############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL scde ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'scde' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bwpca.cpp -o bwpca.o bwpca.cpp: In function 'void set_random_matrix(arma::mat&, arma::mat&)': bwpca.cpp:24:18: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 24 | for(int j=0;j<target.n_rows;j++) { | ~^~~~~~~~~~~~~~ bwpca.cpp:31:18: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 31 | for(int i=0;i<target.n_cols;i++) { | ~^~~~~~~~~~~~~~ bwpca.cpp:34:22: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 34 | for(int j=0;j<target.n_rows;j++) { | ~^~~~~~~~~~~~~~ bwpca.cpp: In function 'void set_random_matrices(arma::mat&, arma::mat&, arma::mat&, arma::mat&)': bwpca.cpp:44:18: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 44 | for(int j=0;j<target1.n_rows;j++) { | ~^~~~~~~~~~~~~~~ bwpca.cpp:51:18: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 51 | for(int i=0;i<target1.n_cols;i++) { | ~^~~~~~~~~~~~~~~ bwpca.cpp:54:22: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 54 | for(int j=0;j<target1.n_rows;j++) { | ~^~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c jpmatLogBoot.cpp -o jpmatLogBoot.o jpmatLogBoot.cpp: In function 'SEXPREC* logBootPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': jpmatLogBoot.cpp:200:24: warning: unused variable 'maxv' [-Wunused-variable] 200 | double maxv=nbp.max(maxij); | ^~~~ jpmatLogBoot.cpp: In function 'SEXPREC* logBootBatchPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': jpmatLogBoot.cpp:443:24: warning: unused variable 'maxv' [-Wunused-variable] 443 | double maxv=nbp.max(maxij); | ^~~~ g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matSlideMult.cpp -o matSlideMult.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pagoda.cpp -o pagoda.o g++ -std=gnu++17 -shared -s -static-libgcc -o scde.dll tmp.def bwpca.o jpmatLogBoot.o matSlideMult.o pagoda.o -lpthread -LE:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lRlapack -LE:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-scde/00new/scde/libs/x64 ** R ** data *** moving datasets to lazyload DB ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scde)