############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MutationalPatterns_3.4.1.tar.gz && rm -rf MutationalPatterns.buildbin-libdir && mkdir MutationalPatterns.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MutationalPatterns.buildbin-libdir MutationalPatterns_3.4.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MutationalPatterns_3.4.1.zip && rm MutationalPatterns_3.4.1.tar.gz MutationalPatterns_3.4.1.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 43 2124k 43 925k 0 0 1362k 0 0:00:01 --:--:-- 0:00:01 1362k 100 2124k 100 2124k 0 0 1709k 0 0:00:01 0:00:01 --:--:-- 1710k install for i386 * installing *source* package 'MutationalPatterns' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'MutationalPatterns' finding HTML links ... done MutationalPatterns-defunct html MutationalPatterns-package html bin_mutation_density html binomial_test html calculate_lesion_segregation html cluster_signatures html context_potential_damage_analysis html convert_sigs_to_ref html cos_sim html cos_sim_matrix html count_dbs_contexts html count_indel_contexts html count_mbs_contexts html determine_regional_similarity html enrichment_depletion_test html extract_signatures html fit_to_signatures html fit_to_signatures_bootstrapped html fit_to_signatures_strict html genomic_distribution html get_dbs_context html get_indel_context html get_known_signatures html get_mut_type html get_sim_tb html lengthen_mut_matrix html merge_signatures html mut_192_occurrences html mut_96_occurrences html mut_context html mut_matrix html mut_matrix_stranded html mut_strand html mut_type html mut_type_occurrences html mutations_from_vcf html plot_192_profile html plot_96_profile html plot_bootstrapped_contribution html plot_compare_dbs html plot_compare_indels html plot_compare_mbs html plot_compare_profiles html plot_contribution html plot_contribution_heatmap html plot_correlation_bootstrap html plot_cosine_heatmap html plot_dbs_contexts html plot_enrichment_depletion html plot_indel_contexts html plot_lesion_segregation html plot_main_dbs_contexts html plot_main_indel_contexts html plot_mbs_contexts html plot_original_vs_reconstructed html plot_profile_heatmap html plot_profile_region html plot_rainfall html plot_regional_similarity html plot_river html plot_signature_strand_bias html plot_spectrum html plot_spectrum_region html plot_strand html plot_strand_bias html pool_mut_mat html read_vcfs_as_granges html region_cossim-class html rename_nmf_signatures html show-region_cossim-method html signature_potential_damage_analysis html split_muts_region html strand_bias_test html strand_occurrences html type_context 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 'MutationalPatterns' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'MutationalPatterns' as MutationalPatterns_3.4.1.zip * DONE (MutationalPatterns) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'MutationalPatterns' successfully unpacked and MD5 sums checked