After switch from R 4.3.3 to 4.4.1 issues in reading site-library 'Permission denied' due to staff usergroup bug, hence all packages broken

[peterwolf4]

Container image name

rocker/rstudio:4.4.1

Container image digest

rocker/rstudio@sha256:f5c8b1c2817860fcefd3105c92c60bedb1fbcb76093f0783345e9e4379c2bad4

What operating system are you seeing the problem on?

Linux

System information

• Docker version 27.0.3, build 7d4bcd8
• 5.15.0-1067-azure (Ubuntu 20.04.6 LTS)

Bug description

We use Rserver instances as reproducible environment for R&D, but since a new package requires a switch to 4.4.1 I have not been able to get the previous functionality and cannot seem to find anyone who shares the problem.

Working (Minimal) Setup:

FROM rocker/rstudio:4.3.3

RUN R -e "install.packages('cowplot')"

Now when I update to the recent version of R 4.4.1 all packages install fine during build time.
However, when I run the container all packages installed during build (and also preinstalled ones such as the ones included in the tidyverse container) won't be available. Here I emulate the Rserver user that users would usually use through the webbrowser frontent by directly logging into a bash sessions as rstudio user (This (should always) yield the same outputs as when a user tries to navigate the files from within the Rstudio terminal in the webbrowser, where the same permission denied error occurs when trying to open site-library.):

docker run -ti --rm testrserver:4.4.1 su -s /bin/bash rstudio

rstudio@d701b2f206b4:~$ ls -l /usr/local/lib/R
total 44
drwxr-xr-x+  3 root root   4096 Jun 14 10:22 bin
-rw-r--r--+  1 root root  18011 Jun 14 10:22 COPYING
drwxr-xr-x+  4 root root   4096 Jun 14 10:22 doc
drwxr-xr-x+  1 root root     35 Jul 19 12:53 etc
drwxr-xr-x+  3 root root   4096 Jun 14 10:22 include
drwxr-xr-x+  2 root root     21 Jun 14 10:22 lib
drwxr-xr-x+ 32 root root   4096 Jun 14 10:22 library
drwxr-xr-x+  2 root root     73 Jun 14 10:22 modules
drwxr-xr-x+ 11 root root    165 Jun 14 10:22 share
drwxrwsr-x+  1 root staff  4096 Jul 19 12:53 site-library
-rw-r--r--+  1 root root     46 Jun 14 10:22 SVN-REVISION

rstudio@d701b2f206b4:~$ ls -l /usr/local/lib/R/site-library/
ls: cannot open directory '/usr/local/lib/R/site-library/': Permission denied

I was able to find out that the ** cause is a permission error to access /usr/local/lib/R/site-library** however, chanigng the permission does not resolve the issue!; Neither should it persist in the first place since read and execute is set allowed for all users.
When logging in as root to remove the staff usergroup it works again, eg. to root:root :

docker run -ti --rm testrserver:4.4.1 bash

root@febff26b4a43:/# chown root:root /usr/local/lib/R/site-library/
root@febff26b4a43:/# su -s /bin/bash rstudio
rstudio@febff26b4a43:/$ ll /usr/local/lib/R/site-library/
total 96
drwxrwsr-x+  1 root root     6 Jul 19 12:53 ./
drwxr-xr-x+  1 root root    65 Jul 19 14:35 ../
drwxrwxr-x+ 11 root staff 4096 Jul 19 12:53 cli/
drwxrwxr-x+ 13 root staff 4096 Jul 19 12:53 colorspace/
drwxrwxr-x+  8 root staff 4096 Jul 19 12:53 cowplot/

At this stage we can see cowplot in autocomplete again when calling library() in the Rstudio IDE, however when loading the package it will error because the underlying directory is still owned by staff.

