* installing *source* package ‘ontologySimilarity’ ...
** this is package ‘ontologySimilarity’ version ‘2.7’
** package ‘ontologySimilarity’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
using SDK: ‘MacOSX26.2.sdk’
clang++ -mmacos-version-min=26 -std=gnu++20 -I"/Users/ripley/R/R-devel/include" -DNDEBUG  -I'/Users/ripley/R/Library/Rcpp/include' -isystem /opt/R/arm64/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion   -c Interface.cpp -o Interface.o
In file included from Interface.cpp:1:
In file included from ./Interface.h:1:
In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp.h:27:
In file included from /Users/ripley/R/Library/Rcpp/include/RcppCommon.h:192:
/Users/ripley/R/Library/Rcpp/include/Rcpp/internal/wrap.h:71:47: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
   71 |             return Rf_mkCharLen(st.data(), st.size());
      |                    ~~~~~~~~~~~~            ~~~^~~~~~
Interface.cpp:39:63: error: reference to 'identity' is ambiguous
   39 |         ReduceSim r(use_mean ? &add : &worst, use_mean ? &by_size : &identity, use_mean ? 0.0 : INFINITY);
      |                                                                      ^
./TermSetSimData.h:21:8: note: candidate found by name lookup is 'identity'
   21 | double identity(double a, int b);
      |        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/identity.h:45:8: note: candidate found by name lookup is 'std::identity'
   45 | struct identity {
      |        ^
Interface.cpp:59:63: error: reference to 'identity' is ambiguous
   59 |         ReduceSim r(use_mean ? &add : &worst, use_mean ? &by_size : &identity, use_mean ? 0.0 : INFINITY);
      |                                                                      ^
./TermSetSimData.h:21:8: note: candidate found by name lookup is 'identity'
   21 | double identity(double a, int b);
      |        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/identity.h:45:8: note: candidate found by name lookup is 'std::identity'
   45 | struct identity {
      |        ^
Interface.cpp:65:75: warning: implicit conversion loses integer precision: 'R_xlen_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
   65 |         simple_sampler simple = simple_sampler(sim_mat->population_size(), group.length());
      |                                 ~~~~~~~~~~~~~~                             ~~~~~~^~~~~~~~
Interface.cpp:89:63: error: reference to 'identity' is ambiguous
   89 |         ReduceSim r(use_mean ? &add : &worst, use_mean ? &by_size : &identity, use_mean ? 0.0 : INFINITY);
      |                                                                      ^
./TermSetSimData.h:21:8: note: candidate found by name lookup is 'identity'
   21 | double identity(double a, int b);
      |        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/identity.h:45:8: note: candidate found by name lookup is 'std::identity'
   45 | struct identity {
      |        ^
Interface.cpp:121:47: warning: implicit conversion loses integer precision: 'R_xlen_t' (aka 'long') to 'const int' [-Wshorten-64-to-32]
  121 |         NumericMatrix result(terms1.length(), terms2.length());
      |                       ~~~~~~                  ~~~~~~~^~~~~~~~
Interface.cpp:121:30: warning: implicit conversion loses integer precision: 'R_xlen_t' (aka 'long') to 'const int' [-Wshorten-64-to-32]
  121 |         NumericMatrix result(terms1.length(), terms2.length());
      |                       ~~~~~~ ~~~~~~~^~~~~~~~
In file included from Interface.cpp:1:
In file included from ./Interface.h:1:
In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp.h:41:
In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp/Vector.h:57:
/Users/ripley/R/Library/Rcpp/include/Rcpp/vector/Matrix.h:138:76: warning: implicit conversion loses integer precision: 'const size_t' (aka 'const unsigned long') to 'int' [-Wshorten-64-to-32]
  138 |       return static_cast< Vector<RTYPE>* >( this )->operator[]( offset( i, j ) ) ;
      |                                                                 ~~~~~~     ^
Interface.cpp:125:10: note: in instantiation of member function 'Rcpp::Matrix<14>::operator()' requested here
  125 |                         result(i1, i2) = 0.0;
      |                               ^
In file included from Interface.cpp:1:
In file included from ./Interface.h:1:
In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp.h:41:
In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp/Vector.h:57:
/Users/ripley/R/Library/Rcpp/include/Rcpp/vector/Matrix.h:138:73: warning: implicit conversion loses integer precision: 'const size_t' (aka 'const unsigned long') to 'int' [-Wshorten-64-to-32]
  138 |       return static_cast< Vector<RTYPE>* >( this )->operator[]( offset( i, j ) ) ;
      |                                                                 ~~~~~~  ^
6 warnings and 3 errors generated.
