We are trying to use pak on the Posit Workbench to install R packages, but this occasionally fails with an error in install_extracted_binary():
Unfortunately, this is not really reproducible, but one assumption is that it fails if the affected package is currently loaded in another session. Restarting the R session prior to installation does not seem to fix the problem.
Posit Workbench runs in a Kubernetes cluster.
sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: cet
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] pak_0.9.0
loaded via a namespace (and not attached):
[1] compiler_4.4.0 tools_4.4.0
pak::pak_siterep()
* pak version:
- 0.9.0
* Version information:
- pak platform: x86_64-pc-linux-gnu (current: x86_64-pc-linux-gnu, compatible)
- pak repository: - (local install?)
* Optional packages installed:
- pillar
* Library path:
- /nfs-data/rhome/rgi/R/x86_64-pc-linux-gnu-library/4.4
- /opt/R/4.4.0/lib/R/library
* pak is installed at /nfs-data/rhome/rgi/R/x86_64-pc-linux-gnu-library/4.4/pak.
* Dependency versions:
- callr 3.7.6
- cli 3.6.5
- curl 5.2.3
- desc 1.4.3
- filelock 1.0.3
- jsonlite 2.0.0
- keyring 1.4.0
- lpSolve 5.6.23
- pkgbuild 1.4.8
- pkgcache 2.2.4
- pkgdepends 0.9.0
- pkgsearch 3.1.5
- processx 3.8.6
- ps 1.9.1
- R6 2.5.1
- yaml 2.3.10
- zip 2.3.3
* Dependencies can be loaded
@alexmic95
We are trying to use pak on the Posit Workbench to install R packages, but this occasionally fails with an error in
install_extracted_binary():Unfortunately, this is not really reproducible, but one assumption is that it fails if the affected package is currently loaded in another session. Restarting the R session prior to installation does not seem to fix the problem.
Posit Workbench runs in a Kubernetes cluster.
@alexmic95