"Permission denied" when renv tries to delete temporary sandbox after rendering a .qmd file using renv::embed

[venpopov]

I used renv::embed("file.qmd") as described here.

echo "---\ntitle: "renvtest"\n---" > test.qmd
Rscript -e "renv::embed('test.qmd')"
quarto render test.qmd

I get a bunch of permission errors when renv tries to delete temporary library files:

processing file: test.qmd
1/3           
2/3 [lockfile]
3/3           
output file: test.knit.md

rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/MASS: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/.renv-sandbox: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/cluster: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/parallel: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/tools: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/methods: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/boot: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/datasets: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/nnet: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/tcltk: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/utils: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/stats4: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/rpart: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/lattice: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/nlme: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/splines: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/grDevices: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/class: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/mgcv: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/codetools: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/spatial: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/graphics: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/foreign: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/compiler: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/Matrix: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/KernSmooth: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/base: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/stats: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/survival: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox/grid: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf/renv-sandbox: Permission denied
rm: /var/folders/6q/td28f3fx31x94xnn2_07qpbh0000gn/T//RtmpKrPnXf: Permission denied
pandoc 
  to: html
  output-file: test.html
  standalone: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  title: renvtest
  
Output created: test.html

My user is the owner and has full permissions to read, write and execute files from the temporary folder:

total 0
-rw-r--r--@ 1 venpopov  staff     0B Jan 15 13:09 .renv-sandbox
lrwxr-xr-x@ 1 venpopov  staff    79B Jan 15 13:09 KernSmooth -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/KernSmooth
lrwxr-xr-x@ 1 venpopov  staff    73B Jan 15 13:09 MASS -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/MASS
lrwxr-xr-x@ 1 venpopov  staff    75B Jan 15 13:09 Matrix -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Matrix
lrwxr-xr-x@ 1 venpopov  staff    73B Jan 15 13:09 base -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/base
lrwxr-xr-x@ 1 venpopov  staff    73B Jan 15 13:09 boot -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/boot
lrwxr-xr-x@ 1 venpopov  staff    74B Jan 15 13:09 class -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/class
lrwxr-xr-x@ 1 venpopov  staff    76B Jan 15 13:09 cluster -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cluster
lrwxr-xr-x@ 1 venpopov  staff    78B Jan 15 13:09 codetools -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/codetools
lrwxr-xr-x@ 1 venpopov  staff    77B Jan 15 13:09 compiler -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/compiler
lrwxr-xr-x@ 1 venpopov  staff    77B Jan 15 13:09 datasets -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/datasets
lrwxr-xr-x@ 1 venpopov  staff    76B Jan 15 13:09 foreign -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/foreign
lrwxr-xr-x@ 1 venpopov  staff    78B Jan 15 13:09 grDevices -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/grDevices
lrwxr-xr-x@ 1 venpopov  staff    77B Jan 15 13:09 graphics -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/graphics
lrwxr-xr-x@ 1 venpopov  staff    73B Jan 15 13:09 grid -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/grid
lrwxr-xr-x@ 1 venpopov  staff    76B Jan 15 13:09 lattice -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/lattice
lrwxr-xr-x@ 1 venpopov  staff    76B Jan 15 13:09 methods -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/methods
lrwxr-xr-x@ 1 venpopov  staff    73B Jan 15 13:09 mgcv -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/mgcv
lrwxr-xr-x@ 1 venpopov  staff    73B Jan 15 13:09 nlme -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/nlme
lrwxr-xr-x@ 1 venpopov  staff    73B Jan 15 13:09 nnet -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/nnet
lrwxr-xr-x@ 1 venpopov  staff    77B Jan 15 13:09 parallel -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/parallel
lrwxr-xr-x@ 1 venpopov  staff    74B Jan 15 13:09 rpart -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rpart
lrwxr-xr-x@ 1 venpopov  staff    76B Jan 15 13:09 spatial -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/spatial
lrwxr-xr-x@ 1 venpopov  staff    76B Jan 15 13:09 splines -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/splines
lrwxr-xr-x@ 1 venpopov  staff    74B Jan 15 13:09 stats -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/stats
lrwxr-xr-x@ 1 venpopov  staff    75B Jan 15 13:09 stats4 -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/stats4
lrwxr-xr-x@ 1 venpopov  staff    77B Jan 15 13:09 survival -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/survival
lrwxr-xr-x@ 1 venpopov  staff    74B Jan 15 13:09 tcltk -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/tcltk
lrwxr-xr-x@ 1 venpopov  staff    74B Jan 15 13:09 tools -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/tools
lrwxr-xr-x@ 1 venpopov  staff    74B Jan 15 13:09 utils -> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/utils

but not for the parent directory "renv-sandbox":

dr-xr-xr-x@ 32 venpopov  staff   1.0K Jan 15 13:09 renv-sandbox

[hutch3232]

I get this error as well in a CI/CD process where I call renv::use. It hasn't caused issues for me though, just more of a minor nuisance.

Looks related to this

renv/R/sandbox.R

Line 246 in 65bf458

mode == 365L # as.integer(as.octmode("0555"))

But I haven't looked in depth.

[kevinushey]

Thanks for the bug report -- I'm going to take a look.