precommit deps-in-desc hook failing after upgrade to R 4.3.0 in renv locked package

[yogat3ch]

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
The precommit deps-in-desc hook appears to be failing after upgrading to R 4.3.0. I'm using the precommit package with a renv locked repository and attempting to make a commit on a file without using any new dependencies.

I'm getting the following error:

deps-in-desc.............................................................Failed
- hook id: deps-in-desc
- exit code: 1

ℹ Using R 4.3.0 (lockfile was generated with R 4.2.1)
ℹ Using R 4.3.0 (lockfile was generated with R 4.2.1)
Error in loadNamespace(x) : there is no package called ‘docopt’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted

The renv.lock file was snapshotted using R 4.3.0, so those warnings are puzzling.
The package I'm working in does not use docopt. docopt is installed in both the renv locked libpath and the global R library.
It almost seems like precommit is working from an entirely different R installation and directory than the one I'm trying to commit in?

Expected behavior
No warnings from the deps-in-desc hook since there are no new dependencies.

Additional context

• My operating system is: MacOSX Ventura 13.3.1 (a)
• My project uses {renv}.
• the output of packageVersion('renv'): 0.17.2

My .pre-commit-config.yaml

# All available hooks: https://pre-commit.com/hooks.html
# R specific hooks: https://github.com/lorenzwalthert/precommit
repos:
-   repo: https://github.com/lorenzwalthert/precommit
    rev: v0.3.2.9007
    default_stages: [push]
    hooks:
    # -   id: style-files
    #     args: [--style_pkg=styler, --style_fun=tidyverse_style]
    -   id: use-tidy-description
    -   id: spell-check
        exclude: >
          (?x)^(
          .*\.[rR]|
          .*\.feather|
          .*\.jpeg|
          .*\.pdf|
          .*\.png|
          .*\.py|
          .*\.RData|
          .*\.rds|
          .*\.Rds|
          .*\.Rproj|
          .*\.sh|
          .*\.scss|
          .*\.css|
          .*\.csv|
          .*\.svg|
          (.*/|)\.gitignore|
          (.*/|)\.gitlab-ci\.yml|
          (.*/|)\.lintr|
          (.*/|)\.pre-commit-.*|
          (.*/|)\.Rbuildignore|
          (.*/|)\.Renviron|
          (.*/|)\.Rprofile|
          (.*/|)\.travis\.yml|
          (.*/|)appveyor\.yml|
          (.*/|)NAMESPACE|
          (.*/|)DESCRIPTION|
          (.*/|)renv/settings\.dcf|
          (.*/|)renv\.lock|
          (.*/|)WORDLIST|
          man/.*|
          \.github/workflows/.*|
          data/.*|
          )$
    -   id: readme-rmd-rendered
    -   id: parsable-R
    -   id: no-browser-statement
        exclude: >
          (?x)^(
          (.*/|)utils_server.R|
          )
    -   id: no-debug-statement
    -   id: deps-in-desc
        exclude: >
          (?x)^(
          (.*/|)deprecated/*\.R|
          (.*/|)\.reprex/*\.R*|
          ^scripts/.*\.R*|
          (.*/|)app_data_sync\.R|
          (.*/|)activate\.R*
          )
        args: [--allow_private_imports]
-   repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.4.0
    hooks:
    -   id: check-added-large-files
        args: ['--maxkb=25000']
    -   id: file-contents-sorter
        files: '^\.(Rbuildignore|gitignore)$'
    -   id: end-of-file-fixer
        exclude: >
         (?x)^(
          (.*/|)*\.Rd|
          (.*/|)*\.css*|
          )
-   repo: https://github.com/pre-commit-ci/pre-commit-ci-config
    rev: v1.5.1
    hooks:
    # Only reuiqred when https://pre-commit.ci is used for config validation
    -   id: check-pre-commit-ci-config
-   repo: local
    hooks:
    -   id: forbid-to-commit
        name: Don't commit common R artifacts
        entry: Cannot commit .Rhistory, .RData, .Renviron
        language: fail
        files: '\.(Rhistory|RData|Renviron)$'
        # `exclude: <regex>` to allow committing specific files

ci:
    autoupdate_schedule: monthly

devtools::session_info()

─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.0 (2023-04-21)
 os       macOS Ventura 13.3.1
 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/Denver
 date     2023-05-13
 rstudio  2023.03.1+446 Cherry Blossom (desktop)
 pandoc   NA

