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

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 (R 4.1.0)
    backports                1.3.0      2021-10-27 [1] CRAN (R 4.1.0)
    beachmat                 2.10.0     2021-10-26 [1] Bioconductor
    beeswarm                 0.4.0      2021-06-01 [1] CRAN (R 4.1.0)
    benchmarkme              1.0.7      2021-03-21 [1] CRAN (R 4.1.0)
    benchmarkmeData          1.0.4      2020-04-23 [1] CRAN (R 4.1.0)
    Biobase                * 2.54.0     2021-10-26 [1] Bioconductor
    BiocCheck                1.30.0     2021-10-26 [1] Bioconductor
    BiocFileCache            2.2.0      2021-10-26 [1] Bioconductor
    BiocGenerics           * 0.40.0     2021-10-26 [1] Bioconductor
    BiocIO                   1.4.0      2021-10-26 [1] Bioconductor
    BiocManager              1.30.16    2021-06-15 [1] CRAN (R 4.1.0)
    BiocNeighbors            1.12.0     2021-10-26 [1] Bioconductor
    BiocParallel             1.28.0     2021-10-26 [1] Bioconductor
    BiocSingular             1.10.0     2021-10-26 [1] Bioconductor
    biocthis                 1.4.0      2021-10-26 [1] Bioconductor
    BiocVersion              3.14.0     2021-05-19 [1] Bioconductor
    biocViews                1.62.1     2021-11-02 [1] Bioconductor
    biomaRt                  2.50.0     2021-10-26 [1] Bioconductor
    Biostrings               2.62.0     2021-10-26 [1] Bioconductor
    bit                      4.0.4      2020-08-04 [1] CRAN (R 4.1.0)
    bit64                    4.0.5      2020-08-30 [1] CRAN (R 4.1.0)
    bitops                   1.0-7      2021-04-24 [1] CRAN (R 4.1.0)
    blob                     1.2.2      2021-07-23 [1] CRAN (R 4.1.0)
    bslib                    0.3.1      2021-10-06 [1] CRAN (R 4.1.0)
    cachem                   1.0.6      2021-08-19 [1] CRAN (R 4.1.0)
    callr                    3.7.0      2021-04-20 [1] CRAN (R 4.1.0)
    cli                      3.1.0      2021-10-27 [1] CRAN (R 4.1.0)
    codetools                0.2-18     2020-11-04 [1] CRAN (R 4.1.2)
    colorout                 1.2-2      2021-11-05 [1] Github (jalvesaq/colorout@79931fd)
    colorspace               2.0-2      2021-06-24 [1] CRAN (R 4.1.0)
    commonmark               1.7        2018-12-01 [1] CRAN (R 4.1.0)
    config                   0.3.1      2020-12-17 [1] CRAN (R 4.1.0)
    cowplot                  1.1.1      2020-12-30 [1] CRAN (R 4.1.0)
    crayon                   1.4.2      2021-10-29 [1] CRAN (R 4.1.0)
    curl                     4.3.2      2021-06-23 [1] CRAN (R 4.1.0)
    data.table               1.14.2     2021-09-27 [1] CRAN (R 4.1.0)
    DBI                      1.1.1      2021-01-15 [1] CRAN (R 4.1.0)
    dbplyr                   2.1.1      2021-04-06 [1] CRAN (R 4.1.0)
    DelayedArray             0.20.0     2021-10-26 [1] Bioconductor
    DelayedMatrixStats       1.16.0     2021-10-26 [1] Bioconductor
    desc                     1.4.0      2021-09-28 [1] CRAN (R 4.1.0)
    devtools               * 2.4.2      2021-06-07 [1] CRAN (R 4.1.0)
    digest                   0.6.28     2021-09-23 [1] CRAN (R 4.1.0)
    dockerfiler              0.1.4      2021-09-03 [1] CRAN (R 4.1.0)
    doParallel               1.0.16     2020-10-16 [1] CRAN (R 4.1.0)
    dotCall64                1.0-1      2021-02-11 [1] CRAN (R 4.1.0)
    dplyr                    1.0.7      2021-06-18 [1] CRAN (R 4.1.0)
    dqrng                    0.3.0      2021-05-01 [1] CRAN (R 4.1.0)
