Installing to site-library with a different user fails

[AlexAxthelm]

Hi, loving the utility and flexibility of pak!

I've encountered what might be an edge-case issue, but if I can find a solution, it would really help.

I'm calling pak as part of my docker build process, and when I try to run pak multiple times, as different (unix) users (which are part of the staff group, which has permissions to site-library), the process is failing, with similar messages to those reported in #310.

#12 33.01 Error:
#12 33.01 ! error in pak subprocess
#12 33.01 Caused by error in `verify_extracted_package(filename, pkg_cache)`:
#12 33.01 !
#12 33.01 '/tmp/Rtmp9AYWUh/file3614634922/src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.3/praise_1.0.0.tar.gz'
#12 33.01 is not a valid R package, it is an empty archive.
#12 33.01 ---
#12 33.01 Backtrace:
#12 33.01 1. pak::pak("praise")
#12 33.01 2. pak::pkg_install(pkg, ...)
#12 33.01 3. pak:::remote(function(...) get("pkg_install_do_plan", asNamespace("pak"))(...), …
#12 33.01 4. err$throw(res$error)
#12 33.01 ---

---

Repro Steps

I've constructed a (mostly) minimal Dockerfile that demonstrates the issue. In it, I:

1. set the CRAN repo to Posit Package manager (binaries)
2. Install pak
3. Install a package, using pak
4. Add and set a demo user (adding them to the staff group)
5. Prove that the new user has write permissions to site-library
6. (Attempt to) install another package.

FROM docker.io/rocker/r-ver:4.3.1 AS base

# set frozen CRAN repo and RProfile.site
RUN echo "options(repos = c(CRAN = 'https://packagemanager.posit.co/cran/__linux__/jammy/2023-10-30'))" \
  > "${R_HOME}/etc/Rprofile.site"

# Install pak
RUN Rscript -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'

RUN whoami

RUN Rscript -e 'pak::pak("base64enc")'

# Create and use non-root user
# -m creates a home directory,
# -G adds user to staff group allowing R package installation.
RUN useradd \
      -m \
      -G staff \
      demo-user
USER demo-user
WORKDIR /home/demo-user

# prove that we have permissions on site-library
RUN whoami \
      && touch /usr/local/lib/R/site-library/foo.txt \
      && rm /usr/local/lib/R/site-library/foo.txt

RUN Rscript -e "\
    pak::pak('praise'); \
    "

In this example, praise can be installed under any of the following conditions:

• The first pak::pak() command is not run
• the first package is intalled with install.packages
• The user is not changed

Things that do not get the second package to install:

• running pak::cache_clean()
• Installing from source, rather than binaries (Posit Package Manager)

Docker Build Logs

Build Log

$ docker build --no-cache . -t pak_demo
#0 building with "desktop-linux" instance using docker driver

#1 [internal] load .dockerignore
#1 transferring context: 2B done
#1 DONE 0.0s

#2 [internal] load build definition from Dockerfile
#2 transferring dockerfile: 932B done
#2 DONE 0.0s

#3 [internal] load metadata for docker.io/rocker/r-ver:4.3.1
#3 DONE 0.0s

#4 [1/9] FROM docker.io/rocker/r-ver:4.3.1
#4 CACHED

#5 [2/9] RUN echo "options(repos = c(CRAN = 'https://packagemanager.posit.co/cran/__linux__/jammy/2023-10-30'))"   > "/usr/local/lib/R/etc/Rprofile.site"
#5 DONE 0.1s

#6 [3/9] RUN Rscript -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
#6 1.175 Installing package into ‘/usr/local/lib/R/site-library’
#6 1.175 (as ‘lib’ is unspecified)
#6 1.807 trying URL 'https://r-lib.github.io/p/pak/stable/source/linux-gnu/x86_64/src/contrib/../../../../../linux/x86_64/pak_0.7.2_R-4-3_x86_64-linux.tar.gz'
#6 2.270 Content type 'application/gzip' length 8038050 bytes (7.7 MB)
#6 2.377 ==================================================
#6 2.861 downloaded 7.7 MB
#6 2.861
#6 6.852 * installing *binary* package ‘pak’ ...
#6 6.924 * DONE (pak)
#6 6.982
#6 6.982 The downloaded source packages are in
#6 6.982        ‘/tmp/RtmpHREPme/downloaded_packages’
#6 DONE 7.1s