─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 !  package     * version date (UTC) lib source
 P  cachem        1.0.7   2023-02-24 [?] CRAN (R 4.3.0)
    callr         3.7.3   2022-11-02 [1] CRAN (R 4.3.0)
 P  cli           3.6.1   2023-03-23 [?] CRAN (R 4.3.0)
 P  crayon        1.5.2   2022-09-29 [?] CRAN (R 4.3.0)
    devtools      2.4.5   2022-10-11 [1] CRAN (R 4.3.0)
    digest        0.6.31  2022-12-11 [1] CRAN (R 4.3.0)
    ellipsis      0.3.2   2021-04-29 [1] CRAN (R 4.3.0)
 P  fansi         1.0.4   2023-01-22 [?] CRAN (R 4.3.0)
    fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
 VP fs            1.6.2   2023-02-06 [?] CRAN (R 4.3.0) (on disk 1.6.1)
 P  glue          1.6.2   2022-02-24 [?] CRAN (R 4.3.0)
    htmltools     0.5.5   2023-03-23 [1] CRAN (R 4.3.0)
    htmlwidgets   1.6.2   2023-03-17 [1] CRAN (R 4.3.0)
    httpuv        1.6.9   2023-02-14 [1] CRAN (R 4.3.0)
 P  later         1.3.0   2021-08-18 [?] CRAN (R 4.3.0)
 P  lifecycle     1.0.3   2022-10-07 [?] CRAN (R 4.3.0)
 P  magrittr      2.0.3   2022-03-30 [?] CRAN (R 4.3.0)
    memoise       2.0.1   2021-11-26 [1] CRAN (R 4.3.0)
    mime          0.12    2021-09-28 [1] CRAN (R 4.3.0)
    miniUI        0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
 P  pillar        1.9.0   2023-03-22 [?] CRAN (R 4.3.0)
    pkgbuild      1.4.0   2022-11-27 [1] CRAN (R 4.3.0)
 P  pkgconfig     2.0.3   2019-09-22 [?] CRAN (R 4.3.0)
    pkgload       1.3.2   2022-11-16 [1] CRAN (R 4.3.0)
 P  plyr          1.8.8   2022-11-11 [?] CRAN (R 4.3.0)
    prettyunits   1.1.1   2020-01-24 [1] CRAN (R 4.3.0)
 P  processx      3.8.0   2022-10-26 [?] CRAN (R 4.3.0)
 P  profvis       0.3.7   2020-11-02 [?] CRAN (R 4.3.0)
    promises      1.2.0.1 2021-02-11 [1] CRAN (R 4.3.0)
 P  ps            1.7.4   2023-04-02 [?] CRAN (R 4.3.0)
 P  purrr         1.0.1   2023-01-10 [?] CRAN (R 4.3.0)
 P  R6            2.5.1   2021-08-19 [?] CRAN (R 4.3.0)
 P  Rcpp          1.0.10  2023-01-22 [?] CRAN (R 4.3.0)
 P  remotes       2.4.2   2021-11-30 [?] CRAN (R 4.3.0)
    renv          0.17.2  2023-03-17 [1] CRAN (R 4.3.0)
 VP rlang         1.1.1   2023-03-14 [?] CRAN (R 4.3.0) (on disk 1.1.0)
 P  rstudioapi    0.14    2022-08-22 [?] CRAN (R 4.3.0)
    sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
    shiny         1.7.4   2022-12-15 [1] CRAN (R 4.3.0)
    stringi       1.7.12  2023-01-11 [1] CRAN (R 4.3.0)
    stringr       1.5.0   2022-12-02 [1] CRAN (R 4.3.0)
 P  tibble        3.2.1   2023-03-20 [?] CRAN (R 4.3.0)
    urlchecker    1.0.1   2021-11-30 [1] CRAN (R 4.3.0)
 P  usethis       2.1.6   2022-05-25 [?] CRAN (R 4.3.0)
 P  utf8          1.2.3   2023-01-31 [?] CRAN (R 4.3.0)
 VP vctrs         0.6.2   2023-03-22 [?] CRAN (R 4.3.0) (on disk 0.6.1)
    xtable        1.8-4   2019-04-21 [1] CRAN (R 4.3.0)

 [1] /Users/stephenholsenbeck/Library/Caches/org.R-project.R/R/renv/library/dmdu-4393acb2/R-4.3/aarch64-apple-darwin20
 [2] /Users/stephenholsenbeck/Library/Caches/org.R-project.R/R/renv/sandbox/R-4.3/aarch64-apple-darwin20/84ba8b13

 V ── Loaded and on-disk version mismatch.
 P ── Loaded and on-disk path mismatch.

──────────────────────────────────────────────────────────────────────────────────────────────────────────────────

`renv::diagnostics()`

Diagnostics Report [renv 0.17.2]
================================

# Session Info =======================
R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Denver
tzcode source: internal

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

loaded via a namespace (and not attached):
 [1] utf8_1.2.3      magrittr_2.0.3  glue_1.6.2      tibble_3.2.1   
 [5] pkgconfig_2.0.3 lifecycle_1.0.3 cli_3.6.1       fansi_1.0.4    
 [9] vctrs_0.6.2     renv_0.17.2     compiler_4.3.0  plyr_1.8.8     
[13] purrr_1.0.1     rstudioapi_0.14 tools_4.3.0     pillar_1.9.0   
[17] Rcpp_1.0.10     rlang_1.1.1     fs_1.6.2       

