############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/monocle_2.20.0.tar.gz && rm -rf monocle.buildbin-libdir && mkdir monocle.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=monocle.buildbin-libdir monocle_2.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL monocle_2.20.0.zip && rm monocle_2.20.0.tar.gz monocle_2.20.0.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 0 9403k 0 33775 0 0 157k 0 0:00:59 --:--:-- 0:00:59 157k 30 9403k 30 2907k 0 0 2464k 0 0:00:03 0:00:01 0:00:02 2463k 68 9403k 68 6415k 0 0 2939k 0 0:00:03 0:00:02 0:00:01 2938k 100 9403k 100 9403k 0 0 3357k 0 0:00:02 0:00:02 --:--:-- 3357k install for i386 * installing *source* package 'monocle' ... ** 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:/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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c clustering.cpp -o clustering.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o monocle.dll tmp.def RcppExports.o clustering.o -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/monocle.buildbin-libdir/00LOCK-monocle/00new/monocle/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 'monocle' finding HTML links ... done BEAM html CellDataSet-methods html CellDataSet html CellType html CellTypeHierarchy html addCellType html branchTest html buildBranchCellDataSet html calABCs html calILRs html calibrate_per_cell_total_proposal html cellPairwiseDistances-set html cellPairwiseDistances html clusterCells html finding level-2 HTML links ... done clusterGenes html compareModels html detectBifurcationPoint html detectGenes html diff_test_helper html differentialGeneTest html dispersionTable html estimateDispersionsForCellDataSet html estimateSizeFactorsForMatrix html estimate_t html exportCDS html extract_good_branched_ordering html fitModel html fit_model_helper html genSmoothCurveResiduals html genSmoothCurves html get_classic_muscle_markers html importCDS html load_HSMM html load_HSMM_markers html load_lung html markerDiffTable html mcesApply html minSpanningTree-set html minSpanningTree html newCellDataSet html newCellTypeHierarchy html orderCells html order_p_node html package-deprecated html plot_cell_clusters html plot_cell_trajectory html plot_clusters html plot_coexpression_matrix html plot_complex_cell_trajectory html plot_genes_branched_heatmap html plot_genes_branched_pseudotime html plot_genes_in_pseudotime html plot_genes_jitter html plot_genes_positive_cells html plot_genes_violin html plot_multiple_branches_heatmap html plot_multiple_branches_pseudotime html plot_ordering_genes html plot_pc_variance_explained html plot_pseudotime_heatmap html plot_rho_delta html pq_helper html reduceDimension html reducedDimA-set html reducedDimA html reducedDimK-set html reducedDimK html reducedDimS-set html reducedDimS html reducedDimW-set html reducedDimW html relative2abs html residualMatrix html responseMatrix html selectTopMarkers html setOrderingFilter html spike_df html vstExprs 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 'monocle' ... ** 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:/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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c clustering.cpp -o clustering.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o monocle.dll tmp.def RcppExports.o clustering.o -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/monocle.buildbin-libdir/monocle/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'monocle' as monocle_2.20.0.zip * DONE (monocle) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'monocle' successfully unpacked and MD5 sums checked