[Rcpp-devel] building shared library error with sourceCpp

[Fatima Batool]

Ah, I guess something else is wrong. The Flags are already there. Please
see the attached file which is Makevars in .R.

Simon can you guess what else it could be? I didn't change things myself.
Do you recommend doing all installations again? If so in which order?

On Sat, Dec 28, 2019 at 9:50 PM Balamuta, James Joseph <
balamut2 at illinois.edu> wrote:

> Fatima,
>
>
>
> I think the ~/.R/Makevars didn’t get created correctly. In particular, the
> ${R_HOME} path didn’t get extended:
>
>
>
> >  -Wl,-rpath,/lib /lib/libc++abi.1.dylib
>
>
>
> Could you modify the ~/.R/Makevars file and ensure it has:
>
>
>
> # clang: start
>
> CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
>
> CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
>
> CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
>
> CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> -I/usr/local/include
>
>
>
> SHLIB_CXXLDFLAGS+=-Wl,-rpath,${R_HOME}/lib ${R_HOME}/lib/libc++abi.1.dylib
>
> SHLIB_CXX14LDFLAGS+=-Wl,-rpath,${R_HOME}/lib
> ${R_HOME}/lib/libc++abi.1.dylib
>
> # clang: end
>
>
>
> - JJB
>
>
>
>
>
> *From: *Rcpp-devel <rcpp-devel-bounces at lists.r-forge.r-project.org> on
> behalf of Fatima Batool <gbatoolfatima at gmail.com>
> *Date: *Saturday, December 28, 2019 at 5:05 PM
> *To: *Simon Urbanek <simon.urbanek at r-project.org>
> *Cc: *"rcpp-devel at lists.r-forge.r-project.org" <
> rcpp-devel at lists.r-forge.r-project.org>
> *Subject: *Re: [Rcpp-devel] building shared library error with sourceCpp
>
>
>
> 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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