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 <[email protected]> on behalf of
Fatima Batool <[email protected]>
Date: Saturday, December 28, 2019 at 5:05 PM
To: Simon Urbanek <[email protected]>
Cc: "[email protected]"
<[email protected]>
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
<[email protected]<mailto:[email protected]>> wrote:
Did you follow the instructions I sent you?
Sent from my iPhone
On Dec 28, 2019, at 12:38, Fatima Batool
<[email protected]<mailto:[email protected]>> 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
<[email protected]<mailto:[email protected]>> 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
> <[email protected]<mailto:[email protected]>> 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
> [email protected]<mailto:[email protected]>
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