############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/SC3_1.20.0.tar.gz && rm -rf SC3.buildbin-libdir && mkdir SC3.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SC3.buildbin-libdir SC3_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL SC3_1.20.0.zip && rm SC3_1.20.0.tar.gz SC3_1.20.0.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 72 1742k 72 1255k 0 0 1399k 0 0:00:01 --:--:-- 0:00:01 1399k 100 1742k 100 1742k 0 0 1551k 0 0:00:01 0:00:01 --:--:-- 1552k install for i386 * installing *source* package 'SC3' ... ** using staged installation ** libs "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:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.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:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cppFunctions.cpp -o cppFunctions.o cppFunctions.cpp: In function 'arma::mat consmx(arma::mat)': cppFunctions.cpp:63:16: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for (j = 0; j < dat.n_cols; j++) { ~~^~~~~~~~~~~~ cppFunctions.cpp:64:17: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for (i = 0; i < dat.n_rows; i++) { ~~^~~~~~~~~~~~ cppFunctions.cpp:65:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for (k = i + 1; k < dat.n_rows; k++) { ~~^~~~~~~~~~~~ C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o SC3.dll tmp.def RcppExports.o cppFunctions.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -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/SC3.buildbin-libdir/00LOCK-SC3/00new/SC3/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 'SC3' finding HTML links ... done ED1 html ED2 html ann html calculate_distance html calculate_stability html consensus_matrix html consmx html estkTW html get_auroc html get_biolgy html get_de_genes html get_marker_genes html get_outl_cells html get_processed_dataset html markers_for_heatmap html norm_laplacian html organise_de_genes html organise_marker_genes html prepare_for_svm html reindex_clusters html sc3 html sc3_calc_biology html sc3_calc_consens html sc3_calc_dists html sc3_calc_transfs html sc3_estimate_k html sc3_export_results_xls html sc3_interactive html sc3_kmeans html sc3_plot_cluster_stability html sc3_plot_consensus html sc3_plot_de_genes html sc3_plot_expression html sc3_plot_markers html sc3_plot_silhouette html sc3_prepare html sc3_run_svm html support_vector_machines html tmult html transformation html yan 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 'SC3' ... ** libs "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:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.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:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cppFunctions.cpp -o cppFunctions.o cppFunctions.cpp: In function 'arma::mat consmx(arma::mat)': cppFunctions.cpp:63:16: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for (j = 0; j < dat.n_cols; j++) { ~~^~~~~~~~~~~~ cppFunctions.cpp:64:17: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for (i = 0; i < dat.n_rows; i++) { ~~^~~~~~~~~~~~ cppFunctions.cpp:65:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for (k = i + 1; k < dat.n_rows; k++) { ~~^~~~~~~~~~~~ C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o SC3.dll tmp.def RcppExports.o cppFunctions.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -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/SC3.buildbin-libdir/SC3/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'SC3' as SC3_1.20.0.zip * DONE (SC3) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'SC3' successfully unpacked and MD5 sums checked