Install log for 'COMIX'

* installing *source* package ‘COMIX’ ...
** package ‘COMIX’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppNumerical/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -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'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppNumerical/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -fPIC  -falign-functions=64 -Wall -g -O2   -c armaMunkres.cpp -o armaMunkres.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppNumerical/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -fPIC  -falign-functions=64 -Wall -g -O2   -c calibrateSN.cpp -o calibrateSN.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppNumerical/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -fPIC  -falign-functions=64 -Wall -g -O2   -c main.cpp -o main.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppNumerical/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -fPIC  -falign-functions=64 -Wall -g -O2   -c perturbedSN_helpers.cpp -o perturbedSN_helpers.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppNumerical/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -fPIC  -falign-functions=64 -Wall -g -O2   -c perturbedSN_pmc.cpp -o perturbedSN_pmc.o
In file included from RcppExports.cpp:5:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:26:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseCore:61:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from perturbedSN_helpers.cpp:5:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:26:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseCore:61:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from RcppExports.cpp:5:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseLU:35:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from perturbedSN_helpers.cpp:5:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/Sparse:29:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/SparseLU:35:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from RcppExports.cpp:5:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from perturbedSN_helpers.cpp:5:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from RcppExports.cpp:5:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
In file included from perturbedSN_helpers.cpp:5:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppNumerical/include/RcppNumerical.h:10:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppNumerical/include' -I/opt/R/x86_64/include    -DARMA_64BIT_WORD -fPIC  -falign-functions=64 -Wall -g -O2   -c relabel.cpp -o relabel.o
5 warnings generated.
5 warnings generated.
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 COMIX.so RcppExports.o armaMunkres.o calibrateSN.o main.o perturbedSN_helpers.o perturbedSN_pmc.o relabel.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 /Volumes/Builds/packages/big-sur-x86_64/results/4.4/COMIX.Rcheck/00LOCK-COMIX/00new/COMIX/libs
** generating debug symbols (dSYM)
** 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 (COMIX)