make[1]: *** [Interface.o] Error 1
clang++ -mmacos-version-min=26 -std=gnu++20 -I"/Users/ripley/R/R-devel/include" -DNDEBUG  -I'/Users/ripley/R/Library/Rcpp/include' -isystem /opt/R/arm64/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion   -c PVal.cpp -o PVal.o
In file included from PVal.cpp:1:
In file included from ./PVal.h:1:
In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp.h:27:
In file included from /Users/ripley/R/Library/Rcpp/include/RcppCommon.h:192:
/Users/ripley/R/Library/Rcpp/include/Rcpp/internal/wrap.h:71:47: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
   71 |             return Rf_mkCharLen(st.data(), st.size());
      |                    ~~~~~~~~~~~~            ~~~^~~~~~
1 warning generated.
clang++ -mmacos-version-min=26 -std=gnu++20 -I"/Users/ripley/R/R-devel/include" -DNDEBUG  -I'/Users/ripley/R/Library/Rcpp/include' -isystem /opt/R/arm64/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion   -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp.h:27:
In file included from /Users/ripley/R/Library/Rcpp/include/RcppCommon.h:192:
/Users/ripley/R/Library/Rcpp/include/Rcpp/internal/wrap.h:71:47: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
   71 |             return Rf_mkCharLen(st.data(), st.size());
      |                    ~~~~~~~~~~~~            ~~~^~~~~~
1 warning generated.
clang++ -mmacos-version-min=26 -std=gnu++20 -I"/Users/ripley/R/R-devel/include" -DNDEBUG  -I'/Users/ripley/R/Library/Rcpp/include' -isystem /opt/R/arm64/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion   -c Sampling.cpp -o Sampling.o
In file included from Sampling.cpp:1:
In file included from ./Sampling.h:1:
In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp.h:27:
In file included from /Users/ripley/R/Library/Rcpp/include/RcppCommon.h:192:
/Users/ripley/R/Library/Rcpp/include/Rcpp/internal/wrap.h:71:47: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
   71 |             return Rf_mkCharLen(st.data(), st.size());
      |                    ~~~~~~~~~~~~            ~~~^~~~~~
Sampling.cpp:9:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'typename storage_type<13>::type' (aka 'int') [-Wshorten-64-to-32]
    9 |         item[i] = i;
      |                 ~ ^
Sampling.cpp:69:6: warning: variable 'total_items' set but not used [-Wunused-but-set-variable]
   69 |         int total_items = 0;
      |             ^
Sampling.cpp:67:32: warning: implicit conversion loses integer precision: 'R_xlen_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
   67 |         int num_strata = strata_sizes.length();
      |             ~~~~~~~~~~   ~~~~~~~~~~~~~^~~~~~~~
4 warnings generated.
clang++ -mmacos-version-min=26 -std=gnu++20 -I"/Users/ripley/R/R-devel/include" -DNDEBUG  -I'/Users/ripley/R/Library/Rcpp/include' -isystem /opt/R/arm64/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion   -c SimMatrix.cpp -o SimMatrix.o
In file included from SimMatrix.cpp:1:
In file included from ./SimMatrix.h:1:
In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp.h:27:
In file included from /Users/ripley/R/Library/Rcpp/include/RcppCommon.h:192:
/Users/ripley/R/Library/Rcpp/include/Rcpp/internal/wrap.h:71:47: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
   71 |             return Rf_mkCharLen(st.data(), st.size());
      |                    ~~~~~~~~~~~~            ~~~^~~~~~
In file included from SimMatrix.cpp:1:
In file included from ./SimMatrix.h:1:
In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp.h:41:
In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp/Vector.h:57:
/Users/ripley/R/Library/Rcpp/include/Rcpp/vector/Matrix.h:138:76: warning: implicit conversion loses integer precision: 'const size_t' (aka 'const unsigned long') to 'int' [-Wshorten-64-to-32]
  138 |       return static_cast< Vector<RTYPE>* >( this )->operator[]( offset( i, j ) ) ;
      |                                                                 ~~~~~~     ^
SimMatrix.cpp:21:39: note: in instantiation of member function 'Rcpp::Matrix<14>::operator()' requested here
   21 |                                         best_term = max(term_term_sim_mat(t1, t2), best_term);
      |                                                                          ^
In file included from SimMatrix.cpp:1:
In file included from ./SimMatrix.h:1:
In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp.h:41:
In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp/Vector.h:57:
/Users/ripley/R/Library/Rcpp/include/Rcpp/vector/Matrix.h:138:73: warning: implicit conversion loses integer precision: 'const size_t' (aka 'const unsigned long') to 'int' [-Wshorten-64-to-32]
  138 |       return static_cast< Vector<RTYPE>* >( this )->operator[]( offset( i, j ) ) ;
      |                                                                 ~~~~~~  ^
3 warnings generated.
