############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL messina ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘messina’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c Classifier.cpp -o Classifier.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c Data.cpp -o Data.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c crossval.cpp -o crossval.o crossval.cpp: In function ‘STATUS CrossVal::cv(int32_t, uint16_t, Classifier&, Result*, bool, bool)’: crossval.cpp:229:40: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 229 | delete train_indices; | ^~~~~~~~~~~~~ crossval.cpp:184:52: note: returned from ‘void* operator new [](std::size_t)’ 184 | if ((train_indices = new int32_t[train_size]) == NULL) | ^ crossval.cpp:230:40: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 230 | delete test_indices; | ^~~~~~~~~~~~ crossval.cpp:187:50: note: returned from ‘void* operator new [](std::size_t)’ 187 | if ((test_indices = new int32_t[test_size]) == NULL) | ^ crossval.cpp:231:40: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 231 | delete in_test_set; | ^~~~~~~~~~~ crossval.cpp:193:44: note: returned from ‘void* operator new [](std::size_t)’ 193 | if ((in_test_set = new bool[n_samps]) == NULL) | ^ crossval.cpp:238:32: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 238 | delete train_indices; | ^~~~~~~~~~~~~ crossval.cpp:184:52: note: returned from ‘void* operator new [](std::size_t)’ 184 | if ((train_indices = new int32_t[train_size]) == NULL) | ^ crossval.cpp:239:32: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 239 | delete test_indices; | ^~~~~~~~~~~~ crossval.cpp:187:50: note: returned from ‘void* operator new [](std::size_t)’ 187 | if ((test_indices = new int32_t[test_size]) == NULL) | ^ crossval.cpp:240:32: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 240 | delete in_test_set; | ^~~~~~~~~~~ crossval.cpp:193:44: note: returned from ‘void* operator new [](std::size_t)’ 193 | if ((in_test_set = new bool[n_samps]) == NULL) | ^ crossval.cpp:246:32: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 246 | delete train_indices; | ^~~~~~~~~~~~~ crossval.cpp:184:52: note: returned from ‘void* operator new [](std::size_t)’ 184 | if ((train_indices = new int32_t[train_size]) == NULL) | ^ crossval.cpp:247:32: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 247 | delete test_indices; | ^~~~~~~~~~~~ crossval.cpp:187:50: note: returned from ‘void* operator new [](std::size_t)’ 187 | if ((test_indices = new int32_t[test_size]) == NULL) | ^ crossval.cpp:248:32: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 248 | delete in_test_set; | ^~~~~~~~~~~ crossval.cpp:193:44: note: returned from ‘void* operator new [](std::size_t)’ 193 | if ((in_test_set = new bool[n_samps]) == NULL) | ^ crossval.cpp:254:32: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 254 | delete train_indices; | ^~~~~~~~~~~~~ crossval.cpp:184:52: note: returned from ‘void* operator new [](std::size_t)’ 184 | if ((train_indices = new int32_t[train_size]) == NULL) | ^ crossval.cpp:255:32: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 255 | delete test_indices; | ^~~~~~~~~~~~ crossval.cpp:187:50: note: returned from ‘void* operator new [](std::size_t)’ 187 | if ((test_indices = new int32_t[test_size]) == NULL) | ^ crossval.cpp:256:32: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 256 | delete in_test_set; | ^~~~~~~~~~~ crossval.cpp:193:44: note: returned from ‘void* operator new [](std::size_t)’ 193 | if ((in_test_set = new bool[n_samps]) == NULL) | ^ crossval.cpp:268:16: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 268 | delete train_indices; | ^~~~~~~~~~~~~ crossval.cpp:184:52: note: returned from ‘void* operator new [](std::size_t)’ 184 | if ((train_indices = new int32_t[train_size]) == NULL) | ^ crossval.cpp:269:16: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 269 | delete test_indices; | ^~~~~~~~~~~~ crossval.cpp:187:50: note: returned from ‘void* operator new [](std::size_t)’ 187 | if ((test_indices = new int32_t[test_size]) == NULL) | ^ crossval.cpp:270:16: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 270 | delete in_test_set; | ^~~~~~~~~~~ crossval.cpp:193:44: note: returned from ‘void* operator new [](std::size_t)’ 193 | if ((in_test_set = new bool[n_samps]) == NULL) | ^ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c errors.cpp -o errors.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c init.cpp -o init.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c messinaExtern.cpp -o messinaExtern.o messinaExtern.cpp: In function ‘STATUS convertRMatrix2Data(Rcpp::NumericMatrix&, Rcpp::LogicalVector&, Data&)’: messinaExtern.cpp:138:16: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 138 | delete exprs_array; | ^~~~~~~~~~~ messinaExtern.cpp:115:61: note: returned from ‘void* operator new [](std::size_t)’ 115 | if ((exprs_array = new uint16_t[n_probes * n_samples]) == NULL) | ^ messinaExtern.cpp:139:16: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 139 | delete class_array; | ^~~~~~~~~~~ messinaExtern.cpp:119:46: note: returned from ‘void* operator new [](std::size_t)’ 119 | if ((class_array = new bool[n_samples]) == NULL) | ^ messinaExtern.cpp: In function ‘Rcpp::List messinaC(Rcpp::NumericMatrix, Rcpp::LogicalVector, uint32_t, uint32_t, float, float, bool, bool)’: messinaExtern.cpp:86:24: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 86 | delete results; | ^~~~~~~ messinaExtern.cpp:78:51: note: returned from ‘void* operator new [](std::size_t)’ 78 | if ((results = new Result[data.getNGenes()]) == NULL) | ^ messinaExtern.cpp:92:16: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 92 | delete results; | ^~~~~~~ messinaExtern.cpp:78:51: note: returned from ‘void* operator new [](std::size_t)’ 78 | if ((results = new Result[data.getNGenes()]) == NULL) | ^ g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o messina.so Classifier.o Data.o RcppExports.o crossval.o errors.o init.o messinaExtern.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-messina/00new/messina/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 (messina)