# Project ============================
Project path: "~/Documents/R/Contributor_Repos/VirgaLabs/dmdu"

# Status =============================
* The project is already synchronized with the lockfile.

# Packages ===========================
       Library Source   Lockfile Source Path Dependency
1     1.22.1-2   CRAN   1.22.1-2   CRAN  [1]   indirect
2     1.81.0-1   CRAN   1.81.0-1   CRAN  [1]   indirect
3        0.4.0 GitHub      0.4.0 GitHub  [1]     direct
4        1.1.3   CRAN      1.1.3   CRAN  [1]   indirect
5        0.4.0 GitHub      0.4.0 GitHub  [1]     direct
6         0.27   CRAN       0.27   CRAN  [1]     direct
7        1.2-5   CRAN      1.2-5   CRAN  [1]   indirect
8      2.23-20   CRAN       <NA>   <NA>  [2]       <NA>
9     7.3-58.3   CRAN   7.3-58.3   CRAN  [1]   indirect
10       1.5-4   CRAN      1.5-4   CRAN  [2]   indirect
11       1.0.0 GitHub      1.0.0 GitHub  [1]     direct
12        <NA>   <NA>       <NA>   <NA> <NA>     direct
13      0.16.0   CRAN       <NA>   <NA>  [1]       <NA>
14       2.5.1   CRAN      2.5.1   CRAN  [1]     direct
15       1.1-3   CRAN      1.1-3   CRAN  [1]     direct
16     0.10.25   CRAN    0.10.25   CRAN  [1]   indirect
17      1.0.10   CRAN     1.0.10   CRAN  [1]   indirect
18      1.23.9 GitHub     1.23.9 GitHub  [1]     direct
19       0.3.9   CRAN      0.3.9   CRAN  [1]   indirect
20         1.1   CRAN        1.1   CRAN  [1]   indirect
21       0.2.1   CRAN      0.2.1   CRAN  [1]   indirect
22       0.3.1   CRAN      0.3.1   CRAN  [1]   indirect
23       1.4.1   CRAN      1.4.1   CRAN  [1]   indirect
24       0.1-3   CRAN      0.1-3   CRAN  [1]   indirect
25      0.13.0   CRAN     0.13.0   CRAN  [1]   indirect
26       4.0.5   CRAN      4.0.5   CRAN  [1]   indirect
27       4.0.5   CRAN      4.0.5   CRAN  [1]   indirect
28       1.2.4   CRAN      1.2.4   CRAN  [1]   indirect
29    1.3-28.1   CRAN       <NA>   <NA>  [2]       <NA>
30       1.0-8   CRAN      1.0-8   CRAN  [1]   indirect
31       1.1.3   CRAN      1.1.3   CRAN  [1]   indirect
32       1.0.4   CRAN      1.0.4   CRAN  [1]   indirect
33       2.2.1 GitHub      2.2.1 GitHub  [1]     direct
34       0.4.2   CRAN      0.4.2   CRAN  [1]   indirect
35       1.0.7   CRAN      1.0.7   CRAN  [1]   indirect
36       3.7.3   CRAN      3.7.3   CRAN  [1]   indirect
37       1.1.0   CRAN      1.1.0   CRAN  [1]   indirect
38       2.1.0   CRAN      2.1.0   CRAN  [1]   indirect
39  0.1.1.9001 GitHub 0.1.1.9001 GitHub  [1]     direct
40  1.0.5.9000 GitHub 1.0.5.9000 GitHub  [1]     direct
41      7.3-21   CRAN       <NA>   <NA>  [2]       <NA>
42       3.6.1   CRAN      3.6.1   CRAN  [1]     direct
43       0.8.0   CRAN      0.8.0   CRAN  [1]   indirect
44       2.1.4   CRAN       <NA>   <NA>  [2]       <NA>
45      0.2-19   CRAN     0.2-19   CRAN  [2]   indirect
46       2.1-0   CRAN      2.1-0   CRAN  [1]     direct
47       1.9.0   CRAN      1.9.0   CRAN  [1]   indirect
48        <NA>   <NA>       <NA>   <NA>  [2]   indirect
49       0.3.1   CRAN      0.3.1   CRAN  [1]     direct
50       0.8.3   CRAN      0.8.3   CRAN  [1]   indirect
51        0.92   CRAN       0.92   CRAN  [1]   indirect
52       1.4.0   CRAN      1.4.0   CRAN  [1]   indirect
53        <NA>   <NA>       <NA>   <NA> <NA>     direct
54       0.4.3   CRAN      0.4.3   CRAN  [1]   indirect
55       1.5.2   CRAN      1.5.2   CRAN  [1]   indirect
56       1.3.2   CRAN      1.3.2   CRAN  [1]   indirect