#7 [4/9] RUN whoami
#7 0.285 root
#7 DONE 0.3s

#8 [5/9] RUN Rscript -e 'pak::pak("base64enc")'
#8 5.155
#8 9.011 ✔ Updated metadata database: 3.59 MB in 9 files.
#8 9.014
#8 9.018 ℹ Updating metadata database
#8 25.54 ✔ Updating metadata database ... done
#8 25.55
#8 26.09
#8 26.12 → Will install 1 package.
#8 26.19 → Will download 1 package with unknown size.
#8 26.20 + base64enc   0.1-3 [dl]
#8 26.21
#8 26.71 ℹ Getting 1 pkg with unknown size
#8 27.80 ✔ Got base64enc 0.1-3 (x86_64-pc-linux-gnu-ubuntu-22.04) (26.09 kB)
#8 28.25 ✔ Installed base64enc 0.1-3  (155ms)
#8 28.30 ✔ 1 pkg: added 1, dld 1 (26.09 kB) [27s]
#8 DONE 28.5s

#9 [6/9] RUN useradd       -m       -G staff       demo-user
#9 DONE 0.3s

#10 [7/9] WORKDIR /home/demo-user
#10 DONE 0.0s

#11 [8/9] RUN whoami       && touch /usr/local/lib/R/site-library/foo.txt       && rm /usr/local/lib/R/site-library/foo.txt
#11 0.199 demo-user
#11 DONE 0.2s

#12 [9/9] RUN Rscript -e "    pak::pak('praise');     "
#12 5.353
#12 9.093 ✔ Updated metadata database: 3.59 MB in 9 files.
#12 9.097
#12 9.100 ℹ Updating metadata database
#12 25.54 ✔ Updating metadata database ... done
#12 25.54
#12 26.21
#12 26.24 → Will install 1 package.
#12 26.30 → Will download 1 package with unknown size.
#12 26.32 + praise   1.0.0 [dl]
#12 26.33
#12 26.86 ℹ Getting 1 pkg with unknown size
#12 28.19 ✔ Got praise 1.0.0 (x86_64-pc-linux-gnu-ubuntu-22.04) (16.15 kB)
#12 33.01 Error:
#12 33.01 ! error in pak subprocess
#12 33.01 Caused by error in `verify_extracted_package(filename, pkg_cache)`:
#12 33.01 !
#12 33.01 '/tmp/Rtmp9AYWUh/file3614634922/src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.3/praise_1.0.0.tar.gz'
#12 33.01 is not a valid R package, it is an empty archive.
#12 33.01 ---
#12 33.01 Backtrace:
#12 33.01 1. pak::pak("praise")
#12 33.01 2. pak::pkg_install(pkg, ...)
#12 33.01 3. pak:::remote(function(...) get("pkg_install_do_plan", asNamespace("pak"))(...), …
#12 33.01 4. err$throw(res$error)
#12 33.01 ---
#12 33.01 Subprocess backtrace:
#12 33.01  1. base::withCallingHandlers(cli_message = function(msg) { …
#12 33.01  2. get("pkg_install_do_plan", asNamespace("pak"))(...)
#12 33.01  3. proposal$install()
#12 33.01  4. pkgdepends::install_package_plan(plan, lib = private$library, num_workers = nw, …
#12 33.01  5. base::withCallingHandlers({ …
#12 33.01  6. pkgdepends:::handle_events(state, events)
#12 33.01  7. pkgdepends:::handle_event(state, i)
#12 33.01  8. proc$get_result()
#12 33.01  9. processx:::process_get_result(self, private)
#12 33.01 10. private$post_process()
#12 33.01 11. pkgdepends:::install_extracted_binary(filename, lib_cache, pkg_cache, lib, …
#12 33.01 12. pkgdepends:::verify_extracted_package(filename, pkg_cache)
#12 33.01 13. base::throw(pkg_error("{.path {filename}} is not a valid R package, it is an emp…
#12 33.01 14. | base::signalCondition(cond)
#12 33.01 15. global (function (e) …
#12 33.01 Execution halted
#12 ERROR: process "/bin/sh -c Rscript -e \"    pak::pak('praise');     \"" did not complete successfully: exit code: 1
------
 > [9/9] RUN Rscript -e "    pak::pak('praise');     ":
33.01  7. pkgdepends:::handle_event(state, i)
33.01  8. proc$get_result()
33.01  9. processx:::process_get_result(self, private)
33.01 10. private$post_process()
33.01 11. pkgdepends:::install_extracted_binary(filename, lib_cache, pkg_cache, lib, …
33.01 12. pkgdepends:::verify_extracted_package(filename, pkg_cache)
33.01 13. base::throw(pkg_error("{.path {filename}} is not a valid R package, it is an emp…
33.01 14. | base::signalCondition(cond)
33.01 15. global (function (e) …
33.01 Execution halted
------
Dockerfile:29
--------------------
  28 |
  29 | >>> RUN Rscript -e "\
  30 | >>>     pak::pak('praise'); \
  31 | >>>     "
  32 |
--------------------
ERROR: failed to solve: process "/bin/sh -c Rscript -e \"    pak::pak('praise');     \"" did not complete successfully: exit code: 1