    DropletUtils             1.14.0     2021-10-26 [1] Bioconductor
    DT                       0.19       2021-09-02 [1] CRAN (R 4.1.0)
    edgeR                    3.36.0     2021-10-26 [1] Bioconductor
    ellipsis                 0.3.2      2021-04-29 [1] CRAN (R 4.1.0)
    evaluate                 0.14       2019-05-28 [1] CRAN (R 4.1.0)
    ExperimentHub            2.2.0      2021-10-26 [1] Bioconductor
    fansi                    0.5.0      2021-05-25 [1] CRAN (R 4.1.0)
    fastmap                  1.1.0      2021-01-25 [1] CRAN (R 4.1.0)
    fields                   13.3       2021-10-30 [1] CRAN (R 4.1.0)
    filelock                 1.0.2      2018-10-05 [1] CRAN (R 4.1.0)
    fontawesome              0.2.2      2021-07-02 [1] CRAN (R 4.1.0)
    foreach                  1.5.1      2020-10-15 [1] CRAN (R 4.1.0)
    formatR                  1.11       2021-06-01 [1] CRAN (R 4.1.0)
    fs                       1.5.0      2020-07-31 [1] CRAN (R 4.1.0)
    futile.logger          * 1.4.3      2016-07-10 [1] CRAN (R 4.1.0)
    futile.options           1.0.1      2018-04-20 [1] CRAN (R 4.1.0)
    generics                 0.1.1      2021-10-25 [1] CRAN (R 4.1.0)
    GenomeInfoDb           * 1.30.0     2021-10-26 [1] Bioconductor
    GenomeInfoDbData         1.2.7      2021-11-05 [1] Bioconductor
    GenomicAlignments        1.30.0     2021-10-26 [1] Bioconductor
    GenomicFeatures          1.46.1     2021-10-27 [1] Bioconductor
    GenomicRanges          * 1.46.0     2021-10-26 [1] Bioconductor
    getopt                   1.20.3     2019-03-22 [1] CRAN (R 4.1.0)
    ggbeeswarm               0.6.0      2017-08-07 [1] CRAN (R 4.1.0)
    ggplot2                  3.3.5      2021-06-25 [1] CRAN (R 4.1.0)
    ggrepel                  0.9.1      2021-01-15 [1] CRAN (R 4.1.0)
    glue                     1.4.2      2020-08-27 [1] CRAN (R 4.1.0)
    golem                    0.3.1      2021-04-17 [1] CRAN (R 4.1.0)
    graph                    1.72.0     2021-10-26 [1] Bioconductor
    gridExtra                2.3        2017-09-09 [1] CRAN (R 4.1.0)
    gtable                   0.3.0      2019-03-25 [1] CRAN (R 4.1.0)
    HDF5Array                1.22.0     2021-10-26 [1] Bioconductor
    here                     1.0.1      2020-12-13 [1] CRAN (R 4.1.0)
    hms                      1.1.1      2021-09-26 [1] CRAN (R 4.1.0)
    htmltools                0.5.2      2021-08-25 [1] CRAN (R 4.1.0)
    htmlwidgets              1.5.4      2021-09-08 [1] CRAN (R 4.1.0)
    httpuv                   1.6.3      2021-09-09 [1] CRAN (R 4.1.0)
    httr                     1.4.2      2020-07-20 [1] CRAN (R 4.1.0)
    interactiveDisplayBase   1.32.0     2021-10-26 [1] Bioconductor
    IRanges                * 2.28.0     2021-10-26 [1] Bioconductor
    irlba                    2.3.3      2019-02-05 [1] CRAN (R 4.1.0)
    iterators                1.0.13     2020-10-15 [1] CRAN (R 4.1.0)
    jquerylib                0.1.4      2021-04-26 [1] CRAN (R 4.1.0)
    jsonlite                 1.7.2      2020-12-09 [1] CRAN (R 4.1.0)
    KEGGREST                 1.34.0     2021-10-26 [1] Bioconductor
    knitr                    1.36       2021-09-29 [1] CRAN (R 4.1.0)
    lambda.r                 1.2.4      2019-09-18 [1] CRAN (R 4.1.0)
    later                    1.3.0      2021-08-18 [1] CRAN (R 4.1.0)
    lattice                  0.20-45    2021-09-22 [1] CRAN (R 4.1.2)
