Hello 👋
You don't seem to have an issue template, so here is best effort (please do request more info as needed):
Output of pak::pak_sitrep() command:
> pak::pak_sitrep()
* pak version:
- 0.11.1
* Version information:
- pak platform: x86_64-pc-linux-gnu (current: x86_64-pc-linux-gnu, compatible)
- pak repository: - (local install?)
* Optional packages installed:
- pillar
...
* Dependency versions:
- callr 3.7.6
- cli 3.6.6
- curl 7.1.0
- desc 1.4.3
- filelock 1.0.3
- jsonlite 2.0.0
- keyring 1.4.1
- lpSolve 5.6.23
- pkgbuild 1.4.8
- pkgcache 2.2.5.9000
- pkgdepends 0.9.1.9000
- pkgsearch 3.1.5
- processx 3.8.7
- ps 1.9.2
- R6 2.5.1
- tsitter 0.0.0.9000
- tstoml 0.0.0.9000
- yaml 2.3.12
- zip 3.0.1.9000
* Dependencies can be loaded
*
R version: 4.6.1 (also happens in RStudio Server 2026.05.1 Build 225)
Operating system: Ubuntu 24.04.4 running inside an Apptainer container on a Rocky 9.6 host
Environment: HPC cluster running Slurm and Open OnDemand
Expected Behavior:
pak::pak("<github_user>/<github_repo>") pulls all required packages and source tarballs to install a package
Actual Behavior:
pak::pak("<github_user>/<github_repo>") fails on any GitHub zipballs stored at https://api.github.com/repos/<github_user>/<github_repo>/zipball/<user>
Steps to Reproduce the Problem:
Install pak using:
install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))
pak::pak_install_extra()Install a package from GitHub using pak:
pak::pak("<github_user>/<github_repo>")e.g.
pak::pak("cole-trapnell-lab/monocle3")Further details:
Really enjoying the benefits that pak can bring, but have hit a nasty snag.
Recently, when trying to use pak to install from a GitHub repo, e.g:
pak::pak("cole-trapnell-lab/monocle3")I'm hitting:
> pak::pak("cole-trapnell-lab/monocle3")
→ Will install 22 packages.
→ Will download 22 packages with unknown size.
+ assertthat 0.2.1 [dl]
+ BPCells 0.3.1 [bld][cmp][dl] (GitHub: 0162964)
+ distributional 0.8.1 [dl]
+ furrr 0.4.0 [dl]
+ ggdist 3.3.3 [dl]
+ ggforce 0.5.0 [dl]
+ hexbin 1.28.6 [dl]
+ leidenbase 0.1.37 [dl]
+ monocle3 1.4.27 [bld][cmp][dl] (GitHub: 536f103)
+ pbmcapply 1.5.1 [dl]
+ pheatmap 1.0.13 [dl]
+ pscl 1.5.9 [dl]
+ RhpcBLASctl 0.23-42 [dl]
+ rsample 1.3.2 [dl]
+ slam 0.1-56 [dl]
+ slider 0.3.3 [dl]
+ spData 2.3.5 [dl]
+ spdep 1.4-2 [dl]
+ speedglm 0.3-4 [bld][cmp][dl] (GitHub: ca34b4e)
+ tweenr 2.0.3 [dl]
+ viridis 0.6.5 [dl]
+ warp 0.2.3 [dl]
✔ All system requirements are already installed.
