############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf destiny.buildbin-libdir && mkdir destiny.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh destiny_3.19.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R destiny.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=destiny.buildbin-libdir destiny_3.19.0.tar.gz' >>>>>>> * installing *source* package ‘destiny’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -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/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/grDevices/include' -I/opt/R/x86_64/include -ggdb -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -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/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/grDevices/include' -I/opt/R/x86_64/include -ggdb -fPIC -falign-functions=64 -Wall -g -O2 -c censoring.cpp -o censoring.o censoring.cpp:60:15: warning: variable 'm0' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ censoring.cpp:71:20: note: uninitialized use occurs here * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) ) ^~ censoring.cpp:60:11: note: remove the 'if' if its condition is always true } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ censoring.cpp:60:15: warning: variable 'm0' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized] } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~ censoring.cpp:71:20: note: uninitialized use occurs here * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) ) ^~ censoring.cpp:60:15: note: remove the '&&' if its condition is always true } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~~~~ censoring.cpp:55:13: note: initialize the variable 'm0' to silence this warning double m0, m1; ^ = 0.0 censoring.cpp:60:15: warning: variable 'm1' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ censoring.cpp:71:48: note: uninitialized use occurs here * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) ) ^~ censoring.cpp:60:11: note: remove the 'if' if its condition is always true } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ censoring.cpp:60:15: warning: variable 'm1' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized] } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~ censoring.cpp:71:48: note: uninitialized use occurs here * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) ) ^~ censoring.cpp:60:15: note: remove the '&&' if its condition is always true } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~~~~ censoring.cpp:55:17: note: initialize the variable 'm1' to silence this warning double m0, m1; ^ = 0.0 censoring.cpp:60:15: warning: variable 'use_d' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ censoring.cpp:66:21: note: uninitialized use occurs here const double v = use_d ? d : c; ^~~~~ censoring.cpp:60:11: note: remove the 'if' if its condition is always true } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ censoring.cpp:60:15: warning: variable 'use_d' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized] } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~ censoring.cpp:66:21: note: uninitialized use occurs here const double v = use_d ? d : c; ^~~~~ censoring.cpp:60:15: note: remove the '&&' if its condition is always true } else if (!one_uncertain && one_missing) { ^~~~~~~~~~~~~~~~~ censoring.cpp:18:12: note: initialize the variable 'use_d' to silence this warning bool use_d; ^ = false 6 warnings generated. clang++ -arch x86_64 -std=gnu++11 -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/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/grDevices/include' -I/opt/R/x86_64/include -ggdb -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o destiny.so RcppExports.o censoring.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/destiny.buildbin-libdir/00LOCK-destiny/00new/destiny/libs ** R ** data ** demo ** 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 (destiny) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR destiny.buildbin-libdir/destiny/libs/destiny.so >>>>>>> >>>>>>> Paths before fix: destiny.buildbin-libdir/destiny/libs/destiny.so: destiny.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/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-x86_64/Resources/lib/libgcc_s.1.1.dylib" "destiny.buildbin-libdir/destiny/libs/destiny.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" "destiny.buildbin-libdir/destiny/libs/destiny.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" "destiny.buildbin-libdir/destiny/libs/destiny.so" >>>>>>> Paths after fix: destiny.buildbin-libdir/destiny/libs/destiny.so: destiny.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/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)