jamesmbaazam
commented
2 months ago trying to re-install epichains to test some updates and got error with {pak}, solved with {devtools}, and generated output with gh::gh_rate_limits()
I also report the usethis::git_sitrep() and .Last.error output
Here I paste the outputs:
> pak::pak("epiverse-trace/epichains") #> Error: #> ! error in pak subprocess #> Caused by error: #> ! Could not solve package dependencies: #> * epiverse-trace/epichains: ! pkgdepends resolution error for epiverse-trace/epichains. #> Caused by error: #> ! Bad GitHub credentials, make sure that your GitHub token is valid. #> Caused by error in `stop(http_error(resp))`: #> ! Unauthorized (HTTP 401). #> Type .Last.error to see the more details. > devtools::install_github("epiverse-trace/epichains") #> Downloading GitHub repo epiverse-trace/epichains@HEAD #> These packages have more recent versions available. #> It is recommended to update all of them. #> Which would you like to update? #> #> 1: All #> 2: CRAN packages only #> 3: None #> 4: backports (1.4.1 -> 1.5.0) [CRAN] #> #> Enter one or more numbers, or an empty line to skip updates: 2 #> backports (1.4.1 -> 1.5.0) [CRAN] #> Installing 1 packages: backports #> Installing package into 'C:/Users/AndreeValleCampos/Documents/0projects/epicatador/renv/library/R-4.3/x86_64-w64-mingw32' #> (as 'lib' is unspecified) #> trying URL 'https://packagemanager.posit.co/cran/latest/bin/windows/contrib/4.3/backports_1.5.0.zip' #> Content type 'binary/octet-stream' length 122005 bytes (119 KB) #> downloaded 119 KB #> #> package 'backports' successfully unpacked and MD5 sums checked #> #> The downloaded binary packages are in #> C:\Users\AndreeValleCampos\AppData\Local\Temp\Rtmp84bXTU\downloaded_packages #> Registered S3 methods overwritten by 'callr': #> method from #> format.callr_status_error #> print.callr_status_error #> ── R CMD build ────────────────────────────────────────────────────────────────────── #> ✔ checking for file 'C:\Users\AndreeValleCampos\AppData\Local\Temp\Rtmp84bXTU\remotes28d82391169\epiverse-trace-epichains-4375575/DESCRIPTION' (414ms) #> ─ preparing 'epichains': (1.2s) #> ✔ checking DESCRIPTION meta-information ... #> ─ checking for LF line-endings in source and make files and shell scripts (380ms) #> ─ checking for empty or unneeded directories #> ─ building 'epichains_0.1.0.tar.gz' #> #> Installing package into 'C:/Users/AndreeValleCampos/Documents/0projects/epicatador/renv/library/R-4.3/x86_64-w64-mingw32' #> (as 'lib' is unspecified) #> - One or more packages recorded in the lockfile are not installed. #> - Use `renv::status()` for more details. #> * installing *source* package 'epichains' ... #> ** using staged installation #> ** R #> ** data #> *** moving datasets to lazyload DB #> ** inst #> ** byte-compile and prepare package for lazy loading #> ** help #> *** installing help indices #> *** copying figures #> ** building package indices #> ** installing vignettes #> ** testing if installed package can be loaded from temporary location #> ** testing if installed package can be loaded from final location #> ** testing if installed package keeps a record of temporary installation path #> * DONE (epichains) #> Warning messages: #> 1: In untar2(tarfile, files, list, exdir, restore_times) : #> skipping pax global extended headers #> 2: In untar2(tarfile, files, list, exdir, restore_times) : #> skipping pax global extended headers > gh::gh_rate_limits() #> type limit used remaining reset mins_left #> 1 core 5000 4 4996 2024-05-30 20:34:37 58.1 #> 2 search 30 0 30 2024-05-30 19:37:33 1.0 #> 3 graphql 5000 0 5000 2024-05-30 