pak
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20 hours ago •
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Error: Cannot open lock file: Permission denied
Many thanks for the awesome pak package. I've just installed R 4.1.2 and am trying to
install a large number of pacakges using pak. But I keep running into an error in the pak
installation.
First, I restarted R/RStudio and ran the following command to install the latest version of pak:
install.packages("pak", repos = "https://r-lib.github.io/p/pak/devel/")
I then restarted R/RStudio again, and ran the following installation script to install the packages in one go (based on a modified version of Garrick Aiden Buie's excellent code)
Installation script (causing issue)
# Packages developed by Garrick Aden‑Buie
gabuie_pkgs <- c(
"xaringanExtra", "js4shiny", "shrtcts",
"rsthemes", "ermoji", "regexplain"
)
# Get the github repos for installation
gabuie_pkgs_gh <- paste0("gadenbuie/", gabuie_pkgs)
REQ_PKGS <- c(
# Package development related
"devtools",
"here",
"pkgdown",
"Rdpack",
"remotes",
"roxygen2",
"styler",
"usethis",
"testthat",
# VSCode
"rstudioapi",
# VSCode
"languageserver",
# Publishing RMarkdown related
"bookdown",
"distill",
"knitr",
"pagedown",
"rmarkdown",
"xaringan",
"postcards",
"tjmahr/WrapRmd",
# Geospatial
"sf",
"mapsf",
# Reproducibility
"details",
"reprex",
# Citation related
"crsh/citr",
# Dates and formatting
"lubridate",
"scales",
# CV
"vitae",
# File management
"fs",
# Tidyverse and data wrangling
"broom",
"forcats",
"janitor",
"patchwork",
"skimr",
"tidyverse",
"vroom",
# Modeling
"tidymodels",
"stacks",
# Packages developed by Garrick Aden‑Buie
gabuie_pkgs_gh,
# More RStudio addins
"MilesMcBain/datapasta",
"seasmith/AlignAssign",
"remedy"
)
# Install all of the packages
pak::pkg_install(pkg = REQ_PKGS)
It keeps returning the following output (with error), even if just try installing one of the packages (and comment out all other packages):
Output (with error)
✓ Loading metadata database ... done
→ Will install 22 packages.
→ Will update 30 packages.
→ Will download 1 CRAN package (1.10 MB), cached: 44 (153.52 MB).
→ Will download 7 packages with unknown size.
+ bibtex 0.4.2.3
+ bookdown 0.24
+ broom 0.7.8 → 0.7.10
+ citr 0.3.2 👷🏿♂️🔧 ⬇ (GitHub: 0e8243d)
+ details 0.2.1
+ devtools 2.4.3
+ dials 0.0.9 → 0.0.10
+ distill 1.3
+ downlit 0.2.1 → 0.4.0
+ fs 1.5.0 → 1.5.2
+ hardhat 0.1.5 → 0.1.6
+ here 1.0.1
+ infer 0.5.4 → 1.0.0
+ ipred 0.9-11 → 0.9-12
+ js4shiny 0.0.28 → 0.0.28 👷🏻♀️🔧 ⬇ (GitHub: b201cbf)
+ languageserver 0.3.12
+ lubridate 1.7.10 → 1.8.0
+ mapsf 0.2.0 → 0.3.0
+ modeldata 0.1.0 → 0.1.1
+ pagedown 0.16
+ parsnip 0.1.6 → 0.1.7
+ pillar 1.6.1 → 1.6.4
+ pkgdown 2.0.1
+ postcards 0.2.2
+ Rdpack 2.1.3
+ recipes 0.1.16 → 0.1.17
+ RefManageR 1.3.0
+ remotes 2.4.2
+ roxygen2 7.1.2
+ rsthemes 0.2.1.9000 → 0.3.1 👷🏻♂️🔧 ⬇ (GitHub: bbe73ca)
+ s2 1.0.6 → 1.0.7
+ sass 0.4.0.9000 → 0.4.0.9000 👷🏼♀️🔧 ⬇ (GitHub: f7a9540)
+ servr 0.22 → 0.24
+ sf 1.0-5
+ shinyjs 2.1.0 ⬇ (1.10 MB)
+ shrtcts 0.1.0 → 0.1.1 👷🏻🔧 ⬇ (GitHub: 4691bfc)
+ stacks 0.2.0 → 0.2.1
+ styler 1.6.2
+ testthat 3.1.1
+ tibble 3.1.2 → 3.1.6
+ tidymodels 0.1.3 → 0.1.4
+ tidyr 1.1.3 → 1.1.4
+ tune 0.1.5 → 0.1.6
+ usethis 2.1.5
+ vitae 0.4.2 → 0.5.1
+ vroom 1.5.2 → 1.5.7
+ wk 0.4.1 → 0.5.0
+ workflows 0.2.2 → 0.2.4
+ workflowsets 0.0.2 → 0.1.0
+ WrapRmd 0.0.0.9004 👷🏿🔧 ⬇ (GitHub: d1a31a2)
+ xaringan 0.22
+ xaringanExtra 0.5.4 → 0.5.5 👷🏻♀️🔧 ⬇ (GitHub: cc1f613)
? Do you want to continue (Y/n) Y
ℹ Getting 1 pkg (1.10 MB) and 7 pkgs with unknown sizes, 44 (153.52 MB) cached
✓ Cached copy of xaringanExtra 0.5.5 (source) is the latest build
✓ Cached copy of js4shiny 0.0.28 (source) is the latest build
✓ Cached copy of shrtcts 0.1.1 (source) is the latest build
✓ Cached copy of WrapRmd 0.0.0.9004 (source) is the latest build
✓ Cached copy of citr 0.3.2 (source) is the latest build
✓ Cached copy of rsthemes 0.3.1 (source) is the latest build
✓ Cached copy of sass 0.4.0.9000 (source) is the latest build
✓ Cached copy of shinyjs 2.1.0 (x86_64-apple-darwin17.0) is the latest build
✓ No downloads needed, all packages are cached
ℹ Packaging xaringanExtra 0.5.5
ℹ Packaging WrapRmd 0.0.0.9004
Error: Cannot open lock file: Permission denied
I tried to check whether tidyr it had installed correctly just in case:
> packageVersion("tidyr")
[1] ‘1.1.3’
Which is not the 1.1.4 version that pak was trying to install above. So the error indicates that the pak installation had not worked as intended.
