Installing SC3: gfortran error on Mac M1
0
0
Entering edit mode
krp • 0
@ac451ac2
Last seen 8 weeks 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 • 320 views
ADD COMMENT
0
Entering edit mode

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
0
Entering edit mode

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
0
Entering edit mode

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

Login before adding your answer.

Traffic: 306 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