spencerlong1
commented
1 year ago UPDATE ON THIS STEP: I HAVE SINCE RESOLVED ISSUE ON THIS SYSTEM AND INSTALLED- followed advice in this thread https://github.com/zdk123/SpiecEasi/issues/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?
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):
include_next
1 error generated. make: *** [/Library/Frameworks/R.framework/Resources/etc/Makeconf:175: ADMM.o] Error 1 ERROR: compilation failed for package ‘SpiecEasi’
Do you know what may solve this? is it an rcpp issue?
Thanks