ld error on macos when building C code that links Rlib.

[lgautier]

Describe the bug

I am using the action r-setup in GHA pipelines to build rpy2, a bridge between Python and R using their respective C APIs. Over the last weeks build errors specific to macos and happening during the linking step appeared:
https://github.com/rpy2/rpy2/actions/runs/13741000014/job/38430240207#step:10:25

The error is about deflate not found and seems similar to #965 , even though my error is with R release.

If an issue with a FORTRAN update, should it be address by this action, upstream by GitHub, or by users? I don't have a macos system to troubleshoot.

To Reproduce

See CI pipeline link above.

Expected behavior
Compilation and linking used to work.

Additional context
NA.

[gaborcsardi]

Why do you think that this is a bug in setup-r? The CRAN R 4.4.x macOS build does not link to libdeflate. What can setup-r do about that?

[lgautier]

Why do you think that this is a bug in setup-r?

As mentioned, just a speculation based on the following similarity with #965:

• build error appears without explainable cause in code base or CI pipeline using r-setup.
• also about ld error regarding a library that cannot be found.

The CRAN R 4.4.x macOS build does not link to libdeflate.

Ah. This rules out r-setup then. Something else must have changed in Github's runners for macos.

What can setup-r do about that?

This is a question I am asking. Under the "similar to #965" hypothesis, something like #966. From the note right the hypothesis does not seem correct. I'll keep looking what is the source of the issue upstream. Thanks for the quick reply.

[gaborcsardi]

I think this is a bug in whatever adds the -ldeflate flag, not in setup-r.

[gaborcsardi]

Actually, it seems that R 4.4.3 adds that.

A potential fix for you is to install libdeflate from here:
https://mac.r-project.org/bin/darwin20/arm64/
https://mac.r-project.org/bin/

curl -LO https://mac.r-project.org/bin/darwin20/arm64/libdeflate-1.23-darwin.20-arm64.tar.xz
tar xzf libdeflate-1.23-darwin.20-arm64.tar.xz -C /

You might need sudo for the second one.

Another potential fix is to remove -ldeflate from the R config file.

[lgautier]

Thanks. This put me on the right track.

• small fix to extract the archive. It should be tar xJf
• the library zstd also had to be added. With both deflate and zstd, building is working again.

The fix is needed for R 4.4.3 (current release) and 4.5.0-dev (current devel).

[gaborcsardi]

Emailed CRAN about this here:
https://stat.ethz.ch/pipermail/r-sig-mac/2025-March/015124.html

[github-actions]

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