Hence I'll need to completely purge staff usergroup out of the 4.4.1 site-library install directories to fix the installed R packages.

root@febff26b4a43:/# chown root:root -R /usr/local/lib/R/site-library/

For now I will bypass this issue by including the purge fix into the dockerfile like so:

FROM rocker/rstudio:4.4.1

RUN R -e "install.packages('cowplot')"
RUN chown root:root -R /usr/local/lib/R/site-library/

Does anyone got a clue where this staff permission error originates from? Afterall, both versions build from the same install scripts and it feels very unsatisfying to recursively own filetrees.

1. I could not figure out how there can be a change to the staff group between something as R version increments?
2. What would trigger permission errors despite the folder clearly allowing for read access to all users, let alone if the user is part of the same group that is triggering the permission errors in the first place?

Bootup and install logs etc all look fine, looking forward to hear your thoughts and ideas to narrow down the root cause of this issue! Thanks for your time and the great maintenance!

How to reproduce this bug?

#Dockerfile:
FROM rocker/rstudio:4.4.1
RUN R -e "install.packages('cowplot')"

#Docker run:
docker run -ti --rm testrserver:4.4.1 su -s /bin/bash rstudio

#Try to access usr/local/lib/R/site-library default installation folder for all packages during build time without root permission to check if rstudio can read packages:

ls -l /usr/local/lib/R/site-library

[eitsupi]

I can't reproduce.

Details

❯ docker run --rm -it --user rstudio rocker/rstudio:latest bash
Unable to find image 'rocker/rstudio:latest' locally
latest: Pulling from rocker/rstudio
7646c8da3324: Already exists
2a532d0e6beb: Already exists
db5aa940be08: Already exists
7ccbc6ce8ef9: Already exists
a2977a275248: Already exists
aae3293b611a: Already exists
36b2aee4e980: Pull complete
ae7ddf798c0e: Pull complete
3063c6ebd52c: Pull complete
461dc934c656: Pull complete
14f9cc122a80: Pull complete
c56be56146bb: Pull complete
9f7fb49c0af0: Pull complete
d89986be3a9e: Pull complete
1c6b0e896726: Pull complete
a332ee746205: Pull complete
5dceea08366f: Pull complete
290821724b21: Pull complete
Digest: sha256:f5c8b1c2817860fcefd3105c92c60bedb1fbcb76093f0783345e9e4379c2bad4
Status: Downloaded newer image for rocker/rstudio:latest
rstudio@07940d327f9d:/$ ls -l /usr/local/lib/R/site-library
total 8
drwxrwxr-x  8 root staff 4096 Jun 14 10:23 docopt
drwxrwxr-x 12 root staff 4096 Jun 14 10:23 littler
rstudio@07940d327f9d:/$ R -e "install.packages('cowplot')"

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages('cowplot')
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
also installing the dependencies ‘utf8’, ‘fansi’, ‘magrittr’, ‘pillar’, ‘pkgconfig’, ‘colorspace’, ‘cli’, ‘glue’, ‘isoband’, ‘lifecycle’, ‘tibble’, ‘vctrs’, ‘withr’, ‘farver’, ‘labeling’, ‘munsell’, ‘R6’, ‘RColorBrewer’, ‘viridisLite’, ‘ggplot2’, ‘gtable’, ‘rlang’, ‘scales’

