle,
    tools,
    stats,
    methods,
    S4Vectors,
    grDevices,
    basilisk,
    zellkonverter,
    SummarizedExperiment,
    SingleCellExperiment,
    SpatialExperiment
Suggests: 
    testthat,
    knitr,
    covr,
    bslib,
    pkgdown,
    rmarkdown,
    purrr,
    rjson,
    Seurat,
    SeuratDisk,
    Giotto

[vjcitn]

I am sorry about the delay in reviewing this package. The pkgdown orientation leads to a help.start() page that is difficult to navigate. We need to think a little more about the client-side rendering and will get back to you soon.

[keller-mark]

Thank you. I have been trying to debug the pkgdown issue as well. It seems to only happen locally since the github action can successfully build and deploy the site.

The error seems to occur inside the callr::r_safe function so the underlying error is not yet clear to me.

[keller-mark]

I am not sure, but the issue may be related to the merge_js function in the package which I added to get around the 5MB Bioconductor file size limit (the JS code for the htmlwidget is more than 5MB). Do you recommend a different solution for this problem?

[vjcitn]

Let me know if you need more assistance here; I was in touch with Ludwig Geistlinger whom I understand is collaborating on this.

[vjcitn]

Checking in again.

[keller-mark]

Hi @vjcitn, Due to other obligations I will likely not be able to prioritize the refactor of this package until mid-April, would you prefer that I close this and re-open at that point?

[vjcitn]

take your time @lshep can advise if u should close

[lshep]

yes lets mark as inactive for now. When you are ready with changes, simply comment back here that you would like the issue reopened. Cheers,

[bioc-issue-bot]

This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.

Thank you for your interest in Bioconductor.