problem in installing Sleuth to Jupyter Notebok
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Entering edit mode
6 months ago

Hello everyone, so I am trying to install sleuth package to Jupyter Notebook using R kernel but it always returns with error. the latest code I tried is:

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install()
library("devtools")
BiocManager::install("pachterlab/sleuth")

an it returns like this:

  There is a binary version available but the source version is later:
        binary source needs_compilation
stringi  1.4.6  1.5.3              TRUE

  Binaries will be installed
package 'stringi' successfully unpacked and MD5 sums checked
Error: Failed to install 'sleuth' from GitHub:
  (converted from warning) cannot remove prior installation of package 'stringi'
Traceback:

1. BiocManager::install("pachterlab/sleuth")
2. .install(pkgs, repos = repos, ...)
3. .install_github(todo, lib = lib, lib.loc = lib.loc, repos = repos, 
 .     ...)
4. remotes::install_github(repo, lib = lib, ...)
5. install_remotes(remotes, auth_token = auth_token, host = host, 
 .     dependencies = dependencies, upgrade = upgrade, force = force, 
 .     quiet = quiet, build = build, build_opts = build_opts, build_manual = build_manual, 
 .     build_vignettes = build_vignettes, repos = repos, type = type, 
 .     ...)
6. tryCatch(res[[i]] <- install_remote(remotes[[i]], ...), error = function(e) {
 .     stop(remote_install_error(remotes[[i]], e))
 . })
7. tryCatchList(expr, classes, parentenv, handlers)
8. tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. value[[3L]](cond)

Thanks for the help

RNA-Seq R • 196 views
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