ℹ Getting 22 pkgs with unknown sizes
✖ Failed to download monocle3 1.4.27 (source)
✖ Failed to download BPCells 0.3.1 (source)
✖ Failed to download speedglm 0.3-4 (source)
✔ Got assertthat 0.2.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (56.98 kB)
✔ Got pbmcapply 1.5.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (41.85 kB)
✔ Got distributional 0.8.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (625.34 kB)
✔ Got RhpcBLASctl 0.23-42 (x86_64-pc-linux-gnu-ubuntu-24.04) (15.92 kB)
✔ Got leidenbase 0.1.37 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.35 MB)
✔ Got pheatmap 1.0.13 (x86_64-pc-linux-gnu-ubuntu-24.04) (79.96 kB)
✔ Got slam 0.1-56 (x86_64-pc-linux-gnu-ubuntu-24.04) (189.70 kB)
✔ Got ggforce 0.5.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.99 MB)
✔ Got slider 0.3.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (311.65 kB)
✔ Got rsample 1.3.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.72 MB)
✔ Got ggdist 3.3.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.83 MB)
✔ Got tweenr 2.0.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (474.01 kB)
✔ Cached copy of hexbin 1.28.6 (x86_64-pc-linux-gnu-ubuntu-24.04) is the latest build
✔ Got warp 0.2.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (67.73 kB)
✔ Got pscl 1.5.9 (x86_64-pc-linux-gnu-ubuntu-24.04) (3.41 MB)
✔ Got spData 2.3.5 (x86_64-pc-linux-gnu-ubuntu-24.04) (3.90 MB)
✔ Got viridis 0.6.5 (x86_64-pc-linux-gnu-ubuntu-24.04) (3.01 MB)
✔ Got spdep 1.4-2 (x86_64-pc-linux-gnu-ubuntu-24.04) (5.57 MB)
✔ Got furrr 0.4.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.02 MB)
✖ Failed to download 3 packages.
Error:
! error in pak subprocess
Caused by error:
! Failed to download monocle3 from `https://api.github.com/repos/cole-trapnell-lab/monocle3/zipball/536f1033d6de7c957f26a1f403f81efbd825e0db`.
Failed to download BPCells from `https://api.github.com/repos/bnprks/BPCells/zipball/016296413cd7a5725c8b35816df02365d7def853`.
Failed to download speedglm from `https://api.github.com/repos/cole-trapnell-lab/speedglm/zipball/ca34b4e53319424b60c442bb550adf3574b4bfec`.
Type .Last.error to see the more details.And here is the output of .Last.error:
> .Last.error
<callr_error/rlib_error_3_0/rlib_error/error>
Error:
! error in pak subprocess
Caused by error:
! Failed to download monocle3 from `https://api.github.com/repos/cole-trapnell-lab/monocle3/zipball/536f1033d6de7c957f26a1f403f81efbd825e0db`.
Failed to download BPCells from `https://api.github.com/repos/bnprks/BPCells/zipball/016296413cd7a5725c8b35816df02365d7def853`.
Failed to download speedglm from `https://api.github.com/repos/cole-trapnell-lab/speedglm/zipball/ca34b4e53319424b60c442bb550adf3574b4bfec`.
---
Backtrace:
1. pak::pak("cole-trapnell-lab/monocle3")
2. pak::pkg_install(pkg, ...)
3. pak:::remote(function(...) get("pkg_install_do_plan", asNamespace("pak"))(...), …
4. err$throw(res$error)
---
Subprocess backtrace:
1. base::withCallingHandlers(cli_message = function(msg) { …
2. get("pkg_install_do_plan", asNamespace("pak"))(...)
3. proposal$stop_for_download_error()
4. private$plan$stop_for_solution_download_error()
5. pkgdepends:::pkgplan_stop_for_solution_download_error(self, private)
6. pkgdepends:::stop(err)
7. | base::throw(add_class(args[[1]], c("rlib_error_3_0", "rlib_error"), …
8. | base::signalCondition(cond)
9. global (function (e) …If I run the same test using the same Apptainer container locally on a Fedora Kinoite 44 host, it's fine:
> pak::pak("cole-trapnell-lab/monocle3")
! Using bundled GitHub PAT. Please add your own PAT using `gitcreds::gitcreds_set()`.
→ Package library at /tmp/rlibrary.
→ Will install 106 packages.
→ Will download 106 packages with unknown size.
