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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sRACIPE
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘sRACIPE’ ...
** this is package ‘sRACIPE’ version ‘2.3.2’
** using staged installation
** libs
specified C++11
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c generateThresholds.cpp -o generateThresholds.o
generateThresholds.cpp:43:41: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   43 |   size_t interactionsNumber[numberGene][interactionTypes];
      |                                         ^~~~~~~~~~~~~~~~
generateThresholds.cpp:43:41: note: read of non-const variable 'interactionTypes' is not allowed in a constant expression
generateThresholds.cpp:31:10: note: declared here
   31 |   size_t interactionTypes = static_cast<size_t>(hyperParameters[8]);
      |          ^
generateThresholds.cpp:43:29: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   43 |   size_t interactionsNumber[numberGene][interactionTypes];
      |                             ^~~~~~~~~~
generateThresholds.cpp:43:29: note: read of non-const variable 'numberGene' is not allowed in a constant expression
generateThresholds.cpp:38:10: note: declared here
   38 |   size_t numberGene=geneInteraction.nrow();
      |          ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c header.cpp -o header.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c limitcycle.cpp -o limitcycle.o
limitcycle.cpp:33:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   33 |     double fX2_arr[number_gene]; //fX2_arr saves fX values for degradation part
      |                    ^~~~~~~~~~~
limitcycle.cpp:33:20: note: function parameter 'number_gene' with unknown value cannot be used in a constant expression
limitcycle.cpp:21:26: note: declared here
   21 | void cal_fX_E(const int &number_gene,
      |                          ^
limitcycle.cpp:86:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   86 | double exprxGeneH1[number_gene]; //array for temp gene expression values
      |                    ^~~~~~~~~~~
limitcycle.cpp:86:20: note: function parameter 'number_gene' with unknown value cannot be used in a constant expression
limitcycle.cpp:73:26: note: declared here
   73 | void cal_fX_R(const int &number_gene,
      |                          ^
limitcycle.cpp:87:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   87 | double exprxGeneH2[number_gene]; //array for temp gene expression values
      |                    ^~~~~~~~~~~
limitcycle.cpp:87:20: note: function parameter 'number_gene' with unknown value cannot be used in a constant expression
limitcycle.cpp:73:26: note: declared here
   73 | void cal_fX_R(const int &number_gene,
      |                          ^
limitcycle.cpp:88:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   88 | double exprxGeneH3[number_gene]; //array for temp gene expression values
      |                    ^~~~~~~~~~~
limitcycle.cpp:88:20: note: function parameter 'number_gene' with unknown value cannot be used in a constant expression
limitcycle.cpp:73:26: note: declared here
   73 | void cal_fX_R(const int &number_gene,
      |                          ^
limitcycle.cpp:89:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   89 | double exprxGeneH4[number_gene]; //array for temp gene expression values
      |                    ^~~~~~~~~~~
limitcycle.cpp:89:20: note: function parameter 'number_gene' with unknown value cannot be used in a constant expression
limitcycle.cpp:73:26: note: declared here
   73 | void cal_fX_R(const int &number_gene,
      |                          ^
limitcycle.cpp:329:17: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  329 |     int periodT[MaxPeriods]; //saves the periods
      |                 ^~~~~~~~~~
limitcycle.cpp:329:17: note: function parameter 'MaxPeriods' with unknown value cannot be used in a constant expression
limitcycle.cpp:316:24: note: declared here
  316 |             const int &MaxPeriods,
      |                        ^
limitcycle.cpp:327:9: warning: variable 'countSameMinDist' set but not used [-Wunused-but-set-variable]
  327 |     int countSameMinDist=0;
      |         ^
limitcycle.cpp:621:23: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  621 |     int LC_period_arr[maxLCs];
      |                       ^~~~~~
limitcycle.cpp:621:23: note: function parameter 'maxLCs' with unknown value cannot be used in a constant expression
limitcycle.cpp:610:25: note: declared here
  610 |              const int &maxLCs,
      |                         ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c simulateGRC.cpp -o simulateGRC.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c steppers.cpp -o steppers.o
steppers.cpp:118:21: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  118 |   double exprxGeneH[numberGene]; //array for temp gene expression values
      |                     ^~~~~~~~~~
steppers.cpp:118:21: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:93:25: note: declared here
   93 |              const int &numberGene,
      |                         ^
steppers.cpp:245:21: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  245 |   double exprxGeneH[numberGene]; //array for temp gene expression values
      |                     ^~~~~~~~~~
steppers.cpp:245:21: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:219:25: note: declared here