Could anyone please help me with completing this installation?
current session info
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.1.2 (2021-11-01)
os macOS Monterey 12.0.1
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2021-12-25
─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] standard (@0.2.1)
backports 1.2.1 2020-12-09 [1] standard (@1.2.1)
broom 0.7.8 2021-06-24 [1] standard (@0.7.8)
callr 3.7.0 2021-04-20 [1] standard (@3.7.0)
cellranger 1.1.0 2016-07-27 [1] standard (@1.1.0)
cli 3.1.0 2021-10-27 [1] CRAN (R 4.1.0)
clipr 0.7.1 2020-10-08 [1] standard (@0.7.1)
colorspace 2.0-2 2021-06-24 [1] standard (@2.0-2)
crayon 1.4.1 2021-02-08 [1] standard (@1.4.1)
DBI 1.1.1 2021-01-15 [1] standard (@1.1.1)
dbplyr 2.1.1 2021-04-06 [1] standard (@2.1.1)
desc 1.4.0 2021-09-28 [1] CRAN (R 4.1.0)
details 0.2.1 2020-01-12 [1] CRAN (R 4.1.0)
dplyr * 1.0.7 2021-06-18 [1] standard (@1.0.7)
ellipsis 0.3.2 2021-04-29 [1] standard (@0.3.2)
fansi 0.5.0 2021-05-25 [1] standard (@0.5.0)
forcats * 0.5.1 2021-01-27 [1] standard (@0.5.1)
fs 1.5.0 2020-07-31 [1] standard (@1.5.0)
generics 0.1.0 2020-10-31 [1] standard (@0.1.0)
ggplot2 * 3.3.5 2021-06-25 [1] standard (@3.3.5)
glue 1.4.2 2020-08-27 [1] standard (@1.4.2)
gtable 0.3.0 2019-03-25 [1] standard (@0.3.0)
haven 2.4.1 2021-04-23 [1] standard (@2.4.1)
hms 1.1.0 2021-05-17 [1] standard (@1.1.0)
httr 1.4.2 2020-07-20 [1] standard (@1.4.2)
jsonlite 1.7.2 2020-12-09 [1] standard (@1.7.2)
knitr 1.37 2021-12-16 [1] CRAN (R 4.1.0)
lifecycle 1.0.0 2021-02-15 [1] standard (@1.0.0)
lubridate 1.7.10 2021-02-26 [1] standard (@1.7.10)
magrittr 2.0.1 2020-11-17 [1] standard (@2.0.1)
modelr 0.1.8 2020-05-19 [1] standard (@0.1.8)
munsell 0.5.0 2018-06-12 [1] standard (@0.5.0)
pak 0.2.0.9000 2021-12-21 [1] local
pillar 1.6.1 2021-05-16 [1] standard (@1.6.1)
pkgconfig 2.0.3 2019-09-22 [1] standard (@2.0.3)
png 0.1-7 2013-12-03 [1] standard (@0.1-7)
processx 3.5.2 2021-04-30 [1] standard (@3.5.2)
ps 1.6.0 2021-02-28 [1] standard (@1.6.0)
purrr * 0.3.4 2020-04-17 [1] standard (@0.3.4)
R6 2.5.0 2020-10-28 [1] standard (@2.5.0)
Rcpp 1.0.7 2021-07-07 [1] CRAN (R 4.1.0)
readr * 1.4.0 2020-10-05 [1] standard (@1.4.0)
readxl 1.3.1 2019-03-13 [1] standard (@1.3.1)
reprex 2.0.1 2021-08-05 [1] CRAN (R 4.1.0)
rlang 0.4.11 2021-04-30 [1] standard (@0.4.11)
rprojroot 2.0.2 2020-11-15 [1] standard (@2.0.2)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0)
rvest 1.0.0 2021-03-09 [1] standard (@1.0.0)
scales 1.1.1 2020-05-11 [1] standard (@1.1.1)
sessioninfo 1.1.1 2018-11-05 [1] standard (@1.1.1)
stringi 1.6.2 2021-05-17 [1] standard (@1.6.2)
stringr * 1.4.0 2019-02-10 [1] standard (@1.4.0)
tibble * 3.1.2 2021-05-16 [1] standard (@3.1.2)
tidyr * 1.1.3 2021-03-03 [1] standard (@1.1.3)
tidyselect 1.1.1 2021-04-30 [1] standard (@1.1.1)
tidyverse * 1.3.1 2021-04-15 [1] CRAN (R 4.1.0)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.0)
vctrs 0.3.8 2021-04-29 [1] standard (@0.3.8)
withr 2.4.2 2021-04-18 [1] standard (@2.4.2)
xfun 0.29 2021-12-14 [1] CRAN (R 4.1.0)
xml2 1.3.2 2020-04-23 [1] standard (@1.3.2)
[1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
Do you have write access to the package library?
I believe so. For background, I'm running the above installation on my personal macbook. So I checked the following:
> .libPaths()
[1] "/Library/Frameworks/R.framework/Versions/4.1/Resources/library"
I went to this directory and checked that I have read-write access. As Admin I do have it.
Should I be checking another directory for pak? Or should I be setting some option in pak
manually to enable it to have write access to this directory?
Also the results of the Last error trace are as follows:
Last error trace
> .Last.error.trace
Stack trace:
12. (function (...) ...
13. base:::withCallingHandlers(cli_message = function(msg) { ...
14. get("pkg_install_do_plan", asNamespace("pak"))(...)
15. pkgdepends::install_package_plan(plan = plan, lib = lib, num_workers = num_ ...
16. base:::withCallingHandlers({ ...
17. pkgdepends:::handle_events(state, events)
18. pkgdepends:::handle_event(state, i)
19. proc$get_result()
20. processx:::process_get_result(self, private)
21. private$post_process()
22. pkgdepends:::install_extracted_binary(filename, lib_cache, pkg_cache, ...
23. pkgdepends:::lock_cache(lib_cache, pkg_name, getOption("install.lock"))
24. filelock:::lock(lockfile)
25. base:::.handleSimpleError(function (e) ...
26. h(simpleError(msg, call))
27. base:::stop(e)
28. (function (e) ...
x Cannot open lock file: Permission denied
I am experiencing something similar on an Intel Mac:
> pak::pkg_install("broom")
→ Will update 1 package.
→ Will download 1 CRAN package (1.80 MB).
+ broom 0.7.10 → 0.7.11 ⬇ (1.80 MB)
? Do you want to continue (Y/n) y
ℹ Getting 1 pkg (1.80 MB)
✓ Got broom 0.7.11 (x86_64-apple-darwin17.0) (1.80 MB)
✓ Downloaded 1 package (1.80 MB)in 768ms
Error: Cannot open lock file: Permission denied
Type .Last.error.trace to see where the error occurred
It seems to work fine with utils::install_packages():
> install.packages("broom")
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/broom_0.7.11.tgz'
Content type 'application/x-gzip' length 1800952 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
The downloaded binary packages are in
/var/folders/wx/zjw1jzk11s76vchhc2xym7xw0000gn/T//RtmpVRtFFr/downloaded_packages
Session info
> session_info()
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.1.1 (2021-08-10)
os macOS Monterey 12.1
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_GB.UTF-8
ctype en_GB.UTF-8
tz Europe/London
date 2022-01-20
rstudio 2021.09.1+372 Ghost Orchid (desktop)
pandoc 2.14.0.3 @ /Applications/RStudio.app/Contents/MacOS/pandoc/ (via rmarkdown)
─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.0)
callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.0)
cli 3.1.0 2021-10-27 [1] CRAN (R 4.1.0)
clipr 0.7.1 2020-10-08 [1] CRAN (R 4.1.0)
crayon 1.4.2 2021-10-29 [1] CRAN (R 4.1.0)
desc 1.4.0 2021-09-28 [1] CRAN (R 4.1.0)
devtools * 2.4.3.9000 2021-12-09 [1] Github (r-lib/devtools@91a8758)
digest 0.6.29 2021-12-01 [1] CRAN (R 4.1.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0)
evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.0)
fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.0)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0)
flow * 0.0.2 2021-08-13 [1] CRAN (R 4.1.0)
fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.1)
glue 1.6.0 2021-12-17 [1] CRAN (R 4.1.0)
highr 0.9 2021-04-16 [1] CRAN (R 4.1.0)
htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.1.1)
knitr 1.36 2021-09-29 [1] CRAN (R 4.1.0)
lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.1)
lookup * 1.0 2021-04-14 [1] CRAN (R 4.1.0)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.1.0)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.1.0)
pak * 0.2.1 2021-12-20 [1] CRAN (R 4.1.0)
pillar 1.6.4 2021-10-18 [1] CRAN (R 4.1.0)
pkgbuild 1.3.0 2021-12-09 [1] CRAN (R 4.1.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
pkgload 1.2.4 2021-11-30 [1] CRAN (R 4.1.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0)
processx 3.5.2 2021-04-30 [1] CRAN (R 4.1.0)
prompt * 1.0.1 2021-06-26 [1] Github (gaborcsardi/prompt@fc2ac94)
ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.0)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.0)
remotes 2.4.2 2021-11-30 [1] CRAN (R 4.1.0)
reprex * 2.0.1 2021-08-05 [1] CRAN (R 4.1.0)
rlang 0.4.12 2021-10-18 [1] CRAN (R 4.1.0)
rmarkdown 2.11 2021-09-14 [1] CRAN (R 4.1.1)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.0)
rsthemes * 0.3.1 2021-12-14 [1] Github (gadenbuie/rsthemes@bbe73ca)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.0)
testthat * 3.1.1 2021-12-03 [1] CRAN (R 4.1.0)
tibble 3.1.6 2021-11-07 [1] CRAN (R 4.1.0)
usethis * 2.1.5 2021-12-09 [1] CRAN (R 4.1.1)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.0)
vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.0)
withr 2.4.3 2021-11-30 [1] CRAN (R 4.1.0)
xfun 0.29 2021-12-14 [1] CRAN (R 4.1.0)
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.1.0)
[1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
─────────────────────────────────────────────────────────────────────────────────────────────────────────────
In my R package library (.libPaths()[1])) I have a folder named _cache which holds quite a number of .lock files which seem to be responsible for the error above. Once I deleted broom.lock, pak::pkg_install("broom") ran successfully.