+ askpass 1.2.1 [dl]
+ assertthat 0.2.1 [dl]
+ bit 4.6.0 [dl]
+ bit64 4.8.4 [dl]
+ BPCells 0.3.1 [bld][cmp][dl] (GitHub: 0162964)
+ bslib 0.12.0 [dl]
+ cachem 1.1.0 [dl]
+ classInt 0.4-11 [dl]
+ clipr 0.8.1 [dl] + ✔ libx11-dev
+ commonmark 2.0.0 [dl]
+ crayon 1.5.3 [dl]
+ crosstalk 1.2.2 [dl]
+ curl 7.1.0 [dl] + ✔ libcurl4-openssl-dev, ✔ libssl-dev
+ data.table 1.18.4 [dl]
+ DBI 1.3.0 [dl]
+ deldir 2.0-4 [dl]
+ digest 0.6.39 [dl]
+ distributional 0.8.1 [dl]
+ dplyr 1.2.1 [dl]
+ e1071 1.7-17 [dl]
+ evaluate 1.0.5 [dl]
+ fastmap 1.2.0 [dl]
+ FNN 1.1.4.1 [dl]
+ fontawesome 0.5.3 [dl]
+ fs 2.1.0 [dl] + ✔ cmake, ✔ make, ✔ libuv1-dev
+ furrr 0.4.0 [dl]
+ future 1.75.0 [dl]
+ ggdist 3.3.3 [dl]
+ ggforce 0.5.0 [dl]
+ ggrepel 0.9.8 [dl]
+ globals 0.19.1 [dl]
+ gridExtra 2.3.1 [dl]
+ hexbin 1.28.6 [dl]
+ highr 0.12 [dl]
+ hms 1.1.4 [dl]
+ htmltools 0.5.9 [dl]
+ htmlwidgets 1.6.4 [dl]
+ httpuv 1.6.17 [dl] + ✔ make, ✔ zlib1g-dev
+ httr 1.4.8 [dl]
+ jquerylib 0.1.4 [dl]
+ knitr 1.51 [dl] + ✔ pandoc
+ later 1.4.8 [dl]
+ lazyeval 0.2.3 [dl]
+ leidenbase 0.1.37 [dl]
+ listenv 1.0.0 [dl]
+ lmtest 0.9-40 [dl]
+ memoise 2.0.1 [dl]
+ mime 0.13 [dl]
+ monocle3 1.4.27 [bld][cmp][dl] (GitHub: 536f103)
+ numDeriv 2016.8-1.1 [dl]
+ openssl 2.4.2 [dl] + ✔ libssl-dev
+ otel 0.2.0 [dl]
+ parallelly 1.48.0 [dl]
+ patchwork 1.3.2 [dl]
+ pbapply 1.7-4 [dl]
+ pbmcapply 1.5.1 [dl]
+ pheatmap 1.0.13 [dl]
+ plotly 4.12.1 [dl]
+ plyr 1.8.9 [dl]
+ polyclip 1.10-7 [dl]
+ promises 1.5.0 [dl]
+ proxy 0.4-29 [dl]
+ pscl 1.5.9 [dl]
+ purrr 1.2.2 [dl]
+ quadprog 1.5-8 [dl]
+ RANN 2.6.2 [dl]
+ rappdirs 0.3.4 [dl]
+ RcppAnnoy 0.0.23 [dl]
+ RcppHNSW 0.7.0 [dl]
+ readr 2.2.0 [dl]
+ reshape2 1.4.5 [dl]
+ RhpcBLASctl 0.23-42 [dl]
+ rmarkdown 2.31 [dl] + ✔ pandoc
+ rsample 1.3.2 [dl]
+ RSpectra 0.16-2 [dl]
+ Rtsne 0.17 [dl]
+ s2 1.1.11 [dl] + ✔ libabsl-dev, ✔ cmake, ✔ libssl-dev
+ sass 0.4.10 [dl] + ✔ make
+ scattermore 1.2 [dl]
+ sf 1.1-2 [dl] + ✔ libgdal-dev, ✔ gdal-bin, ✔ libgeos-dev, ✔ libproj-dev, ✔ libsqlite3-dev
+ shiny 1.14.0 [dl]
+ slam 0.1-56 [dl]
+ slider 0.3.3 [dl]
+ sourcetools 0.1.7-2 [dl]
+ sp 2.2-3 [dl]
+ spData 2.3.5 [dl]
+ spdep 1.4-2 [dl]
+ speedglm 0.3-4 [bld][cmp][dl] (GitHub: ca34b4e)
+ stringr 1.6.0 [dl]
+ sys 3.4.3 [dl]
+ tibble 3.3.1 [dl]
+ tidyr 1.3.2 [dl]
+ tidyselect 1.2.1 [dl]
+ tinytex 0.60 [dl]
+ tweenr 2.0.3 [dl]
+ tzdb 0.5.0 [dl]
+ units 1.0-1 [dl] + ✔ libudunits2-dev
+ uwot 0.2.4 [dl]
+ viridis 0.6.5 [dl]
+ vroom 1.7.1 [dl]
+ warp 0.2.3 [dl]
+ wk 0.9.5 [dl]
+ xfun 0.60 [dl]
+ xtable 1.8-8 [dl]
+ yaml 2.3.12 [dl]
+ zoo 1.9-0 [dl]
✔ All system requirements are already installed.
ℹ Getting 106 pkgs with unknown sizes
✔ Got speedglm 0.3-4 (source) (44.03 kB)
✔ Got askpass 1.2.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (23.67 kB)
✔ Got assertthat 0.2.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (56.98 kB)