  219 |              const int &numberGene,
      |                         ^
steppers.cpp:246:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  246 |   double currNoise[numberGene]; //array for temp gene expression values
      |                    ^~~~~~~~~~
steppers.cpp:246:20: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:219:25: note: declared here
  219 |              const int &numberGene,
      |                         ^
steppers.cpp:381:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  381 | double exprxGeneH1[numberGene]; //array for temp gene expression values
      |                    ^~~~~~~~~~
steppers.cpp:381:20: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:359:25: note: declared here
  359 |              const int &numberGene,
      |                         ^
steppers.cpp:382:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  382 | double exprxGeneH2[numberGene]; //array for temp gene expression values
      |                    ^~~~~~~~~~
steppers.cpp:382:20: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:359:25: note: declared here
  359 |              const int &numberGene,
      |                         ^
steppers.cpp:383:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  383 | double exprxGeneH3[numberGene]; //array for temp gene expression values
      |                    ^~~~~~~~~~
steppers.cpp:383:20: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:359:25: note: declared here
  359 |              const int &numberGene,
      |                         ^
steppers.cpp:384:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  384 | double exprxGeneH4[numberGene]; //array for temp gene expression values
      |                    ^~~~~~~~~~
steppers.cpp:384:20: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:359:25: note: declared here
  359 |              const int &numberGene,
      |                         ^
steppers.cpp:669:21: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  669 |   double exprxGeneH[numberGene]; //array for temp gene expression values
      |                     ^~~~~~~~~~
steppers.cpp:669:21: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:648:26: note: declared here
  648 |               const int &numberGene,
      |                          ^
steppers.cpp:670:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  670 |   double exprxGeneH1[numberGene]; //array for temp gene expression values
      |                      ^~~~~~~~~~
steppers.cpp:670:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:648:26: note: declared here
  648 |               const int &numberGene,
      |                          ^
steppers.cpp:671:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  671 |   double exprxGeneH2[numberGene]; //array for temp gene expression values
      |                      ^~~~~~~~~~
steppers.cpp:671:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:648:26: note: declared here
  648 |               const int &numberGene,
      |                          ^
steppers.cpp:672:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  672 |   double exprxGeneH3[numberGene]; //array for temp gene expression values
      |                      ^~~~~~~~~~
steppers.cpp:672:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:648:26: note: declared here
  648 |               const int &numberGene,
      |                          ^
steppers.cpp:673:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  673 |   double exprxGeneH4[numberGene]; //array for temp gene expression values
      |                      ^~~~~~~~~~
steppers.cpp:673:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:648:26: note: declared here
  648 |               const int &numberGene,
      |                          ^
steppers.cpp:674:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  674 |   double exprxGeneH5[numberGene]; //array for temp gene expression values
      |                      ^~~~~~~~~~
steppers.cpp:674:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:648:26: note: declared here
  648 |               const int &numberGene,
      |                          ^
steppers.cpp:675:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  675 |   double exprxGeneH6[numberGene]; //array for temp gene expression values
      |                      ^~~~~~~~~~
steppers.cpp:675:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:648:26: note: declared here
  648 |               const int &numberGene,
      |                          ^
steppers.cpp:676:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  676 |   double exprxGeneH7[numberGene]; //array for temp gene expression values
      |                      ^~~~~~~~~~
steppers.cpp:676:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppers.cpp:648:26: note: declared here
  648 |               const int &numberGene,
      |                          ^
15 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c steppersConv.cpp -o steppersConv.o
steppersConv.cpp:30:21: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   30 |   double exprxGeneH[numberGene]; //array for temp gene expression values
      |                     ^~~~~~~~~~
steppersConv.cpp:30:21: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:10:25: note: declared here
   10 |              const int &numberGene,
