############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/cola_1.8.1.tar.gz && rm -rf cola.buildbin-libdir && mkdir cola.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cola.buildbin-libdir cola_1.8.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL cola_1.8.1.zip && rm cola_1.8.1.tar.gz cola_1.8.1.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 10.7M 0 16224 0 0 135k 0 0:01:21 --:--:-- 0:01:21 135k 21 10.7M 21 2406k 0 0 2157k 0 0:00:05 0:00:01 0:00:04 2157k 49 10.7M 49 5485k 0 0 2573k 0 0:00:04 0:00:02 0:00:02 2574k 69 10.7M 69 7691k 0 0 2457k 0 0:00:04 0:00:03 0:00:01 2458k 94 10.7M 94 10.1M 0 0 2509k 0 0:00:04 0:00:04 --:--:-- 2509k 100 10.7M 100 10.7M 0 0 2543k 0 0:00:04 0:00:04 --:--:-- 2610k install for i386 * installing *source* package 'cola' ... ** 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 atc.cpp -o atc.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 cal_consensus_mat.cpp -o cal_consensus_mat.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 pdist.cpp -o pdist.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o cola.dll tmp.def RcppExports.o atc.o cal_consensus_mat.o pdist.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/cola.buildbin-libdir/00LOCK-cola/00new/cola/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'cola' finding HTML links ... done ATC html ATC_approx html ConsensusPartition-class html ConsensusPartitionList-class html DownSamplingConsensusPartition-class html Extract.ConsensusPartitionList html Extract.HierarchicalPartition html ExtractExtract.ConsensusPartitionList html ExtractExtract.HierarchicalPartition html FCC html HierarchicalPartition-class html PAC html aPAC html adjust_matrix html adjust_outlier html all_leaves-HierarchicalPartition-method html all_nodes-HierarchicalPartition-method html all_partition_methods html all_top_value_methods html cola html cola_opt html cola_report-ConsensusPartition-method html cola_report-ConsensusPartitionList-method html cola_report-HierarchicalPartition-method html cola_report-dispatch html cola_rl html collect_classes-ConsensusPartition-method html collect_classes-ConsensusPartitionList-method html collect_classes-HierarchicalPartition-method html collect_classes-dispatch html collect_plots-ConsensusPartition-method html collect_plots-ConsensusPartitionList-method html collect_plots-dispatch html collect_stats-ConsensusPartition-method html collect_stats-ConsensusPartitionList-method html collect_stats-dispatch html colnames-ConsensusPartition-method html colnames-ConsensusPartitionList-method html colnames-DownSamplingConsensusPartition-method html colnames-HierarchicalPartition-method html colnames-dispatch html compare_partitions-ConsensusPartition-method html compare_signatures-ConsensusPartition-method html compare_signatures-HierarchicalPartition-method html compare_signatures-dispatch html concordance html config_ATC html consensus_heatmap-ConsensusPartition-method html consensus_partition html consensus_partition_by_down_sampling html correspond_between_rankings html correspond_between_two_rankings html david_enrichment html dim.ConsensusPartition html dim.ConsensusPartitionList html dim.DownSamplingConsensusPartition html dim.HierarchicalPartition html dimension_reduction-ConsensusPartition-method html dimension_reduction-DownSamplingConsensusPartition-method html dimension_reduction-HierarchicalPartition-method html dimension_reduction-dispatch html dimension_reduction-matrix-method html find_best_km html functional_enrichment-ANY-method html functional_enrichment-ConsensusPartition-method html functional_enrichment-ConsensusPartitionList-method html functional_enrichment-HierarchicalPartition-method html functional_enrichment-dispatch html get_anno-ConsensusPartition-method html get_anno-ConsensusPartitionList-method html get_anno-DownSamplingConsensusPartition-method html get_anno-HierarchicalPartition-method html get_anno-dispatch html get_anno_col-ConsensusPartition-method html get_anno_col-ConsensusPartitionList-method html get_anno_col-HierarchicalPartition-method html get_anno_col-dispatch html get_children_nodes-HierarchicalPartition-method html get_classes-ConsensusPartition-method html get_classes-ConsensusPartitionList-method html