Warning messages on Apple M1 BigSur
1
0
Entering edit mode
Alexandre • 0
@095e334e
Last seen 20 months 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 • 4.0k views
ADD COMMENT
2
Entering edit mode
@vincent-j-carey-jr-4
Last seen 6 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.

0
Entering edit mode

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

ADD REPLY
2
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 804 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6