Strugglebussing while trying to upgrade rocker versions (from r-ver:4.2.3 to 4.4.1) and I think I've narrowed it down to either a pak or a littler issue:
FROM rocker/r-ver:4.4.1
RUN install2.r -e -r https://r-lib.github.io/p/pak/stable/source/linux-gnu/x86_64 pak
# littler's "r" doesn't work but somehow normal R does work ... ?
RUN r -e "pak::pkg_install('dplyr')"
returns this error on build:
[13:02:01] tan@mudkip🌊 ~/test_docker
❯ docker build .
[+] Building 3.7s (6/6) FINISHED docker:default
=> [internal] load build definition from Dockerfile 0.0s
=> => transferring dockerfile: 188B 0.0s
=> [internal] load metadata for docker.io/rocker/r-ver:4.4.1 0.0s
=> [internal] load .dockerignore 0.0s
=> => transferring context: 2B 0.0s
=> [1/3] FROM docker.io/rocker/r-ver:4.4.1 0.0s
=> CACHED [2/3] RUN install2.r -e -r https://r-lib.github.io/p 0.0s
=> ERROR [3/3] RUN r -e "pak::pkg_install('dplyr')" 3.6s
------
> [3/3] RUN r -e "pak::pkg_install('dplyr')":
3.581 Error:
3.581 ! error in pak subprocess
3.581 Caused by error in `download.file(url, tmp, quiet = TRUE)`:
3.581 ! could not find function "download.file"
3.581 ---
3.581 Backtrace:
3.581 1. pak::pkg_install("dplyr")
3.581 2. pak:::remote(function(...) get("pkg_install_make_plan", asNamespace("pak"))(...)…
3.581 3. err$throw(res$error)
3.581 ---
3.581 Subprocess backtrace:
3.581 1. base::withCallingHandlers(cli_message = function(msg) { …
3.581 2. get("pkg_install_make_plan", asNamespace("pak"))(...)
3.581 3. pkgdepends::new_pkg_installation_proposal(pkg, config = list(library = lib…
3.581 4. pkg_installation_proposal$new(refs, config = config, ...)
3.581 5. local initialize(...)
3.581 6. pkg_plan$new(refs, config = config, library = config$library, …
3.581 7. local initialize(...)
3.581 8. pkgdepends:::pkgplan_init(self, private, refs, config, library, remote_types, …
3.581 9. pkgcache::cranlike_metadata_cache$new(replica_path = private$config$get("m…
3.581 10. local initialize(...)
3.581 11. pkgcache:::cmc_init(self, private, primary_path, replica_path, platforms, …
3.581 12. pkgcache:::cmc__get_repos(repos, bioc, cran_mirror, r_version)
3.581 13. bioconductor$get_repos()
3.581 14. local get_bioc_version(getRversion(), forget)
3.581 15. local get_matching_bioc_version(r_version, forget = forget)
3.581 16. local get_version_map(forget = forget)
3.581 17. local get_yaml_config(forget)
3.581 18. base::stop(new)
3.581 19. global (function (e) …
------
Dockerfile:5
--------------------
3 | RUN install2.r -e -r https://r-lib.github.io/p/pak/stable/source/linux-gnu/x86_64 pak
4 |
5 | >>> RUN r -e "pak::pkg_install('dplyr')"
6 |
--------------------
ERROR: failed to solve: process "/bin/sh -c r -e \"pak::pkg_install('dplyr')\"" did not complete successfully: exit code: 1
Strugglebussing while trying to upgrade rocker versions (from r-ver:4.2.3 to 4.4.1) and I think I've narrowed it down to either a pak or a littler issue:
returns this error on build:
This error seems to stem from https://github.com/r-lib/pak/blob/64a34ee61afa3885057fbf5dde41863549a6b3e3/src/library/pkgcache/R/bioc.R#L295 where it fails to call
download.file
?