error in installing devtools::install_github("zdebruine/RcppML")

[Rose-Hedderman]

devtools::install_github("zdebruine/RcppML") Using GitHub PAT from the git credential store. Downloading GitHub repo zdebruine/RcppML@HEAD These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: xfun (0.42 -> 0.43) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1 xfun (0.42 -> 0.43) [CRAN] Installing 1 packages: xfun trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.3/xfun_0.42.tgz' Content type 'application/x-gzip' length 475932 bytes (464 KB)

downloaded 464 KB

The downloaded binary packages are in /var/folders/xf/8l51mcd939x_wh_596kx9lpw0000gn/T//RtmpSU7Lxl/downloaded_packages ── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/private/var/folders/xf/8l51mcd939x_wh_596kx9lpw0000gn/T/RtmpSU7Lxl/remotes5088378f0bf2/zdebruine-RcppML-5449a5b/DESCRIPTION’ ... ─ preparing ‘RcppML’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories NB: this package now depends on R (>= 3.5.0) WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: ‘RcppML/data/aml.rdata’ ‘RcppML/data/hawaiibirds.rdata’ ‘RcppML/data/movielens.rdata’ ─ building ‘RcppML_0.5.6.tar.gz’

• installing source package ‘RcppML’ ... using staged installation libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’ using C++11 using SDK: ‘MacOSX14.4.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DEIGEN_INITIALIZE_MATRICES_BY_ZERO -DEIGEN_NO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from ./../inst/include/RcppML.h:13: ../inst/include/RcppML/SparseMatrix.h:96:63: warning: private field 'ssize' is not used [-Wunused-private-field] int col, index, max_index, s_max_index, s_index = 0, s_size; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DEIGEN_INITIALIZE_MATRICES_BY_ZERO -DEIGEN_NO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c RcppFunctions.cpp -o RcppFunctions.o In file included from RcppFunctions.cpp:9: ./../inst/include/RcppML/SparseMatrix.h:96:63: warning: private field 'ssize' is not used [-Wunused-private-field] int col, index, max_index, s_max_index, s_index = 0, s_size; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DEIGEN_INITIALIZE_MATRICES_BY_ZERO -DEIGEN_NO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c bipartiteMatch.cpp -o bipartiteMatch.o clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o RcppML.so RcppExports.o RcppFunctions.o bipartiteMatch.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: search path '/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0' not found ld: warning: search path '/opt/gfortran/lib' not found ld: library 'gfortran' not found clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [RcppML.so] Error 1 ERROR: compilation failed for package ‘RcppML’
• removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppML’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppML’ Warning message: In i.p(...) : installation of package ‘/var/folders/xf/8l51mcd939x_wh_596kx9lpw0000gn/T//RtmpSU7Lxl/file508859f9f10d/RcppML_0.5.6.tar.gz’ had non-zero exit status

any thoughts on how to solve this?

[zdebruine]

Sounds like you need to install gfortran. I'm guessing you're on a linux HPC system and you just need to load a module or contact your system administrator. This is not an issue with the package, you will have issues installing many packages, particularly those depending on he RcppEigen package.