✔ Got cachem 1.1.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (76.21 kB)
✔ Got evaluate 1.0.5 (x86_64-pc-linux-gnu-ubuntu-24.04) (105.40 kB)
✔ Got distributional 0.8.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (625.34 kB)
✔ Got commonmark 2.0.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (149.77 kB)
✔ Got tinytex 0.60 (x86_64-pc-linux-gnu-ubuntu-24.04) (151.29 kB)
✔ Got furrr 0.4.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.02 MB)
✔ Got classInt 0.4-11 (x86_64-pc-linux-gnu-ubuntu-24.04) (498.64 kB)
✔ Got pheatmap 1.0.13 (x86_64-pc-linux-gnu-ubuntu-24.04) (79.96 kB)
✔ Got bslib 0.12.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (6.23 MB)
✔ Got leidenbase 0.1.37 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.35 MB)
✔ Got monocle3 1.4.27 (source) (4.02 MB)
✔ Got quadprog 1.5-8 (x86_64-pc-linux-gnu-ubuntu-24.04) (32.74 kB)
✔ Got knitr 1.51 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.07 MB)
✔ Got fastmap 1.2.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (74.67 kB)
✔ Got viridis 0.6.5 (x86_64-pc-linux-gnu-ubuntu-24.04) (3.01 MB)
✔ Got xfun 0.60 (x86_64-pc-linux-gnu-ubuntu-24.04) (655.68 kB)
✔ Got fs 2.1.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (247.42 kB)
✔ Got rmarkdown 2.31 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.65 MB)
✔ Got BPCells 0.3.1 (source) (4.58 MB)
✔ Got polyclip 1.10-7 (x86_64-pc-linux-gnu-ubuntu-24.04) (126.43 kB)
✔ Got otel 0.2.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (283.12 kB)
✔ Got tzdb 0.5.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (675.39 kB)
✔ Got readr 2.2.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (851.25 kB)
✔ Got ggforce 0.5.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.99 MB)
✔ Got htmltools 0.5.9 (x86_64-pc-linux-gnu-ubuntu-24.04) (357.10 kB)
✔ Got RANN 2.6.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (45.74 kB)
✔ Got spdep 1.4-2 (x86_64-pc-linux-gnu-ubuntu-24.04) (5.57 MB)
✔ Got clipr 0.8.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (56.45 kB)
✔ Got RcppAnnoy 0.0.23 (x86_64-pc-linux-gnu-ubuntu-24.04) (311.26 kB)
✔ Got parallelly 1.48.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (640.22 kB)
✔ Got gridExtra 2.3.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (527.59 kB)
✔ Got digest 0.6.39 (x86_64-pc-linux-gnu-ubuntu-24.04) (236.15 kB)
✔ Got tibble 3.3.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (653.87 kB)
✔ Got crosstalk 1.2.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (416.48 kB)
✔ Got slam 0.1-56 (x86_64-pc-linux-gnu-ubuntu-24.04) (189.70 kB)
✔ Got zoo 1.9-0 (x86_64-pc-linux-gnu-ubuntu-24.04) (990.59 kB)
✔ Got sys 3.4.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (42.27 kB)
✔ Got tweenr 2.0.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (474.01 kB)
✔ Got e1071 1.7-17 (x86_64-pc-linux-gnu-ubuntu-24.04) (589.66 kB)
✔ Got warp 0.2.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (67.73 kB)
✔ Got yaml 2.3.12 (x86_64-pc-linux-gnu-ubuntu-24.04) (123.84 kB)
✔ Got lazyeval 0.2.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (190.56 kB)
✔ Got pbapply 1.7-4 (x86_64-pc-linux-gnu-ubuntu-24.04) (102.21 kB)
✔ Got bit 4.6.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (629.40 kB)
✔ Got hexbin 1.28.6 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.60 MB)
✔ Got httpuv 1.6.17 (x86_64-pc-linux-gnu-ubuntu-24.04) (680.86 kB)
✔ Got fontawesome 0.5.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.40 MB)
✔ Got data.table 1.18.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.98 MB)
✔ Got memoise 2.0.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (53.16 kB)
✔ Got ggrepel 0.9.8 (x86_64-pc-linux-gnu-ubuntu-24.04) (372.26 kB)
✔ Got later 1.4.8 (x86_64-pc-linux-gnu-ubuntu-24.04) (161.95 kB)
✔ Got curl 7.1.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (776.79 kB)
✔ Got htmlwidgets 1.6.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (818.17 kB)
✔ Got sp 2.2-3 (x86_64-pc-linux-gnu-ubuntu-24.04) (5.32 MB)
✔ Got pscl 1.5.9 (x86_64-pc-linux-gnu-ubuntu-24.04) (3.41 MB)
✔ Got openssl 2.4.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.28 MB)
✔ Got plyr 1.8.9 (x86_64-pc-linux-gnu-ubuntu-24.04) (793.73 kB)
✔ Got tidyr 1.3.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.19 MB)
✔ Got bit64 4.8.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (561.49 kB)
✔ Got reshape2 1.4.5 (x86_64-pc-linux-gnu-ubuntu-24.04) (127.97 kB)
✔ Got sourcetools 0.1.7-2 (x86_64-pc-linux-gnu-ubuntu-24.04) (50.83 kB)
✔ Got DBI 1.3.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (944.07 kB)
✔ Got Rtsne 0.17 (x86_64-pc-linux-gnu-ubuntu-24.04) (121.41 kB)
✔ Got jquerylib 0.1.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (529.71 kB)
✔ Got FNN 1.1.4.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (130.38 kB)
✔ Got plotly 4.12.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (4.02 MB)
✔ Got mime 0.13 (x86_64-pc-linux-gnu-ubuntu-24.04) (46.70 kB)
✔ Got purrr 1.2.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (558.15 kB)
✔ Got RhpcBLASctl 0.23-42 (x86_64-pc-linux-gnu-ubuntu-24.04) (15.92 kB)
✔ Got globals 0.19.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (170.15 kB)
✔ Got sf 1.1-2 (x86_64-pc-linux-gnu-ubuntu-24.04) (4.18 MB)
✔ Got slider 0.3.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (311.65 kB)
✔ Got tidyselect 1.2.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (228.26 kB)
✔ Got uwot 0.2.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.03 MB)
✔ Got crayon 1.5.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (167.83 kB)
✔ Got highr 0.12 (x86_64-pc-linux-gnu-ubuntu-24.04) (39.94 kB)
