Install log for 'secr'

* installing *source* package ‘secr’ ...
** package ‘secr’ 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  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c autils.cpp -o autils.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c autoini.cpp -o autoini.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c detectfn.cpp -o detectfn.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c getdenom.cpp -o getdenom.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c geth.cpp -o geth.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c hdot.cpp -o hdot.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c integral1D.cpp -o integral1D.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c integral2D.cpp -o integral2D.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c makegk.cpp -o makegk.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c makegkpoly.cpp -o makegkpoly.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c makelookup.cpp -o makelookup.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c nkpoint.cpp -o nkpoint.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c pdot.cpp -o pdot.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c polygonNR.cpp -o polygonNR.o
polygonNR.cpp:30:9: warning: private field 'fn' is not used [-Wunused-private-field]
    int fn;
        ^
polygonNR.cpp:120:9: warning: private field 'fn' is not used [-Wunused-private-field]
    int fn;
        ^
polygonNR.cpp:162:19: warning: private field 'fn' is not used [-Wunused-private-field]
        const int fn;
                  ^
polygonNR.cpp:163:19: warning: private field 'n1' is not used [-Wunused-private-field]
              int n1;
                  ^
polygonNR.cpp:164:19: warning: private field 'n2' is not used [-Wunused-private-field]
              int n2;
                  ^
polygonNR.cpp:306:19: warning: private field 'fn' is not used [-Wunused-private-field]
        const int fn;
                  ^
polygonNR.cpp:309:22: warning: private field 'ay' is not used [-Wunused-private-field]
        const double ay;
                     ^
polygonNR.cpp:310:22: warning: private field 'by' is not used [-Wunused-private-field]
        const double by;
                     ^
polygonNR.cpp:515:9: warning: private field 'fn' is not used [-Wunused-private-field]
    int fn;
        ^
polygonNR.cpp:535:9: warning: private field 'fn' is not used [-Wunused-private-field]
    int fn;
        ^
10 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c prwifastproximity.cpp -o prwifastproximity.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c prwipolygon.cpp -o prwipolygon.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c prwipolygonfxi.cpp -o prwipolygonfxi.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c prwisignal.cpp -o prwisignal.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c prwisimple.cpp -o prwisimple.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c prwisimplefxi.cpp -o prwisimplefxi.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c sighting.cpp -o sighting.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c sightingchat.cpp -o sightingchat.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c sightingexpectedmusk.cpp -o sightingexpectedmusk.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c simsecr.cpp -o simsecr.o
simsecr.cpp:1192:14: warning: unused variable 'ik' [-Wunused-variable]
    int    i,ik,k,s,x;
             ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c transectutils.cpp -o transectutils.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppNumerical/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c trapping.cpp -o trapping.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o secr.so RcppExports.o autils.o autoini.o detectfn.o getdenom.o geth.o hdot.o integral1D.o integral2D.o makegk.o makegkpoly.o makelookup.o nkpoint.o pdot.o polygonNR.o prwifastproximity.o prwipolygon.o prwipolygonfxi.o prwisignal.o prwisimple.o prwisimplefxi.o sighting.o sightingchat.o sightingexpectedmusk.o simsecr.o transectutils.o trapping.o -L/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/lib -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Builds/packages/big-sur-arm64/results/4.4/secr.Rcheck/00LOCK-secr/00new/secr/libs
** generating debug symbols (dSYM)
** R
** data
*** moving datasets to lazyload DB
** 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 (secr)