<div dir="ltr">Ah, I guess something else is wrong. The Flags are already there. Please see the attached file which is Makevars in .R. <div><br></div><div>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? </div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Dec 28, 2019 at 9:50 PM Balamuta, James Joseph <<a href="mailto:balamut2@illinois.edu">balamut2@illinois.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
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<p class="MsoNormal">Fatima,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I think the ~/.R/Makevars didn’t get created correctly. In particular, the ${R_HOME} path didn’t get extended:<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">> -Wl,-rpath,/lib /lib/libc++abi.1.dylib<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Could you modify the ~/.R/Makevars file and ensure it has:<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"># clang: start<u></u><u></u></p>
<p class="MsoNormal">CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk<u></u><u></u></p>
<p class="MsoNormal">CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk<u></u><u></u></p>
<p class="MsoNormal">CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk<u></u><u></u></p>
<p class="MsoNormal">CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">SHLIB_CXXLDFLAGS+=-Wl,-rpath,${R_HOME}/lib ${R_HOME}/lib/libc++abi.1.dylib<u></u><u></u></p>
<p class="MsoNormal">SHLIB_CXX14LDFLAGS+=-Wl,-rpath,${R_HOME}/lib ${R_HOME}/lib/libc++abi.1.dylib<u></u><u></u></p>
<p class="MsoNormal"># clang: end<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">- JJB<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><b><span style="font-size:12pt;color:black">From: </span></b><span style="font-size:12pt;color:black">Rcpp-devel <<a href="mailto:rcpp-devel-bounces@lists.r-forge.r-project.org" target="_blank">rcpp-devel-bounces@lists.r-forge.r-project.org</a>> on behalf of Fatima Batool <<a href="mailto:gbatoolfatima@gmail.com" target="_blank">gbatoolfatima@gmail.com</a>><br>
<b>Date: </b>Saturday, December 28, 2019 at 5:05 PM<br>
<b>To: </b>Simon Urbanek <<a href="mailto:simon.urbanek@r-project.org" target="_blank">simon.urbanek@r-project.org</a>><br>
<b>Cc: </b>"<a href="mailto:rcpp-devel@lists.r-forge.r-project.org" target="_blank">rcpp-devel@lists.r-forge.r-project.org</a>" <<a href="mailto:rcpp-devel@lists.r-forge.r-project.org" target="_blank">rcpp-devel@lists.r-forge.r-project.org</a>><br>
<b>Subject: </b>Re: [Rcpp-devel] building shared library error with sourceCpp<u></u><u></u></span></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">That's nothing extra, it's the first step in the link.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">On Sat, Dec 28, 2019 at 2:14 PM Simon Urbanek <<a href="mailto:simon.urbanek@r-project.org" target="_blank">simon.urbanek@r-project.org</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal" style="margin-bottom:12pt">Did you follow the instructions I sent you?<u></u><u></u></p>
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<p class="MsoNormal">Sent from my iPhone<u></u><u></u></p>
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<p class="MsoNormal"><br>
<br>
<u></u><u></u></p>
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<p class="MsoNormal" style="margin-bottom:12pt">On Dec 28, 2019, at 12:38, Fatima Batool <<a href="mailto:gbatoolfatima@gmail.com" target="_blank">gbatoolfatima@gmail.com</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal">Hi Drik and Simon, <u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:-webkit-standard,serif;color:black">thanks you for the help!</span><u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">I have followed all the instructions Drik mentioned here: <u>
<span style="color:blue"><a href="https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/" target="_blank">https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/</a></span></u> and then run a hello
world.cpp example but unfortunately the error is still there. <u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><span style="color:blue">> Rcpp::sourceCpp('/Users/fatimabatool/documents/New/Rcodes/ASW/helloworld.cpp')</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="color:blue">clang-7: error: no such file or directory: '/lib/libc++abi.1.dylib'</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="color:blue">make: *** [sourceCpp_6.so] Error 1</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="color:black">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</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="color:black">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</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="color:red">Error in Rcpp::sourceCpp("/Users/fatimabatool/documents/New/Rcodes/ASW/helloworld.cpp") : </span><u></u><u></u></p>
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<p class="MsoNormal"><span style="color:red"> Error 1 occurred building shared library.</span><u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<div>
<p class="MsoNormal"><span style="color:black">Have removed old installation files, installed command line tools, upgraded to clang-7 and gfotron6.1. I have added set of compilation files to </span><span style="font-size:12pt;font-family:"Times New Roman",serif;color:rgb(16,23,48);background-color:rgb(250,248,248);background-position:initial initial;background-repeat:initial initial"> </span><code><span style="font-size:12pt;font-family:Consolas;color:rgb(16,23,48);border:1pt none windowtext;padding:0in;background-color:rgb(236,232,232);background-position:initial initial;background-repeat:initial initial">~/.R/Makevars</span></code><span style="color:black"><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="color:black"> 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?<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="color:black"><u></u> <u></u></span></p>
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<p class="MsoNormal">Best wishes, <u></u><u></u></p>
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<p class="MsoNormal">Fatima<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">On Sat, Dec 28, 2019 at 11:45 AM Simon Urbanek <<a href="mailto:simon.urbanek@r-project.org" target="_blank">simon.urbanek@r-project.org</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal" style="margin-bottom:12pt">Fatima,<br>
<br>
it means you don't have command line tools installed (they are independent of Xcode and Apple OS upgrades delete things, unfortunately) - try<br>
<br>
sudo xcode-select —install<br>
<br>
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.<br>
<br>
Cheers,<br>
Simon<br>
<br>
<br>
<br>
> On Dec 27, 2019, at 8:16 PM, Fatima Batool <<a href="mailto:gbatoolfatima@gmail.com" target="_blank">gbatoolfatima@gmail.com</a>> wrote:<br>
> <br>
> Hi all, <br>
> <br>
> Could anyone please advice what is going on in the following error and how can I fix it?<br>
> <br>
> sourceCpp("/Users/fatimabatool/documents/New/Rcodes/trial.cpp") <br>
> 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<br>
> Error in sourceCpp("/Users/fatimabatool/documents/New/Rcodes/trial.cpp") : <br>
> Error 1 occurred building shared library.<br>
> clang: warning: no such sysroot directory: '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk' [-Wmissing-sysroot]<br>
> In file included from trial.cpp:9:<br>
> In file included from /Users/fatimabatool/Documents/New/Rcodes/trial.hpp:12:<br>
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' file not found<br>
> #include_next <stdio.h><br>
> ^~~~~~~~~<br>
> 1 error generated.<br>
> make: *** [trial.o] Error 1<br>
> <br>
> <br>
> 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.
<br>
> <br>
> I have Library/Developer but no ../CommandLineTools/SDKs/MAcOSX.sdk subdirectories exist there.
<br>
> <br>
> <br>
> <br>
> Best wishes, <br>
> Fatima<br>
> _______________________________________________<br>
> Rcpp-devel mailing list<br>
> <a href="mailto:Rcpp-devel@lists.r-forge.r-project.org" target="_blank">Rcpp-devel@lists.r-forge.r-project.org</a><br>
> <a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel" target="_blank">
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel</a><u></u><u></u></p>
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<p class="MsoNormal"><Makevars><u></u><u></u></p>
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