############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data immunoClust ### ############################################################################## ############################################################################## * checking for file ‘immunoClust/DESCRIPTION’ ... OK * preparing ‘immunoClust’: * checking DESCRIPTION meta-information ... OK * cleaning src * running ‘cleanup’ * installing the package to build vignettes ----------------------------------- * installing *source* package ‘immunoClust’ ... ** using staged installation checking for pkg-config... /opt/homebrew/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for GSL... yes configure: creating ./config.status config.status: creating src/Makevars ** libs clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_meta.cpp -o R_meta.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_model.cpp -o R_model.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dist_mvn.cpp -o dist_mvn.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c em_meta.cpp -o em_meta.o em_meta.cpp:412:16: warning: variable 'sndLike' set but not used [-Wunused-but-set-variable] double sndLike = 0.0; ^ em_meta.cpp:697:16: warning: variable 'maxLike' set but not used [-Wunused-but-set-variable] double maxLike = 0.0; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c em_meta_bc.cpp -o em_meta_bc.o em_meta_bc.cpp:237:16: warning: variable 'maxLike' set but not used [-Wunused-but-set-variable] double maxLike = 0.0; ^ em_meta_bc.cpp:523:16: warning: variable 'maxLike' set but not used [-Wunused-but-set-variable] double maxLike = 0.0; ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c em_meta_kl.cpp -o em_meta_kl.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c em_mvn.cpp -o em_mvn.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c em_mvt.cpp -o em_mvt.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c em_mvt2.cpp -o em_mvt2.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hc_meta.cpp -o hc_meta.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hc_mvn.cpp -o hc_mvn.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c immunoClust.c -o immunoClust.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c meta_norm.cpp -o meta_norm.o meta_norm.cpp:275:16: warning: variable 'sw' set but not used [-Wunused-but-set-variable] double sw = 0; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c meta_scale.cpp -o meta_scale.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c normalize.cpp -o normalize.o normalize.cpp:284:16: warning: variable 'sw' set but not used [-Wunused-but-set-variable] double sw = 0; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sub_mvn.cpp -o sub_mvn.o In file included from sub_mvn.cpp:10: ./sub_mvn.h:21:16: warning: private field 'W' is not used [-Wunused-private-field] const double* W; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c util.cpp -o util.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vs_htrans.cpp -o vs_htrans.o clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o immunoClust.so R_meta.o R_model.o dist_mvn.o em_meta.o em_meta_bc.o em_meta_kl.o em_mvn.o em_mvt.o em_mvt2.o hc_meta.o hc_mvn.o immunoClust.o meta_norm.o meta_scale.o normalize.o sub_mvn.o util.o vs_htrans.o -L/usr/local/lib -lgsl -lgslcblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: ignoring file /usr/local/lib/libgslcblas.a, building for macOS-arm64 but attempting to link with file built for macOS-x86_64 ld: warning: ignoring file /usr/local/lib/libgsl.a, building for macOS-arm64 but attempting to link with file built for macOS-x86_64 installing to /private/tmp/RtmpETeUWs/Rinstdf4b4f9b4e8f/00LOCK-immunoClust/00new/immunoClust/libs ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘immunoClust’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/private/tmp/RtmpETeUWs/Rinstdf4b4f9b4e8f/00LOCK-immunoClust/00new/immunoClust/libs/immunoClust.so': dlopen(/private/tmp/RtmpETeUWs/Rinstdf4b4f9b4e8f/00LOCK-immunoClust/00new/immunoClust/libs/immunoClust.so, 0x0006): symbol not found in flat namespace '_gsl_cdf_chisq_Pinv' Error: loading failed Execution halted ERROR: loading failed * removing ‘/private/tmp/RtmpETeUWs/Rinstdf4b4f9b4e8f/immunoClust’ ----------------------------------- ERROR: package installation failed