However, the broom.lock file is back (after the installation), but this time {pak} does not mind it (it probably can open it).
I'm not sure what the purpose of the _cache folder or the .lock files is or why {pak} cannot read older .lock files .
Installing a package with utils::install.packages() does not create a .lock file in cache. Could all those .lock files be from an older version of {pak}?
Oh, right, so one of the way this can happen if there is another (frozen?) process installing the same package into the same library. The fix for that is to find that process and kill it.
Removing the lock file is not as a good workaround, because it is unpredictable what the end result of the two concurrent install processes would be. If the other process is frozen then it it probably OK.
I'll try to give a better error message for this, and also print the process id of the locking process if possible.
Thanks, Gábor. In my case there was only one R process active, so maybe those lock files were leftover from a frozen process that got killed a while ago. Would that be possible?
That's only possible if the lock file was created by another user, e.g. root, and your current user has no rights to open it. This would happen if you use another user to install packages into this library. Or, again, a frozen background process is locking it.
pak uses a proper locks with fcntl(F_SETLK), the presence of a lock does not mean that there is a lock on the package.
Or of course it also just could be a bug in pak.
@gaborcsardi @dragosmg - thanks for the updates on this.
I tried reinstalling both R/RStudio multiple times (and also restarting my macbook), and running my above script. Unfortunately I still get the same type of error:
> pak::pkg_install(pkg = REQ_PKGS)
✓ Updated metadata database: 4.86 MB in 8 files.
✓ Updating metadata database ... done
→ Will install 5 packages.
→ Will update 26 packages.
→ Will download 14 CRAN packages (123.69 MB), cached: 16 (21.83 MB).
→ Will download 1 package with unknown size.
+ bibtex 0.4.2.3
+ broom 0.7.10 → 0.7.12 ⬇ (1.80 MB)
+ bslib 0.2.5.1 → 0.3.1 ⬇ (4.78 MB)
+ citr 0.3.2 👷🏿🔧 ⬇ (GitHub: 0e8243d)
+ dials 0.0.9 → 0.1.0 ⬇ (783.28 kB)
+ hardhat 0.1.5 → 0.2.0 ⬇ (773.77 kB)
+ infer 0.5.4 → 1.0.0
+ ipred 0.9-11 → 0.9-12
+ lubridate 1.7.10 → 1.8.0
+ mapsf 0.2.0 → 0.4.0 ⬇ (2.21 MB)
+ modeldata 0.1.0 → 0.1.1
+ parsnip 0.1.6 → 0.1.7
+ pillar 1.6.1 → 1.7.0 ⬇ (742.25 kB)
+ pkgdown 2.0.1 → 2.0.2 ⬇ (718.13 kB)
+ postcards 0.2.2 → 0.2.3 ⬇ (3.17 MB)
+ Rdpack 2.1.3
+ recipes 0.1.16 → 0.1.17
+ RefManageR 1.3.0
+ rsample 0.1.0 → 0.1.1 ⬇ (418.09 kB)
+ sf 1.0-5 → 1.0-6 ⬇ (100.54 MB)
+ shinyjs 2.1.0
+ stacks 0.2.0 → 0.2.2 ⬇ (3.57 MB)
+ testthat 3.1.1 → 3.1.2 ⬇ (2.96 MB)
+ tibble 3.1.2 → 3.1.6
+ tidymodels 0.1.3 → 0.1.4
+ tidyr 1.1.3 → 1.2.0 ⬇ (1.00 MB)
+ tune 0.1.5 → 0.1.6
+ vitae 0.4.2 → 0.5.1
+ withr 2.4.2 → 2.4.3 ⬇ (213.90 kB)
+ workflows 0.2.2 → 0.2.4
+ workflowsets 0.0.2 → 0.1.0
! pillar, tibble, withr, lubridate, broom, and tidyr are loaded in the current
R session, you probably need to restart R after the installation.
? Do you want to continue (Y/n) Y
ℹ Getting 14 pkgs (123.69 MB) and 1 pkg with unknown size, 16 (21.83 MB) cached
✓ Cached copy of citr 0.3.2 (source) is the latest build
✓ Got withr 2.4.3 (x86_64-apple-darwin17.0) (213.90 kB)
✓ Got pkgdown 2.0.2 (x86_64-apple-darwin17.0) (718.13 kB)
✓ Got pillar 1.7.0 (x86_64-apple-darwin17.0) (742.25 kB)
✓ Got hardhat 0.2.0 (x86_64-apple-darwin17.0) (773.77 kB)
✓ Got tidyr 1.2.0 (x86_64-apple-darwin17.0) (1.00 MB)
✓ Got rsample 0.1.1 (x86_64-apple-darwin17.0) (418.09 kB)
✓ Got dials 0.1.0 (x86_64-apple-darwin17.0) (783.28 kB)
✓ Got broom 0.7.12 (x86_64-apple-darwin17.0) (1.80 MB)
✓ Got testthat 3.1.2 (x86_64-apple-darwin17.0) (2.96 MB)
✓ Got postcards 0.2.3 (x86_64-apple-darwin17.0) (3.17 MB)
✓ Got mapsf 0.4.0 (x86_64-apple-darwin17.0) (2.21 MB)
✓ Got bslib 0.3.1 (x86_64-apple-darwin17.0) (4.78 MB)
✓ Got stacks 0.2.2 (x86_64-apple-darwin17.0) (3.57 MB)
✓ Got sf 1.0-6 (x86_64-apple-darwin17.0) (100.54 MB)
✓ Downloaded 14 packages (123.69 MB)in 26.3s
Error: Cannot open lock file: Permission denied
Type .Last.error.trace to see where the error occurred
Looking into .Last.error.trace gives the following:
Stack trace:
12. (function (...) ...