57       1.2.1 GitHub      1.2.1 GitHub  [1]     direct
58       1.0.0 GitHub      1.0.0 GitHub  [1]     direct
59       5.0.0   CRAN      5.0.0   CRAN  [1]     direct
60      1.14.8   CRAN     1.14.8   CRAN  [1]   indirect
61       1.0.0   CRAN      1.0.0   CRAN  [1]   indirect
62        <NA>   <NA>       <NA>   <NA>  [2]   indirect
63       0.7.1   CRAN      0.7.1   CRAN  [1]   indirect
64       2.3.2   CRAN      2.3.2   CRAN  [1]   indirect
65       1.4.2   CRAN      1.4.2   CRAN  [1]   indirect
66       2.4.5   CRAN      2.4.5   CRAN  [1]     direct
67       0.3.5   CRAN      0.3.5   CRAN  [1]   indirect
68      0.6.31   CRAN     0.6.31   CRAN  [1]     direct
69        <NA>   <NA>       <NA>   <NA> <NA>     direct
70       0.7.1   CRAN       <NA>   <NA>  [1]       <NA>
71       0.4.2   CRAN      0.4.2   CRAN  [1]   indirect
72       1.1.1   CRAN      1.1.1   CRAN  [1]     direct
73       0.4.4   CRAN      0.4.4   CRAN  [1]     direct
74       0.5.1 GitHub      0.5.1 GitHub  [1]     direct
75       1.4.5   CRAN      1.4.5   CRAN  [1]     direct
76       0.8.3   CRAN      0.8.3   CRAN  [1]   indirect
77       0.3.2   CRAN      0.3.2   CRAN  [1]   indirect
78       1.2-6   CRAN      1.2-6   CRAN  [1]     direct
79        0.20   CRAN       0.20   CRAN  [1]   indirect
80       1.0.4   CRAN      1.0.4   CRAN  [1]   indirect
81       2.1.1   CRAN      2.1.1   CRAN  [1]   indirect
82       1.1.1   CRAN      1.1.1   CRAN  [1]   indirect
83       0.5.0   CRAN      0.5.0   CRAN  [1]   indirect
84      0.8-84   CRAN       <NA>   <NA>  [2]       <NA>
85       0.2.0   CRAN      0.2.0   CRAN  [1]   indirect
86       1.6.1   CRAN      1.6.1   CRAN  [1]     direct
87       1.3.0   CRAN      1.3.0   CRAN  [1]     direct
88       0.1.3   CRAN      0.1.3   CRAN  [1]   indirect
89       1.9.2   CRAN      1.9.2   CRAN  [1]   indirect
90       3.4.2   CRAN      3.4.2   CRAN  [1]     direct
91       1.4.0   CRAN      1.4.0   CRAN  [1]   indirect
92       0.1.2   CRAN      0.1.2   CRAN  [1]   indirect
93      0.16.2   CRAN     0.16.2   CRAN  [1]   indirect
94       1.6.2   CRAN      1.6.2   CRAN  [1]     direct
95        <NA>   <NA>       <NA>   <NA> <NA>     direct
96       0.4.0   CRAN      0.4.0   CRAN  [1]     direct
97       2.1.0   CRAN      2.1.0   CRAN  [1]     direct
98       1.1.0   CRAN      1.1.0   CRAN  [1]     direct
99        <NA>   <NA>       <NA>   <NA>  [2]     direct
100       <NA>   <NA>       <NA>   <NA>  [2]   indirect
101       <NA>   <NA>       <NA>   <NA>  [2]   indirect
102      0.3.3   CRAN      0.3.3   CRAN  [1]   indirect
103      1.3.0   CRAN      1.3.0   CRAN  [1]   indirect
104      1.0.1   CRAN      1.0.1   CRAN  [1]   indirect
105       <NA>   <NA>       <NA>   <NA> <NA>     direct
106       0.10   CRAN       0.10   CRAN  [1]   indirect
107      1.1.3   CRAN      1.1.3   CRAN  [1]   indirect
108      0.5.5   CRAN      0.5.5   CRAN  [1]     direct
109      1.6.2   CRAN      1.6.2   CRAN  [1]     direct
110      1.6.9   CRAN      1.6.9   CRAN  [1]   indirect
111      1.4.5   CRAN      1.4.5   CRAN  [1]   indirect
112      0.2.2   CRAN      0.2.2   CRAN  [1]   indirect
113      1.0.1   CRAN      1.0.1   CRAN  [1]   indirect
114      0.3.1   CRAN      0.3.1   CRAN  [1]   indirect
115     0.19.1   CRAN     0.19.1   CRAN  [1]   indirect
116      1.0-5   CRAN      1.0-5   CRAN  [1]   indirect
