* installing *source* package ‘MasterBayes’ ... ** this is package ‘MasterBayes’ version ‘2.59’ ** package ‘MasterBayes’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘clang version 23.1.1’ using C++ compiler: ‘clang version 23.1.1’ make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang/MasterBayes/src' /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c ErrorMat.cc -o ErrorMat.o In file included from ErrorMat.cc:1: In file included from ./ErrorMat.h:44: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from ErrorMat.cc:1: In file included from ./ErrorMat.h:44: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c LikFunctions.cc -o LikFunctions.o 3 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c MCMCped.cc -o MCMCped.o In file included from LikFunctions.cc:1: In file included from ./LikFunctions.h:3: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from LikFunctions.cc:1: In file included from ./LikFunctions.h:3: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ In file included from MCMCped.cc:1: In file included from ./MCMCped.h:2: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from MCMCped.cc:1: In file included from ./MCMCped.h:2: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ 3 warnings generated. 3 warnings generated. /usr/local/clang23/bin/clang-23 -std=gnu23 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c MasterBayes_init.c -o MasterBayes_init.o /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c Read_in_data.cc -o Read_in_data.o In file included from Read_in_data.cc:1: In file included from ./Read_in_data.h:3: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from Read_in_data.cc:1: In file included from ./Read_in_data.h:3: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ 3 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c SampD.cc -o SampD.o In file included from SampD.cc:1: In file included from ./SampD.h:3: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from SampD.cc:1: In file included from ./SampD.h:3: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ 3 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c SampDomG.cc -o SampDomG.o In file included from SampDomG.cc:1: In file included from ./SampDomG.h:3: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from SampDomG.cc:1: In file included from ./SampDomG.h:3: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ 3 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c SampG.cc -o SampG.o /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c SampGC.cc -o SampGC.o In file included from SampG.cc:1: In file included from ./SampG.h:3: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from SampG.cc:1: In file included from ./SampG.h:3: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ In file included from SampGC.cc:1: In file included from ./SampGC.h:3: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from SampGC.cc:1: In file included from ./SampGC.h:3: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ 3 warnings generated. 3 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c SampP.cc -o SampP.o In file included from SampP.cc:1: In file included from ./SampP.h:3: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from SampP.cc:1: In file included from ./SampP.h:3: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c SampS.cc -o SampS.o 3 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c SpecRand.cc -o SpecRand.o In file included from SampS.cc:1: In file included from ./SampS.h:3: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from SampS.cc:1: In file included from ./SampS.h:3: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ In file included from SpecRand.cc:1: In file included from ./SpecRand.h:3: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from SpecRand.cc:1: In file included from ./SpecRand.h:3: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ 3 warnings generated. 3 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c calcX_G.cc -o calcX_G.o In file included from calcX_G.cc:1: In file included from ./calcX_G.h:3: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from calcX_G.cc:1: In file included from ./calcX_G.h:3: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ 3 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c calcX_GD.cc -o calcX_GD.o In file included from calcX_GD.cc:1: In file included from ./calcX_G.h:3: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from calcX_GD.cc:1: In file included from ./calcX_G.h:3: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ 3 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c calcX_GS.cc -o calcX_GS.o /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c calcX_Gcervus.cc -o calcX_Gcervus.o /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c calcX_GcervusD.cc -o calcX_GcervusD.o In file included from calcX_GS.cc:1: In file included from ./calcX_G.h:3: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from calcX_GS.cc:1: In file included from ./calcX_G.h:3: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ In file included from calcX_Gcervus.cc:1: In file included from ./calcX_G.h:3: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from calcX_Gcervus.cc:1: In file included from ./calcX_G.h:3: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ calcX_Gcervus.cc:32:16: warning: variable 'q' set but not used [-Wunused-but-set-variable] 32 | double q; | ^ 3 warnings generated. 4 warnings generated. In file included from calcX_GcervusD.cc:1: In file included from ./calcX_G.h:3: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from calcX_GcervusD.cc:1: In file included from ./calcX_G.h:3: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ 3 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c calcX_GcervusS.cc -o calcX_GcervusS.o In file included from calcX_GcervusS.cc:1: In file included from ./calcX_G.h:3: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from calcX_GcervusS.cc:1: In file included from ./calcX_G.h:3: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ 3 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c calcX_Gmm.cc -o calcX_Gmm.o In file included from calcX_Gmm.cc:1: In file included from ./calcX_G.h:3: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from calcX_Gmm.cc:1: In file included from ./calcX_G.h:3: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c fillXG.cc -o fillXG.o 3 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c legalG.cc -o legalG.o In file included from fillXG.cc:1: In file included from ./MCMCped.h:2: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from fillXG.cc:1: In file included from ./MCMCped.h:2: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ 3 warnings generated. In file included from legalG.cc:1: In file included from ./MCMCped.h:2: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from legalG.cc:1: In file included from ./MCMCped.h:2: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ 3 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c mismatches.cc -o mismatches.o In file included from mismatches.cc:1: In file included from ./MCMCped.h:2: In file included from ./General.h:6: In file included from ./matrix.h:61: In file included from ./algorithm.h:41: ./matrix_random_access_iterator.h:202:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 202 | inline const reference operator* () const | ^~~~~ ./matrix_random_access_iterator.h:287:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 287 | inline const reference operator[] (difference_type n) const | ^~~~~ In file included from mismatches.cc:1: In file included from ./MCMCped.h:2: In file included from ./General.h:6: In file included from ./matrix.h:66: ./matrix_bidirectional_iterator.h:217:14: warning: 'const' qualifier on reference type 'reference' (aka 'T_type &') has no effect [-Wignored-reference-qualifiers] 217 | inline const reference operator* () const | ^~~~~ 3 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -shared -L/usr/local/clang/lib64 -L/usr/local/clang23/lib -L/usr/local/clang23/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o MasterBayes.so ErrorMat.o LikFunctions.o MCMCped.o MasterBayes_init.o Read_in_data.o SampD.o SampDomG.o SampG.o SampGC.o SampP.o SampS.o SpecRand.o calcX_G.o calcX_GD.o calcX_GS.o calcX_Gcervus.o calcX_GcervusD.o calcX_GcervusS.o calcX_Gmm.o fillXG.o legalG.o mismatches.o make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-clang/MasterBayes/src' make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang/MasterBayes/src' make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-clang/MasterBayes/src' installing to /data/localhost/ripley/R/packages/tests-clang/MasterBayes.Rcheck/00LOCK-MasterBayes/00new/MasterBayes/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 (MasterBayes)