13. base:::withCallingHandlers(cli_message = function(msg) { ...
14. get("pkg_install_do_plan", asNamespace("pak"))(...)
15. pkgdepends::install_package_plan(plan = plan, lib = lib, num_workers = num_ ...
16. base:::withCallingHandlers({ ...
17. pkgdepends:::handle_events(state, events)
18. pkgdepends:::handle_event(state, i)
19. proc$get_result()
20. processx:::process_get_result(self, private)
21. private$post_process()
22. pkgdepends:::install_extracted_binary(filename, lib_cache, pkg_cache, ...
23. pkgdepends:::lock_cache(lib_cache, pkg_name, getOption("install.lock"))
24. filelock:::lock(lockfile)
25. base:::.handleSimpleError(function (e) ...
26. h(simpleError(msg, call))
27. base:::stop(e)
28. (function (e) ...
x Cannot open lock file: Permission denied
For background here is my sessioninfo::session_info() .
current session info
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.1.2 (2021-11-01)
os macOS Monterey 12.1
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2022-02-07
─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] standard (@0.2.1)
backports 1.2.1 2020-12-09 [1] standard (@1.2.1)
broom 0.7.10 2021-10-31 [1] CRAN (R 4.1.0)
callr 3.7.0 2021-04-20 [1] standard (@3.7.0)
cellranger 1.1.0 2016-07-27 [1] standard (@1.1.0)
cli 3.1.1 2022-01-20 [1] CRAN (R 4.1.2)
clipr 0.7.1 2020-10-08 [1] standard (@0.7.1)
colorspace 2.0-2 2021-06-24 [1] standard (@2.0-2)
crayon 1.4.1 2021-02-08 [1] standard (@1.4.1)
DBI 1.1.1 2021-01-15 [1] standard (@1.1.1)
dbplyr 2.1.1 2021-04-06 [1] standard (@2.1.1)
desc 1.4.0 2021-09-28 [1] CRAN (R 4.1.0)
details 0.2.1 2020-01-12 [1] CRAN (R 4.1.0)
dplyr * 1.0.7 2021-06-18 [1] standard (@1.0.7)
ellipsis 0.3.2 2021-04-29 [1] standard (@0.3.2)
fansi 0.5.0 2021-05-25 [1] standard (@0.5.0)
forcats * 0.5.1 2021-01-27 [1] CRAN (R 4.1.0)
fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.0)
generics 0.1.0 2020-10-31 [1] standard (@0.1.0)
ggplot2 * 3.3.5 2021-06-25 [1] standard (@3.3.5)
glue 1.6.1 2022-01-22 [1] CRAN (R 4.1.2)
gtable 0.3.0 2019-03-25 [1] standard (@0.3.0)
haven 2.4.1 2021-04-23 [1] standard (@2.4.1)
hms 1.1.1 2021-09-26 [1] CRAN (R 4.1.0)
httr 1.4.2 2020-07-20 [1] standard (@1.4.2)
jsonlite 1.7.2 2020-12-09 [1] standard (@1.7.2)
knitr 1.37 2021-12-16 [1] CRAN (R 4.1.0)
lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.0)
lubridate 1.7.10 2021-02-26 [1] standard (@1.7.10)
magrittr 2.0.2 2022-01-26 [1] CRAN (R 4.1.2)
modelr 0.1.8 2020-05-19 [1] standard (@0.1.8)
munsell 0.5.0 2018-06-12 [1] standard (@0.5.0)
pak 0.2.0.9000 2021-12-21 [1] local
pillar 1.6.1 2021-05-16 [1] standard (@1.6.1)
pkgconfig 2.0.3 2019-09-22 [1] standard (@2.0.3)
png 0.1-7 2013-12-03 [1] standard (@0.1-7)
processx 3.5.2 2021-04-30 [1] standard (@3.5.2)
ps 1.6.0 2021-02-28 [1] standard (@1.6.0)
purrr * 0.3.4 2020-04-17 [1] standard (@0.3.4)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.0)
Rcpp 1.0.7 2021-07-07 [1] CRAN (R 4.1.0)
readr * 1.4.0 2020-10-05 [1] standard (@1.4.0)
readxl 1.3.1 2019-03-13 [1] standard (@1.3.1)
reprex 2.0.1 2021-08-05 [1] CRAN (R 4.1.0)
rlang 1.0.0 2022-01-26 [1] CRAN (R 4.1.2)
rprojroot 2.0.2 2020-11-15 [1] standard (@2.0.2)
rsthemes 0.3.1 2022-02-02 [1] Github (gadenbuie/rsthemes@bbe73ca)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0)
rvest 1.0.0 2021-03-09 [1] standard (@1.0.0)
scales 1.1.1 2020-05-11 [1] standard (@1.1.1)
sessioninfo 1.1.1 2018-11-05 [1] standard (@1.1.1)
stringi 1.7.6 2021-11-29 [1] CRAN (R 4.1.0)
stringr * 1.4.0 2019-02-10 [1] standard (@1.4.0)
tibble * 3.1.2 2021-05-16 [1] standard (@3.1.2)
tidyr * 1.1.3 2021-03-03 [1] standard (@1.1.3)
tidyselect 1.1.1 2021-04-30 [1] standard (@1.1.1)
tidyverse * 1.3.1 2021-04-15 [1] CRAN (R 4.1.0)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.0)
vctrs 0.3.8 2021-04-29 [1] standard (@0.3.8)
withr 2.4.2 2021-04-18 [1] standard (@2.4.2)
xfun 0.29 2021-12-14 [1] CRAN (R 4.1.0)
xml2 1.3.2 2020-04-23 [1] standard (@1.3.2)
[1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
@gaborcsardi - given this is on a new version of RStudio/R, how would you recommend proceed to get these pak installations working? I'm inclined to believe that this is a bug in pak, but I may be mistaken.
@shamindras What's the output of these commands from a terminal?
