################################################################################################################################################################## Running command:###### rm -rf mnem.buildbin-libdir && mkdir mnem.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh mnem_1.26.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R mnem.buildbin-libdir###############################################################################################################################################################>>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=mnem.buildbin-libdir mnem_1.26.0.tar.gz'>>>>>>> * installing *source* package ‘mnem’ ...** this is package ‘mnem’ version ‘1.26.0’** using staged installation** libsusing C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’using SDK: ‘MacOSX11.3.1.sdk’clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.oIn file included from RcppExports.cpp:4:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] Index count = 0; ^In file included from RcppExports.cpp:4:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^In file included from RcppExports.cpp:4:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] Index replacements = 0; ^In file included from RcppExports.cpp:4:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] int count = 0; ^5 warnings generated.clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mm.cpp -o mm.oIn file included from mm.cpp:5:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] Index count = 0; ^In file included from mm.cpp:5:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^In file included from mm.cpp:5:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] Index replacements = 0; ^In file included from mm.cpp:5:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] int count = 0; ^5 warnings generated.clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o mnem.so RcppExports.o mm.o -F/Library/Frameworks/R.framework/.. -framework Rinstalling to /Users/biocbuild/bbs-3.22-bioc/meat/mnem.buildbin-libdir/00LOCK-mnem/00new/mnem/libs** R** data*** moving datasets to lazyload DB** 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 (mnem)>>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR mnem.buildbin-libdir/mnem/libs/mnem.so>>>>>>> >>>>>>> Paths before fix:mnem.buildbin-libdir/mnem/libs/mnem.so:mnem.so (compatibility version 0.0.0, current version 0.0.0)/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.2)/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/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "mnem.buildbin-libdir/mnem/libs/mnem.so"install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "mnem.buildbin-libdir/mnem/libs/mnem.so"install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "mnem.buildbin-libdir/mnem/libs/mnem.so">>>>>>> Paths after fix:mnem.buildbin-libdir/mnem/libs/mnem.so:mnem.so (compatibility version 0.0.0, current version 0.0.0)/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.2)/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)
