error installing via Rstudio

[spencerlong1]

Hi,
I am having the current error when installing via R-studio on personal macbook (sorry if this is already covered somewhere else, but couldnt find it when searching):

library("devtools")
install_github("zdk123/SpiecEasi")
Downloading GitHub repo zdk123/SpiecEasi@HEAD
✔ checking for file ‘/private/var/folders/lj/w_2_h2hx29jcfj_0r46j1j0m0000gp/T/Rtmpgd9ImH/remotes195f53884e54/zdk123-SpiecEasi-c463727/DESCRIPTION’ ...
─ 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_1.1.2.tar.gz’

• installing source package ‘SpiecEasi’ ...
  ** using staged installation
  ** libs
  clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ADMM.cpp -o ADMM.o
  In file included from ADMM.cpp:1:
  In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
  In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
  In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/RcppCommon.h:30:
  In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
  In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
  In file included from /Users/sdl1c18/opt/miniconda3/bin/../include/c++/v1/cmath:308:
  /Users/sdl1c18/opt/miniconda3/bin/../include/c++/v1/math.h:300:15: fatal error: 'math.h' file not found
  #include_next <math.h>
  ^~~~~~~~
  1 error generated.
  make: *** [/Library/Frameworks/R.framework/Resources/etc/Makeconf:175: ADMM.o] Error 1
  ERROR: compilation failed for package ‘SpiecEasi’
• removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/SpiecEasi’
  Warning message:
  In i.p(...) :
  installation of package ‘/var/folders/lj/w_2_h2hx29jcfj_0r46j1j0m0000gp/T//Rtmpgd9ImH/file195f19ce97a4/SpiecEasi_1.1.2.tar.gz’ had non-zero exit status

Do you know what may solve this? is it an rcpp issue?

Thanks

[spencerlong1]

UPDATE ON THIS STEP: I HAVE SINCE RESOLVED ISSUE ON THIS SYSTEM AND INSTALLED- followed advice in this thread #217

Hi, to update this, on my work (more used) macbook I don't seem to get the above erroor. However, now when I try and install on R on this machine I get the following:

Downloading GitHub repo zdk123/SpiecEasi@HEAD
✔ checking for file ‘/private/var/folders/lj/w_2_h2hx29jcfj_0r46j1j0m0000gp/T/RtmpuY8PIr/remotes24f2948a28a/zdk123-SpiecEasi-c463727/DESCRIPTION’ ...
─ 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_1.1.2.tar.gz’

• installing source package ‘SpiecEasi’ ...
  ** using staged installation
  ** libs
  clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ADMM.cpp -o ADMM.o
  clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/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'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c matops.cpp -o matops.o
  clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c sqrtNewton.cpp -o sqrtNewton.o
  clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c svthresh.cpp -o svthresh.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 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/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: *** [SpiecEasi.so] Error 1
  ERROR: compilation failed for package ‘SpiecEasi’
• removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/SpiecEasi’
  Warning message:
  In i.p(...) :
  installation of package ‘/var/folders/lj/w_2_h2hx29jcfj_0r46j1j0m0000gp/T//RtmpuY8PIr/file24f56fe74ad/SpiecEasi_1.1.2.tar.gz’ had non-zero exit status

This seem to be a gfortran issue, but is not something I am sure how to fix. Do you know how I would get round this? Admittedly I am not an expert on the gfortran side of things, so unsure where this unfound library may be or how I would resolve it. As far as I know, xcode is already installed and I have updated it in the terminal via softwareupdate --install -a , but this doesnt seem to help the issue?