I am experiencing a similar issue as this .When I try to install clusterExperiment on macOS it errors out as follows
BiocManager::install("clusterExperiment")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
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 'https://bioconductor.org/packages/3.14/bioc/src/contrib/clusterExperiment_2.14.0.tar.gz'
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 clusterExperiment.so 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: *** [clusterExperiment.so] 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
‘/private/var/folders/9h/zbzv_b3j3wz2r6mdgw9s2p04000lw8/T/Rtmp7IVGlJ/downloaded_packages’
Installation paths not writeable, unable to update packages
path: /Library/Frameworks/R.framework/Versions/4.1/Resources/library
packages:
MASS
Old packages: 'quantreg'
Update all/some/none? [a/s/n]: