Question

BiocGenerics binary is outdated for macOS ARM

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Michael Steinbaugh ▴ 90

@mjsteinbaugh

Last seen 12 months ago

Cambridge, MA

Hi Bioconductor team,

I noticed that the current binary file for BiocGenerics is outdated for macOS ARM (Apple Silicon):

Source Package  BiocGenerics_0.46.0.tar.gz
Windows Binary  BiocGenerics_0.46.0.zip
macOS Binary (x86_64)   BiocGenerics_0.46.0.tgz
macOS Binary (arm64)    BiocGenerics_0.45.3.tgz

Best, Mike

BiocGenerics • 877 views

ADD COMMENT • link 18 months ago Michael Steinbaugh ▴ 90

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That is because it is failing from dependencies not being available. https://bioconductor.org/checkResults/3.17/bioc-mac-arm64-LATEST/BiocGenerics/kjohnson2-checksrc.html

ADD REPLY • link 18 months ago shepherl 4.1k

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Thanks, Mike, for posting about this and thanks to Lori for noticing the lock. I removed it and RProtoBufLib passes R CMD check. Unfortunately, since this build is slow and runs only once a week, we won't see the new binary propagated until next week, Friday June 9.

ADD REPLY • link 18 months ago jennifer.wokaty ▴ 70

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Awesome thanks, for reference here's the lock issue:

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RProtoBufLib
###
##############################################################################
##############################################################################


* installing to library '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library'
ERROR: failed to lock directory '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library' for modifying
Try removing '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-RProtoBufLib'

https://bioconductor.org/checkResults/3.17/bioc-mac-arm64-LATEST/RProtoBufLib/kjohnson2-checksrc.html

ADD REPLY • link 18 months ago Michael Steinbaugh ▴ 90

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Ah thanks for the update. Yeah I see that the flowClust release is the culprit: https://www.bioconductor.org/packages/release/bioc/html/flowClust.html

Package suggested but not available: 'flowClust'

See builds here: https://bioconductor.org/checkResults/3.17/bioc-mac-arm64-LATEST/flowClust/

ADD REPLY • link 18 months ago Michael Steinbaugh ▴ 90