Error linking to Rhdf5lib in Rcpp package on macOS arm64 CRAN check.

[jdstamp]

Hi,

I link to Rhdf5lib in my R package which I have submitted to CRAN (https://cran.r-project.org/package=smer). The automated checks on CRAN fail only for macOS: https://www.r-project.org/nosvn/R.check/r-release-macos-arm64/smer-00install.html and https://www.r-project.org/nosvn/R.check/r-release-macos-x86_64/smer-00install.html .

Specifically, the check fails when loading the temporary installed version of the package with an error that looks for the HDF5 symbol _H5Treclaim

Error: package or namespace load failed for ‘smer’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Volumes/Builds/packages/big-sur-arm64/results/4.4/smer.Rcheck/00LOCK-smer/00new/smer/libs/smer.so':
  dlopen(/Volumes/Builds/packages/big-sur-arm64/results/4.4/smer.Rcheck/00LOCK-smer/00new/smer/libs/smer.so, 0x0006): symbol not found in flat namespace '_H5Treclaim'
Error: loading failed
Execution halted
ERROR: loading failed

Both Windows and Linux work on CRAN. My github R CMD check on macOS is working too (https://github.com/lcrawlab/sme/actions/workflows/r-cmd-check.yml).

I would like to fix this error on CRAN, but as of now I have no starting point to understand how to fix it. Does anyone have any idea how I could go about understanding this issue?

[Bisaloo]

Thanks for the report!

You are using Rhdf5lib as the HDF5 lib provider for HighFive? I need to think a bit more about it but I'm not completely convinced it can work as expected.

If Rhdf5lib is installed after HighFive, then HighFive is compiled against the system HDF5 library.

If the system HDF5 library differs from the version provided by Rhdf5lib, I think it could explain what you are seeing 🤔 .