Installation issue

[courtney0thomas]

Hi, I'm trying to install shaman on R 3.6.1 using the code provided:

Load shiny packages

if(!require('shiny')){
install.packages('shiny')
library(shiny)
}

Install dependencies, download last version of SHAMAN from github and run shaman in one command :

runGitHub('aghozlane/shaman')

and I get a lot of warning messages but ultimately R studio says this:

runGitHub('aghozlane/shaman')
Downloading https://github.com/aghozlane/shaman/archive/master.tar.gz
Loading required package: DESeq2shaman
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘DESeq2shaman’
Downloading GitHub repo aghozlane/DESeq2shaman@master
✔ checking for file ‘/private/var/folders/_s/s02mpvvn6_7494rb08sycqgr0000gp/T/RtmpmMteBC/remotesf622370c5c16/aghozlane-DESeq2shaman-282594b/DESCRIPTION’
─ preparing ‘DESeq2shaman’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
✔ checking vignette meta-information
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘DESeq2shaman_1.6.3.tar.gz’

• installing source package ‘DESeq2shaman’ ...
  ** using staged installation
  ** libs
  #lists libraries#
  clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
  clang++ -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 DESeq2shaman.so DESeq2.o RcppExports.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-darwin15/6.1.0 -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-darwin15/6.1.0'
  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: *** [DESeq2shaman.so] Error 1
  ERROR: compilation failed for package ‘DESeq2shaman’
• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/DESeq2shaman’
  Error: Failed to install 'DESeq2shaman' from GitHub:
  (converted from warning) installation of package ‘/var/folders/_s/s02mpvvn6_7494rb08sycqgr0000gp/T//RtmpmMteBC/filef622c71c496/DESeq2shaman_1.6.3.tar.gz’ had non-zero exit status

[aghozlane]

Hi you need to install gfortran to build tools on mac https://cran.r-project.org/bin/macosx/tools/

this one should be the most appropriate for your version of mac: https://cran.r-project.org/bin/macosx/tools/gfortran-6.1.pkg