[Rcpp-devel] building shared library error with sourceCpp

[Simon Urbanek]

Did you follow the instructions I sent you?

Sent from my iPhone

> On Dec 28, 2019, at 12:38, Fatima Batool <gbatoolfatima at gmail.com> wrote:
> 
> 
> 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/ 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.urbanek at 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 <gbatoolfatima at 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 at lists.r-forge.r-project.org
>> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>> 
> 
> <Makevars>
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