Error installing on macOS Monterey 12.5 Intel based

[LilEigenValue]

Hello,

Ive been trying to install this package for a week. I installed a bunch of Fortran files and moved libraries but to no avail. Any help would be appreciated.

ibrary(devtools)
Loading required package: usethis

install_github("zdk123/SpiecEasi")
Downloading GitHub repo zdk123/SpiecEasi@HEAD
✔ checking for file ‘/private/var/folders/w7/h6vx0pj1107c1dkkv1q46jmw0000gn/T/RtmpFUwB7w/remotesd7b83baa7d28/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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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: malformed universal file: slice content is not mach-o or a static library file '/usr/local/lib/libgfortran.dylib'
  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/4.2/Resources/library/SpiecEasi’
  Warning message:
  In i.p(...) :
  installation of package ‘/var/folders/w7/h6vx0pj1107c1dkkv1q46jmw0000gn/T//RtmpFUwB7w/filed7b844487317/SpiecEasi_1.1.2.tar.gz’ had non-zero exit status

[zdk123]

Thanks... Will test macOS install on 4.2...

[zdk123]

working on Big-Sur with an M1 chip. It looks like the wrong compiler is getting used though. I'll have to dig into this some more. Maybe use the pre-compiled package via bioconda in the meantime?

[mljaniczek]

Hi! I was having this issue and tried a few things before finally was able to get SpiecEasy installed.
I did the following:

1. Thought Xcode might need to be updated. Followed an answer from stackoverflow and put the following commands in the command line to update it:
   softwareupdate --list --verbose
   Then:
   softwareupdate -i Command\ Line\ Tools\ for\ Xcode-13.2

Restarted R, still didn't resolve.

2. So then I used Kevin Ushey's answer from this stackoverflow question and added the following to the file ~/.R/Makevars:
   FLIBS=-L/opt/local/lib/gcc48/

3. Restarted R, then was able to install SpiecEasi!

I'm not sure precisely what was going on but something about using gcc vs clang?

(I'm on macOS Big Sur 11.5.1 btw)

[azmigueldario]

The answer by @mljaniczek also worked for me. I could not find the Makevars file initially, so if it is not in your $HOME path, then just create it.

# check if it exists
ls $HOME/.R

# create folder
mkdir -p $HOME/.R

# save command into new file Makevars
echo "FLIBS=-L/opt/local/lib/gcc48/" > $HOME/.R/Makevars

[zdk123]

Thanks for the answers all. I should put this in the README.

[finally-jay]

azmigueldario
Thank you very much, this answer works for me !