get_classes-DownSamplingConsensusPartition-method html get_classes-HierarchicalPartition-method html get_classes-dispatch html get_consensus-ConsensusPartition-method html get_matrix-ConsensusPartition-method html get_matrix-ConsensusPartitionList-method html get_matrix-HierarchicalPartition-method html get_matrix-dispatch html get_membership-ConsensusPartition-method html get_membership-ConsensusPartitionList-method html get_membership-dispatch html get_param-ConsensusPartition-method html get_signatures-ConsensusPartition-method html get_signatures-DownSamplingConsensusPartition-method html get_signatures-HierarchicalPartition-method html get_signatures-dispatch html get_stats-ConsensusPartition-method html get_stats-ConsensusPartitionList-method html get_stats-dispatch html golub_cola html golub_cola_ds html golub_cola_rh html hierarchical_partition html is_best_k-ConsensusPartition-method html is_best_k-ConsensusPartitionList-method html is_best_k-dispatch html is_leaf_node-HierarchicalPartition-method html is_stable_k-ConsensusPartition-method html is_stable_k-ConsensusPartitionList-method html is_stable_k-dispatch html knee_finder2 html knitr_add_tab_item html knitr_insert_tabs html map_to_entrez_id html max_depth-HierarchicalPartition-method html membership_heatmap-ConsensusPartition-method html merge_node-HierarchicalPartition-method html merge_node_param html ncol-ConsensusPartition-method html ncol-ConsensusPartitionList-method html ncol-DownSamplingConsensusPartition-method html ncol-HierarchicalPartition-method html ncol-dispatch html node_info-HierarchicalPartition-method html node_level-HierarchicalPartition-method html nrow-ConsensusPartition-method html nrow-ConsensusPartitionList-method html nrow-HierarchicalPartition-method html nrow-dispatch html plot_ecdf-ConsensusPartition-method html predict_classes-ConsensusPartition-method html finding level-2 HTML links ... done predict_classes-dispatch html predict_classes-matrix-method html print.hc_table_suggest_best_k html recalc_stats html register_NMF html register_SOM html register_partition_methods html register_top_value_methods html relabel_class html remove_partition_methods html remove_top_value_methods html rownames-ConsensusPartition-method html rownames-ConsensusPartitionList-method html rownames-HierarchicalPartition-method html rownames-dispatch html run_all_consensus_partition_methods html select_partition_number-ConsensusPartition-method html show-ConsensusPartition-method html show-ConsensusPartitionList-method html show-DownSamplingConsensusPartition-method html show-HierarchicalPartition-method html show-dispatch html split_node-HierarchicalPartition-method html suggest_best_k-ConsensusPartition-method html suggest_best_k-ConsensusPartitionList-method html suggest_best_k-HierarchicalPartition-method html suggest_best_k-dispatch html test_between_factors html test_to_known_factors-ConsensusPartition-method html test_to_known_factors-ConsensusPartitionList-method html test_to_known_factors-DownSamplingConsensusPartition-method html test_to_known_factors-HierarchicalPartition-method html test_to_known_factors-dispatch html top_elements_overlap html top_rows_heatmap-ConsensusPartition-method html top_rows_heatmap-ConsensusPartitionList-method html top_rows_heatmap-HierarchicalPartition-method html top_rows_heatmap-dispatch html top_rows_heatmap-matrix-method html top_rows_overlap-ConsensusPartitionList-method html top_rows_overlap-HierarchicalPartition-method html top_rows_overlap-dispatch html top_rows_overlap-matrix-method 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 'cola' ... ** 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 atc.cpp -o atc.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 cal_consensus_mat.cpp -o cal_consensus_mat.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 pdist.cpp -o pdist.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o cola.dll tmp.def RcppExports.o atc.o cal_consensus_mat.o pdist.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/cola.buildbin-libdir/cola/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'cola' as cola_1.8.1.zip * DONE (cola) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'cola' successfully unpacked and MD5 sums checked