clang++ -mmacos-version-min=26 -std=gnu++20 -I"/Users/ripley/R/R-devel/include" -DNDEBUG  -I'/Users/ripley/R/Library/Rcpp/include' -isystem /opt/R/arm64/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion   -c TermList.cpp -o TermList.o
In file included from TermList.cpp:1:
In file included from ./TermList.h:1:
In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp.h:27:
In file included from /Users/ripley/R/Library/Rcpp/include/RcppCommon.h:192:
/Users/ripley/R/Library/Rcpp/include/Rcpp/internal/wrap.h:71:47: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
   71 |             return Rf_mkCharLen(st.data(), st.size());
      |                    ~~~~~~~~~~~~            ~~~^~~~~~
TermList.cpp:23:34: warning: implicit conversion loses integer precision: 'R_xlen_t' (aka 'long') to 'typename storage_type<13>::type' (aka 'int') [-Wshorten-64-to-32]
   23 |         case_to[num_cases-1] = case_ids.length();
      |                              ~ ~~~~~~~~~^~~~~~~~
2 warnings generated.
clang++ -mmacos-version-min=26 -std=gnu++20 -I"/Users/ripley/R/R-devel/include" -DNDEBUG  -I'/Users/ripley/R/Library/Rcpp/include' -isystem /opt/R/arm64/include    -fPIC  -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion   -c TermSetSimData.cpp -o TermSetSimData.o
In file included from TermSetSimData.cpp:1:
In file included from ./TermSetSimData.h:1:
In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp.h:27:
In file included from /Users/ripley/R/Library/Rcpp/include/RcppCommon.h:192:
/Users/ripley/R/Library/Rcpp/include/Rcpp/internal/wrap.h:71:47: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
   71 |             return Rf_mkCharLen(st.data(), st.size());
      |                    ~~~~~~~~~~~~            ~~~^~~~~~
TermSetSimData.cpp:35:47: warning: implicit conversion loses integer precision: 'R_xlen_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
   35 | int VectorSim::population_size() { return vec.length(); }
      |                                    ~~~~~~ ~~~~^~~~~~~~
TermSetSimData.cpp:39:16: warning: implicit conversion loses integer precision: 'R_xlen_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
   39 |         int n = group.length();
      |             ~   ~~~~~~^~~~~~~~
TermSetSimData.cpp:110:50: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wfloat-conversion]
  110 |         return reducer.norm(agg, ((double)(n * (n - 1)) * 0.5));
      |                ~~~~~~~            ~~~~~~~~~~~~~~~~~~~~~~^~~~~
TermSetSimData.cpp:103:16: warning: implicit conversion loses integer precision: 'R_xlen_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
  103 |         int n = group.length();
      |             ~   ~~~~~~^~~~~~~~
In file included from TermSetSimData.cpp:1:
In file included from ./TermSetSimData.h:1:
In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp.h:41:
In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp/Vector.h:57:
/Users/ripley/R/Library/Rcpp/include/Rcpp/vector/Matrix.h:138:76: warning: implicit conversion loses integer precision: 'const size_t' (aka 'const unsigned long') to 'int' [-Wshorten-64-to-32]
  138 |       return static_cast< Vector<RTYPE>* >( this )->operator[]( offset( i, j ) ) ;
      |                                                                 ~~~~~~     ^
TermSetSimData.cpp:137:65: note: in instantiation of member function 'Rcpp::Matrix<14>::operator()' requested here
  137 | double pre_computed_matrix::pairsim(int i1, int i2) { return mat(i1, i2); }
      |                                                                 ^
In file included from TermSetSimData.cpp:1:
In file included from ./TermSetSimData.h:1:
In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp.h:41:
In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp/Vector.h:57:
/Users/ripley/R/Library/Rcpp/include/Rcpp/vector/Matrix.h:138:73: warning: implicit conversion loses integer precision: 'const size_t' (aka 'const unsigned long') to 'int' [-Wshorten-64-to-32]
  138 |       return static_cast< Vector<RTYPE>* >( this )->operator[]( offset( i, j ) ) ;
      |                                                                 ~~~~~~  ^
7 warnings generated.
make[1]: Target `all' not remade because of errors.
ERROR: compilation failed for package ‘ontologySimilarity’
* removing ‘/Users/ripley/R/packages/tests-devel/ontologySimilarity.Rcheck/ontologySimilarity’