* installing *source* package ‘unityForest’ ...
** this is package ‘unityForest’ version ‘0.1.0’
** package ‘unityForest’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C++ compiler: ‘clang version 21.1.8’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/unityForest/src'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c AAA_check_cpp11.cpp -o AAA_check_cpp11.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c Data.cpp -o Data.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c DataChar.cpp -o DataChar.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c DataFloat.cpp -o DataFloat.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c DataSparse.cpp -o DataSparse.o
In file included from DataSparse.cpp:29:
In file included from ./DataSparse.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from DataSparse.cpp:29:
In file included from ./DataSparse.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/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]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
In file included from DataSparse.cpp:29:
In file included from ./DataSparse.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
72 | Index replacements = 0;
| ^
In file included from DataSparse.cpp:29:
In file included from ./DataSparse.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
246 | int count = 0;
| ^
In file included from DataSparse.cpp:29:
./DataSparse.h:53:12: warning: unused variable 'col_permuted' [-Wunused-variable]
53 | size_t col_permuted = col;
| ^~~~~~~~~~~~
6 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c Forest.cpp -o Forest.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c ForestClassification.cpp -o ForestClassification.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c ForestProbability.cpp -o ForestProbability.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c ForestRegression.cpp -o ForestRegression.o
ForestRegression.cpp:124:9: warning: variable 'value' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
124 | if (divfortype == 1) {
| ^~~~~~~~~~~~~~~
ForestRegression.cpp:128:38: note: uninitialized use occurs here
128 | predictions[0][0][sampleID] += value;
| ^~~~~
ForestRegression.cpp:124:5: note: remove the 'if' if its condition is always true
124 | if (divfortype == 1) {
| ^~~~~~~~~~~~~~~~~~~~
ForestRegression.cpp:123:19: note: initialize the variable 'value' to silence this warning
123 | double value;
| ^
| = 0.0
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c Hungarian.cpp -o Hungarian.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RcppExports.cpp -o RcppExports.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c Tree.cpp -o Tree.o
In file included from RcppExports.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from RcppExports.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/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]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
In file included from RcppExports.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
72 | Index replacements = 0;
| ^
In file included from RcppExports.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
246 | int count = 0;
| ^
Tree.cpp:1826:12: warning: variable 'num_vars' set but not used [-Wunused-but-set-variable]
1826 | size_t num_vars = data->getNumCols();
| ^
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c TreeClassification.cpp -o TreeClassification.o
5 warnings generated.
TreeClassification.cpp:673:30: warning: unused variable 'class_weights_ref' [-Wunused-variable]
673 | const std::vector<double>& class_weights_ref = *class_weights;
| ^~~~~~~~~~~~~~~~~
TreeClassification.cpp:1252:15: warning: unused variable 'split_criterion_unweighted' [-Wunused-variable]
1252 | double split_criterion_unweighted = HungAlgo.Solve(class_proportions, assignment);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c TreeProbability.cpp -o TreeProbability.o
TreeProbability.cpp:1017:15: warning: unused variable 'split_criterion_unweighted' [-Wunused-variable]
1017 | double split_criterion_unweighted = HungAlgo.Solve(class_proportions, assignment);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
TreeProbability.cpp:1200:30: warning: unused variable 'class_weights_ref' [-Wunused-variable]
1200 | const std::vector<double>& class_weights_ref = *class_weights;
| ^~~~~~~~~~~~~~~~~
2 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c TreeRegression.cpp -o TreeRegression.o
2 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c divforCpp.cpp -o divforCpp.o
In file included from divforCpp.cpp:28:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from divforCpp.cpp:28:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/gannet/ripley/R/test-clang/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]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
In file included from divforCpp.cpp:28:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
72 | Index replacements = 0;
| ^
In file included from divforCpp.cpp:28:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37:
In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
246 | int count = 0;
| ^
In file included from divforCpp.cpp:43:
./DataSparse.h:53:12: warning: unused variable 'col_permuted' [-Wunused-variable]
53 | size_t col_permuted = col;
| ^~~~~~~~~~~~
6 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c utility.cpp -o utility.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_BUILD -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c utilityRcpp.cpp -o utilityRcpp.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o unityForest.so AAA_check_cpp11.o Data.o DataChar.o DataFloat.o DataSparse.o Forest.o ForestClassification.o ForestProbability.o ForestRegression.o Hungarian.o RcppExports.o Tree.o TreeClassification.o TreeProbability.o TreeRegression.o divforCpp.o utility.o utilityRcpp.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/unityForest/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/unityForest/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/unityForest/src'
installing to /data/gannet/ripley/R/packages/tests-clang/unityForest.Rcheck/00LOCK-unityForest/00new/unityForest/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (unityForest)