Warning messages on Apple M1 BigSur
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Alexandre • 0
@095e334e
Last seen 2 days ago
Hong Kong

Hi,

Does bioconductor supports the binary of R created specifically for arm chips already ?

I get the following warning when trying to install any Bioconductor packages:

1: In .inet_warning(msg) :
  unable to access index for repository http://bioconductor.org/packages/3.13/bioc/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'http://bioconductor.org/packages/3.13/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES' 

The packages are being installed however, I've tried Deseq2 and it installed from source.

Thanks

Bioconductor • 313 views
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@vincent-j-carey-jr-4
Last seen 10 days ago
United States

We are not producing M1 binaries at this time. If you use the intel version of R under Rosetta 2 you can use the intel mac binaries.

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ok thanks, but that means R will run slower right ? Since Rosetta 2 is emulation environment, correct ?

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Try it. https://www.anaconda.com/blog/apple-silicon-transition includes the following on Rosetta2:

"You can download the macOS x86-64 installer for Anaconda (or conda-forge) and install it on an M1 Mac, and everything will work. You will see a warning from the installer that the “architecture does not appear to be 64-bit,” but you can safely ignore that warning. When running Python applications, you may notice a pause (sometimes long!) when starting Python or importing a package for the first time, as Rosetta2 translates machine code from x86-64 to ARM64. However, that pause will disappear on subsequent runs. The main limitation is that packages that require AVX will not run."

There are some comparisons concerning R available on the web. The Bioc core developer team is discussing how to support distribution of M1-based binaries, which will require investment in hardware, and this will likely take place during the development of release 3.15.

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