[Fix] installing Rhdf5lib on M1/M2 OSX with conda version of R

[eyalbenda]

So, after a long and miserable time trying to get Rhdf5lib installed on the M1 OSX (binary version couldn't work for me) I traced the issue and found a solution. Note, this has been tested by me using the conda-forge version of R(4.3.1).

See: #45 #51

apparently hdf5's configure script gets the build alias from $host_alias or $build_alias if they're defined. The following command allowed a clean install from inside R with BiocManager::install("Rhdf5lib")

unset host_alias unset build_alias

I'm putting it here as a fix. This could potentially be fixed by the package's install script, for your consideration.

[grimbough]

Thanks for the report @eyalbenda

Just so I'm clear, what was the symptom of the issue for you? The error messages in #45 and #51 look different to me.

[eyalbenda]

That’s because #51 already tries to install the binary, which isn’t installed correctly on conda R builds. Unsetting the flags allows installation from source, solving #45 and obviating the need for binary installation.

On Thu, Sep 14, 2023 at 12:27 AM Mike Smith @.***> wrote:

Thanks for the report @eyalbenda https://github.com/eyalbenda

Just so I'm clear, what was the symptom of the issue for you? The error messages in #45 https://github.com/grimbough/Rhdf5lib/issues/45 and #51 https://github.com/grimbough/Rhdf5lib/issues/51 look different to me.

— Reply to this email directly, view it on GitHub https://github.com/grimbough/Rhdf5lib/issues/54#issuecomment-1718909611, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACQHDYIOEDHDLJTSJNTCMD3X2KWXLANCNFSM6AAAAAA4UCZTTA . You are receiving this because you were mentioned.Message ID: @.***>

[wakelin-g]

I can confirm that with conda-forge R (4.3.2), this is still an issue and this fix continues to work.

R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20.0.0 (64-bit)
Running under: macOS Sonoma 14.2.1

Matrix products: default
BLAS/LAPACK: /Users/griffen/mambaforge/envs/r-osca/lib/libopenblas.0.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Halifax
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Rhdf5lib_1.24.1

loaded via a namespace (and not attached):
[1] BiocManager_1.30.22 compiler_4.3.2      tools_4.3.2

[grimbough]

Now GitHub have made and M1 Mac available as an Actions runner it much more likely I'll be able to reproduce and test this. I'll report back here when I have done so.

[grimbough]

I think this should now be sorted. I updated some of the scripts bundled with the HDF5 source which were quite out of date and didn't recognise the combination of conda and arm64 Mac. It's available in Rhdf5lib version 1.24.2, which I guess might take a few days to be available via the Bioconductor repository.