romagnolid
commented
2 years ago Hi @biostars-nyc, it looks like an issue related to the Mac environment. I don't know your expertise so forgive me if I suggest something obvious. First of all you you need to install Xcode. Second, I found this related issue on stackexchange which redirects to this guide to install R compiler tools on MacOS.
biostars-nyc
I get the following output + errors when attempting to install via dev tools:
ownloading GitHub repo cgplab/Rockermeth@HEAD Skipping 3 packages not available: IRanges, GenomicRanges, S4Vectors ✓ checking for file ‘/private/var/folders/2w/dgzchz7j45sbkqfppwffx2gr0000gq/T/RtmpyoRRoX/remotes11f81c729d90/cgplab-Rockermeth-15dfe35/DESCRIPTION’ (894ms) ─ preparing ‘Rockermeth’: (505ms) ✓ 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 ─ building ‘Rockermeth_0.1.0.tar.gz’
installing source package ‘Rockermeth’ ... using staged installation libs gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c MethLibrary.f -o MethLibrary.o MethLibrary.f:8:40:
8 | DOUBLE PRECISION NDELTA(KTILDE,T),PDELTA(KTILDE,T) | 1 Warning: Unused variable 'ndelta' declared at (1) [-Wunused-variable] MethLibrary.f:5:28:
5 | DOUBLE PRECISION NORM,NORM1,NUMMAX | 1 Warning: Unused variable 'norm' declared at (1) [-Wunused-variable] MethLibrary.f:5:34:
5 | DOUBLE PRECISION NORM,NORM1,NUMMAX | 1 Warning: Unused variable 'norm1' declared at (1) [-Wunused-variable] MethLibrary.f:8:57:
8 | DOUBLE PRECISION NDELTA(KTILDE,T),PDELTA(KTILDE,T) | 1 Warning: Unused variable 'pdelta' declared at (1) [-Wunused-variable] clang -mmacosx-version-min=10.13 -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 Rockermeth.so MethLibrary.o -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: *** [Rockermeth.so] Error 1 ERROR: compilation failed for package ‘Rockermeth’