Error in installing packages

[jlche]

Hi, I am trying to install the package on my laptop (macOS Monterey 12.7.2) using the RStudio (Version 2023.12.0), but it failed to visit and download via the routine as shown below. May I try the other way or do you know how to solve this error? Thanks a lot.

install_github("zdk123/SpiecEasi") Downloading GitHub repo zdk123/SpiecEasi@HEAD ── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/private/var/folders/57/435jclf55xx08_k5bhcr6j940000gn/T/RtmpHLktoK/remotes370e29da7798/zdk123-SpiecEasi-5f396da/DESCRIPTION’ (355ms) ─ preparing ‘SpiecEasi’: ✔ 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 Removed empty directory ‘SpiecEasi/inst’ ─ looking to see if a ‘data/datalist’ file should be added ─ building ‘SpiecEasi_1.1.3.tar.gz’

• installing source package ‘SpiecEasi’ ... using staged installation libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX13.1.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ADMM.cpp -o ADMM.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matops.cpp -o matops.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sqrtNewton.cpp -o sqrtNewton.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c svthresh.cpp -o svthresh.o clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o SpiecEasi.so ADMM.o RcppExports.o matops.o sqrtNewton.o svthresh.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: directory not found for option '-L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0' ld: warning: directory not found for option '-L/opt/gfortran/lib' ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin20/12.2.0' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [SpiecEasi.so] Error 1 ERROR: compilation failed for package ‘SpiecEasi’
• removing ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/SpiecEasi’ Warning message: In i.p(...) : installation of package ‘/var/folders/57/435jclf55xx08_k5bhcr6j940000gn/T//RtmpHLktoK/file370e45e1b19f/SpiecEasi_1.1.3.tar.gz’ had non-zero exit status

[JiatingH]

It works for me in https://github.com/zdk123/SpiecEasi/issues/217#issuecomment-1489172072

[jlche]

It has been solved. create folder name .R ; then create subfolder name it with Makevars, input below code into Makevars： FC = /usr/local/gcc/bin/gfortran E77 = /usr/local/opt/gcc/bin/gfortran FLIBS = -L/usr/local/opt/gcc/lib

[jlche]

It has been solved. create folder name .R ; then create subfolder name it with Makevars, input below code into Makevars： FC = /usr/local/gcc/bin/gfortran E77 = /usr/local/opt/gcc/bin/gfortran FLIBS = -L/usr/local/opt/gcc/lib

    ------------------ Original ------------------ From: @.>; Date:  Thu, Feb 1, 2024 03:04 PM To: @.>; Cc: @.>; @.>; Subject:  Re: [zdk123/SpiecEasi] Error in installing packages (Issue #253)

 

I have encountered the same issue. Have you managed to resolve it?

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