genefilter not available for R v4.1/arm64
1
0
Entering edit mode
jeremymsimon ▴ 20
@4174dc58
Last seen 12 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 • 1.2k views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 2 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?

ADD COMMENT
0
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.

ADD REPLY

Login before adding your answer.

Traffic: 637 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