xzhoulab/SPARK

Cannot install package on Mac

Anjan-stat opened this issue · 3 comments

Anjan-stat commented

I'm trying to install SPARK on Mac but getting the following error
R version: 4.3.1
MacOC: M1 Pro

if(!require("SPARK", quietly = TRUE)){

  • devtools::install_github('xzhoulab/SPARK')
  • }
    Downloading GitHub repo xzhoulab/SPARK@HEAD
    ── R CMD build ─────────────────────────────────────────────────────────────────────────────
    ✔ checking for file ‘/private/var/folders/vy/r4cjr09n25j20vl1tfz6_glc0000gq/T/RtmpVBFa4H/remotesd7bb8837a4e/xzhoulab-SPARK-a8b4bf2/DESCRIPTION’ ...
    ─ preparing ‘SPARK’:
    ✔ checking DESCRIPTION meta-information ...
    ─ cleaning src
    ─ installing the package to process help pages
    -----------------------------------
    ─ installing source package ‘SPARK’ ...
    ** using staged installation
    ** libs
    using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
    using C++11
    using SDK: ‘MacOSX13.3.sdk’
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c RcppExports.cpp -o RcppExports.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c rcpparma_hello_world.cpp -o rcpparma_hello_world.o
    clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_64BIT_WORD=1 -fPIC -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c spark_float.cpp -o spark_float.o
    clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o SPARK.so RcppExports.o rcpparma_hello_world.o spark_float.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    ld: warning: directory not found for option '-L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0'
    ld: warning: directory not found for option '-L/opt/gfortran/lib'
    ld: library not found for -lgfortran
    clang: error: linker command failed with exit code 1 (use -v to see invocation)
    make: *** [SPARK.so] Error 1
    ERROR: compilation failed for package ‘SPARK’
    ─ removing ‘/private/var/folders/vy/r4cjr09n25j20vl1tfz6_glc0000gq/T/RtmpLNv8Gq/Rinstd83d752bd7fe/SPARK’
    -----------------------------------
    ERROR: package installation failed
    Error: Failed to install 'SPARK' from GitHub:
    ! System command 'R' failed
Streisenberg commented

I have reinstalled gfortran, deleted and reinstalled xcode-build tool, edited and rebuilt the Makevars file (I may have made a mistake here). But I still get the same error. I would be very happy if someone could help. Thank you!

My machine info:
Platform : aarch64-apple-darwin20
R.version : 4.2.2
MacOS : Monterey (12.6.5)
Chip : Apple M1 Max

ANWANGJHU commented

Here is my solution:

  1. brew install gcc
  2. in terminal, type which gfortran. In my case, it returns /opt/homebrew/bin/gfortran

In terminal, type

mkdir -p ~/.R  
nano ~/.R/Makevars
  1. In the ~/.R/Makevars, add
FC = /opt/homebrew/bin/gfortran
F77 = /opt/homebrew/bin/gfortran
FLIBS = -L/opt/homebrew/lib/gcc/14 -lgfortran -lquadmath -lm

Note: /opt/homebrew/lib/gcc is the location of the gcc installed by homebrew, do ls /opt/homebrew/lib/gcc in terminal to find which number is available, in my case it is 14

laleoarrow commented

Here is my solution:

  1. brew install gcc
  2. in terminal, type which gfortran. In my case, it returns /opt/homebrew/bin/gfortran
  3. in terminal, type

In terminal, type

mkdir -p ~/.R  
nano ~/.R/Makevars
  1. In the ~/.R/Makevars, add
FC = /opt/homebrew/bin/gfortran
F77 = /opt/homebrew/bin/gfortran
FLIBS = -L/opt/homebrew/lib/gcc/14 -lgfortran -lquadmath -lm

Note: /opt/homebrew/lib/gcc is the location of the gcc installed by homebrew, do ls /opt/homebrew/lib/gcc in terminal to find which number is available, in my case it is 14

This approach can be applied to various R packages that require compilation for M-chip MacBooks. Thank you for providing such a valuable solution!

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