ls -ld /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/_cache
ls -l /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/_cache
@gaborcsardi - those directories threw an error for me, but I adjusted slightly. Please see the output as follows:
terminal output
╭─ ~ ✔ base system
╰─ ls -ld /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/_cache
ls: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/_cache: No such file or directory
╭─ ~ 1 ✘ base system
╰─ ls -l /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/_cache
ls: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/_cache: No such file or directory
╭─ ~ 1 ✘ base system
╰─ \ls -ld /Library/Frameworks/R.framework/Versions/4.1/Resources/library/_cache
drwxrwxr-x 614 root admin 19648 Feb 7 18:36 /Library/Frameworks/R.framework/Versions/4.1/Resources/library/_cache
╭─ ~ ✔ base system
╰─ \ls -l /Library/Frameworks/R.framework/Versions/4.1/Resources/library/_cache
total 0
-rw--w---- 1 root admin 0 Jul 8 2021 AlignAssign.lock
-rw--w---- 1 root admin 0 Jul 8 2021 DBI.lock
-rw--w---- 1 root admin 0 Jul 8 2021 DT.lock
-rw--w---- 1 root admin 0 Jul 8 2021 DiceDesign.lock
-rw--w---- 1 root admin 0 Jul 8 2021 GPfit.lock
-rw--w---- 1 root admin 0 Jul 8 2021 R.cache.lock
-rw--w---- 1 root admin 0 Jul 8 2021 R.methodsS3.lock
-rw--w---- 1 root admin 0 Jul 8 2021 R.oo.lock
-rw--w---- 1 root admin 0 Jul 8 2021 R.utils.lock
-rw--w---- 1 root admin 0 Jul 8 2021 R6.lock
-rw--w---- 1 root admin 0 Jul 8 2021 RColorBrewer.lock
-rw--w---- 1 root admin 0 Sep 15 15:52 RCurl.lock
-rw--w---- 1 root admin 0 Sep 8 16:00 RPostgreSQL.lock
-rw--w---- 1 root admin 0 Nov 18 09:14 RSQLite.lock
-rw--w---- 1 root admin 0 Jul 8 2021 Rcpp.lock
-rw--w---- 1 root admin 0 Jul 11 2021 RcppArmadillo.lock
-rw--w---- 1 root admin 0 Jul 8 2021 Rdpack.lock
-rw--w---- 1 root admin 0 Jul 8 2021 SQUAREM.lock
-rw--w---- 1 root admin 0 Sep 29 15:39 USAboundaries.lock
-rw--w---- 1 root admin 0 Jul 9 2021 WrapRmd.lock
-rw--w---- 1 root admin 0 Jul 31 2021 XML.lock
-rw--w---- 1 root admin 0 Jul 8 2021 abind.lock
drwxrwxr-x 2 root admin 64 Sep 14 12:17 allcontributors
-rw--w---- 1 root admin 0 Sep 12 13:09 allcontributors.lock
-rw--w---- 1 root admin 0 Jul 8 2021 askpass.lock
-rw--w---- 1 root admin 0 Jul 8 2021 assertthat.lock
-rw--w---- 1 root admin 0 Jul 8 2021 backports.lock
-rw--w---- 1 root admin 0 Jul 8 2021 base64enc.lock
-rw--w---- 1 root admin 0 Jul 8 2021 bit.lock
-rw--w---- 1 root admin 0 Jul 8 2021 bit64.lock
-rw--w---- 1 root admin 0 Sep 15 15:52 bitops.lock
-rw--w---- 1 root admin 0 Jul 8 2021 blob.lock
-rw--w---- 1 root admin 0 Jul 8 2021 blogdown.lock
-rw--w---- 1 root admin 0 Jul 8 2021 bookdown.lock
-rw--w---- 1 root admin 0 Jul 8 2021 brew.lock
-rw--w---- 1 root admin 0 Jul 8 2021 brio.lock
-rw--w---- 1 root admin 0 Jul 8 2021 broom.lock
-rw--w---- 1 root admin 0 Jul 8 2021 bslib.lock
-rw--w---- 1 root admin 0 Jul 8 2021 butcher.lock
-rw--w---- 1 root admin 0 Jul 8 2021 cachem.lock
-rw--w---- 1 root admin 0 Jul 8 2021 callr.lock
-rw--w---- 1 root admin 0 Jul 8 2021 cellranger.lock
-rw--w---- 1 root admin 0 Jul 8 2021 classInt.lock
-rw--w---- 1 root admin 0 Jul 8 2021 cli.lock
-rw--w---- 1 root admin 0 Aug 14 14:01 cliapp.lock
-rw--w---- 1 root admin 0 Jul 8 2021 clipr.lock
-rw--w---- 1 root admin 0 Jul 8 2021 collections.lock
-rw--w---- 1 root admin 0 Jul 8 2021 colorspace.lock
-rw--w---- 1 root admin 0 Jul 31 2021 colourlovers.lock
-rw--w---- 1 root admin 0 Jul 8 2021 combinat.lock
-rw--w---- 1 root admin 0 Jul 8 2021 commonmark.lock
-rw--w---- 1 root admin 0 Jul 8 2021 conflicted.lock
-rw--w---- 1 root admin 0 Sep 15 15:52 cowplot.lock
-rw--w---- 1 root admin 0 Jul 8 2021 cpp11.lock
-rw--w---- 1 root admin 0 Jul 8 2021 crayon.lock
-rw--w---- 1 root admin 0 Jul 8 2021 credentials.lock
-rw--w---- 1 root admin 0 Jul 8 2021 crosstalk.lock
-rw--w---- 1 root admin 0 Sep 12 13:09 crul.lock
-rw--w---- 1 root admin 0 Jul 8 2021 curl.lock
-rw--w---- 1 root admin 0 Jul 8 2021 cyclocomp.lock
-rw--w---- 1 root admin 0 Jul 8 2021 data.table.lock
-rw--w---- 1 root admin 0 Jul 8 2021 datapasta.lock
-rw--w---- 1 root admin 0 Jul 8 2021 dbplyr.lock
-rw--w---- 1 root admin 0 Jul 8 2021 desc.lock
-rw--w---- 1 root admin 0 Sep 13 13:05 details.lock
-rw--w---- 1 root admin 0 Jul 8 2021 devtools.lock
-rw--w---- 1 root admin 0 Jul 8 2021 dials.lock
-rw--w---- 1 root admin 0 Jul 8 2021 diffobj.lock
-rw--w---- 1 root admin 0 Jul 8 2021 digest.lock
-rw--w---- 1 root admin 0 Jul 8 2021 distill.lock
-rw--w---- 1 root admin 0 Jul 8 2021 downlit.lock
-rw--w---- 1 root admin 0 Jul 8 2021 dplyr.lock
-rw--w---- 1 root admin 0 Jul 8 2021 dtplyr.lock
-rw--w---- 1 root admin 0 Jul 8 2021 e1071.lock
-rw--w---- 1 root admin 0 Jul 8 2021 ellipsis.lock
-rw--w---- 1 root admin 0 Jul 8 2021 emo.lock
-rw--w---- 1 root admin 0 Jul 8 2021 ermoji.lock
-rw--w---- 1 root admin 0 Jul 8 2021 evaluate.lock
-rw--w---- 1 root admin 0 Jul 8 2021 fansi.lock
-rw--w---- 1 root admin 0 Jul 8 2021 farver.lock
-rw--w---- 1 root admin 0 Jul 8 2021 fastmap.lock
drwxrwxr-x 2 root admin 64 Aug 14 14:01 file10825777adb49