117      0.2.7   CRAN      0.2.7   CRAN  [1]   indirect
118      0.1.4   CRAN      0.1.4   CRAN  [1]   indirect
119      1.8.4   CRAN      1.8.4   CRAN  [1]     direct
120       1.42   CRAN       1.42   CRAN  [1]   indirect
121      0.4.2   CRAN      0.4.2   CRAN  [1]   indirect
122      1.3.0   CRAN      1.3.0   CRAN  [1]   indirect
123    0.20-45   CRAN    0.20-45   CRAN  [1]   indirect
124      0.2.2   CRAN      0.2.2   CRAN  [1]   indirect
125     0.11.3   CRAN     0.11.3   CRAN  [1]   indirect
126      1.0-9   CRAN      1.0-9   CRAN  [1]   indirect
127      1.0.3   CRAN      1.0.3   CRAN  [1]   indirect
128      1.9.2   CRAN      1.9.2   CRAN  [1]     direct
129      2.0.3   CRAN      2.0.3   CRAN  [1]   indirect
130        1.5   CRAN        1.5   CRAN  [1]   indirect
131      2.0.1   CRAN      2.0.1   CRAN  [1]   indirect
132       <NA>   <NA>       <NA>   <NA>  [2]   indirect
133     1.8-42   CRAN     1.8-42   CRAN  [2]   indirect
134       0.12   CRAN       0.12   CRAN  [1]   indirect
135    0.1.1.1   CRAN    0.1.1.1   CRAN  [1]   indirect
136      0.8.6   CRAN      0.8.6   CRAN  [1]   indirect
137      0.5.0   CRAN      0.5.0   CRAN  [1]   indirect
138      1.1-3   CRAN      1.1-3   CRAN  [1]   indirect
139    3.1-162   CRAN    3.1-162   CRAN  [2]   indirect
140     7.3-18   CRAN       <NA>   <NA>  [2]       <NA>
141       <NA>   <NA>       <NA>   <NA> <NA>     direct
142      2.0.6   CRAN      2.0.6   CRAN  [1]   indirect
143      0.1.3   CRAN      0.1.3   CRAN  [1]   indirect
144       <NA>   <NA>       <NA>   <NA>  [2]   indirect
145     0.20.2   CRAN     0.20.2   CRAN  [1]   indirect
146      1.0.4   CRAN      1.0.4   CRAN  [1]     direct
147     1.2-19   CRAN     1.2-19   CRAN  [1]   indirect
148     0.10.2   CRAN     0.10.2   CRAN  [1]   indirect
149      1.9.0   CRAN      1.9.0   CRAN  [1]   indirect
150      2.0.2   CRAN      2.0.2   CRAN  [1]   indirect
151      1.4.0   CRAN      1.4.0   CRAN  [1]   indirect
152      2.0.3   CRAN      2.0.3   CRAN  [1]   indirect
153      2.0.7   CRAN      2.0.7   CRAN  [1]   indirect
154      1.3.2   CRAN      1.3.2   CRAN  [1]     direct
155     4.10.1   CRAN     4.10.1   CRAN  [1]     direct
156      1.8.8   CRAN      1.8.8   CRAN  [1]     direct
157      1.0.1   CRAN      1.0.1   CRAN  [1]   indirect
158      1.0.0   CRAN      1.0.0   CRAN  [1]   indirect
159 0.3.2.9008 GitHub       <NA>   <NA>  [1]       <NA>
160      1.1.1   CRAN      1.1.1   CRAN  [1]   indirect
161      3.8.0   CRAN      3.8.0   CRAN  [1]   indirect
162      0.3.7   CRAN      0.3.7   CRAN  [1]   indirect
163      1.2.2   CRAN      1.2.2   CRAN  [1]   indirect
164    1.2.0.1   CRAN    1.2.0.1   CRAN  [1]   indirect
165      1.7.4   CRAN      1.7.4   CRAN  [1]   indirect
166      1.0.1   CRAN      1.0.1   CRAN  [1]     direct
167      1.2.5   CRAN      1.2.5   CRAN  [1]   indirect
168      0.3.3   CRAN      0.3.3   CRAN  [1]   indirect
169      1.4.0   CRAN      1.4.0   CRAN  [1]   indirect
170      2.1.4   CRAN      2.1.4   CRAN  [1]     direct
171      1.0.1   CRAN      1.0.1   CRAN  [1]   indirect
172      2.1.2   CRAN      2.1.2   CRAN  [1]   indirect
173      2.4.2   CRAN      2.4.2   CRAN  [1]   indirect
174     0.17.2   CRAN     0.17.2   CRAN  [1]     direct
175       <NA>   <NA>       <NA>   <NA> <NA>     direct
176      1.1.0   CRAN      1.1.0   CRAN  [1]     direct
177       <NA>   <NA>       <NA>   <NA>  [1]     direct
