############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf BASiCS.buildbin-libdir && mkdir BASiCS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BASiCS_2.17.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BASiCS.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BASiCS.buildbin-libdir BASiCS_2.17.0.tar.gz' >>>>>>> * installing *source* package ‘BASiCS’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BASiCS.cpp -o BASiCS.o In file included from BASiCS.cpp:1: In file included from ./updates.h:4: ./utils.h:357:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if( arma::is_finite(log_aux(i)) & arma::is_finite(y(i)) ) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && ./utils.h:357:9: note: cast one or both operands to int to silence this warning ./utils.h:358:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if((log(u(i)) < log_aux(i)) & (y(i) > threshold)) { ind(i) = 1; } ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && ./utils.h:358:10: note: cast one or both operands to int to silence this warning In file included from BASiCS.cpp:1: ./updates.h:163:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if(all(prop_var * phi1 < 2.5327372760800758e+305) & ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./updates.h:163:6: note: cast one or both operands to int to silence this warning ./updates.h:163:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if(all(prop_var * phi1 < 2.5327372760800758e+305) & ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./updates.h:163:6: note: cast one or both operands to int to silence this warning ./updates.h:163:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if(all(prop_var * phi1 < 2.5327372760800758e+305) & ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && ./updates.h:163:6: note: cast one or both operands to int to silence this warning ./updates.h:258:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if (!R_IsNA(chi(j)) & (chi(j) > 0)) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && ./updates.h:258:11: note: cast one or both operands to int to silence this warning ./updates.h:266:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if (!(chi(j) < 0) & (lambda(j) > 0)) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && ./updates.h:266:13: note: cast one or both operands to int to silence this warning In file included from BASiCS.cpp:3: ./updatesNoSpikes.h:76:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if ((log(u(iAux)) < log_aux(iAux)) & (mu1(iAux) > mintol)) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && ./updatesNoSpikes.h:76:11: note: cast one or both operands to int to silence this warning ./updatesNoSpikes.h:102:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if ((log(u(iAux)) < log_aux(iAux)) & (mu1(iAux) > mintol)) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && ./updatesNoSpikes.h:102:9: note: cast one or both operands to int to silence this warning In file included from BASiCS.cpp:4: ./updatesRegNoSpikes.h:107:10: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if((log(u(iAux)) < log_aux(iAux)) & (mu1(iAux) > mintol)) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && ./updatesRegNoSpikes.h:107:10: note: cast one or both operands to int to silence this warning ./updatesRegNoSpikes.h:139:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if ((log(u(iAux)) < log_aux(iAux)) & (mu1(iAux) > mintol)) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && ./updatesRegNoSpikes.h:139:9: note: cast one or both operands to int to silence this warning In file included from BASiCS.cpp:6: ./MCMCReg.h:383:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if ((det(V1) != 0) & all(arma::eig_sym(sigma2Aux * VAux) > 0)) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && ./MCMCReg.h:383:9: note: cast one or both operands to int to silence this warning In file included from BASiCS.cpp:8: ./MCMCRegNoSpikes.h:382:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if((det(V1)!=0) & all(arma::eig_sym(sigma2Aux * VAux) > 0)) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && ./MCMCRegNoSpikes.h:382:8: note: cast one or both operands to int to silence this warning 13 warnings generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o BASiCS.so BASiCS.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/BASiCS.buildbin-libdir/00LOCK-BASiCS/00new/BASiCS/libs ** R ** data ** inst ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BASiCS) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR BASiCS.buildbin-libdir/BASiCS/libs/BASiCS.so >>>>>>> >>>>>>> Paths before fix: BASiCS.buildbin-libdir/BASiCS/libs/BASiCS.so: BASiCS.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "BASiCS.buildbin-libdir/BASiCS/libs/BASiCS.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "BASiCS.buildbin-libdir/BASiCS/libs/BASiCS.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "BASiCS.buildbin-libdir/BASiCS/libs/BASiCS.so" install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "BASiCS.buildbin-libdir/BASiCS/libs/BASiCS.so" install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "BASiCS.buildbin-libdir/BASiCS/libs/BASiCS.so" >>>>>>> Paths after fix: BASiCS.buildbin-libdir/BASiCS/libs/BASiCS.so: BASiCS.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)