    lazyeval                 0.2.2      2019-03-15 [1] CRAN (R 4.1.0)
    lifecycle                1.0.1      2021-09-24 [1] CRAN (R 4.1.0)
    limma                    3.50.0     2021-10-26 [1] Bioconductor
    locfit                   1.5-9.4    2020-03-25 [1] CRAN (R 4.1.0)
    magick                   2.7.3      2021-08-18 [1] CRAN (R 4.1.0)
    magrittr                 2.0.1      2020-11-17 [1] CRAN (R 4.1.0)
    maps                     3.4.0      2021-09-25 [1] CRAN (R 4.1.0)
    markdown                 1.1        2019-08-07 [1] CRAN (R 4.1.0)
    Matrix                   1.3-4      2021-06-01 [1] CRAN (R 4.1.2)
    MatrixGenerics         * 1.6.0      2021-10-26 [1] Bioconductor
    matrixStats            * 0.61.0     2021-09-17 [1] CRAN (R 4.1.0)
    memoise                  2.0.0      2021-01-26 [1] CRAN (R 4.1.0)
    mime                     0.12       2021-09-28 [1] CRAN (R 4.1.0)
    munsell                  0.5.0      2018-06-12 [1] CRAN (R 4.1.0)
    optparse                 1.7.1      2021-10-08 [1] CRAN (R 4.1.0)
    OrganismDbi              1.36.0     2021-10-26 [1] Bioconductor
    pillar                   1.6.4      2021-10-18 [1] CRAN (R 4.1.0)
    pkgbuild                 1.2.0      2020-12-15 [1] CRAN (R 4.1.0)
    pkgconfig                2.0.3      2019-09-22 [1] CRAN (R 4.1.0)
    pkgload                  1.2.3      2021-10-13 [1] CRAN (R 4.1.0)
    plotly                   4.10.0     2021-10-09 [1] CRAN (R 4.1.0)
    png                      0.1-7      2013-12-03 [1] CRAN (R 4.1.0)
    Polychrome               1.3.1      2021-07-16 [1] CRAN (R 4.1.0)
    prettyunits              1.1.1      2020-01-24 [1] CRAN (R 4.1.0)
    processx                 3.5.2      2021-04-30 [1] CRAN (R 4.1.0)
    progress                 1.2.2      2019-05-16 [1] CRAN (R 4.1.0)
    promises                 1.2.0.1    2021-02-11 [1] CRAN (R 4.1.0)
    pryr                     0.1.5      2021-07-26 [1] CRAN (R 4.1.0)
    ps                       1.6.0      2021-02-28 [1] CRAN (R 4.1.0)
    purrr                    0.3.4      2020-04-17 [1] CRAN (R 4.1.0)
    R.cache                  0.15.0     2021-04-30 [1] CRAN (R 4.1.0)
    R.methodsS3              1.8.1      2020-08-26 [1] CRAN (R 4.1.0)
    R.oo                     1.24.0     2020-08-26 [1] CRAN (R 4.1.0)
    R.utils                  2.11.0     2021-09-26 [1] CRAN (R 4.1.0)
    R6                       2.5.1      2021-08-19 [1] CRAN (R 4.1.0)
    rappdirs                 0.3.3      2021-01-31 [1] CRAN (R 4.1.0)
    RBGL                     1.70.0     2021-10-26 [1] Bioconductor
    RColorBrewer             1.1-2      2014-12-07 [1] CRAN (R 4.1.0)
    Rcpp                     1.0.7      2021-07-07 [1] CRAN (R 4.1.0)
    RCurl                    1.98-1.5   2021-09-17 [1] CRAN (R 4.1.0)
    rematch2                 2.1.2      2020-05-01 [1] CRAN (R 4.1.0)
    remotes                  2.4.1      2021-09-29 [1] CRAN (R 4.1.0)
    restfulr                 0.0.13     2017-08-06 [1] CRAN (R 4.1.0)
    rhdf5                    2.38.0     2021-10-26 [1] Bioconductor
    rhdf5filters             1.6.0      2021-10-26 [1] Bioconductor
    Rhdf5lib                 1.16.0     2021-10-26 [1] Bioconductor
    rjson                    0.2.20     2018-06-08 [1] CRAN (R 4.1.0)
    rlang                    0.4.12     2021-10-18 [1] CRAN (R 4.1.0)
    rmarkdown                2.11       2021-09-14 [1] CRAN (R 4.1.0)