✔ Got patchwork 1.3.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (3.35 MB)
✔ Got units 1.0-1 (x86_64-pc-linux-gnu-ubuntu-24.04) (494.83 kB)
✔ Got httr 1.4.8 (x86_64-pc-linux-gnu-ubuntu-24.04) (484.62 kB)
✔ Got stringr 1.6.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (342.59 kB)
✔ Got hms 1.1.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (106.29 kB)
✔ Got sass 0.4.10 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.46 MB)
✔ Got RcppHNSW 0.7.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (240.79 kB)
✔ Got s2 1.1.11 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.21 MB)
✔ Got pbmcapply 1.5.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (41.85 kB)
✔ Got dplyr 1.2.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.53 MB)
✔ Got rsample 1.3.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.72 MB)
✔ Got promises 1.5.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.67 MB)
✔ Got ggdist 3.3.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.83 MB)
✔ Got spData 2.3.5 (x86_64-pc-linux-gnu-ubuntu-24.04) (3.90 MB)
✔ Got vroom 1.7.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.03 MB)
✔ Got listenv 1.0.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (130.90 kB)
✔ Got deldir 2.0-4 (x86_64-pc-linux-gnu-ubuntu-24.04) (281.56 kB)
✔ Got scattermore 1.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (342.45 kB)
✔ Got proxy 0.4-29 (x86_64-pc-linux-gnu-ubuntu-24.04) (174.32 kB)
✔ Got numDeriv 2016.8-1.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (116.26 kB)
✔ Got lmtest 0.9-40 (x86_64-pc-linux-gnu-ubuntu-24.04) (405.92 kB)
✔ Got shiny 1.14.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (4.57 MB)
✔ Got rappdirs 0.3.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (48.73 kB)
✔ Got wk 0.9.5 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.74 MB)
✔ Got xtable 1.8-8 (x86_64-pc-linux-gnu-ubuntu-24.04) (758.52 kB)
✔ Got RSpectra 0.16-2 (x86_64-pc-linux-gnu-ubuntu-24.04) (535.07 kB)
✔ Got future 1.75.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.03 MB)
✔ Downloaded 106 packages (109.50 MB) in 7.6s
ℹ Packaging speedglm 0.3-4
✔ Packaged speedglm 0.3-4 (499ms)
ℹ Building speedglm 0.3-4
✔ Built speedglm 0.3-4 (1.7s)
✔ Installed askpass 1.2.1 (1s)
✔ Installed assertthat 0.2.1 (1s)
✔ Installed bslib 0.12.0 (72ms)
✔ Installed cachem 1.1.0 (1s)
✔ Installed classInt 0.4-11 (1s)
✔ Installed commonmark 2.0.0 (1s)
✔ Installed crosstalk 1.2.2 (1s)
✔ Installed curl 7.1.0 (1s)
✔ Installed data.table 1.18.4 (1s)
✔ Installed DBI 1.3.0 (1s)
✔ Installed deldir 2.0-4 (1s)
✔ Installed digest 0.6.39 (1s)
✔ Installed distributional 0.8.1 (1s)
✔ Installed dplyr 1.2.1 (1s)
✔ Installed e1071 1.7-17 (1s)
✔ Installed evaluate 1.0.5 (1s)
✔ Installed fastmap 1.2.0 (10ms)
✔ Installed FNN 1.1.4.1 (1s)
✔ Installed fontawesome 0.5.3 (1s)
✔ Installed fs 2.1.0 (1s)
✔ Installed furrr 0.4.0 (1s)
