Error in github_resolve_ref.github_release trying to install IRkernel

[breiter]

Installing IRKernel via remotes in rocker-vesrioned2/scripts/install_jupiter.sh fails with an error Cannot find repo repo IRkernel/IRkernel although it exists and cannot open URL 'https://api.github.com/repos/IRkernel/IRkernel/releases' which also exists.

https://github.com/rocker-org/rocker-versioned2/blob/ef593dcd7b334e02e79188a9e17dcf6149c178b9/scripts/install_jupyter.sh#L36

R --quiet -e 'remotes::install_github("IRkernel/IRkernel@*release")'

41.01 > remotes::install_github("IRkernel/IRkernel@*release")
41.22 Error in github_resolve_ref.github_release(meta$ref %||% ref, meta, host = host,  : 
41.22   Cannot find repo IRkernel/IRkernel.
41.22 cannot open URL 'https://api.github.com/repos/IRkernel/IRkernel/releases'
41.22 Calls: <Anonymous> ... github_resolve_ref -> github_resolve_ref.github_release
41.22 Execution halted
------
Dockerfile:97
--------------------
  95 |     
  96 |     # install jupyter
  97 | >>> RUN /rocker_scripts/install_jupyter.sh
  98 |     
  99 |     # set up renv in order to build cache in ~/.cache/R/renv/library by creating a

I think this is happening in install-github.R in github_resolve_ref.github_release but I'm stumped as to why.

  # Retrieve the ref for the latest release
  #' @export
  github_resolve_ref.github_release <- function(x, params, ..., host, auth_token = github_pat()) {
    # GET /repos/:user/:repo/releases
    path <- paste("repos", params$username, params$repo, "releases", sep = "/")
    response <- tryCatch(
      github_GET(path, host = host, pat = auth_token),
      error = function(e) e
    )
  
    if (methods::is(response, "error") || !is.null(response$message)) {
      stop("Cannot find repo ", params$username, "/", params$repo, ".", "\n",
        response$message)
    }
  
    if (length(response) == 0L)
      stop("No releases found for repo ", params$username, "/", params$repo, ".")
  
    params$ref <- response[[1L]]$tag_name
    params
  }

[gaborcsardi]

Works for me, try a newer version of remotes?

❯ remotes::install_github("IRkernel/IRkernel@*release")
Downloading GitHub repo IRkernel/IRkernel@1.3.2
'/opt/homebrew/bin/git' clone --depth 1 --no-hardlinks --recurse-submodules https://github.com/jupyter/jupyter_kernel_test.git /var/folders/ph/fpcmzfd16rgbbk8mxvy9m2_h0000gn/T//Rtmpt5mdcC/remotes12f45126204ea/IRkernel-IRkernel-1130602/tests/testthat/jkt
Cloning into '/var/folders/ph/fpcmzfd16rgbbk8mxvy9m2_h0000gn/T//Rtmpt5mdcC/remotes12f45126204ea/IRkernel-IRkernel-1130602/tests/testthat/jkt'...
remote: Enumerating objects: 22, done.
remote: Counting objects: 100% (22/22), done.
remote: Compressing objects: 100% (21/21), done.
remote: Total 22 (delta 1), reused 9 (delta 0), pack-reused 0
Receiving objects: 100% (22/22), 17.02 KiB | 2.13 MiB/s, done.
Resolving deltas: 100% (1/1), done.
'/opt/homebrew/bin/git' clone --depth 1 --no-hardlinks --recurse-submodules https://github.com/flying-sheep/ndjson-testrunner.git /var/folders/ph/fpcmzfd16rgbbk8mxvy9m2_h0000gn/T//Rtmpt5mdcC/remotes12f45126204ea/IRkernel-IRkernel-1130602/tests/testthat/njr
Cloning into '/var/folders/ph/fpcmzfd16rgbbk8mxvy9m2_h0000gn/T//Rtmpt5mdcC/remotes12f45126204ea/IRkernel-IRkernel-1130602/tests/testthat/njr'...
remote: Enumerating objects: 10, done.
remote: Counting objects: 100% (10/10), done.
remote: Compressing objects: 100% (8/8), done.
remote: Total 10 (delta 0), reused 6 (delta 0), pack-reused 0
Receiving objects: 100% (10/10), 15.97 KiB | 1.23 MiB/s, done.
Skipping 1 packages ahead of CRAN: cli
Installing 2 packages: pbdZMQ, IRdisplay
Installing packages into ‘/Users/gaborcsardi/Library/R/arm64/4.3/library’
(as ‘lib’ is unspecified)

The downloaded binary packages are in
	/var/folders/ph/fpcmzfd16rgbbk8mxvy9m2_h0000gn/T//Rtmpt5mdcC/downloaded_packages
── R CMD build ─────────────────────────────────────────────────────────────────
   checking for file ‘/private/var/folders/ph/fpcmzfd16rgbbk8mxvy9m2_h0000gn/T/R✔  checking for file ‘/private/var/folders/ph/fpcmzfd16rgbbk8mxvy9m2_h0000gn/T/Rtmpt5mdcC/build-12f45e4587e7/IRkernel/DESCRIPTION’
─  preparing ‘IRkernel’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
   Removed empty directory ‘IRkernel/example-notebooks’
─  building ‘IRkernel_1.3.2.tar.gz’

Installing package into ‘/Users/gaborcsardi/Library/R/arm64/4.3/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘IRkernel’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (IRkernel)

[breiter]

Working directly on the unaltered rocker image, so I need to find the problem somewhere else.

$ docker run --rm -it rocker/rstudio:4 /bin/bash
root@908254633e8c:/# bash /rocker_scripts/install_jupyter.sh 
...
* DONE (IRkernel)
> 
> 
> IRkernel::installspec(user = FALSE)
> 
> 
Check the avalable jupyter kernels...

Available kernels:
  ir         /usr/local/share/jupyter/kernels/ir
  python3    /usr/local/share/jupyter/kernels/python3

Install jupyter, done!

thanks!

[breiter]

I think this was caused by a regression in a security fix for curl in Ubuntu 22.04.

==========================================================================
Ubuntu Security Notice USN-6237-2
July 19, 2023

curl regression

A security issue affects these releases of Ubuntu and its derivatives:

• Ubuntu 22.04 LTS

Summary:

USN-6237-1 introduced a regression in curl.

Software Description:

• curl: HTTP, HTTPS, and FTP client and client libraries

Details:

USN-6237-1 fixed vulnerabilities in curl. The update caused a certificate
wildcard handling regression on Ubuntu 22.04 LTS. This update fixes the
problem.

We apologize for the inconvenience.