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binary packages install are failing when download method gets source

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
45/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Stale
Tech stack
r
Domain
tooling

Research direction

Reproduce the failure with the R example using pkgdepends::new_pkg_installation_proposal, then inspect the download and installation paths named in the report, especially pkgcache::download_one_of and install-binary.R. Check how ip$download() passes a selected source into ip$install() and use the reported backtrace as the starting point. Done means installation no longer fails when a non-binary archive is selected, with coverage for the Archive-source scenario.

Written by the indexing model from the issue text.

Description

bug

ip$install() call fails on verifying the binary package after the installation proposal download call (see below for an example)

  • Fail is random, as it may use the resolution$sources item that is not Archive most of the time
  • Fail sometimes happens if non-archive source is downloaded
    • can be mitigated with another download

This was detected when installing insightsengineering/teal.modules.clinical with 2 problematic binary packages nloptr and urltools (using ppm snapshot or latest).

  • Is there an option to disable resolving the Archive URL?
    • doesn't happen only on Archive URL (however, this one always downloads source packages)
  • Could the method fall back to installing a source package or re-downloading again?
Reproducible example

note: I think this results from a race condition when downloading the file with pkgcache::download_one_of(...) and it downloads a source archive.

config <- list(
  cran_mirror = "https://packagemanager.posit.co/cran/__linux__/noble/2024-04-19", 
  library = tempfile()
)

ip <- pkgdepends::new_pkg_installation_proposal("tern", config = config)

ip$solve()

res <- ip$get_resolution()

# Keep only Archive sources (force failure)
new_sources <- lapply(
  res$sources,
  function(x) {
    if (length(x) > 1 && any(grepl("src/contrib/Archive", x))) {
      x[grepl("src/contrib/Archive", x)]
    } else {
      x
    }
  }
)

ip$.__enclos_env__$private$plan$.__enclos_env__$private$resolution$result$sources <- new_sources

ip$download()
ip$install()

.Last.error
#> <install_input_error/rlib_error_3_0/rlib_error/error>
#> Error in `verify_extracted_package(filename, pkg_cache)` at install-binary.R:5:3:
#> ! 
#> /tmp/Rtmpaxpmb1/file4cf621cf4b41/src/contrib/x86_64-pc-linux-gnu-ubuntu-24.04/4.4/nloptr_2.0.3.tar.gz
#> is not a valid binary, it is missing nloptr/Meta/package.rds.
#> ---
#> Backtrace:
#>  1. ip$install()
#>  2. pkgdepends::install_package_plan(plan, lib = private$library, num_workers = nw, … at pkg-installation.R:466:7
#>  3. base::withCallingHandlers({ … at install-plan.R:107:3
#>  4. pkgdepends:::handle_events(state, events) at install-plan.R:120:7
#>  5. pkgdepends:::handle_event(state, i) at install-plan.R:210:3
#>  6. proc$get_result() at install-plan.R:239:3
#>  7. processx:::process_get_result(self, private) at process.R:576:18
#>  8. private$post_process() at process.R:784:5
#>  9. pkgdepends:::install_extracted_binary(filename, lib_cache, pkg_cache, lib, … at install-binary.R:140:4
#> 10. pkgdepends:::verify_extracted_package(filename, pkg_cache) at install-binary.R:5:3
#> 11. pkgdepends:::throw(pkg_error("{.path {filename}} is not a valid binary, it is missing {miss}."… at install-verify-binary.R:30:5
Dominant language
C
Stars
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Forks
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