✔ Installed future 1.75.0 (1s)
✔ Installed ggdist 3.3.3 (1s)
✔ Installed ggforce 0.5.0 (1s)
✔ Installed ggrepel 0.9.8 (1s)
✔ Installed globals 0.19.1 (1s)
✔ Installed gridExtra 2.3.1 (1s)
✔ Installed highr 0.12 (1s)
✔ Installed htmltools 0.5.9 (1s)
✔ Installed htmlwidgets 1.6.4 (18ms)
✔ Installed httpuv 1.6.17 (1s)
✔ Installed httr 1.4.8 (1s)
✔ Installed jquerylib 0.1.4 (1s)
✔ Installed knitr 1.51 (1s)
✔ Installed later 1.4.8 (1s)
✔ Installed lazyeval 0.2.3 (1s)
✔ Installed leidenbase 0.1.37 (1s)
✔ Installed listenv 1.0.0 (1s)
✔ Installed lmtest 0.9-40 (1s)
✔ Installed memoise 2.0.1 (1s)
✔ Installed mime 0.13 (1s)
✔ Installed numDeriv 2016.8-1.1 (1s)
✔ Installed openssl 2.4.2 (1s)
✔ Installed otel 0.2.0 (1s)
✔ Installed parallelly 1.48.0 (1s)
✔ Installed pbapply 1.7-4 (1s)
✔ Installed pbmcapply 1.5.1 (1s)
✔ Installed pheatmap 1.0.13 (1s)
✔ Installed plotly 4.12.1 (47ms)
✔ Installed plyr 1.8.9 (1s)
✔ Installed polyclip 1.10-7 (1s)
✔ Installed promises 1.5.0 (27ms)
✔ Installed proxy 0.4-29 (1s)
✔ Installed pscl 1.5.9 (1s)
✔ Installed purrr 1.2.2 (1s)
✔ Installed quadprog 1.5-8 (1s)
✔ Installed RANN 2.6.2 (10ms)
✔ Installed rappdirs 0.3.4 (1s)
✔ Installed RcppAnnoy 0.0.23 (1s)
✔ Installed RcppHNSW 0.7.0 (1s)
✔ Installed reshape2 1.4.5 (1s)
✔ Installed RhpcBLASctl 0.23-42 (1s)
✔ Installed rmarkdown 2.31 (1s)
✔ Installed rsample 1.3.2 (1s)
✔ Installed RSpectra 0.16-2 (1s)
✔ Installed Rtsne 0.17 (1s)
✔ Installed s2 1.1.11 (1s)
✔ Installed sass 0.4.10 (1s)
✔ Installed sf 1.1-2 (48ms)
✔ Installed shiny 1.14.0 (1.1s)
✔ Installed slam 0.1-56 (1s)
✔ Installed slider 0.3.3 (1s)
✔ Installed sourcetools 0.1.7-2 (1s)
✔ Installed sp 2.2-3 (1.1s)
✔ Installed spData 2.3.5 (1s)
✔ Installed spdep 1.4-2 (55ms)
✔ Installed stringr 1.6.0 (1s)
✔ Installed sys 3.4.3 (1s)
✔ Installed tibble 3.3.1 (1s)
✔ Installed tidyr 1.3.2 (1s)
✔ Installed tidyselect 1.2.1 (1s)
✔ Installed tinytex 0.60 (1s)
✔ Installed tweenr 2.0.3 (1s)
✔ Installed units 1.0-1 (1s)
✔ Installed uwot 0.2.4 (1s)
✔ Installed viridis 0.6.5 (1s)
✔ Installed warp 0.2.3 (1s)
✔ Installed wk 0.9.5 (1s)
✔ Installed xfun 0.60 (1s)
✔ Installed xtable 1.8-8 (1s)
✔ Installed yaml 2.3.12 (1s)
✔ Installed zoo 1.9-0 (1s)
✔ Installed speedglm 0.3-4 (github::cole-trapnell-lab/speedglm@ca34b4e) (1s)
✔ Installed bit 4.6.0 (1s)
✔ Installed bit64 4.8.4 (1s)
✔ Installed clipr 0.8.1 (1s)
✔ Installed crayon 1.5.3 (1s)
✔ Installed hexbin 1.28.6 (1s)
✔ Installed hms 1.1.4 (1s)
✔ Installed patchwork 1.3.2 (1s)
✔ Installed readr 2.2.0 (1s)
✔ Installed scattermore 1.2 (1s)
✔ Installed tzdb 0.5.0 (1s)
✔ Installed vroom 1.7.1 (1s)
ℹ Packaging BPCells 0.3.1
✔ Packaged BPCells 0.3.1 (1.2s)
ℹ Building BPCells 0.3.1
✔ Built BPCells 0.3.1 (4m 45.4s)
✔ Installed BPCells 0.3.1 (github::bnprks/BPCells@0162964) (796ms)
ℹ Packaging monocle3 1.4.27
✔ Packaged monocle3 1.4.27 (829ms)
