############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL DeMixT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library' * installing *source* package 'DeMixT' ... ** using staged installation ** libs gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DeMixT.c -o DeMixT.o DeMixT.c: In function 'Tdemix': DeMixT.c:37:45: warning: variable 'st2_sig_2' set but not used [-Wunused-but-set-variable] 37 | double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; | ^~~~~~~~~ DeMixT.c:37:33: warning: variable 'st1_sig_2' set but not used [-Wunused-but-set-variable] 37 | double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; | ^~~~~~~~~ DeMixT.c:37:22: warning: variable 'st2_mu_2' set but not used [-Wunused-but-set-variable] 37 | double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; | ^~~~~~~~ DeMixT.c:37:11: warning: variable 'st1_mu_2' set but not used [-Wunused-but-set-variable] 37 | double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; | ^~~~~~~~ DeMixT.c: In function 'gettumor': DeMixT.c:591:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] 591 | double obj_old, obj_new; | ^~~~~~~ DeMixT.c:591:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] 591 | double obj_old, obj_new; | ^~~~~~~ DeMixT.c: In function 'getpi': DeMixT.c:1280:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] 1280 | double obj_old, obj_new; | ^~~~~~~ DeMixT.c:1280:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] 1280 | double obj_old, obj_new; | ^~~~~~~ DeMixT.c: In function 'getspikeinpi': DeMixT.c:1307:18: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] 1307 | double obj_old, obj_new; | ^~~~~~~ DeMixT.c:1307:9: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] 1307 | double obj_old, obj_new; | ^~~~~~~ DeMixT.c: In function 'getpiT': DeMixT.c:1322:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] 1322 | double obj_old, obj_new; | ^~~~~~~ DeMixT.c:1322:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] 1322 | double obj_old, obj_new; | ^~~~~~~ DeMixT.c: In function 'Tdemix': DeMixT.c:195:11: warning: 'Tavgtmp' may be used uninitialized in this function [-Wmaybe-uninitialized] 195 | if(Tavgtmp <= 0) Tavgtmp = exp(10*log(2.0) + p->Tsigma[j]/2.0*pow(log(2.0), 2.0)); | ^ DeMixT.c:240:8: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 240 | CD = calloc(intx ,sizeof(double *)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from DeMixT.c:8: c:\rtools42\x86_64-w64-mingw32.static.posix\include\stdlib.h:535:17: note: in a call to allocation function 'calloc' declared here 535 | void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements); | ^~~~~~ DeMixT.c:94:8: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 94 | FD = calloc(nS ,sizeof(double *)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from DeMixT.c:8: c:\rtools42\x86_64-w64-mingw32.static.posix\include\stdlib.h:535:17: note: in a call to allocation function 'calloc' declared here 535 | void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements); | ^~~~~~ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Profile_2D.cpp -o Profile_2D.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c registerDynamicSymbol.c -o registerDynamicSymbol.o g++ -std=gnu++14 -shared -s -static-libgcc -o DeMixT.dll tmp.def DeMixT.o Profile_2D.o RcppExports.o init.o registerDynamicSymbol.o -fopenmp -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-DeMixT/00new/DeMixT/libs/x64 ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'ggplot2::alpha' by 'psych::alpha' when loading 'DeMixT' Warning: replacing previous import 'SummarizedExperiment::distance' by 'psych::distance' when loading 'DeMixT' Warning: replacing previous import 'ggplot2::%+%' by 'psych::%+%' when loading 'DeMixT' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'ggplot2::alpha' by 'psych::alpha' when loading 'DeMixT' Warning: replacing previous import 'SummarizedExperiment::distance' by 'psych::distance' when loading 'DeMixT' Warning: replacing previous import 'ggplot2::%+%' by 'psych::%+%' when loading 'DeMixT' ** testing if installed package can be loaded from final location Warning: replacing previous import 'ggplot2::alpha' by 'psych::alpha' when loading 'DeMixT' Warning: replacing previous import 'SummarizedExperiment::distance' by 'psych::distance' when loading 'DeMixT' Warning: replacing previous import 'ggplot2::%+%' by 'psych::%+%' when loading 'DeMixT' ** testing if installed package keeps a record of temporary installation path * DONE (DeMixT)