############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/YAPSA_1.20.1.tar.gz && rm -rf YAPSA.buildbin-libdir && mkdir YAPSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=YAPSA.buildbin-libdir YAPSA_1.20.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL YAPSA_1.20.1.zip && rm YAPSA_1.20.1.tar.gz YAPSA_1.20.1.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 23 1293k 23 306k 0 0 630k 0 0:00:02 --:--:-- 0:00:02 631k 100 1293k 100 1293k 0 0 1053k 0 0:00:01 0:00:01 --:--:-- 1054k install for i386 * installing *source* package 'YAPSA' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' ** help *** installing help indices converting help for package 'YAPSA' finding HTML links ... done GenomeOfNl_raw html LCD html LCD_SMC html LCD_complex_cutoff html MutCat_indel_df html SMC html SMC_perPID html YAPSA html add_annotation html add_as_fist_to_list html aggregate_exposures_by_category html annotate_intermut_dist_PID html annotate_intermut_dist_cohort html annotation_exposures_barplot html annotation_exposures_list_barplot html annotation_heatmap_exposures html attribute_nucleotide_exchanges html attribute_sequence_contex_indel html attribution_of_indels html build_gene_list_for_pathway html classify_indels html compare_SMCs html compare_exposures html compare_expousre_sets html compare_sets html compare_to_catalogues html complex_heatmap_exposures html computeLogLik html compute_comparison_stat_df html confIntExp html confidence_indel_calulation html confidence_indel_only_calulation html correct_rounded html cosineDist html cosineMatchDist html create_indel_mut_cat_from_df html create_indel_mutation_catalogue_from_df html create_mutation_catalogue_from_VR html create_mutation_catalogue_from_df html finding level-2 HTML links ... done cut_breaks_as_intervals html cutoffs html cutoffs_pcawg html deriveSigInd_df html disambiguateVector html enrichSigs html exampleINDEL_YAPSA html exampleYAPSA html exchange_colour_vector html exome_mutCatRaw_df html exposures_barplot html extract_names_from_gene_list html find_affected_PIDs html getSequenceContext html get_extreme_PIDs html hclust_exposures html logLikelihood html lymphomaNature2013_mutCat_df html makeVRangesFromDataFrame html make_catalogue_strata_df html make_comparison_matrix html make_strata_df html make_subgroups_df html melt_exposures html merge_exposures html normalizeMotifs_otherRownames html normalize_df_per_dim html plotExchangeSpectra html plotExchangeSpectra_indel html plotExposuresConfidence html plotExposuresConfidence_indel html plot_SMC html plot_exposures html plot_strata html read_entry html relateSigs html repeat_df html round_precision html run_SMC html run_annotate_vcf_pl html run_comparison_catalogues html run_comparison_general html run_kmer_frequency_correction html run_kmer_frequency_normalization html run_plot_strata_general html shapiro_if_possible html sigs html sigs_pcawg html split_exposures_by_subgroups html stat_plot_subgroups html stat_test_SMC html stat_test_subgroups html stderrmean html sum_over_list_of_df html targetCapture_cor_factors html temp_trellis_rainfall_plot html testSigs html test_exposureAffected html test_gene_list_in_exposures html transform_rownames_R_to_MATLAB html translate_to_hg19 html trellis_rainfall_plot html trellis_rainfall_plot_old html variateExp html variateExpSingle html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' ** testing if installed package can be loaded from final location Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'YAPSA' ... ** testing if installed package can be loaded Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' * MD5 sums packaged installation of 'YAPSA' as YAPSA_1.20.1.zip * DONE (YAPSA) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'YAPSA' successfully unpacked and MD5 sums checked