Hi Drik and Simon, thanks you for the help!
I have followed all the instructions Drik mentioned here: *https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/ <https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/>* and then run a hello world.cpp example but unfortunately the error is still there. > Rcpp::sourceCpp('/Users/fatimabatool/documents/New/Rcodes/ASW/helloworld.cpp') clang-7: error: no such file or directory: '/lib/libc++abi.1.dylib' make: *** [sourceCpp_6.so] Error 1 clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -I"/Users/fatimabatool/Documents/New/Rcodes/ASW" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c helloworld.cpp -o helloworld.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -Wl,-rpath,/lib /lib/libc++abi.1.dylib -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o sourceCpp_6.so helloworld.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 Error in Rcpp::sourceCpp("/Users/fatimabatool/documents/New/Rcodes/ASW/helloworld.cpp") : Error 1 occurred building shared library. Have removed old installation files, installed command line tools, upgraded to clang-7 and gfotron6.1. I have added set of compilation files to ~/.R/Makevars as mentioned and the file exist there (attached) but there is still no CommandLineTools directory in Library/Developer. Should I try to create these myself? Best wishes, Fatima On Sat, Dec 28, 2019 at 11:45 AM Simon Urbanek <simon.urba...@r-project.org> wrote: > Fatima, > > it means you don't have command line tools installed (they are independent > of Xcode and Apple OS upgrades delete things, unfortunately) - try > > sudo xcode-select —install > > That should fix the error you see. However, Catalina broke more things so > you may look at the links Dirk pointed out if you get new errors. > > Cheers, > Simon > > > > > On Dec 27, 2019, at 8:16 PM, Fatima Batool <gbatoolfat...@gmail.com> > wrote: > > > > Hi all, > > > > Could anyone please advice what is going on in the following error and > how can I fix it? > > > > sourceCpp("/Users/fatimabatool/documents/New/Rcodes/trial.cpp") > > 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"/Users/fatimabatool/Documents/New/Rcodes" -isysroot > /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include > -fPIC -Wall -g -O2 -c trial.cpp -o trial.o > > Error in sourceCpp("/Users/fatimabatool/documents/New/Rcodes/trial.cpp") > : > > Error 1 occurred building shared library. > > clang: warning: no such sysroot directory: > '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk' [-Wmissing-sysroot] > > In file included from trial.cpp:9: > > In file included from > /Users/fatimabatool/Documents/New/Rcodes/trial.hpp:12: > > > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/stdio.h:108:15: > fatal error: 'stdio.h' file not found > > #include_next <stdio.h> > > ^~~~~~~~~ > > 1 error generated. > > make: *** [trial.o] Error 1 > > > > > > I was able to source all .cpp files before system updates. I have > recently updated my MacOS to Catalina (10.15.2) and using Xcode 11.3. I am > working in R Action of the Toe. Using version 1.0.3 of Rcpp. I have clang > version 4.0.1. > > > > I have Library/Developer but no ../CommandLineTools/SDKs/MAcOSX.sdk > subdirectories exist there. > > > > > > > > Best wishes, > > Fatima > > _______________________________________________ > > Rcpp-devel mailing list > > Rcpp-devel@lists.r-forge.r-project.org > > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel > >
Makevars
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