installation of clusterexperiment fails on 3.14 (BiocManager 1.30.17), R 4.1.3 (2022-03-10) MacOS

I am experiencing a similar issue as this .When I try to install clusterExperiment on macOS it errors out as follows


'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:

Bioconductor version 3.14 (BiocManager 1.30.17), R 4.1.3 (2022-03-10)
Installing package(s) 'clusterExperiment'
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘clusterExperiment’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source package ‘clusterExperiment’

trying URL ''
Content type 'application/x-gzip' length 11065856 bytes (10.6 MB)

downloaded 10.6 MB

  • installing source package ‘clusterExperiment’ ...
    ** using staged installation
    ** libs
    clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/jr35/Library/R/x86_64/4.1/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
    clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/jr35/Library/R/x86_64/4.1/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c search_pairs.cpp -o search_pairs.o
    clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/jr35/Library/R/x86_64/4.1/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c subsampleLoop.cpp -o subsampleLoop.o
    clang++ -mmacosx-version-min=10.13 -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/usr/local/lib -o RcppExports.o search_pairs.o subsampleLoop.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
    ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
    ld: library not found for -lgfortran
    clang: error: linker command failed with exit code 1 (use -v to see invocation)
    make: *** [] Error 1
    ERROR: compilation failed for package ‘clusterExperiment’
  • removing ‘/Users/jr35/Library/R/x86_64/4.1/library/clusterExperiment’

The downloaded source packages are in
Installation paths not writeable, unable to update packages
path: /Library/Frameworks/R.framework/Versions/4.1/Resources/library
Old packages: 'quantreg'
Update all/some/none? [a/s/n]:

You are missing a fortran compiler in your system, try installing the recommended development tools for macOS systems.

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