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

[Edward Zhao]

Thanks for the clarification. Fingers crossed!

Edward

On Wed, Oct 30, 2024 at 7:34 PM Hervé Pagès <hpages.on.github using gmail.com>
wrote:

> Hi Edward,
>
> arrow is a CRAN package with Mac binaries available for R 4.4 so our build
> system just install that. Note that Mac package binaries should be
> self-contained (they use static linking), so they should **never** require
> any external system library.
>
> Not sure why we see this error on lconway. It could be that there was a
> problem with the Mac binary provided by CRAN (it looks like they updated
> the binary on Sept 12), or something went wrong when it landed on lconway,
> hard to know. In any case, I just reinstalled the package on lconway and
> that seems to have solved the problem, that is, now I can library(arrow) in
> an interactive session on the machine.
>
> I might have done this too late for the fix to have any impact on
> tomorrow's build report for 3.20. Let's see how things are going for
> BayesSpace on Friday's report.
>
> Best,
>
> H.
> On 10/23/24 01:29, Edward Zhao wrote:
>
> 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> <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/> <https://bioconductor.org/checkResults/devel/bioc-LATEST/VisiumIO/>,
> SpatialFeatureExperiment<https://bioconductor.org/checkResults/devel/bioc-LATEST/SpatialFeatureExperiment/> <https://bioconductor.org/checkResults/devel/bioc-LATEST/SpatialFeatureExperiment/>).
> Thanks!
>
> Best,
> Edward
>
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>
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> --
> Hervé Pagès
>
> Bioconductor Core Teamhpages.on.github using gmail.com
>
>

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