* installing *source* package ‘gllvm’ ... ** package ‘gllvm’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DTMBAD_FRAMEWORK -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gllvm.cpp -o gllvm.o In file included from gllvm.cpp:2: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/TMB.hpp:83: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Dense:1: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Core:540: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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 gllvm.cpp:2: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/TMB.hpp:83: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Dense:2: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/LU:47: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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 gllvm.cpp:2: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/TMB.hpp:83: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Dense:3: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Cholesky:12: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Jacobi:29: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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 gllvm.cpp:2: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/TMB.hpp:83: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Dense:3: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Cholesky:43: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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 gllvm.cpp:2: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/TMB.hpp:83: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Dense:4: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/QR:15: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Householder:27: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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 gllvm.cpp:2: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/TMB.hpp:83: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Dense:4: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/QR:48: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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 gllvm.cpp:2: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/TMB.hpp:83: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Dense:5: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/SVD:48: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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 gllvm.cpp:2: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/TMB.hpp:83: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Dense:6: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Geometry:58: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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 gllvm.cpp:2: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/TMB.hpp:83: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Dense:7: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Eigenvalues:58: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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 gllvm.cpp:2: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/TMB.hpp:87: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Sparse:26: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/SparseCore:66: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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 gllvm.cpp:2: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/TMB.hpp:87: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Sparse:27: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/OrderingMethods:71: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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 gllvm.cpp:2: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/TMB.hpp:87: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Sparse:29: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/SparseCholesky:43: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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 gllvm.cpp:2: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/TMB.hpp:87: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Sparse:32: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/SparseQR:34: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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 gllvm.cpp:2: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/TMB.hpp:87: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/Sparse:33: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppEigen/include/Eigen/IterativeLinearSolvers:46: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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 gllvm.cpp:2: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/TMB.hpp:112: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/cppad/cppad.hpp:34: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/cppad/ode_gear.hpp:489:6: warning: variable 'sign' set but not used [-Wunused-but-set-variable] int sign; ^ In file included from gllvm.cpp:2: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/TMB.hpp:112: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/cppad/cppad.hpp:39: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/cppad/romberg_mul.hpp:277:10: warning: variable 'pow2' set but not used [-Wunused-but-set-variable] size_t pow2 = 1; ^ In file included from gllvm.cpp:2: In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/TMB.hpp:123: /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/TMBad/TMBad.cpp:4324:10: warning: variable 'total' set but not used [-Wunused-but-set-variable] size_t total = 0; ^ gllvm.cpp:310:16: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if((random(0)==0)){ ~~~~~~~~~^~~ gllvm.cpp:310:16: note: remove extraneous parentheses around the comparison to silence this warning if((random(0)==0)){ ~ ^ ~ gllvm.cpp:310:16: note: use '=' to turn this equality comparison into an assignment if((random(0)==0)){ ^~ = gllvm.cpp:310:16: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if((random(0)==0)){ ~~~~~~~~~^~~ /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/tmb_core.hpp:1277:6: note: in instantiation of member function 'objective_function::operator()' requested here F(); // Run through user template (modifies reportvector) ^ gllvm.cpp:310:16: note: remove extraneous parentheses around the comparison to silence this warning if((random(0)==0)){ ~ ^ ~ gllvm.cpp:310:16: note: use '=' to turn this equality comparison into an assignment if((random(0)==0)){ ^~ = gllvm.cpp:310:16: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if((random(0)==0)){ ~~~~~~~~~^~~ /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/TMB/include/tmb_core.hpp:2031:34: note: in instantiation of member function 'objective_function::operator()' requested here PROTECT( res = asSEXP( pf->operator()() ) ); ^ gllvm.cpp:310:16: note: remove extraneous parentheses around the comparison to silence this warning if((random(0)==0)){ ~ ^ ~ gllvm.cpp:310:16: note: use '=' to turn this equality comparison into an assignment if((random(0)==0)){ ^~ = gllvm.cpp:1815:23: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if((y(i,j)==0)){ ~~~~~~^~~ gllvm.cpp:1815:23: note: remove extraneous parentheses around the comparison to silence this warning if((y(i,j)==0)){ ~ ^ ~ gllvm.cpp:1815:23: note: use '=' to turn this equality comparison into an assignment if((y(i,j)==0)){ ^~ = gllvm.cpp:1819:30: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] } else if((y(i,j)==1)){ ~~~~~~^~~ gllvm.cpp:1819:30: note: remove extraneous parentheses around the comparison to silence this warning } else if((y(i,j)==1)){ ~ ^ ~ gllvm.cpp:1819:30: note: use '=' to turn this equality comparison into an assignment } else if((y(i,j)==1)){ ^~ = 22 warnings generated. clang++ -arch arm64 -std=gnu++17 -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 gllvm.so gllvm.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Volumes/Builds/packages/big-sur-arm64/results/4.3/gllvm.Rcheck/00LOCK-gllvm/00new/gllvm/libs ** generating debug symbols (dSYM) ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning message: In checkMatrixPackageVersion() : Package version inconsistency detected. TMB was built with Matrix version 1.6.0 Current Matrix version is 1.6.1 Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in checkMatrixPackageVersion() : Package version inconsistency detected. TMB was built with Matrix version 1.6.0 Current Matrix version is 1.6.1 Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning in checkMatrixPackageVersion() : Package version inconsistency detected. TMB was built with Matrix version 1.6.0 Current Matrix version is 1.6.1 Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package ** testing if installed package keeps a record of temporary installation path * DONE (gllvm)