drwxrwxr-x 2 root admin 64 Jul 13 2021 file12ca94cc76095
drwxrwxr-x 2 root admin 64 Jul 13 2021 file12ca9a3b1b08
drwxrwxr-x 2 root admin 64 Jul 8 2021 file13d632d9bb2a4
drwxrwxr-x 2 root admin 64 Jul 8 2021 file13d6360a7c028
drwxrwxr-x 2 root admin 64 Jul 8 2021 file1425810c863c1
drwxrwxr-x 2 root admin 64 Jul 8 2021 file1425828cac5ea
drwxrwxr-x 2 root admin 64 Jul 8 2021 file14258540d1c82
drwxrwxr-x 2 root admin 64 Jul 8 2021 file146c72619ac37
drwxrwxr-x 2 root admin 64 Jul 8 2021 file146c72d06f634
drwxrwxr-x 2 root admin 64 Jul 8 2021 file146c75f79626b
drwxrwxr-x 2 root admin 64 Jul 8 2021 file146c77983777c
drwxrwxr-x 2 root admin 64 Jul 8 2021 file146c7cb9ca1a
drwxrwxr-x 2 root admin 64 Jul 8 2021 file1472247300d8b
drwxrwxr-x 2 root admin 64 Jul 8 2021 file1472250182eb5
drwxrwxr-x 2 root admin 64 Jul 8 2021 file1472263a29627
drwxrwxr-x 2 root admin 64 Jul 8 2021 file14722653c37b4
drwxrwxr-x 2 root admin 64 Sep 8 16:00 file157b217fc2efc
drwxrwxr-x 2 root admin 64 Sep 8 16:00 file157b22d70aeb1
drwxrwxr-x 2 root admin 64 Sep 8 16:00 file157b234f653de
drwxrwxr-x 2 root admin 64 Sep 8 16:00 file157b260a9f0a6
drwxrwxr-x 2 root admin 64 Jul 9 2021 file157db509f3cfa
drwxrwxr-x 2 root admin 64 Sep 8 16:00 file157e2723924c9
drwxrwxr-x 3 root admin 96 Sep 8 16:09 file15a4c15123171
drwxrwxr-x 3 root admin 96 Sep 8 16:09 file15a4c2a043de4
drwxrwxr-x 3 root admin 96 Sep 8 16:09 file15a4c3a6fbbd2
drwxrwxr-x 3 root admin 96 Sep 8 16:09 file15a4c54e91f7c
drwxrwxr-x 3 root admin 96 Sep 8 16:09 file15a4c5c8fafad
drwxrwxr-x 3 root admin 96 Sep 8 16:09 file15a4c5d56b654
drwxrwxr-x 3 root admin 96 Sep 8 16:09 file15a4c5d6bfc85
drwxrwxr-x 3 root admin 96 Sep 8 16:09 file15a4c622c5d1
drwxrwxr-x 3 root admin 96 Sep 8 16:09 file15a4c67dc74ab
drwxrwxr-x 3 root admin 96 Sep 8 16:09 file15a4c7d93f5f6
drwxrwxr-x 3 root admin 96 Sep 24 12:50 file1d134bc90c2c
drwxrwxr-x 3 root admin 96 Sep 24 12:50 file1d13670a0744
drwxrwxr-x 3 root admin 96 Sep 24 12:50 file1d3c223eb1be
drwxrwxr-x 3 root admin 96 Dec 25 15:25 file2d9e12e6353f
drwxrwxr-x 3 root admin 96 Dec 25 15:25 file2d9e2017b680
drwxrwxr-x 3 root admin 96 Dec 25 15:25 file2d9e290cffa8
drwxrwxr-x 3 root admin 96 Dec 25 15:25 file2d9e3cb9c5b0
drwxrwxr-x 3 root admin 96 Dec 25 15:25 file2d9e47b1c4ca
drwxrwxr-x 3 root admin 96 Dec 25 15:25 file2d9e4861c4f5
drwxrwxr-x 3 root admin 96 Dec 25 15:25 file2d9e48fd4a0d
drwxrwxr-x 3 root admin 96 Dec 25 15:25 file2d9e52ff11bf
drwxrwxr-x 3 root admin 96 Dec 25 15:25 file2d9e5879bbc9
drwxrwxr-x 3 root admin 96 Dec 25 15:25 file2d9e59b17a92
drwxrwxr-x 3 root admin 96 Dec 25 15:25 file2d9e67e63d2a
drwxrwxr-x 3 root admin 96 Dec 25 15:25 file2d9e67eece8b
drwxrwxr-x 3 root admin 96 Dec 25 15:25 file2d9e6d08c0ea
drwxrwxr-x 3 root admin 96 Dec 25 15:25 file2d9e6f3a3cfb
drwxrwxr-x 3 root admin 96 Dec 25 15:25 file2d9e74ce9df5
drwxrwxr-x 3 root admin 96 Dec 25 15:25 file2d9eac9d5f3
drwxrwxr-x 3 root admin 96 Dec 25 15:27 file2e7e1cd68e2c
drwxrwxr-x 3 root admin 96 Dec 25 15:27 file2e7e20da235c
drwxrwxr-x 3 root admin 96 Dec 25 15:27 file2e7e281bac5a
drwxrwxr-x 3 root admin 96 Dec 25 15:27 file2e7e29e5df47
drwxrwxr-x 3 root admin 96 Dec 25 15:27 file2e7e30d05d48
drwxrwxr-x 3 root admin 96 Dec 25 15:27 file2e7e32a5c3ce
drwxrwxr-x 3 root admin 96 Dec 25 15:27 file2e7e33a97200
drwxrwxr-x 3 root admin 96 Dec 25 15:27 file2e7e3f9c3b01
drwxrwxr-x 3 root admin 96 Dec 25 15:27 file2e7e4842d984
drwxrwxr-x 3 root admin 96 Dec 25 15:27 file2e7e4a0ff97e
drwxrwxr-x 3 root admin 96 Dec 25 15:27 file2e7e50a25f9d
drwxrwxr-x 3 root admin 96 Dec 25 15:27 file2e7e543365c6
drwxrwxr-x 3 root admin 96 Dec 25 15:27 file2e7e5923f754
drwxrwxr-x 3 root admin 96 Dec 25 15:27 file2e7e5ec4e52e
drwxrwxr-x 3 root admin 96 Dec 25 15:27 file2e7e680904d2
drwxrwxr-x 3 root admin 96 Dec 25 15:27 file2e7e7a5ed559
drwxrwxr-x 3 root admin 96 Dec 25 15:28 file2f0e1ed37cc7
drwxrwxr-x 3 root admin 96 Dec 25 15:28 file2f0e20b30db0
drwxrwxr-x 3 root admin 96 Dec 25 15:28 file2f0e23c75ddd
drwxrwxr-x 3 root admin 96 Dec 25 15:28 file2f0e25663c93
drwxrwxr-x 3 root admin 96 Dec 25 15:28 file2f0e35837230
drwxrwxr-x 3 root admin 96 Dec 25 15:28 file2f0e36c5b41b
drwxrwxr-x 3 root admin 96 Dec 25 15:28 file2f0e44e9cf7e
drwxrwxr-x 3 root admin 96 Dec 25 15:28 file2f0e48bdc8c2
drwxrwxr-x 3 root admin 96 Dec 25 15:28 file2f0e4b47ae95
drwxrwxr-x 3 root admin 96 Dec 25 15:28 file2f0e4f16decf
drwxrwxr-x 3 root admin 96 Dec 25 15:28 file2f0e5b12ea13
drwxrwxr-x 3 root admin 96 Dec 25 15:28 file2f0e5e73e160
drwxrwxr-x 3 root admin 96 Dec 25 15:28 file2f0e667e1099
drwxrwxr-x 3 root admin 96 Dec 25 15:28 file2f0e6db374b4
drwxrwxr-x 3 root admin 96 Dec 25 15:28 file2f0e75e36a84
drwxrwxr-x 3 root admin 96 Dec 25 15:28 file2f0e9d19612
drwxrwxr-x 3 root admin 96 Dec 25 15:30 file2fdb1c2f1ed1
drwxrwxr-x 3 root admin 96 Dec 25 15:30 file2fdb29454f74
drwxrwxr-x 3 root admin 96 Dec 25 15:30 file2fdb34b4bb19
drwxrwxr-x 3 root admin 96 Dec 25 15:30 file2fdb3e4d5ff7
drwxrwxr-x 3 root admin 96 Dec 25 15:30 file2fdb3ea5d104
drwxrwxr-x 3 root admin 96 Dec 25 15:30 file2fdb45678157
