[Bioc-devel] arrow dependent packages fail to build on macOS

[Edward Zhao]

Hello,

I have made updates to my package BayesSpace on the devel branch and it
shows an error on macOS only due to an error with the arrow dependency:

unable to load shared object
'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/arrow/libs/arrow.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/arrow/libs/arrow.so,
0x0006): symbol not found in flat namespace (_ZSTD_compress)


This is a CRAN package that passes CRAN checks
<https://cran.r-project.org/web/checks/check_results_arrow.html>, but it
seems like they are having problems on macOS (
https://github.com/apache/arrow/issues/44206,
https://github.com/apache/arrow/issues/40667), which is the version on the
build environment. There is a comment here that suggests installing from
r-universe instead of CRAN.

I've been messaging with Martin Grigorov on slack, who suggested that I
should request zstd to be installed on the builder machine. My collaborator
Senbai (cc'd) who has been looking into this also suggested to install
libarrow with "full features" since the current libarrow on the machine
does not support zstd compression type.

Please let me know if there's anything I can do to help get this resolved.
It is affecting not only my package but also others that use arrow (e.g.
VisiumIO <https://bioconductor.org/checkResults/devel/bioc-LATEST/VisiumIO/>,
SpatialFeatureExperiment
<https://bioconductor.org/checkResults/devel/bioc-LATEST/SpatialFeatureExperiment/>).
Thanks!

Best,
Edward

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