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/utf8_1.2.4.tar.gz'
Content type 'binary/octet-stream' length 148199 bytes (144 KB)
==================================================
downloaded 144 KB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/fansi_1.0.6.tar.gz'
Content type 'binary/octet-stream' length 317685 bytes (310 KB)
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downloaded 310 KB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/magrittr_2.0.3.tar.gz'
Content type 'binary/octet-stream' length 223920 bytes (218 KB)
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downloaded 218 KB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/pillar_1.9.0.tar.gz'
Content type 'binary/octet-stream' length 653066 bytes (637 KB)
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downloaded 637 KB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/pkgconfig_2.0.3.tar.gz'
Content type 'binary/octet-stream' length 18180 bytes (17 KB)
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trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/colorspace_2.1-0.tar.gz'
Content type 'binary/octet-stream' length 2597662 bytes (2.5 MB)
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downloaded 2.5 MB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/cli_3.6.3.tar.gz'
Content type 'binary/octet-stream' length 1302054 bytes (1.2 MB)
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downloaded 1.2 MB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/glue_1.7.0.tar.gz'
Content type 'binary/octet-stream' length 153022 bytes (149 KB)
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downloaded 149 KB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/isoband_0.2.7.tar.gz'
Content type 'binary/octet-stream' length 1644164 bytes (1.6 MB)
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downloaded 1.6 MB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/lifecycle_1.0.4.tar.gz'
Content type 'binary/octet-stream' length 125136 bytes (122 KB)
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downloaded 122 KB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/tibble_3.2.1.tar.gz'
Content type 'binary/octet-stream' length 678614 bytes (662 KB)
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downloaded 662 KB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/vctrs_0.6.5.tar.gz'
Content type 'binary/octet-stream' length 1318491 bytes (1.3 MB)
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downloaded 1.3 MB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/withr_3.0.0.tar.gz'
Content type 'binary/octet-stream' length 242104 bytes (236 KB)
==================================================
downloaded 236 KB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/farver_2.1.2.tar.gz'
Content type 'binary/octet-stream' length 1466846 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/labeling_0.4.3.tar.gz'
Content type 'binary/octet-stream' length 61014 bytes (59 KB)
==================================================
downloaded 59 KB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/munsell_0.5.1.tar.gz'
Content type 'binary/octet-stream' length 243199 bytes (237 KB)
==================================================
downloaded 237 KB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/R6_2.5.1.tar.gz'
Content type 'binary/octet-stream' length 83250 bytes (81 KB)
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downloaded 81 KB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/RColorBrewer_1.1-3.tar.gz'
Content type 'binary/octet-stream' length 51979 bytes (50 KB)
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downloaded 50 KB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/viridisLite_0.4.2.tar.gz'
Content type 'binary/octet-stream' length 1297630 bytes (1.2 MB)
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downloaded 1.2 MB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/ggplot2_3.5.1.tar.gz'
Content type 'binary/octet-stream' length 5005937 bytes (4.8 MB)
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downloaded 4.8 MB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/gtable_0.3.5.tar.gz'
Content type 'binary/octet-stream' length 217472 bytes (212 KB)
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downloaded 212 KB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/rlang_1.1.4.tar.gz'
Content type 'binary/octet-stream' length 1600805 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/scales_1.3.0.tar.gz'
Content type 'binary/octet-stream' length 711428 bytes (694 KB)
==================================================
downloaded 694 KB

trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/cowplot_1.1.3.tar.gz'
Content type 'binary/octet-stream' length 1380530 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

* installing *binary* package ‘utf8’ ...
* DONE (utf8)
* installing *binary* package ‘fansi’ ...
* DONE (fansi)
* installing *binary* package ‘magrittr’ ...
* DONE (magrittr)
* installing *binary* package ‘pkgconfig’ ...
* DONE (pkgconfig)
* installing *binary* package ‘colorspace’ ...
* DONE (colorspace)
* installing *binary* package ‘cli’ ...
* DONE (cli)
* installing *binary* package ‘glue’ ...
* DONE (glue)
* installing *binary* package ‘isoband’ ...
* DONE (isoband)
* installing *binary* package ‘withr’ ...
* DONE (withr)
* installing *binary* package ‘farver’ ...
* DONE (farver)
* installing *binary* package ‘labeling’ ...
* DONE (labeling)
* installing *binary* package ‘R6’ ...
* DONE (R6)
* installing *binary* package ‘RColorBrewer’ ...
* DONE (RColorBrewer)
* installing *binary* package ‘viridisLite’ ...
* DONE (viridisLite)
* installing *binary* package ‘rlang’ ...
* DONE (rlang)
* installing *binary* package ‘lifecycle’ ...
* DONE (lifecycle)
* installing *binary* package ‘munsell’ ...
* DONE (munsell)
* installing *binary* package ‘vctrs’ ...
* DONE (vctrs)
* installing *binary* package ‘gtable’ ...
* DONE (gtable)
* installing *binary* package ‘scales’ ...
* DONE (scales)
* installing *binary* package ‘pillar’ ...
* DONE (pillar)
* installing *binary* package ‘tibble’ ...
* DONE (tibble)
* installing *binary* package ‘ggplot2’ ...
* DONE (ggplot2)
* installing *binary* package ‘cowplot’ ...
* DONE (cowplot)