drwxrwxr-x 3 root admin 96 Dec 25 15:30 file2fdb49d77115
drwxrwxr-x 3 root admin 96 Dec 25 15:30 file2fdb4cc1b8a5
drwxrwxr-x 3 root admin 96 Dec 25 15:30 file2fdb5036cef5
drwxrwxr-x 3 root admin 96 Dec 25 15:30 file2fdb5635dd7
drwxrwxr-x 3 root admin 96 Dec 25 15:30 file2fdb5a3ae3a2
drwxrwxr-x 3 root admin 96 Dec 25 15:30 file2fdb5f413f92
drwxrwxr-x 3 root admin 96 Dec 25 15:30 file2fdb61999213
drwxrwxr-x 3 root admin 96 Dec 25 15:30 file2fdb783d7dbd
drwxrwxr-x 3 root admin 96 Dec 25 15:30 file2fdbd0a40f7
drwxrwxr-x 3 root admin 96 Dec 25 15:30 file2fdbe5c9a5a
drwxrwxr-x 3 root admin 96 Dec 25 15:34 file30ba12bc52e0
drwxrwxr-x 3 root admin 96 Dec 25 15:34 file30ba17c7aab7
drwxrwxr-x 3 root admin 96 Dec 25 15:34 file30ba1c4c9b6c
drwxrwxr-x 3 root admin 96 Dec 25 15:34 file30ba241fd126
drwxrwxr-x 3 root admin 96 Dec 25 15:34 file30ba24dc2851
drwxrwxr-x 3 root admin 96 Dec 25 15:34 file30ba3598e093
drwxrwxr-x 3 root admin 96 Dec 25 15:34 file30ba47bfee62
drwxrwxr-x 3 root admin 96 Dec 25 15:34 file30ba4a2f4e60
drwxrwxr-x 3 root admin 96 Dec 25 15:34 file30ba5cf38457
drwxrwxr-x 3 root admin 96 Dec 25 15:34 file30ba67c2a6ac
drwxrwxr-x 3 root admin 96 Dec 25 15:34 file30ba71daf0be
drwxrwxr-x 3 root admin 96 Dec 25 15:34 file30ba770db1fa
drwxrwxr-x 3 root admin 96 Dec 25 15:34 file30ba77759b6d
drwxrwxr-x 3 root admin 96 Dec 25 15:34 file30ba9bb88bb
drwxrwxr-x 3 root admin 96 Dec 25 15:34 file30ba9e4f9bc
drwxrwxr-x 3 root admin 96 Dec 25 15:34 file30bad38f4ab
drwxrwxr-x 3 root admin 96 Dec 25 15:44 file312c129e5693
drwxrwxr-x 3 root admin 96 Dec 25 15:44 file312c12ef25db
drwxrwxr-x 3 root admin 96 Dec 25 15:39 file312c12fcfed4
drwxrwxr-x 3 root admin 96 Dec 25 15:39 file312c1a416162
drwxrwxr-x 3 root admin 96 Dec 25 15:39 file312c1b4f6dcf
drwxrwxr-x 3 root admin 96 Dec 25 15:39 file312c1e74ac80
drwxrwxr-x 3 root admin 96 Dec 25 15:39 file312c1fbe1a09
drwxrwxr-x 3 root admin 96 Dec 25 15:44 file312c29bce99d
drwxrwxr-x 3 root admin 96 Dec 25 15:44 file312c2c3095d5
drwxrwxr-x 3 root admin 96 Dec 25 15:44 file312c2d5dd10d
drwxrwxr-x 3 root admin 96 Dec 25 15:44 file312c318d57d3
drwxrwxr-x 3 root admin 96 Dec 25 15:39 file312c35008a03
drwxrwxr-x 3 root admin 96 Dec 25 15:39 file312c3664e624
drwxrwxr-x 3 root admin 96 Dec 25 15:39 file312c37b6eb42
drwxrwxr-x 3 root admin 96 Dec 25 15:39 file312c3a607665
drwxrwxr-x 3 root admin 96 Dec 25 15:44 file312c3b889f0d
drwxrwxr-x 3 root admin 96 Dec 25 15:39 file312c4a0f56a1
drwxrwxr-x 3 root admin 96 Dec 25 15:39 file312c4b8f702b
drwxrwxr-x 3 root admin 96 Dec 25 15:44 file312c4c5964f2
drwxrwxr-x 3 root admin 96 Dec 25 15:39 file312c51ecf326
drwxrwxr-x 3 root admin 96 Dec 25 15:44 file312c5945d671
drwxrwxr-x 3 root admin 96 Dec 25 15:44 file312c6822d04
drwxrwxr-x 3 root admin 96 Dec 25 15:44 file312c6a47c3bf
drwxrwxr-x 3 root admin 96 Dec 25 15:44 file312c6f8d6632
drwxrwxr-x 3 root admin 96 Dec 25 15:39 file312c7348e8f7
drwxrwxr-x 3 root admin 96 Dec 25 15:44 file312c7801c280
drwxrwxr-x 3 root admin 96 Dec 25 15:39 file312c799f5526
drwxrwxr-x 3 root admin 96 Dec 25 15:39 file312c7bb23f0a
drwxrwxr-x 3 root admin 96 Dec 25 15:39 file312c7de9171e
drwxrwxr-x 3 root admin 96 Dec 25 15:44 file312c8247aa2
drwxrwxr-x 3 root admin 96 Dec 25 15:44 file312cd84671c
drwxrwxr-x 3 root admin 96 Dec 25 15:44 file312cf27307
drwxrwxr-x 3 root admin 96 Dec 25 15:45 file31b811604077
drwxrwxr-x 3 root admin 96 Dec 25 15:45 file31b814afaf48
drwxrwxr-x 3 root admin 96 Dec 25 15:45 file31b81a1caa94
drwxrwxr-x 3 root admin 96 Dec 25 15:45 file31b81cfeaf6f
drwxrwxr-x 3 root admin 96 Dec 25 15:45 file31b82818b84b
drwxrwxr-x 3 root admin 96 Dec 25 15:45 file31b83cec7f21
drwxrwxr-x 3 root admin 96 Dec 25 15:47 file31b84190aa4e
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-rw--w---- 1 root admin 0 Jul 11 2021 zoo.lock
So the issue is that when you use root user, via sudo or another way, you create lock files that are owned by root, and then when you use your non-root user you cannot lock these files, because they belong to root.
The solution is to delete the whole _cache directory.
I'll try yo have a better solution or at least a better error message for this case.
So the issue is that when you use root user, via sudo or another way, you create lock files that are owned by root, and then when you use your non-root user you cannot lock these files, because they belong to root.
The solution is to delete the whole
_cachedirectory.
Ah - interesting. Thanks for looking into this. So you mean I should just do as root the following:
rm -rf /Library/Frameworks/R.framework/Versions/4.1/Resources/library/_cache
And then re-run the pak installation?
I'll try yo have a better solution or at least a better error message for this case.
This would be great going forward. If you can flag it to this thread or tag me with updates on this, I'd appreciate it.
As a background, I TA our Stat computing course and am trying to get more students to use pak to simplify large scale package installation. However due to such issues we can't use pak as the preferred installation method currently.
