Install log for 'gllvm'

* 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<TMBad::global::ad_aug>::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<double>::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)