Installing package from GitHub repository containing symlink fails

[matt-graham]

On trying to install a package bridgestan using a github package reference with subdirectory specifier using pak with

pak::pkg_install("github::roualdes/bridgestan/R@v2.6.2")

locally (on Ubuntu 24.04 or within a posit/r-base:4.5-noble Docker container, both with pak@v0.9.0) or on macos-latest / ubuntu-latest GitHub Actions runners I get an error

<callr_error/rlib_error_3_0/rlib_error/error>
Error:
! error in pak subprocess
Caused by error in `stop_task_package_uncompress(state, worker)`:
! Failed to uncompress bridgestan from /tmp/Rtmp9FJYBP/file2d24eb3b88/src/contrib/bridgestan_2.6.2_2fc2521.tar.gz-t.
---
Backtrace:
1. pak::pkg_install("github::roualdes/bridgestan/R@v2.6.2")
2. pak:::remote(function(...) get("pkg_install_do_plan", asNamespace("pak"))(...), …
3. err$throw(res$error)
---
Subprocess backtrace:
 1. base::withCallingHandlers(cli_message = function(msg) { …
 2. get("pkg_install_do_plan", asNamespace("pak"))(...)
 3. proposal$install()
 4. pkgdepends::install_package_plan(plan, lib = private$library, num_workers = nw, …
 5. base::withCallingHandlers({ …
 6. pkgdepends:::handle_events(state, events)
 7. pkgdepends:::handle_event(state, i)
 8. pkgdepends:::stop_task(state, worker)
 9. pkgdepends:::stop_task_package(state, worker)
10. pkgdepends:::stop_task_package_uncompress(state, worker)
11. base::throw(pkg_error("Failed to uncompress {.pkg {pkg}} from\n      {.path {state$plan$file[[pkgidx]]}}.", …
12. | base::signalCondition(cond)
13. global (function (e) …

As far as I can tell the package reference follows the format specified in the documentation.

Installing via remotes::install_github instead using

remotes::install_github("https://github.com/roualdes/bridgestan", subdir="R", ref="v2.6.2")

works without issues.

I originally noticed this issue as a series of GitHub Actions workflows using setup-r-dependencies with bridgestan specified in the extra-packages argument started failing on MacOS / Ubuntu due to the above error (UCL/rmcmc#92) - interestingly however the installation proceeds without errors when running on the Windows runners - for example see the logs from this workflow run.

From a bit of further investigation locally: the downloaded package file bridgestan_2.6.2_2fc2521.tar.gz-t appears from the extension as if it should be a gzipped tar file but in practice running

tar -xvzf bridgestan_2.6.2_2fc2521.tar.gz-t

gives an error

gzip: stdin has more than one entry--rest ignored
tar: Child returned status 2
tar: Error is not recoverable: exiting now

Running

file bridgestan_2.6.2_2fc2521.tar.gz-t

outputs

bridgestan_2.6.2_2fc2521.tar.gz-t: Zip archive data, at least v1.0 to extract, compression method=store

suggesting it is instead a zip archive, and this appears to be the case as running

unzip bridgestan_2.6.2_2fc2521.tar.gz-t

succeeds.

So possibly the issue here is that the automatic identification of the archive type and so correct command to uncompress the archive is failing?

[gaborcsardi]

This boils down to

> zip::unzip("/var/folders/ph/fpcmzfd16rgbbk8mxvy9m2_h0000gn/T//Rtmp4cSHSI/file2aea3ae50d2d/src/contrib/bridgestan_2.6.2_ef91341.tar.gz-t", exdir="/tmp/uz")
Error during wrapup: zip error: Cannot set permissions for `roualdes-bridgestan-ef91341/rust/src/bridgestan.h` from archive `/private/var/folders/ph/fpcmzfd16rgbbk8mxvy9m2_h0000gn/T/Rtmp4cSHSI/file2aea3ae50d2d/src/contrib/bridgestan_2.6.2_ef91341.tar.gz-t` in file zip.c:276

and it happens because that file is a symlink.

[ccasar]

I believe the same issue also happens with bnprks/BPCells. This remotes::install_github("bnprks/BPCells/r") works, but pak::pkg_install("github::bnprks/BPCells/r") does not.

x Failed to uncompress BPCells 0.3.1
Error: 
! error in pak subprocess
Caused by error in `stop_task_package_uncompress(state, worker)`:
! Failed to uncompress BPCells from
/tmp/RtmpOxl1ew/file14d5e772c8b14/src/contrib/BPCells_0.3.1_c293a0a.tar.gz-t.
---
Backtrace:
1. renv::restore(prompt = FALSE)
2. renv:::renv_pak_restore(lockfile = lockfile, packages = packages, exclude = exclude, ...
3. pak$pkg_install(pkg = remotes, ask = prompt)
4. pak:::remote(function(...) get("pkg_install_do_plan", asNamespace("pak"))(...), ...
5. err$throw(res$error)

As @gaborcsardi described unzipping here fails also because of a symlink:

Error in zip::unzip("/tmp/RtmpRpgX7x/file76fa2168713a6/src/contrib/BPCells_0.3.1_c293a0a.tar.gz-t") : 
  zip error: Cannot set permissions for `bnprks-BPCells-c293a0a/cpp/bpcells-cpp` from archive `/tmp/RtmpRpgX7x/file76fa2168713a6/src/contrib/BPCells_0.3.1_c293a0a.tar.gz-t` in file zip.c:276

finishing deferred symbolic links:
  bnprks-BPCells-c293a0a/cpp/bpcells-cpp -> ../r/src/bpcells-cpp
  bnprks-BPCells-c293a0a/cpp/vendor -> ../r/src/vendor
  bnprks-BPCells-c293a0a/python/src/bpcells-cpp -> ../../cpp/bpcells-cpp
  bnprks-BPCells-c293a0a/python/src/vendor -> ../../r/src/vendor