178      7.2.3   CRAN      7.2.3   CRAN  [1]     direct
179     4.1.19   CRAN     4.1.19   CRAN  [2]     direct
180      3.1.1   CRAN      3.1.1   CRAN  [1]     direct
181      2.0.3   CRAN      2.0.3   CRAN  [1]   indirect
182       0.14   CRAN       0.14   CRAN  [1]     direct
183      2.1.2   CRAN      2.1.2   CRAN  [1]   indirect
184       <NA>   <NA>       <NA>   <NA> <NA>     direct
185      0.4.5   CRAN      0.4.5   CRAN  [1]     direct
186      1.2.1   CRAN      1.2.1   CRAN  [1]     direct
187      0.7.5   CRAN      0.7.5   CRAN  [1]     direct
188      1.2.2   CRAN      1.2.2   CRAN  [1]   indirect
189      1.7.4   CRAN      1.7.4   CRAN  [1]     direct
190      0.2.2 GitHub      0.2.2 GitHub  [1]     direct
191     0.23.1 GitHub     0.23.1 GitHub  [1]     direct
192      0.7.6   CRAN      0.7.6   CRAN  [1]     direct
193      2.1.0   CRAN      2.1.0   CRAN  [1]     direct
194 0.2.1.9000 GitHub 0.2.1.9000 GitHub  [1]     direct
195      0.1.2   CRAN      0.1.2   CRAN  [1]     direct
196     0.11.0   CRAN     0.11.0   CRAN  [1]     direct
197      0.5.0 GitHub      0.5.0 GitHub  [1]     direct
198    0.1.7-1   CRAN    0.1.7-1   CRAN  [1]   indirect
199     7.3-16   CRAN       <NA>   <NA>  [2]       <NA>
200       <NA>   <NA>       <NA>   <NA>  [2]   indirect
201       <NA>   <NA>       <NA>   <NA>  [2]     direct
202     1.7.12   CRAN     1.7.12   CRAN  [1]   indirect
203      1.5.0   CRAN      1.5.0   CRAN  [1]     direct
204      3.5-5   CRAN      3.5-5   CRAN  [2]   indirect
205      3.4.1   CRAN      3.4.1   CRAN  [1]   indirect
206      1.0.4   CRAN      1.0.4   CRAN  [1]   indirect
207      3.1.7   CRAN      3.1.7   CRAN  [1]     direct
208      0.3.6   CRAN      0.3.6   CRAN  [1]   indirect
209      3.2.1   CRAN      3.2.1   CRAN  [1]     direct
210      1.3.0   CRAN      1.3.0   CRAN  [1]     direct
211      0.1.5   CRAN      0.1.5   CRAN  [1]     direct
212      1.2.0   CRAN      1.2.0   CRAN  [1]     direct
213      0.2.0   CRAN      0.2.0   CRAN  [1]   indirect
214       0.44   CRAN       0.44   CRAN  [1]   indirect
215      1.0.0 GitHub      1.0.0 GitHub  [1]     direct
216       <NA>   <NA>       <NA>   <NA>  [2]   indirect
217      0.3.0   CRAN      0.3.0   CRAN  [1]   indirect
218      1.0.1   CRAN      1.0.1   CRAN  [1]   indirect
219      2.1.6   CRAN      2.1.6   CRAN  [1]     direct
220      1.2.3   CRAN      1.2.3   CRAN  [1]   indirect
221       <NA>   <NA>       <NA>   <NA>  [2]     direct
222      1.1-0   CRAN      1.1-0   CRAN  [1]   indirect
223      0.6.1   CRAN      0.6.1   CRAN  [1]     direct
224      0.5.0 GitHub      0.5.0 GitHub  [1]     direct
225      0.4.1   CRAN      0.4.1   CRAN  [1]   indirect
226      1.6.1   CRAN      1.6.1   CRAN  [1]   indirect
227      0.2.5   CRAN      0.2.5   CRAN  [1]   indirect
228      0.4.0   CRAN      0.4.0   CRAN  [1]   indirect
229      1.4.1   CRAN      1.4.1   CRAN  [1]   indirect
230      0.4.1   CRAN      0.4.1   CRAN  [1]   indirect
231      2.5.0   CRAN      2.5.0   CRAN  [1]   indirect
232       0.38   CRAN       0.38   CRAN  [1]   indirect
233      1.3.3   CRAN      1.3.3   CRAN  [1]     direct
234      1.0.0   CRAN      1.0.0   CRAN  [1]   indirect
235      1.8-4   CRAN      1.8-4   CRAN  [1]   indirect
236      2.3.7   CRAN      2.3.7   CRAN  [1]   indirect
237      1.1.0   CRAN      1.1.0   CRAN  [1]     direct
238      2.2.2   CRAN      2.2.2   CRAN  [1]   indirect

