############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf destiny.buildbin-libdir && mkdir destiny.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh destiny_3.14.0.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_3.14.0.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 arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/grDevices/include' -I/opt/R/arm64/include -ggdb -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Core:540: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:2: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/LU:47: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Cholesky:12: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Jacobi:29: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Cholesky:43: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/QR:15: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Householder:27: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/QR:48: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:5: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SVD:48: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:6: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Geometry:58: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:66: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:27: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:32: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseQR:34: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:33: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:32: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:35: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:39: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:40: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ 18 warnings generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/grDevices/include' -I/opt/R/arm64/include -ggdb -fPIC -falign-functions=64 -Wall -g -O2 -c censoring.cpp -o censoring.o In file included from censoring.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Core:540: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from censoring.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:2: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/LU:47: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from censoring.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Cholesky:12: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Jacobi:29: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from censoring.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Cholesky:43: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from censoring.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/QR:15: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Householder:27: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from censoring.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/QR:48: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from censoring.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:5: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SVD:48: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from censoring.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:6: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Geometry:58: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from censoring.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from censoring.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:66: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from censoring.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:27: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from censoring.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from censoring.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:32: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseQR:34: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from censoring.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:33: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from censoring.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:32: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from censoring.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:35: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from censoring.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:39: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from censoring.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:40: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ 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 24 warnings generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/grDevices/include' -I/opt/R/arm64/include -ggdb -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o clang++ -arch arm64 -std=gnu++11 -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 destiny.so RcppExports.o censoring.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /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) /usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/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/4.3-arm64/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/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /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) /usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)