cgplab/Rockermeth

installation issue

biostars-nyc opened this issue · 2 comments

biostars-nyc commented

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’

  • removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rockermeth’
    Warning message:
    In i.p(...) :
    installation of package '/var/folders/2w/dgzchz7j45sbkqfppwffx2gr0000gq/T//RtmpyoRRoX/file11f828c66787/Rockermeth_0.1.0.tar.gz' had non-zero exit status

romagnolid commented

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 commented

Thanks I was able to resolve it!

  • 👍1