The downloaded source packages are in
        ‘/tmp/RtmppJ68PS/downloaded_packages’
>
>
rstudio@07940d327f9d:/$ ls -l /usr/local/lib/R/site-library
total 104
drwxrwxr-x 11 rstudio staff 4096 Jul 20 01:51 cli
drwxrwxr-x 13 rstudio staff 4096 Jul 20 01:51 colorspace
drwxrwxr-x  8 rstudio staff 4096 Jul 20 01:51 cowplot
drwxrwxr-x  8 root    staff 4096 Jun 14 10:23 docopt
drwxrwxr-x  8 rstudio staff 4096 Jul 20 01:51 fansi
drwxrwxr-x  7 rstudio staff 4096 Jul 20 01:51 farver
drwxrwxr-x  8 rstudio staff 4096 Jul 20 01:51 ggplot2
drwxrwxr-x  8 rstudio staff 4096 Jul 20 01:51 glue
drwxrwxr-x  7 rstudio staff 4096 Jul 20 01:51 gtable
drwxrwxr-x  9 rstudio staff 4096 Jul 20 01:51 isoband
drwxrwxr-x  6 rstudio staff 4096 Jul 20 01:51 labeling
drwxrwxr-x  7 rstudio staff 4096 Jul 20 01:51 lifecycle
drwxrwxr-x 12 root    staff 4096 Jun 14 10:23 littler
drwxrwxr-x  8 rstudio staff 4096 Jul 20 01:51 magrittr
drwxrwxr-x  7 rstudio staff 4096 Jul 20 01:51 munsell
drwxrwxr-x  7 rstudio staff 4096 Jul 20 01:51 pillar
drwxrwxr-x  6 rstudio staff 4096 Jul 20 01:51 pkgconfig
drwxrwxr-x  6 rstudio staff 4096 Jul 20 01:51 R6
drwxrwxr-x  6 rstudio staff 4096 Jul 20 01:51 RColorBrewer
drwxrwxr-x  7 rstudio staff 4096 Jul 20 01:51 rlang
drwxrwxr-x  6 rstudio staff 4096 Jul 20 01:51 scales
drwxrwxr-x  8 rstudio staff 4096 Jul 20 01:51 tibble
drwxrwxr-x  8 rstudio staff 4096 Jul 20 01:51 utf8
drwxrwxr-x  9 rstudio staff 4096 Jul 20 01:51 vctrs
drwxrwxr-x  6 rstudio staff 4096 Jul 20 01:51 viridisLite
drwxrwxr-x  7 rstudio staff 4096 Jul 20 01:51 withr

Details

❯ docker run --rm -it --user rstudio rocker/tidyverse:latest bash
Unable to find image 'rocker/tidyverse:latest' locally
latest: Pulling from rocker/tidyverse
7646c8da3324: Already exists
2a532d0e6beb: Already exists
db5aa940be08: Already exists
7ccbc6ce8ef9: Already exists
a2977a275248: Already exists
aae3293b611a: Already exists
565a86b8dc8d: Pull complete
08516011f9e4: Pull complete
7bd8d0b63f2f: Pull complete
2041332265ca: Pull complete
286ca6f97446: Pull complete
5b9c39d18b55: Pull complete
b5c2e531b988: Pull complete
dc90a1a57065: Pull complete
84068eccbae4: Pull complete
b2f9dd331a53: Pull complete
8670ebf4d2d3: Pull complete
8063b8a0feb1: Pull complete
e76623234471: Pull complete
baf0ee110225: Pull complete
Digest: sha256:6201884679072727ce627102ee636c64c51b4dc2dcfb376f2b03105505da9d6f
Status: Downloaded newer image for rocker/tidyverse:latest
rstudio@f14eb9e3f278:/$ R

