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precommit fails to set up environment after upgrade to R 4.2.1 #424

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danielinteractive opened this issue Jun 28, 2022 · 5 comments
Closed
3 tasks done

precommit fails to set up environment after upgrade to R 4.2.1 #424

danielinteractive opened this issue Jun 28, 2022 · 5 comments

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@danielinteractive
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Before filing a bug

  • I have installed the latest dev version of {precommit} with remotes::install_github('lorenzwalthert/precommit')
  • I have installed the latest hook revisions (update with precommit::autoupdate())
  • I have installed the latest release of the upstream Python framework pre-comit as described under the update instructions.

Describe the bug

With R 4.2.1 (just upgraded) I cannot get precommit to run anymore correctly, it fails when setting up the environment.
I also followed the tipps at #342 (comment) but without success.

To Reproduce
Steps to reproduce the behavior:

  1. Clone https://github.com/insightsengineering/tern.mmrm
  2. pre-commit install
  3. touch test
  4. git commit -m "test"
  5. precommit starts and gives following log with error:
[INFO] Installing environment for https://github.com/lorenzwalthert/precommit.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
An unexpected error has occurred: CalledProcessError: command: ('/usr/bin/Rscript', '--no-save', '--no-restore', '--no-site-file', '--no-environ', '-e', 'renv::install(commandArgs(trailingOnly = TRUE))', 'insightsengineering/tern', 'assertthat', 'checkmate', 'dfoptim', 'dplyr', 'emmeans', 'insightsengineering/formatters', 'generics', 'ggplot2', 'lme4', 'lmerTest', 'magrittr', 'optimx', 'parallel', 'rlang', 'rtables', 'stats', 'utils')
return code: 1
expected return code: 0
stdout:
    Retrieving 'https://api.github.com/repos/insightsengineering/tern/tarball/63ec152b1eacfc4ad8a519d249095191c6e0fc7c' ...
    	OK [downloaded 582.7 Kb in 0.3 secs]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/assertthat_0.2.1.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/broom_0.8.0.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/dplyr_1.0.9.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/generics_0.1.2.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/tidyselect_1.1.2.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/tidyr_1.2.0.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/ggplot2_3.3.6.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/gtable_0.3.0.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/isoband_0.2.5.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/scales_1.2.0.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/farver_2.1.0.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/labeling_0.4.2.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/munsell_0.5.0.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/colorspace_2.0-3.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/RColorBrewer_1.1-3.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/viridisLite_0.4.0.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/car_3.1-0.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/abind_1.4-5.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/pbkrtest_0.5.1.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/numDeriv_2016.8-1.1.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/lme4_1.1-29.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/minqa_1.2.4.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/nloptr_2.0.3.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/testthat_3.1.4.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/brio_1.1.3.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/praise_1.0.0.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/waldo_0.4.0.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/diffobj_0.3.5.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/RcppEigen_0.3.3.9.2.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/quantreg_5.93.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/MatrixModels_0.5-0.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/SparseM_1.81.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/maptools_1.1-4.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/sp_1.5-0.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/carData_3.0-5.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/checkmate_2.1.0.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/cowplot_1.1.1.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/emmeans_1.7.5.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/estimability_1.3.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/mvtnorm_1.1-3.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/xtable_1.8-4.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/forcats_0.5.1.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://api.github.com/repos/insightsengineering/formatters/tarball/a5d416318246f2b5305f83168fdd294102d008eb' ...
    	OK [downloaded 2.3 Mb in 0.7 secs]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/htmltools_0.5.2.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/base64enc_0.1-3.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/fastmap_1.1.0.tar.gz' ...
    	OK [file is up to date]
    Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/gridExtra_2.3.tar.gz' ...
    	OK [file is up to date]
    
stderr:
    Fehler in state$requirements[[record$Package]] : 
      falsche Argumente um ein environment zu indizieren
    Ruft auf: <Anonymous> ... handler -> renv_retrieve_impl -> renv_retrieve_incompatible
    Traceback (most recent calls last):
    11: renv::install(commandArgs(trailingOnly = TRUE))
    10: retrieve(names(remotes))
     9: handler(package, renv_retrieve_impl(package))
     8: renv_retrieve_impl(package)
     7: renv_retrieve_github(record)
     6: renv_retrieve_package(record, url, path)
     5: renv_retrieve_successful(record, path)
     4: retrieve(package)
     3: handler(package, renv_retrieve_impl(package))
     2: renv_retrieve_impl(package)
     1: renv_retrieve_incompatible(record)
    Ausführung angehalten
    
Check the log at /home/users/sabanesd/.cache/pre-commit/pre-commit.log

Expected behavior

It should work (it has worked before upgrading R from 4.1.3)

Additional context

> sessionInfo()

R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C               LC_TIME=de_CH.UTF-8       
 [4] LC_COLLATE=de_DE.UTF-8     LC_MONETARY=de_CH.UTF-8    LC_MESSAGES=de_DE.UTF-8   
 [7] LC_PAPER=de_CH.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=de_CH.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] mmrm_0.0.0.9001

loaded via a namespace (and not attached):
 [1] lattice_0.20-45     mvtnorm_1.1-3       grid_4.2.1          lifecycle_1.0.1     xtable_1.8-4       
 [6] nlme_3.1-157        backports_1.4.1     coda_0.19-4         rlang_1.0.3         estimability_1.3   
[11] cli_3.3.0           rstudioapi_0.13     checkmate_2.1.0     tools_4.2.1         emmeans_1.7.5      
[16] numDeriv_2016.8-1.1 parallel_4.2.1      compiler_4.2.1
@lorenzwalthert
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Thanks @danielinteractive. Can you provide the full log from /home/users/sabanesd/.cache/pre-commit/pre-commit.log, as indicated above?

@lorenzwalthert
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Do you think it's related to rstudio/renv#983?

@lorenzwalthert
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Owner

How did you install pre-commit?

@danielinteractive
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thanks @lorenzwalthert , I think I solved it - problem was that one package was on CRAN but I gave the github prefix, plus PAT was missing which limited rate on github.com. Will confirm later tonight.

@danielinteractive
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OK indeed this is fixed by stating dependency of another package this depends on explicitly. See corresponding PR insightsengineering/tern.mmrm#77

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