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.