############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL DeMixT ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'DeMixT' ... ** using staged installation ** libs "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c DeMixT.c -o DeMixT.o DeMixT.c: In function 'Tdemix': DeMixT.c:268:28: warning: implicit declaration of function 'Rprintf'; did you mean 'wprintf'? [-Wimplicit-function-declaration] if (nHavepi != 1) Rprintf("Iteration %d: updating parameters\n", i+1); ^~~~~~~ wprintf DeMixT.c:36:45: warning: variable 'st2_sig_2' set but not used [-Wunused-but-set-variable] double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; ^~~~~~~~~ DeMixT.c:36:33: warning: variable 'st1_sig_2' set but not used [-Wunused-but-set-variable] double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; ^~~~~~~~~ DeMixT.c:36:22: warning: variable 'st2_mu_2' set but not used [-Wunused-but-set-variable] double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; ^~~~~~~~ DeMixT.c:36:11: warning: variable 'st1_mu_2' set but not used [-Wunused-but-set-variable] double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; ^~~~~~~~ DeMixT.c: In function 'gettumor': DeMixT.c:590:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^~~~~~~ DeMixT.c:590:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^~~~~~~ DeMixT.c: In function 'getpi': DeMixT.c:1279:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^~~~~~~ DeMixT.c:1279:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^~~~~~~ DeMixT.c: In function 'getspikeinpi': DeMixT.c:1306:18: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^~~~~~~ DeMixT.c:1306:9: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^~~~~~~ DeMixT.c: In function 'getpiT': DeMixT.c:1321:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^~~~~~~ DeMixT.c:1321:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^~~~~~~ DeMixT.c: In function 'Tdemix': DeMixT.c:194:11: warning: 'Tavgtmp' may be used uninitialized in this function [-Wmaybe-uninitialized] if(Tavgtmp <= 0) Tavgtmp = exp(10*log(2.0) + p->Tsigma[j]/2.0*pow(log(2.0), 2.0)); ^ DeMixT.c:93:8: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] FD = calloc(nS ,sizeof(double *)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from DeMixT.c:8: C:/rtools40/mingw64/x86_64-w64-mingw32/include/stdlib.h:455:17: note: in a call to allocation function 'calloc' declared here void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements); ^~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Profile_2D.cpp -o Profile_2D.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c init.c -o init.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c registerDynamicSymbol.c -o registerDynamicSymbol.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o DeMixT.dll tmp.def DeMixT.o Profile_2D.o RcppExports.o init.o registerDynamicSymbol.o -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to D:/biocbuild/bbs-3.15-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 ** help *** installing help indices converting help for package 'DeMixT' finding HTML links ... done DeMixT html DeMixT_DE html DeMixT_GS html DeMixT_S2 html Optimum_KernelC html simulate_2comp html simulate_3comp html test.data.2comp html test.data.3comp html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DeMixT) Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'ggspavis' is missing or broken Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'RUVcorr' is missing or broken done