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(tidyverse)
── Attaching core tidyverse packages ──────────────────────────────────────────────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.4     ✔ readr     2.1.5
✔ forcats   1.0.0     ✔ stringr   1.5.1
✔ ggplot2   3.5.1     ✔ tibble    3.2.1
✔ lubridate 1.9.3     ✔ tidyr     1.3.1
✔ purrr     1.0.2
── Conflicts ────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
>
rstudio@f14eb9e3f278:/$ ls -l /usr/local/lib/R/site-library
total 624
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 arrow
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 askpass
drwxrwxr-x  6 root staff 4096 Jun 14 12:13 assertthat
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 backports
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 base64enc
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 BiocManager
drwxrwxr-x  8 root staff 4096 Jun 14 12:13 bit
drwxrwxr-x 10 root staff 4096 Jun 14 12:13 bit64
drwxrwxr-x  6 root staff 4096 Jun 14 12:13 blob
drwxrwxr-x  6 root staff 4096 Jun 14 12:13 brew
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 brio
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 broom
drwxrwxr-x 19 root staff 4096 Jun 14 12:13 bslib
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 cachem
drwxrwxr-x  6 root staff 4096 Jun 14 12:13 callr
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 cellranger
drwxrwxr-x 11 root staff 4096 Jun 14 12:13 cli
drwxrwxr-x  8 root staff 4096 Jun 14 12:13 clipr
drwxrwxr-x 13 root staff 4096 Jun 14 12:13 colorspace
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 commonmark
drwxrwxr-x  6 root staff 4096 Jun 14 12:13 conflicted
drwxrwxr-x  8 root staff 4096 Jun 14 12:13 cpp11
drwxrwxr-x  6 root staff 4096 Jun 14 12:13 crayon
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 credentials
drwxrwxr-x  8 root staff 4096 Jun 14 12:13 curl
drwxrwxr-x 11 root staff 4096 Jun 14 12:13 data.table
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 DBI
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 dbplyr
drwxrwxr-x  6 root staff 4096 Jun 14 12:13 desc
drwxrwxr-x  8 root staff 4096 Jun 14 12:13 devtools
drwxrwxr-x 10 root staff 4096 Jun 14 12:13 diffobj
drwxrwxr-x 11 root staff 4096 Jun 14 12:13 digest
drwxrwxr-x  8 root staff 4096 Jun 14 10:23 docopt
drwxrwxr-x  6 root staff 4096 Jun 14 12:13 downlit
drwxrwxr-x  9 root staff 4096 Jun 14 12:13 dplyr
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 dtplyr
drwxrwxr-x 10 root staff 4096 Jun 14 12:13 duckdb
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 ellipsis
drwxrwxr-x  6 root staff 4096 Jun 14 12:13 evaluate
drwxrwxr-x  8 root staff 4096 Jun 14 12:13 fansi
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 farver
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 fastmap
drwxrwxr-x  8 root staff 4096 Jun 14 12:13 fontawesome
drwxrwxr-x  8 root staff 4096 Jun 14 12:13 forcats
drwxrwxr-x  8 root staff 4096 Jun 14 12:13 fs
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 fst
drwxrwxr-x  8 root staff 4096 Jun 14 12:13 fstcore
drwxrwxr-x 11 root staff 4096 Jun 14 12:13 gargle
drwxrwxr-x  6 root staff 4096 Jun 14 12:13 generics
drwxrwxr-x  8 root staff 4096 Jun 14 12:13 gert
drwxrwxr-x  8 root staff 4096 Jun 14 12:13 ggplot2
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 gh
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 gitcreds
drwxrwxr-x  8 root staff 4096 Jun 14 12:13 glue
drwxrwxr-x  9 root staff 4096 Jun 14 12:13 googledrive
drwxrwxr-x  8 root staff 4096 Jun 14 12:13 googlesheets4
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 gtable
drwxrwxr-x  9 root staff 4096 Jun 14 12:13 haven
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 highr
drwxrwxr-x  6 root staff 4096 Jun 14 12:13 hms
drwxrwxr-x  8 root staff 4096 Jun 14 12:13 htmltools
drwxrwxr-x  9 root staff 4096 Jun 14 12:13 htmlwidgets
drwxrwxr-x  9 root staff 4096 Jun 14 12:13 httpuv
drwxrwxr-x  8 root staff 4096 Jun 14 12:13 httr
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 httr2
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 ids
drwxrwxr-x  6 root staff 4096 Jun 14 12:13 ini
drwxrwxr-x  9 root staff 4096 Jun 14 12:13 isoband
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 jquerylib
drwxrwxr-x  8 root staff 4096 Jun 14 12:13 jsonlite
drwxrwxr-x 14 root staff 4096 Jun 14 12:13 knitr
drwxrwxr-x  6 root staff 4096 Jun 14 12:13 labeling
drwxrwxr-x 10 root staff 4096 Jun 14 12:13 Lahman
drwxrwxr-x  9 root staff 4096 Jun 14 12:13 later
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 lifecycle
drwxrwxr-x 12 root staff 4096 Jun 14 10:23 littler
drwxrwxr-x 10 root staff 4096 Jun 14 12:13 lubridate
drwxrwxr-x  8 root staff 4096 Jun 14 12:13 magrittr
drwxrwxr-x  6 root staff 4096 Jun 14 12:13 memoise
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 mime
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 miniUI
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 modelr
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 munsell
drwxrwxr-x  7 root staff 4096 Jun 14 12:13 nycflights13
drwxrwxr-x  8 root staff 4096 Jun 14 12:13 openssl
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[peterwolf4]