[1]: /Users/stephenholsenbeck/Library/Caches/org.R-project.R/R/renv/library/dmdu-4393acb2/R-4.3/aarch64-apple-darwin20
[2]: /Users/stephenholsenbeck/Library/Caches/org.R-project.R/R/renv/sandbox/R-4.3/aarch64-apple-darwin20/84ba8b13     

# ABI ================================
* No ABI conflicts were detected in the set of installed packages.

# User Profile =======================
                              Source Package Require Version   Dev
1 /Users/stephenholsenbeck/.Rprofile   utils                 FALSE

# Settings ===========================
List of 11
 $ bioconductor.version     : chr(0) 
 $ external.libraries       : chr(0) 
 $ ignored.packages         : chr [1:10] "sinew" "sos" "todor" "datapasta" ...
 $ package.dependency.fields: chr [1:3] "Imports" "Depends" "LinkingTo"
 $ r.version                : chr(0) 
 $ snapshot.type            : chr "explicit"
 $ use.cache                : logi TRUE
 $ vcs.ignore.cellar        : logi TRUE
 $ vcs.ignore.library       : logi TRUE
 $ vcs.ignore.local         : logi TRUE
 $ vcs.manage.ignores       : logi TRUE

# Options ============================
List of 10
 $ defaultPackages                     : chr [1:6] "datasets" "utils" "grDevices" "graphics" ...
 $ download.file.method                : chr "libcurl"
 $ download.file.extra                 : NULL
 $ install.packages.compile.from.source: chr "interactive"
 $ pkgType                             : chr "both"
 $ repos                               : Named chr "https://cran.rstudio.com"
  ..- attr(*, "names")= chr "CRAN"
 $ renv.consent                        : logi TRUE
 $ renv.project.path                   : chr "/Users/stephenholsenbeck/Documents/R/Contributor_Repos/VirgaLabs/dmdu"
 $ renv.config.auto.snapshot           : logi TRUE
 $ renv.verbose                        : logi TRUE

# Environment Variables ==============
HOME                        = /Users/stephenholsenbeck
LANG                        = en_US.UTF-8
MAKE                        = make
R_LIBS                      = <NA>
R_LIBS_SITE                 = /Library/Frameworks/R.framework/Resources/site-library
R_LIBS_USER                 = /Users/stephenholsenbeck/Library/Caches/org.R-project.R/R/renv/library/dmdu-4393acb2/R-4.3/aarch64-apple-darwin20:/Users/stephenholsenbeck/Library/Caches/org.R-project.R/R/renv/sandbox/R-4.3/aarch64-apple-darwin20/84ba8b13
RENV_DEFAULT_R_ENVIRON      = <NA>
RENV_DEFAULT_R_ENVIRON_USER = ~/Documents/R/.Renviron
RENV_DEFAULT_R_LIBS         = <NA>
RENV_DEFAULT_R_LIBS_SITE    = /Library/Frameworks/R.framework/Resources/site-library
RENV_DEFAULT_R_LIBS_USER    = /Users/stephenholsenbeck/Library/R/arm64/4.3/library
RENV_DEFAULT_R_PROFILE      = <NA>
RENV_DEFAULT_R_PROFILE_USER = ~/Documents/R/.Rprofile
RENV_DOWNLOAD_FILE_METHOD   = libcurl
RENV_PATHS_CACHE            = /Users/stephenholsenbeck/Documents/R/renv_cache/cache
RENV_PATHS_ROOT             = /Users/stephenholsenbeck/Documents/R/renv_cache
RENV_PROJECT                = /Users/stephenholsenbeck/Documents/R/Contributor_Repos/VirgaLabs/dmdu

# PATH ===============================
- /Users/stephenholsenbeck/opt/anaconda3/bin
- /usr/local/bin
- /System/Cryptexes/App/usr/bin
- /usr/bin
- /bin
- /usr/sbin
- /sbin
- /var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin
- /var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin
- /var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin
- /opt/X11/bin
- /Users/stephenholsenbeck/Applications/quarto/bin
- /Library/TeX/texbin
- /usr/texbin
- /Applications/RStudio.app/Contents/Resources/app/bin/postback

# Cache ==============================
There are a total of 150 package(s) installed in the renv cache.
Cache path: "~/Documents/R/renv_cache/cache/v5/R-4.3/aarch64-apple-darwin20"

[lorenzwalthert]

This seems similar to some problems in #476. I just created a wiki page for this problem: https://github.com/lorenzwalthert/precommit/wiki/Packages-are-not-found-after-R-upgrade. Can you follow these steps and let me know if it helps?

[yogat3ch]

Hi @lorenzwalthert,
Thank you for the gist!
I'm trying to work through it now, and when run pre-commit install --install-hooks it errors.

