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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL atSNP
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘atSNP’ ...
** this is package ‘atSNP’ version ‘1.27.0’
** using staged installation
** libs
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 ImportanceSample.cpp -o ImportanceSample.o
ImportanceSample.cpp:77:9: warning: variable 'mean_sample' set but not used [-Wunused-but-set-variable]
   77 |         double mean_sample = 0;
      |                ^
ImportanceSample.cpp:78:9: warning: variable 'mean_adj_score' set but not used [-Wunused-but-set-variable]
   78 |         double mean_adj_score = 0;
      |                ^
ImportanceSample.cpp:229:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  229 |         double prob_stat[motif_len];
      |                          ^~~~~~~~~
ImportanceSample.cpp:229:19: note: read of non-const variable 'motif_len' is not allowed in a constant expression
ImportanceSample.cpp:222:6: note: declared here
  222 |         int motif_len = pwm.nrow();
      |             ^
ImportanceSample.cpp:309:6: warning: variable 'snp_id' set but not used [-Wunused-but-set-variable]
  309 |         int snp_id = 0;
      |             ^
ImportanceSample.cpp:347:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  347 |         double heap[n_top];
      |                     ^~~~~
ImportanceSample.cpp:347:14: note: read of non-const variable 'n_top' is not allowed in a constant expression
ImportanceSample.cpp:345:6: note: declared here
  345 |         int n_top = scores.size() * p + 1;
      |             ^
5 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 ImportanceSampleChange.cpp -o ImportanceSampleChange.o
ImportanceSampleChange.cpp:51:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   51 |         double score[n_sample][4];
      |                      ^~~~~~~~
ImportanceSampleChange.cpp:51:15: note: function parameter 'n_sample' with unknown value cannot be used in a constant expression
ImportanceSampleChange.cpp:16:219: note: declared here
   16 | Rcpp::List p_value_change(NumericMatrix pwm, NumericMatrix wei_mat, NumericMatrix adj_mat, NumericVector stat_dist, NumericMatrix trans_mat, NumericVector scores, NumericVector pval_ratio, double score_percentile, int n_sample) {
      |                                                                                                                                                                                                                           ^
ImportanceSampleChange.cpp:49:9: warning: variable 'mean_score' set but not used [-Wunused-but-set-variable]
   49 |         double mean_score = 0;
      |                ^
ImportanceSampleChange.cpp:120:17: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  120 |         double adj_sum[motif_len];
      |                        ^~~~~~~~~
ImportanceSampleChange.cpp:120:17: note: read of non-const variable 'motif_len' is not allowed in a constant expression
ImportanceSampleChange.cpp:117:6: note: declared here
  117 |         int motif_len = wei_mat.nrow();
      |             ^
ImportanceSampleChange.cpp:190:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  190 |         double prob_start[motif_len];
      |                           ^~~~~~~~~
ImportanceSampleChange.cpp:190:20: note: read of non-const variable 'motif_len' is not allowed in a constant expression
ImportanceSampleChange.cpp:183:6: note: declared here
  183 |         int motif_len = wei_mat.nrow();
      |             ^
ImportanceSampleChange.cpp:334:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  334 |         double heap[n_top];
      |                     ^~~~~
ImportanceSampleChange.cpp:334:14: note: read of non-const variable 'n_top' is not allowed in a constant expression
ImportanceSampleChange.cpp:332:6: note: declared here
  332 |         int n_top = scores.size() * p + 1;
      |             ^
5 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 ImportanceSampleDiff.cpp -o ImportanceSampleDiff.o
ImportanceSampleDiff.cpp:85:9: warning: variable 'mean_diff' set but not used [-Wunused-but-set-variable]
   85 |         double mean_diff = 0;
      |                ^
ImportanceSampleDiff.cpp:213:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  213 |         double prob_start[motif_len];
      |                           ^~~~~~~~~
ImportanceSampleDiff.cpp:213:20: note: read of non-const variable 'motif_len' is not allowed in a constant expression
ImportanceSampleDiff.cpp:206:6: note: declared here
  206 |         int motif_len = wei_mat.nrow();
      |             ^
ImportanceSampleDiff.cpp:338:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  338 |         double heap[n_top];
      |                     ^~~~~
ImportanceSampleDiff.cpp:338:14: note: read of non-const variable 'n_top' is not allowed in a constant expression
ImportanceSampleDiff.cpp:336:6: note: declared here
  336 |         int n_top = scores.size() * p + 1;
      |             ^
3 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 MotifScore.cpp -o MotifScore.o
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 atSNP.so ImportanceSample.o ImportanceSampleChange.o ImportanceSampleDiff.o MotifScore.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-atSNP/00new/atSNP/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 (atSNP)