Unable to install recently released xfun 0.55 on macOS

[jdblischak]

The macOS GitHub Actions workflow for my R package is currently failing because r-lib/actions/setup-r-dependencies cannot install xfun 0.55, which was released to CRAN today.

##[group]Install/update packages
ℹ Installing lockfile '.github/pkg.lock'
 
→ Will install 2 packages.
→ Will download 1 CRAN package (600.83 kB).
→ Will download 1 package with unknown size.
+ xfun   0.54 🔧 ⬇ (600.83 kB)
  
ℹ Getting 1 pkg (600.83 kB)
✖ Failed to download xfun 0.54 (aarch64-apple-darwin20)
Error: 
! error in pak subprocess
Caused by error in `file(con, "rb")`:
! cannot open the connection
---
Backtrace:
1. pak::lockfile_install(".github/pkg.lock")
2. pak:::remote(function(...) { …
3. err$throw(res$error)
---
Subprocess backtrace:
 1. base::withCallingHandlers(cli_message = function(msg) { …
 2. get("lockfile_install_internal", asNamespace("pak"))(...)
 3. plan$install()
 4. pkgdepends::install_package_plan(plan, lib = private$library, num_workers = nw, …
 5. base::withCallingHandlers({ …
 6. pkgdepends:::start_task(state, task)
 7. pkgdepends:::start_task_install(state, task)
 8. pkgdepends:::make_install_process(filename, lib = lib, metadata = metadata)
 9. pkgdepends:::detect_package_archive_type(filename)
10. base::readBin(file, what = "raw", n = 6)
11. base::file(con, "rb")
12. base::.handleSimpleError(function (e) …
13. global h(simpleError(msg, call))
Execution halted

Update: Forgot to mention yesterday: I manually deleted the GitHub Actions caches, but this didn't fix the installation problem.

My original attempt to reproduce the error locally was a distraction. It failed for an unrelated reason which I later fixed. Click for more details on the original report.

I confirmed this behavior locally. I can install xfun 0.55 with pak::pkg_install("xfun") on Windows. But on my macOS, it fails. In contrast, install.packages("xfun") installs it without any problem.

pak::pkg_install("xfun", upgrade = FALSE, ask = FALSE)
## ✔ Loading metadata database ... done
##
## → Will update 1 package.
## → The package (599.57 kB) is cached.
## + xfun 0.54 → 0.55 🔧
## ℹ No downloads are needed, 1 pkg (599.57 kB) is cached
## Error:
## ! error in pak subprocess
## Caused by error in `filelock::lock(lockfile)`:
## ! Cannot open lock file: Permission denied
## Type .Last.error to see the more details.

.Last.error
## <callr_error/rlib_error_3_0/rlib_error/error>
## Error:
## ! error in pak subprocess
## Caused by error in `filelock::lock(lockfile)`:
## ! Cannot open lock file: Permission denied
## ---
## Backtrace:
## 1. pak::pkg_install("xfun", upgrade = FALSE, ask = FALSE)
## 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. proc$get_result()
##  9. processx:::process_get_result(self, private)
## 10. private$post_process()
## 11. pkgdepends:::install_extracted_binary(filename, lib_cache, pkg_cache, lib, …
## 12. pkgdepends:::lock_cache(lib_cache, pkg_name, getOption("install.lock"))
## 13. filelock::lock(lockfile)
## 14. base::.handleSimpleError(function (e) …
## 15. global h(simpleError(msg, call))

install.packages("xfun")
## trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/xfun_0.55.tgz'
## Content type 'application/x-gzip' length 599566 bytes (585 KB)
## ==================================================
## downloaded 585 KB
##
##
## The downloaded binary packages are in
## 	/var/folders/jc/9zp2w_y517dfqjf6bbfmlbtw0000gn/T//RtmpWejsPk/downloaded_packages

packageVersion("xfun")
## [1] ‘0.55’

sessionInfo()
## R version 4.4.3 (2025-02-28)
## Platform: aarch64-apple-darwin20
## Running under: macOS Sonoma 14.8.2
##
## Matrix products: default
## BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base
##
## loaded via a namespace (and not attached):
## [1] processx_3.8.6    compiler_4.4.3    R6_2.6.1          cli_3.6.5         tools_4.4.3
## [6] rstudioapi_0.17.1 callr_3.7.6       ps_1.9.1          pak_0.9.1

[jdblischak]

Later in the day, the macOS CI is passing again:

  ℹ Installing lockfile '.github/pkg.lock'
   
  → Will install 2 packages.
  → Will download 1 CRAN package (600.83 kB).
  → Will download 1 package with unknown size.
  + xfun   0.55 🔧 ⬇ (600.83 kB)
    
  ℹ Getting 1 pkg (600.83 kB)
  ✔ Got xfun 0.55 (aarch64-apple-darwin20) (600.83 kB)
  ✔ Installed xfun 0.55  (49ms)
  ✔ 1 pkg + 81 deps: kept 81, added 1, dld 1 (600.83 kB) [1.9s]
  ✔ Installed lockfile '.github/pkg.lock'

However, it is still failing when I try to install it locally.

[jdblischak]

I realized the that local error was due to lockfile permissions. I fixed it by deleting the _cache/ directory as recommended in #351 (comment)

rm -r /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/_cache

So the actual issue to troubleshoot is: why couldn't pak download xfun 0.54 when xfun 0.55 was just released to CRAN?

[nanxstats]

I saw a similar issue today with litedown on macOS:

✖ Failed to download litedown 0.8 (aarch64-apple-darwin20)

Still the same error even after removing all macOS caches from Actions.

litedown 0.9 was released on CRAN yesterday. It looks like the exact condition for this (transient) issue to happen is: pak still somehow thinking 0.8 is the latest version, while the macOS binary for that older version is already removed from the repos.

"sources": ["https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.5/litedown_0.8.tgz", "https://mac.r-project.org/bin/macosx/big-sur-arm64/contrib/4.5/litedown_0.8.tgz"],

Might be a similar problem to r-lib/actions#917.

[gaborcsardi]

This is a bug in CRAN, probably not going to be fixed: https://stat.ethz.ch/pipermail/r-sig-mac/2025-December/015293.html