shiny updates break the app in spatialLIBD

[lcolladotor]

The shiny app doesn't seem to work with R 4.1.x and bioc 3.14 (well, the current bioc 3.15 dev version installed on bioc 3.14). This looks like something changed in shiny.

Loading required package: shiny

Listening on http://127.0.0.1:6985
Warning: Navigation containers expect a collection of `bslib::nav()`/`shiny::tabPanel()`s and/or `bslib::nav_menu()`/`shiny::navbarMenu()`s. Consider using `header` or `footer` if you wish to place content above (or below) every panel's contents.
Warning: Error in : Navigation containers expect a collection of `bslib::nav()`/`shiny::tabPanel()`s and/or `bslib::nav_menu()`/`shiny::navbarMenu()`s. Consider using `header` or `footer` if you wish to place content above (or below) every panel's contents.
  84: stop
  83: FUN
  82: lapply
  81: buildTabset
  80: navbarPage_
  79: navs_bar
  74: bslib::page_navbar
  72: navbarPage
  69: ui [/Users/lcollado/Dropbox/Code/spatialLIBD/R/app_ui.R#25]

reprex

## Download and save a local cache of the data provided by 10x Genomics
bfc <- BiocFileCache::BiocFileCache()
lymph.url <-
    paste0(
        "https://cf.10xgenomics.com/samples/spatial-exp/",
        "1.1.0/V1_Human_Lymph_Node/",
        c(
            "V1_Human_Lymph_Node_filtered_feature_bc_matrix.tar.gz",
            "V1_Human_Lymph_Node_spatial.tar.gz",
            "V1_Human_Lymph_Node_analysis.tar.gz"
        )
    )
lymph.data <- sapply(lymph.url, BiocFileCache::bfcrpath, x = bfc)

## Extract the files to a temporary location
## (they'll be deleted once you close your R session)
sapply(lymph.data, utils::untar, exdir = tempdir())

## Download the Gencode v32 GTF file and cache it
gtf_cache <- BiocFileCache::bfcrpath(
    bfc,
    paste0(
        "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/",
        "release_32/gencode.v32.annotation.gtf.gz"
    )
)

## Show the GTF cache location
gtf_cache

## Import the data as a SpatialExperiment object
spe_wrapper <- read10xVisiumWrapper(
    samples = tempdir(),
    sample_id = "lymph",
    type = "sparse", data = "filtered",
    images = c("lowres", "highres"), load = TRUE,
    reference_gtf = gtf_cache
)

## Run our shiny app
if (interactive()) {
    vars <- colnames(colData(spe_wrapper))

    run_app(
        spe_wrapper,
        sce_layer = NULL,
        modeling_results = NULL,
        sig_genes = NULL,
        title = "spatialLIBD: human lymph node by 10x Genomics (made with wrapper)",
        spe_discrete_vars = c(vars[grep("10x_", vars)], "ManualAnnotation"),
        spe_continuous_vars = c("sum_umi", "sum_gene", "expr_chrM", "expr_chrM_ratio"),
        default_cluster = "10x_graphclust"
    )
}

R session info

```R options(width = 120); sessioninfo::session_info() ─ Session info 🍝 🇬🇹 🎐 ───────────────────────────────────────────────────────────────────────────────────────── hash: spaghetti, flag: Guatemala, wind chime setting value version R version 4.1.2 Patched (2021-11-04 r81141) os macOS Monterey 12.0.1 system x86_64, darwin17.0 ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz America/New_York date 2021-11-08 rstudio 2021.09.0+351 Ghost Orchid (desktop) pandoc 2.14.0.3 @ /Applications/RStudio.app/Contents/MacOS/pandoc/ (via rmarkdown) ─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────── ! package * version date (UTC) lib source AnnotationDbi 1.56.1 2021-10-29 [1] Bioconductor AnnotationForge 1.36.0 2021-10-26 [1] Bioconductor AnnotationHub 3.2.0 2021-10-26 [1] Bioconductor AnnotationHubData 1.24.0 2021-10-26 [1] Bioconductor assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0) attempt 0.3.1 2020-05-03 [1] CRAN 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P ── Loaded and on-disk path mismatch. ```