An unexpected error has occurred: CalledProcessError: command: ('/Library/Frameworks/R.framework/Resources/bin/Rscript', '--vanilla', '-e', '    options(install.packages.compile.from.source = "never", pkgType = "binary")\n            prefix_dir <- \'/Users/stephenholsenbeck/.cache/pre-commit/repo6fq9kgbf\'\n        options(\n            repos = c(CRAN = "https://cran.rstudio.com"),\n            renv.consent = TRUE\n        )\n        source("renv/activate.R")\n        renv::restore()\n        activate_statement <- paste0(\n          \'suppressWarnings({\',\n          \'old <- setwd("\', getwd(), \'"); \',\n          \'source("renv/activate.R"); \',\n          \'setwd(old); \',\n          \'renv::load("\', getwd(), \'");})\'\n        )\n        writeLines(activate_statement, \'activate.R\')\n        is_package <- tryCatch(\n          {\n              path_desc <- file.path(prefix_dir, \'DESCRIPTION\')\n              suppressWarnings(desc <- read.dcf(path_desc))\n              "Package" %in% colnames(desc)\n          },\n          error = function(...) FALSE\n        )\n        if (is_package) {\n            renv::install(prefix_dir)\n        }\n        \n    ')
return code: 1
...
Error: failed to retrieve 'https://github.com/api/repos/r-lib/styler/tarball/96f859daf39f5973851c06506d7827808eea28a8' [cannot open URL 'https://github.com/api/repos/r-lib/styler/tarball/96f859daf39f5973851c06506d7827808eea28a8']
    In addition: Warning messages:
    1: In (function (url, destfile, method, quiet = FALSE, mode = "w",  :
      downloaded length 0 != reported length 0
    2: In (function (url, destfile, method, quiet = FALSE, mode = "w",  :
      cannot open URL 'https://packagemanager.rstudio.com/all/latest/': HTTP status was '404 Not Found'
    3: In (function (url, destfile, method, quiet = FALSE, mode = "w",  :
      downloaded length 0 != reported length 0
    4: In (function (url, destfile, method, quiet = FALSE, mode = "w",  :
      cannot open URL 'https://github.com/api/repos/r-lib/styler/tarball/96f859daf39f5973851c06506d7827808eea28a8': HTTP status was '401 Unauthorized'
    Traceback (most recent calls last):
    8: renv::restore()
    7: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
    6: retrieve(packages)
    5: handler(package, renv_retrieve_impl(package))
    4: renv_retrieve_impl(package)
    3: renv_retrieve_github(record)
    2: renv_retrieve_package(record, url, path)
    1: stop(status)
    Execution halted

I'm seeing that the command appears to be trying to run renv::restore or something based on the stdout I see. It's using an outdated version of renv: 0.16.0, when my repo is running 0.17.2.

  # Bootstrapping renv 0.16.0 --------------------------------------------------
    * Downloading renv 0.16.0 ... OK
    * Installing renv 0.16.0 ... Done!
    * Successfully installed and loaded renv 0.16.0.
    The following package(s) will be updated:

I've attached the log here:
pre-commit.log

[lorenzwalthert]

The renv.lock file was snapshotted using R 4.3.0, so those warnings are puzzling.

as per the docs, we don’t touch your renv for the project. It’s a different virtual environment installed in a different directory.

I'm seeing that the command appears to be trying to run renv::restore or something based on the stdout I see. It's using an outdated version of renv: 0.16.0, when my repo is running 0.17.2.

same reason.

[lorenzwalthert]

Your next problem seems to relate to your GitHub credentials. If you exceeded the rate limit, then you can try again after some time. Can you try to install that styler package also directly with renv::install(“r-lib/styler@96f859daf39f5973851c06506d7827808eea28a8") anywhere (even in a repo withour renv) to add the package to the cache? If that works successfully, I think you should be able to pre-commit install --install-hooks without problems.

[yogat3ch]

Im sorry, but I'm not following the reasoning here. Where is pre-commit install --install-hooks running from that it's running renv 0.16.0 and for some reason needs the styler package, and my GITHUB_PAT isn't available to it?

The repo from which I'm running the pre-commit install --install-hooks does not use the styler package, and my github credentials worked fine when I recently renv::restored for this repo.

From the log file error it looks like it's running from a random temp directory?
removing ‘/Users/stephenholsenbeck/.cache/pre-commit/repo6fq9kgbf/renv-default/renv/staging/1/pkgload’

[lorenzwalthert]

questions welcome 😄

pre-commit install --install-hooks does:

• clone lorenzwalthert/precommit into its cache and give it a name starting with repo.... On macOS, that repo... lives in ~/.cache/pre-commit/.
• Then, it places an installation script in that repo.
• Then, it runs that script with the working directory being where the script is located, roughly it runs renv::restore().
• As part of running the installation script, it also writes an activation script, that will be executed from your project's working directly, which roughly is 1) change working directory to repo..., 2) renv::load() (which is similar to renv::activate()) and 3) change back to your projects working directory.

When you then run a hook, it sets that activate script as your .Rprofile through an environment variable and executes the hook scripts.

[lorenzwalthert]

I don't think your GITHUB_PAT is available now that I think about it because your .Rprofile is not used for running the hooks or isntalling them. That's why I created #486 to avoid depending on GitHub packages in future hook releases.

[yogat3ch]

Thank you @lorenzwalthert for elaborating that process, the troubleshooting process is making more sense now!
I installed styler and also had to do the same for pkgload but it appears that pre-commit install --install-hooks is now going to work (still going, but it's been going for much longer this time).

Thanks for your work on this package! Do you have a means of taking one-off donations?

[lorenzwalthert]

Welcome @yogat3ch 😄 . I hope it worked out this time?

I also want to find the source of the problem and improve the user experience, so thanks for helping out. On my GitHub Sponsors page, you can make either recurring or one-off donations:

[lorenzwalthert]

thanks for the support @yogat3ch, just to make sure we are on the same page: You selected a monthly donation now.

[yogat3ch]

Indeed @lorenzwalthert , I decided to donate over time!

[lorenzwalthert]

Thanks, I apprecaite that.