I don't think this is a common issue, though.
FWIW a good practice is to create user-library with
dir.create(Sys.getenv("R_LIBS_USER"), recursive=TRUE)
(and then a restart), and then using your regular user to install packages. This keeps the system packages separate, and they are not wiped out for a minor R update. It also decreases the chance that you'd need to use sudo or the root user to install packages.
I think this suggestion (to separate user and system libraries) is very valuable. Do you think it would be useful to make it more prominent in the documentation and / or have a helper function (for which usethis could maybe be a home for)?
@dragosmg pak could print some advice if it sees that it is installing into the system library? (Maybe not on Linux, because containers often use the single library.)
IDK if people would find a helper function by themselves.
@gaborcsardi I think printing some advice would go a long way in helping people use pak. I can imagine users not being persistent (I know I have not been in the past) if they bump into a lock file issue without some indication of how they can get out of it.
thanks @gaborcsardi @dragosmg for the ongoing discussion on this issue. Some comments and queries:
I don't think this is a common issue, though.
That's fair. I was a little cautious recommending pak since this issue was (for me) persistent across R/RStudio installations. If there is a constructive way to get out of the lock, or set things up front to avoid this, I think documenting it would be great in an error msg for the user. It seems like you have a an approach to this, which is great.
FWIW a good practice is to create user-library with
dir.create(Sys.getenv("R_LIBS_USER"), recursive=TRUE)(and then a restart), and then using your regular user to install packages. This keeps the system packages separate, and they are not wiped out for a minor R update. It also decreases the chance that you'd need to use
sudoor the root user to install packages.
So I'd like to understand this more clearly, especially if this is a way to avoid such lock issues going forward. To fix this issue I followed your first suggestion, namely (on a new installation of R/RStudio) I did the following:
-
rm -rf /Library/Frameworks/R.framework/Versions/4.1/Resources/library/_cache - Install
pakusinginstall.packages("pak", repos = "https://r-lib.github.io/p/pak/devel/") - Run the packages installation script using
pakas above
This approach worked. However, I had some queries about your other suggestion. Which seems to be a way to avoid such issues up front.
@gaborcsardi - I don't quite understand what to do with your new approach (assuming starting on a clean R/RStudio installation). Specifically:
- What is
dir.create(Sys.getenv("R_LIBS_USER"), recursive=TRUE)meant to do? - I noticed the following directory already exists:
> Sys.getenv("R_LIBS_USER")
[1] "~/Library/R/x86_64/4.1/library"
Is it still safe to run your suggested line of code in Step 1?
- How does
pakuse this newly created directory? Do I need to do anything as a user during future installations to point to this newly created directory? - How is this separating
userfromrootinpakinstallation? - How do I avoid installing anything as
rootin the first place? I just tried to run mypakpackages installation script fromRStudioas usual, so not sure how this issue came up.
In short, I'm nervous about changing these settings without some more clarification. If you or @dragosmg could kindly help me (and others) understand better, I'd really appreciate it.
Note: @gaborcsardi I think pak is 💯 , and I really want to get more students using it. But need to understand the above better myself before doing so.
What is dir.create(Sys.getenv("R_LIBS_USER"), recursive=TRUE) meant to do?
Create a directory for the current user's package library. (Don't do this as the root user, obviously.) If that directory exists then it does nothing. R automatically uses this library if it exists.
Is it still safe to run your suggested line of code in Step 1?
Yes.
How does pak use this newly created directory?
R adds it to the library path (see .libPaths()) automatically if it exists. pak uses the first library on the library path by default.
Do I need to do anything as a user during future installations to point to this newly created directory?
No.
How is this separating user from root in pak installation?
On macOS you generally don't need to run R as root, ever, not even the installer.
How do I avoid installing anything as root in the first place? I just tried to run my pak packages installation script from RStudio as usual, so not sure how this issue came up.
You never use the root/admin user to start R, e.g. never use sudo. I can't tell what you did exactly, but those files are owned by the root user, which means that they were created by a process running as the root user.
Thanks @gaborcsardi. That does help clarify things. I'm not sure how I installed the pak packages using root.
Just one thing
> Sys.getenv("R_LIBS_USER")
[1] "~/Library/R/x86_64/4.1/library"
> .libPaths()
[1] "/Library/Frameworks/R.framework/Versions/4.1/Resources/library"
> dir.create(Sys.getenv("R_LIBS_USER"), recursive=TRUE)
Warning message:
In dir.create(Sys.getenv("R_LIBS_USER"), recursive = TRUE) :
'/Users/shamindras/Library/R/x86_64/4.1/library' already exists
> .libPaths()
[1] "/Library/Frameworks/R.framework/Versions/4.1/Resources/library"
I don't see the Sys.getenv("R_LIBS_USER") directory added to the .LibPaths(). Am I doing this correctly?
Note, I'm doing a full test of your advice with a clean R/RStudio installation currently.
I don't see the Sys.getenv("R_LIBS_USER") directory added to the .LibPaths(). Am I doing this correctly?
You need to restart R to take effect, because R checks its existence at startup.
Note, I'm doing a full test of your advice with a clean R/RStudio installation currently.
That is not really necessary. If you keep the user's package directory separate, nothing can happen to the R installation.
I don't see the Sys.getenv("R_LIBS_USER") directory added to the .LibPaths(). Am I doing this correctly?
You need to restart R to take effect, because R checks its existence at startup.
Thanks! Sorry I missed this previously. It works now.
Note, I'm doing a full test of your advice with a clean R/RStudio installation currently.
That is not really necessary. If you keep the user's package directory separate, nothing can happen to the R installation.
Agreed, though I was just simulating a fresh installation since something went wrong for me here and led to this issue. I've just consolidated the following steps for convenience of readers, as follows:
- Install the latest
R/RStudio(This can be skipped as @gaborcsardi mentioned). - Open
RStudio. - Run
dir.create(Sys.getenv("R_LIBS_USER"), recursive=TRUE). This creates a directory for the current user's package library - Restart R.
- Check that the user directory is added to the top of the library path by running
.libPaths()in the R console. - Install
pakper the instructions. - Install required packages using
pak, e.g., using a script from this post.
Thanks again @gaborcsardi for pak and your patient help here. Appreciate it.
Just to confirm that this issue affected me as well (for a while now), and I was unable to find a solution until I came here.
I followed the suggestion of @dragosmg and deleted all the *.lock files in file.path(.libPaths()[1],"_cache") and now pak::pak() works like a charm. I did not delete anything else from the _cache dir.
I can confirm that most of the deled files were owned by me, but a chunk was owned by root which probably caused the problem. Not all root-owned files were from the same day, but they were from the same month (last May). I don't usually switch users or run RStudio elevated, but perhaps something caused elevation at some point, and perhaps I left R running for a week or two, updating with pak several times during that period(? because usually I will hit CTRL-0 to restart R before/after any package install), causing a buildup of root-owned lock files that then caused the issue after restarting R with normal privileges.
Agree that improving error messages – perhaps including the full path to the offending lock file – would be sufficient to close this. That would probably have let me fix this in under a minute.
Quick update, I ran into this issue again after updating R+RStudio. Now I did not find a _cache except with an renv directory (that should not have been active), but I deleted it anyway. However, now Sys.getenv("R_LIBS_USER") did not exist, so I ran:
dir.create(Sys.getenv("R_LIBS_USER"), recursive=TRUE)
And now things work again.