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POR package installation is successful on all machines but one
 

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  1. POR package installation is successful on all machines but one
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    <p>We are a team working on an R package containing C/C++ code. The package can successfully be installed on all the machines but one. These all run the same version of Mac OS X. I have provided the log files for the installation of the package on my computer (success) and a colleague's computer (error). The package depends on the Rcpp package and the GSL library, both of which were successfully installed on both machines.</p> <p><strong>My Computer</strong></p> <pre><code>WARNING: ignoring environment value of R_HOME * installing to library '/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15' * installing *source* package 'mrenci' ... ** libs *** arch - x86_64 /opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include" -fPIC -pipe -O2 -m64 -c MRMRTree.cc -o MRMRTree.o /opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include" -fPIC -pipe -O2 -m64 -c Matrix.cc -o Matrix.o /opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include" -fPIC -pipe -O2 -m64 -c MiMBuilder.cc -o MiMBuilder.o /opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include" -fPIC -pipe -O2 -m64 -c SymmetricMatrix.cc -o SymmetricMatrix.o /opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include" -fPIC -pipe -O2 -m64 -c adaptor.cc -o adaptor.o /opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include" -fPIC -pipe -O2 -m64 -c memory.cc -o memory.o /opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include" -fPIC -pipe -O2 -m64 -c tools.cc -o tools.o /opt/local/bin/g++-mp-4.5 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/local/lib -o mrenci.so MRMRTree.o Matrix.o MiMBuilder.o SymmetricMatrix.o adaptor.o memory.o tools.o /Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/lib/x86_64/libRcpp.a -fopenmp -fopenmp -L/opt/local/lib/R/lib/x86_64 -lR installing to /Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/mrenci/libs/x86_64 ** R ** preparing package for lazy loading ** testing if installed package can be loaded * DONE (mrenci) </code></pre> <p><strong>Colleague's Computer</strong></p> <pre><code>WARNING: ignoring environment value of R_HOME * installing to library '/Library/Frameworks/R.framework/Versions/2.15/Resources/library' * installing *source* package 'mrenci' ... ** libs *** arch - x86_64 g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2  -c MRMRTree.cc -o MRMRTree.o MRMRTree.cc: In member function 'double* const MRMRTree::bootstrap(unsigned int)': MRMRTree.cc:73: warning: iteration variable 'i' is unsigned g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2  -c Matrix.cc -o Matrix.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2  -c MiMBuilder.cc -o MiMBuilder.o MiMBuilder.cc: In member function 'Matrix* const MiMBuilder::createMiM(unsigned int*, unsigned int, unsigned int*, unsigned int)': MiMBuilder.cc:102: warning: iteration variable 'i' is unsigned g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2  -c SymmetricMatrix.cc -o SymmetricMatrix.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2  -c adaptor.cc -o adaptor.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2  -c memory.cc -o memory.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2  -c tools.cc -o tools.o g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o mrenci.so MRMRTree.o Matrix.o MiMBuilder.o SymmetricMatrix.o adaptor.o memory.o tools.o /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/lib/x86_64/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/2.15/Resources/library/mrenci/libs/x86_64 ** R ** preparing package for lazy loading ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) :  unable to load shared object '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/mrenci/libs/x86_64/mrenci.so':  dlopen(/Library/Frameworks/R.framework/Versions/2.15/Resources/library/mrenci/libs/x86_64/mrenci.so, 6): Symbol not found: _GOMP_critical_name_end  Referenced from: /Library/Frameworks/R.framework/Versions/2.15/Resources/library/mrenci/libs/x86_64/mrenci.so  Expected in: flat namespace in /Library/Frameworks/R.framework/Versions/2.15/Resources/library/mrenci/libs/x86_64/mrenci.so Error: loading failed Execution halted ERROR: loading failed * removing '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/mrenci' </code></pre> <p>At first, the installation on my colleague's computer would result in the compilation of the package for both architectures, upon which g++ complained about an unknown <code>-arch</code> argument. This issue, however, appears to have been mitigated by forcing the targeting of a single architecture <code>x86_64</code>. It is also worth noting that as a result of these errors, all computers now have several versions of R and g++. Is this an issue with the linker? Does the same compiler need to be used for both R and its packages? In the case of my computer, I never explicitly asked for <code>g++-mp-4.5</code> to be used rather than the default g++ (version 4.2), so I figured R automatically detects it.</p> <p>In case this is of any help, here is what my Makevars contains:</p> <pre><code>PKG_LIBS=`$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(SHLIB_OPENMP_CFLAGS) -fopenmp PKG_CPPFLAGS=$(SHLIB_OPENMP_CXXFLAGS) -fopenmp PKG_CFLAGS=$(SHLIB_OPENMP_CFLAGS) -fopenmp </code></pre> <p>The <code>$(SHLIB_OPENMP_*FLAGS)</code> flags seem to be defined only on my computer; <code>-fopenmp</code> flags were explicitly added for the package to work on all the machines.</p> <p>Has anyone experienced similar issues? Any help would be appreciated.</p>
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    1. COThere seem to be a lot of details still missing in this question.
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    3. COVersions of XCode ? The .Rprofile files seem to be different as well since the libraries being referenced appear to be different.
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