genefilter not available for R v4.1/arm64
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Entering edit mode
@4174dc58
Last seen 3 months ago
United States

Just updated my local machine (M1 macbook) to R v4.1 and bioC 3.14, using the arm64 build, and genefilter/DESeq2 fail to install. It seems genefilter is not yet available for this architecture?

make: /opt/R/arm64/bin/gfortran: No such file or directory
make: *** [ttest.o] Error 1
ERROR: compilation failed for package ‘genefilter’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/genefilter’
ERROR: dependency ‘genefilter’ is not available for package ‘DESeq2’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/DESeq2’

The downloaded source packages are in
    ‘/private/var/folders/q6/jv04nlb917v3mf0c5vvh3cfr0000gn/T/RtmpRQvF4i/downloaded_packages’
Warning messages:
1: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
2: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
3: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
4: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
5: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
6: In .inet_warning(msg) :
  installation of package ‘genefilter’ had non-zero exit status
7: In .inet_warning(msg) :
  installation of package ‘DESeq2’ had non-zero exit status
DESeq2 genefilter • 227 views
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@james-w-macdonald-5106
Last seen 4 hours ago
United States

That's not what the error is telling you. It's saying that gfortran isn't available on your mac, so it can't compile genefilter. That's a different thing than not being available. It's been a while since I have done anything on a mac, but back in the day you had to get the XCode tools to compile things. Or maybe you have gfortran but in a different place, in which case you might need to pass a compiler flag?

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Entering edit mode

Thanks. I found a solution by using the official R v4.1 build, NOT the ARM specific version. There likely is some gfortran/gcc compiler issues, but none of the solutions proposed by others elsewhere seemed to work for me.

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