    roxygen2                 7.1.2      2021-09-08 [1] CRAN (R 4.1.0)
    rprojroot                2.0.2      2020-11-15 [1] CRAN (R 4.1.0)
    Rsamtools                2.10.0     2021-10-26 [1] Bioconductor
    RSQLite                  2.2.8      2021-08-21 [1] CRAN (R 4.1.0)
    rsthemes                 0.2.1.9000 2021-11-05 [1] Github (gadenbuie/rsthemes@19299e5)
    rstudioapi               0.13       2020-11-12 [1] CRAN (R 4.1.0)
    rsvd                     1.0.5      2021-04-16 [1] CRAN (R 4.1.0)
    rtracklayer              1.54.0     2021-10-26 [1] Bioconductor
    RUnit                    0.4.32     2018-05-18 [1] CRAN (R 4.1.0)
    S4Vectors              * 0.32.0     2021-10-26 [1] Bioconductor
    sass                     0.4.0.9000 2021-11-05 [1] Github (rstudio/sass@f95b436)
    ScaledMatrix             1.2.0      2021-10-26 [1] Bioconductor
    scales                   1.1.1      2020-05-11 [1] CRAN (R 4.1.0)
    scater                   1.22.0     2021-10-26 [1] Bioconductor
    scatterplot3d            0.3-41     2018-03-14 [1] CRAN (R 4.1.0)
    scuttle                  1.4.0      2021-10-26 [1] Bioconductor
    sessioninfo              1.2.1      2021-11-02 [1] CRAN (R 4.1.0)
    shiny                  * 1.7.1      2021-10-02 [1] CRAN (R 4.1.0)
    shinyWidgets             0.6.2      2021-09-17 [1] CRAN (R 4.1.0)
    SingleCellExperiment   * 1.16.0     2021-10-26 [1] Bioconductor
    spam                     2.7-0      2021-06-25 [1] CRAN (R 4.1.0)
    sparseMatrixStats        1.6.0      2021-10-26 [1] Bioconductor
    SpatialExperiment      * 1.4.0      2021-10-26 [1] Bioconductor
 VP spatialLIBD            * 1.7.1      2021-10-30 [?] Bioconductor (on disk 1.6.0)
    stringdist               0.9.8      2021-09-09 [1] CRAN (R 4.1.0)
    stringi                  1.7.5      2021-10-04 [1] CRAN (R 4.1.0)
    stringr                  1.4.0      2019-02-10 [1] CRAN (R 4.1.0)
    styler                   1.6.2      2021-09-23 [1] CRAN (R 4.1.0)
    SummarizedExperiment   * 1.24.0     2021-10-26 [1] Bioconductor
    testthat               * 3.1.0      2021-10-04 [1] CRAN (R 4.1.0)
    tibble                   3.1.5      2021-09-30 [1] CRAN (R 4.1.0)
    tidyr                    1.1.4      2021-09-27 [1] CRAN (R 4.1.0)
    tidyselect               1.1.1      2021-04-30 [1] CRAN (R 4.1.0)
    usethis                * 2.1.3      2021-10-27 [1] CRAN (R 4.1.0)
    utf8                     1.2.2      2021-07-24 [1] CRAN (R 4.1.0)
    vctrs                    0.3.8      2021-04-29 [1] CRAN (R 4.1.0)
    vipor                    0.4.5      2017-03-22 [1] CRAN (R 4.1.0)
    viridis                  0.6.2      2021-10-13 [1] CRAN (R 4.1.0)
    viridisLite              0.4.0      2021-04-13 [1] CRAN (R 4.1.0)
    withr                    2.4.2      2021-04-18 [1] CRAN (R 4.1.0)
    xfun                     0.28       2021-11-04 [1] CRAN (R 4.1.1)
    XML                      3.99-0.8   2021-09-17 [1] CRAN (R 4.1.0)
    xml2                     1.3.2      2020-04-23 [1] CRAN (R 4.1.0)
    xtable                   1.8-4      2019-04-21 [1] CRAN (R 4.1.0)
    XVector                  0.34.0     2021-10-26 [1] Bioconductor
    yaml                     2.2.1      2020-02-01 [1] CRAN (R 4.1.0)
    zlibbioc                 1.40.0     2021-10-26 [1] Bioconductor

 [1] /Library/Frameworks/R.framework/Versions/4.1devel/Resources/library

 V ── Loaded and on-disk version mismatch.
 P ── Loaded and on-disk path mismatch.