Question

Installing SC3: gfortran error on Mac M1

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krp • 0

@ac451ac2

Last seen 3.2 years ago

United States

I am trying to install SC3. I am getting an error about install not being able to find an expected directory. I used homebrew to install gcc and gfortran is in /opt/homebrew/bin/gfortran. ISthere a way to specify another directory using BiocManager::install ? Thank you.

ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0'
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with  code 1 (use -v to see invocation)

> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.3.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.16 compiler_4.1.1      tools_4.1.1

SC3 • 3.0k views

ADD COMMENT • link 3.2 years ago krp • 0

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do you have gfortran installed ?

You can install via Brew

https://formulae.brew.sh/formula/gcc#default

Also, make sure it is in your path after installed.

ADD REPLY • link 3.2 years ago Alexandre ▴ 10

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Yep that is what I did

lewy2s-MacBook-Air:~ krp$ which gcc
/usr/bin/gcc
lewy2s-MacBook-Air:~ krp$ which gfortran
/opt/homebrew/bin/gfortran
lewy2s-MacBook-Air:~ krp$

ADD REPLY • link 3.2 years ago krp • 0

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Also thank you for the suggestion. Currently I am looking at this thread: cannot install edgeR on M1 Mac and trying to configure /Library/Frameworks/R.framework/Resources/etc/Makeconf

ADD REPLY • link 3.2 years ago krp • 0