ℹ Building monocle3 1.4.27
✔ Built monocle3 1.4.27 (11.2s)
✔ Installed monocle3 1.4.27 (github::cole-trapnell-lab/monocle3@536f103) (1s)
✔ 1 pkg + 194 deps: kept 83, added 106, dld 106 (NA B) [6m 52.7s]I'm wondering if this is an "us" issue and if our network access from cluster compute nodes is somehow blocking things, or if we are hitting rate-limiting.
Things I've tried already:
- Using a personal GitHub PAT instead of the one
pak bundles (WRT warning "! Using bundled GitHub PAT. Please add your own PAT using gitcreds::gitcreds_set().") - no change
options(pak.download_method = "base") - didn't workSys.setenv(CURL_SSL_BACKEND = "openssl") and options(pak.client_http_version = "1.1") - also didn't work
As I say, could be an "us" issue, but any thoughts anyone have most welcome. Since v.2.5.0 of devtools deprecated its install wrappers in favour of pak, this is quite an issue for us (many of our cluster users are heavy devtools users for installing from GitHub).
Thanking you in advance!
Hello 👋
You don't seem to have an issue template, so here is best effort (please do request more info as needed):
Output of
pak::pak_sitrep()command:R version: 4.6.1 (also happens in RStudio Server 2026.05.1 Build 225)
Operating system: Ubuntu 24.04.4 running inside an Apptainer container on a Rocky 9.6 host
Environment: HPC cluster running Slurm and Open OnDemand
Expected Behavior:
pak::pak("<github_user>/<github_repo>")pulls all required packages and source tarballs to install a packageActual Behavior:
pak::pak("<github_user>/<github_repo>")fails on any GitHub zipballs stored athttps://api.github.com/repos/<github_user>/<github_repo>/zipball/<user>Steps to Reproduce the Problem:
Install
pakusing:Install a package from GitHub using
pak:e.g.
Further details:
Really enjoying the benefits that
pakcan bring, but have hit a nasty snag.Recently, when trying to use
pakto install from a GitHub repo, e.g:pak::pak("cole-trapnell-lab/monocle3")I'm hitting:
And here is the output of
.Last.error:If I run the same test using the same Apptainer container locally on a Fedora Kinoite 44 host, it's fine:
I'm wondering if this is an "us" issue and if our network access from cluster compute nodes is somehow blocking things, or if we are hitting rate-limiting.
Things I've tried already:
pakbundles (WRT warning "! Using bundled GitHub PAT. Please add your own PAT using gitcreds::gitcreds_set().") - no changeoptions(pak.download_method = "base")- didn't workSys.setenv(CURL_SSL_BACKEND = "openssl")andoptions(pak.client_http_version = "1.1")- also didn't workAs I say, could be an "us" issue, but any thoughts anyone have most welcome. Since v.2.5.0 of
devtoolsdeprecated its install wrappers in favour ofpak, this is quite an issue for us (many of our cluster users are heavydevtoolsusers for installing from GitHub).Thanking you in advance!