hbc/bcbioSingleCell

installation error

joys8998 opened this issue · 14 comments

joys8998 commented

Hi there. Sorry i continue to have an error when I try to install this package:
package ‘bcbioSingleCell’ is not available (for R version 4.0.2)

bcbioSingleCell should be available on R >= 4.0

The problem is that I get the same error even when I use R version 4.0.0. How can I solve this problem?
Thank you

mjsteinbaugh commented

Hi @joys8998, what command did you run to install the package?

Refer to the bcbioSingleCell website for current installation recommendations.

Let me know if this works:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
install.packages(
    pkgs = "bcbioSingleCell",
    repos = c(
        "r.acidgenomics.com",
        BiocManager::repositories()
    )
)

We're now recommending users install the latest stable version from our r.acidgenomcs.com repo, until the package is released on Bioconductor.

The error message package ‘bcbioSingleCell’ is not available (for R version 4.0.2) is popping up because the package isn't available on CRAN (or Bioconductor).

joys8998 commented
mjsteinbaugh commented

OK thanks, we need to more troubleshooting.

What returns in R when you try this?

install.packages("https://r.acidgenomics.com/src/contrib/bcbioSingleCell_0.4.14.tar.gz", repos = NULL)

Also, can you post the return for utils::sessionInfo() and sessioninfo::session_info()?

joys8998 commented
mjsteinbaugh commented

OK thanks this is a Windows issue. I'll do some debugging and get back to you.

See how the error is saying SingleCellExperiment isn't available? That shouldn't happen when BiocManager::repositories() is passed to to the repos argument in the install.packages() call.

Can you run BiocManager::repositories() and post the return?

mjsteinbaugh commented

For example, on my machine BiocManager::repositories() looks like:

                                            BioCsoft 
           "https://bioconductor.org/packages/3.11/bioc" 
                                                 BioCann 
"https://bioconductor.org/packages/3.11/data/annotation" 
                                                 BioCexp 
"https://bioconductor.org/packages/3.11/data/experiment" 
                                           BioCworkflows 
      "https://bioconductor.org/packages/3.11/workflows" 
                                                    CRAN 
            "https://packagemanager.rstudio.com/all/342"
joys8998 commented
mjsteinbaugh commented

That looks good. Can you try these commands and see if they work?

BiocManager::install("SingleCellExperiment")
install.packages("SingleCellExperiment", repos = BiocManager::repositories())
mjsteinbaugh commented

Does adding type = "source" to the install.packages() call resolve the issue?

joys8998 commented
mjsteinbaugh commented

OK well clearly I need to troubleshoot this more carefully on a Windows machine. I'm going to create a test environment on Azure and figure this out. It might take me a couple of days, but I'll post an update soon.

joys8998 commented
mjsteinbaugh commented

OK I think I figured it out! This works for me on Windows:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
install.packages(
    pkgs = "bcbioSingleCell",
    repos = c(
        "https://r.acidgenomics.com",
        BiocManager::repositories()
    )
)

Note the addition of "https://" in the repos argument. That seems to do the trick.

joys8998 commented