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 #217 (comment)

[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? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>