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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CNORode
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘CNORode’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c FG_transfer_function.c -o FG_transfer_function.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodea.c -o cvodea.o
cvodea.c:2445:11: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
  int is, retval;
          ^
cvodea.c:2941:7: warning: variable 'flag' set but not used [-Wunused-but-set-variable]
  int flag, retval;
      ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodea_io.c -o cvodea_io.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes.c -o cvodes.o
cvodes.c:8834:20: warning: variable 'rDeltap' set but not used [-Wunused-but-set-variable]
  realtype Deltap, rDeltap;
                   ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_band.c -o cvodes_band.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_bandpre.c -o cvodes_bandpre.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_bbdpre.c -o cvodes_bbdpre.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_dense.c -o cvodes_dense.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_diag.c -o cvodes_diag.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_direct.c -o cvodes_direct.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_io.c -o cvodes_io.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_spbcgs.c -o cvodes_spbcgs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_spgmr.c -o cvodes_spgmr.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_spils.c -o cvodes_spils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c decimal2binary.c -o decimal2binary.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c findStates.c -o findStates.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c fnvector_serial.c -o fnvector_serial.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c getNumBits.c -o getNumBits.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c getNumInputs.c -o getNumInputs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c getStateIndex.c -o getStateIndex.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c getTruthTables.c -o getTruthTables.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c get_count_bits.c -o get_count_bits.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c get_input_index.c -o get_input_index.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c get_support_truth_tables.c -o get_support_truth_tables.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c get_truth_tables_index.c -o get_truth_tables_index.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c hill_function.c -o hill_function.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c linear_transfer_function.c -o linear_transfer_function.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c normHill.c -o normHill.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c normHill_mod.c -o normHill_mod.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c nvector_serial.c -o nvector_serial.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c printAdjMat.c -o printAdjMat.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c printInterMat.c -o printInterMat.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c printNminiTerms.c -o printNminiTerms.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c printTruthTables.c -o printTruthTables.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c rhsODE.c -o rhsODE.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sim_logic_ode.c -o sim_logic_ode.o
sim_logic_ode.c:62:7: warning: variable 'countProtected' set but not used [-Wunused-but-set-variable]
         int countProtected=0;
             ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c simulateODE.c -o simulateODE.o
simulateODE.c:37:14: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
        int i,j,neq,counter,flag;
                    ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_band.c -o sundials_band.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_dense.c -o sundials_dense.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_direct.c -o sundials_direct.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_iterative.c -o sundials_iterative.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_math.c -o sundials_math.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_nvector.c -o sundials_nvector.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_spbcgs.c -o sundials_spbcgs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_spgmr.c -o sundials_spgmr.o
sundials_spgmr.c:439:20: warning: variable 'givens' set but not used [-Wunused-but-set-variable]
  realtype **Hes, *givens, *yg;
                   ^
sundials_spgmr.c:439:29: warning: variable 'yg' set but not used [-Wunused-but-set-variable]
  realtype **Hes, *givens, *yg;
                            ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c sundials_sptfqmr.c -o sundials_sptfqmr.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o CNORode.so FG_transfer_function.o cvodea.o cvodea_io.o cvodes.o cvodes_band.o cvodes_bandpre.o cvodes_bbdpre.o cvodes_dense.o cvodes_diag.o cvodes_direct.o cvodes_io.o cvodes_spbcgs.o cvodes_spgmr.o cvodes_spils.o cvodes_sptfqmr.o decimal2binary.o findStates.o fnvector_serial.o getAdjacencyMatrix.o getNumBits.o getNumInputs.o getStateIndex.o getTruthTables.o get_count_bits.o get_input_index.o get_support_truth_tables.o get_truth_tables_index.o hill_function.o linear_transfer_function.o normHill.o normHill_mod.o nvector_serial.o printAdjMat.o printInterMat.o printNminiTerms.o printTruthTables.o rhsODE.o sim_logic_ode.o simulateODE.o sundials_band.o sundials_dense.o sundials_direct.o sundials_iterative.o sundials_math.o sundials_nvector.o sundials_spbcgs.o sundials_spgmr.o sundials_sptfqmr.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-CNORode/00new/CNORode/libs
** R
** data
** 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 (CNORode)