############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/DeMixT_1.8.0.tar.gz && rm -rf DeMixT.buildbin-libdir && mkdir DeMixT.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DeMixT.buildbin-libdir DeMixT_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL DeMixT_1.8.0.zip && rm DeMixT_1.8.0.tar.gz DeMixT_1.8.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 33 2969k 33 998k 0 0 1563k 0 0:00:01 --:--:-- 0:00:01 1564k 100 2969k 100 2969k 0 0 2144k 0 0:00:01 0:00:01 --:--:-- 2146k install for i386 * installing *source* package 'DeMixT' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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 [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] FD = calloc(nS ,sizeof(double *)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from DeMixT.c:8: C:/rtools40/mingw32/i686-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/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Profile_2D.cpp -o Profile_2D.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c registerDynamicSymbol.c -o registerDynamicSymbol.o C:/rtools40/mingw32/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/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/DeMixT.buildbin-libdir/00LOCK-DeMixT/00new/DeMixT/libs/i386 ** 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 install for x64 * installing *source* package 'DeMixT' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Profile_2D.cpp -o Profile_2D.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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 -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/DeMixT.buildbin-libdir/DeMixT/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'DeMixT' as DeMixT_1.8.0.zip * DONE (DeMixT) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'DeMixT' successfully unpacked and MD5 sums checked