[Rcpp-devel] building shared library error with sourceCpp

[Fatima Batool]

That's nothing extra, it's the first step in the link.

On Sat, Dec 28, 2019 at 2:14 PM Simon Urbanek <simon.urbanek at r-project.org>
wrote:

> 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/
> <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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