@eitsupi
Good for you, I would also love that haha
Really not sure though how there can be differences within the same image :/
To me it seems like then it must be some systemwide user config that interferes within dockre users? But this would only make sense if I had issues under R 4.3.3 as well, which I don't... Really no clue where it is coming, esp. since it seems to be version specific for above 4.4.x...
I included the log of a run exactly how you performed it, with the same error (I know hard to debug when its impossible to reproduce on your end but I am out of guesses as to why I am seeing this error, especially since we are inside a container!)

Rstudio:

docker run --rm -it --user rstudio rocker/rstudio:latest bash
Unable to find image 'rocker/rstudio:latest' locally
latest: Pulling from rocker/rstudio
Digest: sha256:f5c8b1c2817860fcefd3105c92c60bedb1fbcb76093f0783345e9e4379c2bad4
Status: Downloaded newer image for rocker/rstudio:latest
rstudio@0746a5cd5a4f:/$ R

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> q()
rstudio@0746a5cd5a4f:/$ ll /usr/local/lib/R/site-library/
ls: cannot open directory '/usr/local/lib/R/site-library/': Permission denied

And second, same with Tidyverse:

docker run --rm -it --user rstudio rocker/tidyverse:latest bash
Unable to find image 'rocker/tidyverse:latest' locally
latest: Pulling from rocker/tidyverse
Digest: sha256:6201884679072727ce627102ee636c64c51b4dc2dcfb376f2b03105505da9d6f
Status: Downloaded newer image for rocker/tidyverse:latest
rstudio@9cf612317dc4:/$ ll /usr/local/lib/R/site-library/
ls: cannot open directory '/usr/local/lib/R/site-library/': Permission denied