20:36:33 60.0 #> 4 integration_manifest 5000 0 5000 2024-05-30 20:36:33 60.0 #> 5 source_import 100 0 100 2024-05-30 19:37:33 1.0 #> 6 code_scanning_upload 1000 0 1000 2024-05-30 20:36:33 60.0 #> 7 actions_runner_registration 10000 0 10000 2024-05-30 20:36:33 60.0 #> 8 scim 15000 0 15000 2024-05-30 20:36:33 60.0 #> 9 dependency_snapshots 100 0 100 2024-05-30 19:37:33 1.0 #> 10 audit_log 1750 0 1750 2024-05-30 20:36:33 60.0 #> 11 code_search 10 0 10 2024-05-30 19:37:33 1.0 > usethis::git_sitrep() #> ── Git global (user) #> • Name: 'Andree Valle Campos' #> • Email: 'avallecam@gmail.com' #> • Global (user-level) gitignore file: 'C:/Users/AndreeValleCampos/.gitignore' #> • Vaccinated: TRUE #> • Default Git protocol: 'https' #> • Default initial branch name: 'master', 'main' #> #> ── GitHub user #> • Default GitHub host: 'https://github.com' #> • Personal access token for 'https://github.com': '<discovered>' #> • GitHub user: 'avallecam' #> • Token scopes: 'gist, repo, user, workflow' #> • Email(s): 'avallecam@gmail.com (primary)', '11100074@unmsm.edu.pe', 'andree.valle-campos@lshtm.ac.uk' #> #> ── Active usethis project: 'C:/Users/AndreeValleCampos/Documents/0projects/epicatador' ── #> #> ── Git local (project) #> • Name: 'Andree Valle Campos' #> • Email: 'avallecam@gmail.com' #> • Default branch: 'main' #> • Current local branch -> remote tracking branch: #> 'main' -> 'origin/main' #> #> ── GitHub project #> • Type = 'ours' #> • Host = 'https://github.com' #> • Config supports a pull request = TRUE #> • origin = 'avallecam/epicatador' (can push) #> • upstream = <not configured> #> • Desc = 'origin' is both the source and primary repo. #> #> Read more about the GitHub remote configurations that usethis supports at: #> 'https://happygitwithr.com/common-remote-setups.html' > .Last.error #> <callr_error/rlib_error_3_0/rlib_error/error> #> Error: #> ! error in pak subprocess #> Caused by error: #> ! Could not solve package dependencies: #> * epiverse-trace/epichains: ! pkgdepends resolution error for epiverse-trace/epichains. #> Caused by error: #> ! Bad GitHub credentials, make sure that your GitHub token is valid. #> Caused by error in `stop(http_error(resp))`: #> ! Unauthorized (HTTP 401). #> --- #> Backtrace: #> 1. pak::pak("epiverse-trace/epichains") #> 2. pak::pkg_install(pkg, ...) #> 3. pak:::remote(function(...) get("pkg_install_make_plan", asNamespace("pak"))(...), … #> 4. err$throw(res$error) #> --- #> Subprocess backtrace: #> 1. base::withCallingHandlers(cli_message = function(msg) { … #> 2. get("pkg_install_make_plan", asNamespace("pak"))(...) #> 3. prop$stop_for_solution_error() #> 4. private$plan$stop_for_solve_error() #> 5. pkgdepends:::pkgplan_stop_for_solve_error(self, private) #> 6. base::throw(new_error("Could not solve package dependencies:\n", msg, … #> 7. | base::signalCondition(cond) #> 8. global (function (e) …One day after this issue, pak worked fine.
> pak::pak("epiverse-trace/epichains") #> ✔ Loading metadata database ... done #> #> ℹ No downloads are needed #> ✔ 1 pkg + 2 deps: kept 3 [8.1s]
Thanks for reporting this, @avallecam. I think based on the messages from pak, it only "worked" because it actually didn't proceed to install the package since it was already installed.
For now, I will provide an order of installation starting with devtools and then pak.
trying to re-install epichains to test some updates and got error with {pak}, solved with {devtools}, and generated output with gh::gh_rate_limits()
I also report the usethis::git_sitrep() and .Last.error output
Here I paste the outputs:
One day after this issue, pak worked fine.