error loading fgsea package for "panda_gtex_tutorial_server.ipynb" netbook

[wilsonavac]

I tried running the original chunk #2 in the netbook, and then I ran the code to install fgsea alone to get the error message output below.

BiocManager::install("fgsea")

'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.r-project.org/

Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16)

Installing package(s) 'fgsea'

Warning message in install.packages(...):
“'lib = "/opt/conda/envs/rc4/lib/R/library"' is not writable”
Error in install.packages(...): unable to install packages
Traceback:

1. BiocManager::install("fgsea")
2. .install(pkgs, vout[["out_of_date"]], instPkgs = inst, repos = repos,
   . update = update, ask = ask, force = force, ...)
3. .install_repos(pkgs, old_pkgs, instPkgs = instPkgs, lib = lib,
   . repos = repos, force = force, ...)
4. .inet_install.packages(pkgs = doing, lib = lib, repos = repos,
   . ...)
5. withCallingHandlers({
   . tryCatch({
   . install.packages(...)
   . }, error = function(e) {
   . .inet_error(e)
   . invisible(NULL)
   . })
   . }, warning = function(w) {
   . msg <- conditionMessage(w)
   . if (grepl("not available", msg)) {
   . msg <- gsub("this version of R", paste0("Bioconductor version ",
   . "'", version(), "'"), msg)
   . w <- simpleWarning(msg, conditionCall(w))
   . }
   . .inet_warning(w)
   . })
6. tryCatch({
   . install.packages(...)
   . }, error = function(e) {
   . .inet_error(e)
   . invisible(NULL)
   . })
7. tryCatchList(expr, classes, parentenv, handlers)
8. tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. value[3L]
10. .inet_error(e)

[marouenbg]

@wilsonavac It should be fine now, please have a look and let me know!

[wilsonavac]

it works now on the RP2 kernel! thank you

[marouenbg]

Great! RP2 is set by default now so you won't need to change it every time.