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`install_extracted_binary()` fails on Posit Workbench

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
r
Domain
tooling

Research direction

Start at the install_extracted_binary() failure described in the issue and review the supplied sessionInfo() and pak::pak_siterep() output for the Posit Workbench environment. Reproduce the intermittent installation failure in the Kubernetes-based setup, especially when a package is loaded in another session; done means the cause is isolated and the failure has a reliable verification case.

Written by the indexing model from the issue text.

Description

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():

Image

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

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