Updating metadata database ... failed

[jeroen]

As of a few days ago, for all builds in r-universe we very often see:

pak::pkg_sysreqs('.', upgrade = FALSE)
#  ✔ Updated metadata database: 8.82 MB in 16 files.
#  ℹ Updating metadata database
#  ✖ Updating metadata database ... failed

update here is a minimal example: https://github.com/jeroen/pak-tests/actions/runs/14442464229/job/40495486494

---

Perhaps it is the same problem as #764

> pak::pkg_sysreqs('.', upgrade = FALSE)
! Optional package `pillar` is not available for pak.
  Use `pak::pak_install_extra()` to install optional packages.
  Use `options(pak.no_extra_messages = TRUE)` to suppress this message.
✔ Updated metadata database: 6.16 MB in 15 files.
✖ Updating metadata database ... failed
Error:  13  deps for  1/1  pkgs [⠧] Done
! error in pak subprocess
Caused by error in `value$ref %in% private$state$ref && !value$direct`:
! 'length = 12' in coercion to 'logical(1)'
Type .Last.error to see the more details.

[jeroen]

Updated the example with devel pak, still errors: https://github.com/jeroen/pak-tests/actions/runs/14454615834/job/40534917653

Error now says:

ℹ Updating metadata database
✖ Updating metadata database ... failed

Error: 
! error in pak subprocess
Caused by error in `res_one_row_df(entries)`:
! `nrow(out)` must equal `1`.
---
Backtrace:
1. pak::pkg_sysreqs(".", upgrade = FALSE)
2. pak:::remote(function(...) { …
3. err$throw(res$error)
---
Subprocess backtrace:
 1. base::withCallingHandlers(cli_message = function(msg) { …
 2. get("pkg_sysreqs_internal", asNamespace("pak"))(...)
 3. pkgdepends::sysreqs_install_plan(pkg, upgrade = upgrade, config = config)
 4. prop$solve()
 5. private$plan$solve(policy = private$policy)
 6. pkgdepends:::pkgplan_solve(self, private, match.arg(policy))
 7. self$resolve()
 8. pkgdepends:::pkgplan_resolve(self, private)
 9. pkgdepends:::synchronise(self$async_resolve())
10. asNamespace("pkgcache")$synchronise(...)
11. base::stop(priv$value)
12. global (function (e) …

[gaborcsardi]

This is happening because https://bioc.r-universe.dev/bin/linux/noble/4.5/src/contrib/PACKAGES has some packages that do not have a Built fileld, and pak assumes that these are binary packages that have one.

I guess it can assume that the packages without a Built field are source packages.

[gaborcsardi]

This should be fixed now. I started a build for deploying updated nightly builds for Linux.

[jeroen]

Thanks for looking into this!

I guess it can assume that the packages without a Built field are source packages.

How does P3M list packages that do not have a binary? I can change it accordingly.

[gaborcsardi]

Afair p3m does not have a built field at all, but it lists the binary packages is a separate file.