* 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 22.1.2 (https://github.com/llvm/llvm-project 1ab49a973e210e97d61e5db6557180dcb92c3e98)’
using C++ compiler: ‘clang version 22.1.2 (https://github.com/llvm/llvm-project 1ab49a973e210e97d61e5db6557180dcb92c3e98)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/MasterBayes/src'
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 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
| ^~~~~
3 warnings generated.
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 LikFunctions.cc -o LikFunctions.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
| ^~~~~
3 warnings generated.
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 MCMCped.cc -o MCMCped.o
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.
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c MasterBayes_init.c -o MasterBayes_init.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 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.
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 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.
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 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.
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 SampG.cc -o SampG.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
| ^~~~~
3 warnings generated.
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 SampGC.cc -o SampGC.o
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.
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 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
| ^~~~~
3 warnings generated.
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 SampS.cc -o SampS.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
| ^~~~~
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 SpecRand.cc -o SpecRand.o
3 warnings generated.
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.
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 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.
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 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.
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 calcX_GS.cc -o calcX_GS.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 calcX_Gcervus.cc -o calcX_Gcervus.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 calcX_GcervusD.cc -o calcX_GcervusD.o
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 calcX_GcervusS.cc -o calcX_GcervusS.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
| ^~~~~
3 warnings generated.
calcX_Gcervus.cc:32:16: warning: variable 'q' set but not used [-Wunused-but-set-variable]
32 | double q;
| ^
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
| ^~~~~
4 warnings generated.
3 warnings generated.
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.
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 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
| ^~~~~
3 warnings generated.
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 fillXG.cc -o fillXG.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
| ^~~~~
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 legalG.cc -o legalG.o
3 warnings generated.
clang++-22 -stdlib=libc++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -isystem /usr/local/clang22/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 mismatches.cc -o mismatches.o
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.
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.
clang++-22 -stdlib=libc++ -std=gnu++20 -shared -L/usr/local/clang/lib64 -L/usr/local/clang22/lib -L/usr/local/clang22/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/gannet/ripley/R/packages/tests-clang/MasterBayes/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/MasterBayes/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/MasterBayes/src'
installing to /data/gannet/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)