Binary incompatibility of the pre-installed Matrix package

[gaborcsardi]

This (#780) is happening again, because for R 4.4.0 PPM has an lme4 package (+possibly others!) that is built against Matrix 1.6-x, and this are not compatible with the pre-installed Matrix 1.7-x.

Possible workarounds:

• Use R 4.3.

      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: 4.3
          use-public-rspm: true
  

• Turn off PPPM. (But building all packages from source may take a very long time!)

      - uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: false
  

• Request installation of new Matrix, by putting Matrix=?reinstall into extra-packages.

     - uses: r-lib/actions/setup-r-dependencies@v2
       with:
         extra-packages: 'any::pkgdown, local::., Matrix=?reinstall'
  

[gaborcsardi]

I think this should be fixed in PPM eventually.

EDIT: Or actually maybe on CRAN, because they don't have Matrix 1.7-0 available for R 4.4.0. I emailed R-devel: https://stat.ethz.ch/pipermail/r-devel/2024-April/083377.html

[gaborcsardi]

OK, CRAN now has Matrix 1.7-0 in the metadata, and PPM will binaries for it and all the packages that depend on it automatically, I would guess in 1-2 days.

The daily PPM snapshots won't be fixed, though.

I'll keep this issue open until Matrix 1.7-0 is built on PPM.

[CorradoLanera]

Similar issue with {hommel} v1.6

• here - lint
• here - covr
• here - pkgdown
• here - R-CMD-check (linux release only!)
• here - rhub ubuntu release
• here - rhub ubuntu next

For the moment, I take your suggestion to use-public-rspm: false

[gaborcsardi]

@CorradoLanera That is a different issue I believe:

  Error: 
  ! error in pak subprocess
  Caused by error in `verify_extracted_package(filename, pkg_cache)`:
  ! 
  '/tmp/RtmpjTd5Q2/file14075f9f5350/src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.4/hommel_1.6.tar.gz'
  is not a valid binary, it is missing hommel/Meta/package.rds.

[gaborcsardi]

The Matrix problem that this issue is about should be fixed now. PPM has a 1.7-0 binary for R 4.4 now.

[gaborcsardi]

@CorradoLanera The error in #832 (comment) is a different thing, and it is triggered by a change in PPM. It only happens if you set PPM as a repository called CRAN, so a workaround is to call it something else. It will be fixed here: r-lib/pak#623

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