* 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: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ using C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/MasterBayes/src' g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c ErrorMat.cc -o ErrorMat.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c LikFunctions.cc -o LikFunctions.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c MCMCped.cc -o MCMCped.o MCMCped.cc: In function ‘void MCMCped(int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, double*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, double*, double*, double*, double*, double*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*)’: MCMCped.cc:942:11: warning: ‘ppost_G’ may be used uninitialized [-Wmaybe-uninitialized] 942 | delete [] ppost_G; | ^~~~~~~ MCMCped.cc:139:10: note: ‘ppost_G’ was declared here 139 | *ppost_G, | ^~~~~~~ MCMCped.cc:836:31: warning: ‘post_G’ may be used uninitialized [-Wmaybe-uninitialized] 836 | post_G[i][(l*3)+na1] ++; | ~~~~~~~~^ MCMCped.cc:140:11: note: ‘post_G’ was declared here 140 | **post_G; | ^~~~~~ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c MasterBayes_init.c -o MasterBayes_init.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c Read_in_data.cc -o Read_in_data.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c SampD.cc -o SampD.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c SampDomG.cc -o SampDomG.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c SampG.cc -o SampG.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c SampGC.cc -o SampGC.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c SampP.cc -o SampP.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c SampS.cc -o SampS.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c SpecRand.cc -o SpecRand.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c calcX_G.cc -o calcX_G.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c calcX_GD.cc -o calcX_GD.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c calcX_GS.cc -o calcX_GS.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c calcX_Gcervus.cc -o calcX_Gcervus.o calcX_Gcervus.cc: In function ‘void calcX_Gcervus(scythe::Matrix<>*, int*, int, int*, int*, int, scythe::Matrix*, scythe::Matrix*, int**, int, double**, double**, int, int*)’: calcX_Gcervus.cc:32:16: warning: variable ‘q’ set but not used [-Wunused-but-set-variable] 32 | double q; | ^ g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c calcX_GcervusD.cc -o calcX_GcervusD.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c calcX_GcervusS.cc -o calcX_GcervusS.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c calcX_Gmm.cc -o calcX_Gmm.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c fillXG.cc -o fillXG.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c legalG.cc -o legalG.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC -DHAVE_TRUNC -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c mismatches.cc -o mismatches.o g++ -std=gnu++20 -shared -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-devel/MasterBayes/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/MasterBayes/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/MasterBayes/src' installing to /data/gannet/ripley/R/packages/tests-devel/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)