      |                         ^
steppersConv.cpp:37:10: warning: variable 'i' set but not used [-Wunused-but-set-variable]
   37 |   double i=0.0;
      |          ^
steppersConv.cpp:156:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  156 | double exprxGeneH1[numberGene]; //array for temp gene expression values
      |                    ^~~~~~~~~~
steppersConv.cpp:156:20: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:136:25: note: declared here
  136 |              const int &numberGene,
      |                         ^
steppersConv.cpp:157:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  157 | double exprxGeneH2[numberGene]; //array for temp gene expression values
      |                    ^~~~~~~~~~
steppersConv.cpp:157:20: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:136:25: note: declared here
  136 |              const int &numberGene,
      |                         ^
steppersConv.cpp:158:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  158 | double exprxGeneH3[numberGene]; //array for temp gene expression values
      |                    ^~~~~~~~~~
steppersConv.cpp:158:20: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:136:25: note: declared here
  136 |              const int &numberGene,
      |                         ^
steppersConv.cpp:159:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  159 | double exprxGeneH4[numberGene]; //array for temp gene expression values
      |                    ^~~~~~~~~~
steppersConv.cpp:159:20: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:136:25: note: declared here
  136 |              const int &numberGene,
      |                         ^
steppersConv.cpp:170:8: warning: variable 'i' set but not used [-Wunused-but-set-variable]
  170 | double i=0.0;
      |        ^
steppersConv.cpp:396:21: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  396 |   double exprxGeneH[numberGene]; //array for temp gene expression values
      |                     ^~~~~~~~~~
steppersConv.cpp:396:21: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:376:26: note: declared here
  376 |               const int &numberGene,
      |                          ^
steppersConv.cpp:397:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  397 |   double exprxGeneH1[numberGene]; //array for temp gene expression values
      |                      ^~~~~~~~~~
steppersConv.cpp:397:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:376:26: note: declared here
  376 |               const int &numberGene,
      |                          ^
steppersConv.cpp:398:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  398 |   double exprxGeneH2[numberGene]; //array for temp gene expression values
      |                      ^~~~~~~~~~
steppersConv.cpp:398:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:376:26: note: declared here
  376 |               const int &numberGene,
      |                          ^
steppersConv.cpp:399:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  399 |   double exprxGeneH3[numberGene]; //array for temp gene expression values
      |                      ^~~~~~~~~~
steppersConv.cpp:399:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:376:26: note: declared here
  376 |               const int &numberGene,
      |                          ^
steppersConv.cpp:400:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  400 |   double exprxGeneH4[numberGene]; //array for temp gene expression values
      |                      ^~~~~~~~~~
steppersConv.cpp:400:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:376:26: note: declared here
  376 |               const int &numberGene,
      |                          ^
steppersConv.cpp:401:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  401 |   double exprxGeneH5[numberGene]; //array for temp gene expression values
      |                      ^~~~~~~~~~
steppersConv.cpp:401:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:376:26: note: declared here
  376 |               const int &numberGene,
      |                          ^
steppersConv.cpp:402:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  402 |   double exprxGeneH6[numberGene]; //array for temp gene expression values
      |                      ^~~~~~~~~~
steppersConv.cpp:402:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:376:26: note: declared here
  376 |               const int &numberGene,
      |                          ^
steppersConv.cpp:403:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  403 |   double exprxGeneH7[numberGene]; //array for temp gene expression values
      |                      ^~~~~~~~~~
steppersConv.cpp:403:22: note: function parameter 'numberGene' with unknown value cannot be used in a constant expression
steppersConv.cpp:376:26: note: declared here
  376 |               const int &numberGene,
      |                          ^
steppersConv.cpp:422:10: warning: variable 'i' set but not used [-Wunused-but-set-variable]
  422 |   double i=0.0;
      |          ^
16 warnings generated.
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o sRACIPE.so RcppExports.o generateThresholds.o header.o limitcycle.o simulateGRC.o steppers.o steppersConv.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-sRACIPE/00new/sRACIPE/libs
** 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 (sRACIPE)