############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf DifferentialRegulation.buildbin-libdir && mkdir DifferentialRegulation.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DifferentialRegulation_2.4.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R DifferentialRegulation.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DifferentialRegulation.buildbin-libdir DifferentialRegulation_2.4.0.tar.gz' >>>>>>> * installing *source* package ‘DifferentialRegulation’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++17 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rcpp_MCMC.cpp -o Rcpp_MCMC.o Rcpp_MCMC.cpp:135:17: warning: unused variable 'tmp_2' [-Wunused-variable] double tmp_1, tmp_2, tmp_3; ^ Rcpp_MCMC.cpp:135:24: warning: unused variable 'tmp_3' [-Wunused-variable] double tmp_1, tmp_2, tmp_3; ^ Rcpp_MCMC.cpp:135:10: warning: unused variable 'tmp_1' [-Wunused-variable] double tmp_1, tmp_2, tmp_3; ^ 3 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rcpp_MCMC_EC_US.cpp -o Rcpp_MCMC_EC_US.o Rcpp_MCMC_EC_US.cpp:130:10: warning: unused variable 'tmp_1' [-Wunused-variable] double tmp_1, tmp_2, tmp; ^ Rcpp_MCMC_EC_US.cpp:130:17: warning: unused variable 'tmp_2' [-Wunused-variable] double tmp_1, tmp_2, tmp; ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o DifferentialRegulation.so RcppExports.o Rcpp_MCMC.o Rcpp_MCMC_EC_US.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/DifferentialRegulation.buildbin-libdir/00LOCK-DifferentialRegulation/00new/DifferentialRegulation/libs ** R ** 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 (DifferentialRegulation) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR DifferentialRegulation.buildbin-libdir/DifferentialRegulation/libs/DifferentialRegulation.so >>>>>>> >>>>>>> Paths before fix: DifferentialRegulation.buildbin-libdir/DifferentialRegulation/libs/DifferentialRegulation.so: DifferentialRegulation.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.1) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /opt/gfortran/lib/gcc/x86_64-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-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /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-x86_64/Resources/lib/libgcc_s.1.1.dylib" "DifferentialRegulation.buildbin-libdir/DifferentialRegulation/libs/DifferentialRegulation.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "DifferentialRegulation.buildbin-libdir/DifferentialRegulation/libs/DifferentialRegulation.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "DifferentialRegulation.buildbin-libdir/DifferentialRegulation/libs/DifferentialRegulation.so" install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "DifferentialRegulation.buildbin-libdir/DifferentialRegulation/libs/DifferentialRegulation.so" install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "DifferentialRegulation.buildbin-libdir/DifferentialRegulation/libs/DifferentialRegulation.so" >>>>>>> Paths after fix: DifferentialRegulation.buildbin-libdir/DifferentialRegulation/libs/DifferentialRegulation.so: DifferentialRegulation.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.1) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /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)