error about ArchR::installExtraPackages

[1221li]

I'm really sorry to bother you again. The following problem occurred when I was installing the extra package of ArchR

library(ArchR)
library(BSgenome.Btaurus.UCSC.bosTau9)
ArchR::installExtraPackages()
Error: 'installExtraPackages' is not an exported object from 'namespace:ArchR'
Could you please give me some suggestions？I am looking forward to your reply

[rcorces]

If ArchR actually installed correctly, this should never occur. I dont have any suggestions other than to completely restart your R session and reload ArchR.

ArchR/NAMESPACE

Line 127 in 422f0ff

export(installExtraPackages)

> ArchR::installExtraPackages
function (force = FALSE) 
{
    n <- 0
    f <- 0
    fp <- c()
    if (!requireNamespace("Seurat", quietly = TRUE) || force) {
        o <- tryCatch({
            message("Installing Seurat..")
            install.packages("Seurat")
            if (!requireNamespace("Seurat", quietly = TRUE)) {
                stop()
            }
            n <- n + 1
        }, error = function(e) {
            f <- f + 1
            fp <- c(fp, "Seurat")
            message("Error With Seurat Installation")
            message("Try install.packages('Seurat')")
        })
    }
    if (!requireNamespace("Cairo", quietly = TRUE) || force) {
        o <- tryCatch({
            message("Installing Cairo..")
            install.packages("Cairo")
            if (!requireNamespace("Cairo", quietly = TRUE)) {
                stop()
            }
            n <- n + 1
        }, error = function(e) {
            f <- f + 1
            fp <- c(fp, "Cairo")
            message("Error With Cairo Installation")
            message("Try install.packages('Cairo')")
        })
    }
    if (!requireNamespace("harmony", quietly = TRUE) || force) {
        o <- tryCatch({
            message("Installing harmony..")
            devtools::install_github("immunogenomics/harmony", 
                repos = BiocManager::repositories())
            if (!requireNamespace("harmony", quietly = TRUE)) {
                stop()
            }
            n <- n + 1
        }, error = function(e) {
            f <- f + 1
            fp <- c(fp, "harmony")
            message("Error With harmony Installation")
            message("Try devtools::install_github('immunogenomics/harmony', repos = BiocManager::repositories())")
        })
    }
    if (!requireNamespace("presto", quietly = TRUE) || force) {
        o <- tryCatch({
            message("Installing presto..")
            devtools::install_github("immunogenomics/presto", 
                repos = BiocManager::repositories())
            if (!requireNamespace("presto", quietly = TRUE)) {
                stop()
            }
            n <- n + 1
        }, error = function(e) {
            f <- f + 1
            fp <- c(fp, "presto")
            message("Error With presto Installation")
            message("Try devtools::install_github('immunogenomics/presto', repos = BiocManager::repositories())")
        })
    }
    if (!requireNamespace("shiny", quietly = TRUE) || force) {
        o <- tryCatch({
            message("Installing shiny..")
            install.packages("shiny")
            if (!requireNamespace("shiny", quietly = TRUE)) {
                stop()
            }
            n <- n + 1
        }, error = function(e) {
            f <- f + 1
            fp <- c(fp, "shiny")
            message("Error With shiny Installation")
            message("Try install.packages('shiny')")
        })
    }
    if (!requireNamespace("rhandsontable", quietly = TRUE) || 
        force) {
        o <- tryCatch({
            message("Installing rhandsontable..")
            install.packages("rhandsontable")
            if (!requireNamespace("rhandsontable", quietly = TRUE)) {
                stop()
            }
            n <- n + 1
        }, error = function(e) {
            f <- f + 1
            fp <- c(fp, "rhandsontable")
            message("Error With rhandsontable Installation")
            message("Try install.packages('rhandsontable')")
        })
    }
    if (!requireNamespace("shinythemes", quietly = TRUE) || force) {
        o <- tryCatch({
            message("Installing shinythemes..")
            install.packages("shinythemes")
            if (!requireNamespace("shinythemes", quietly = TRUE)) {
                stop()
            }
            n <- n + 1
        }, error = function(e) {
            f <- f + 1
            fp <- c(fp, "rhandsontable")
            message("Error With shinythemes Installation")
            message("Try install.packages('shinythemes')")
        })
    }
    message("Successfully installed ", n, " packages. ", f, " packages failed installation.")
    if (f > 0) {
        message("Failed packages : ", paste0(fp, collapse = ", "))
    }
    return(invisible(0))
}
<bytecode: 0x55e3d5455b80>
<environment: namespace:ArchR>

[lefterov]

on Ubuntu 22.04 LTS:
To install any extra package, in this case, "presto," the first time we see an error message while the Proj is active:

devtools::install_github("immunogenomics/presto")

and then:

saveArchProject(ArchRProj=...)

Restart the computer, then R

load presto

load ArchR, setwd

load proj...

With iMacs, and MacBookPros (Silicon or Intel), all extra packages are there at the beginning...