starting phase `set-SOURCE-DATE-EPOCH'
phase `set-SOURCE-DATE-EPOCH' succeeded after 0.0 seconds
starting phase `set-paths'
environment variable `PATH' set to `/gnu/store/7nxvcm0jk30ipzbbw3k7rbljymmsqpkp-r-minimal-4.0.4/bin:/gnu/store/gww59gv5qxbfijg3vk5y182im7923s06-tar-1.32/bin:/gnu/store/2ayciqwxddkzq183dac82ijljc14j4zj-gzip-1.10/bin:/gnu/store/n1jk0w2wa4vpwmixaqn2y3la1l2sizzi-bzip2-1.0.8/bin:/gnu/store/7p36raqgk6vn47bflxc9bsclqiib3phi-xz-5.2.4/bin:/gnu/store/lpkf3ydcdvxn8gcrzaq9cp3ri05h8qhs-file-5.38/bin:/gnu/store/6gqaw09zqw8w0vcax6simlq71bq7l5r0-diffutils-3.7/bin:/gnu/store/qw20chpgkgbcqmzhs60c8hjl1hmblyc8-patch-2.7.6/bin:/gnu/store/b5y5scfmh2d8kxcpl9p84294z2198cgf-findutils-4.7.0/bin:/gnu/store/9iwlsj7d6ffqhshy8qshf7p4fqwfwrvn-gawk-5.0.1/bin:/gnu/store/q1nfjb24vqjs1cgi8mlnskw34h16y09r-sed-4.8/bin:/gnu/store/4qr6mcvsxyzknxa7x1wny8x30f5i0r3n-grep-3.4/bin:/gnu/store/2v61vg0bizgrhybkqbrki2k7kr094waz-coreutils-8.32/bin:/gnu/store/b7jbh7kzzig0bxfswdj8nfj9bkljyyya-make-4.3/bin:/gnu/store/v1g7f3p4f0851mywrla8qmr9hb8jgfjr-bash-minimal-5.0.16/bin:/gnu/store/dyqxnydqk1810afjfbqzfvh0n83xyl62-ld-wrapper-0/bin:/gnu/store/50lyzn9bz6x4da66648kry29wn8afird-binutils-2.34/bin:/gnu/store/afpgzln8860m6yfhxy6i8n9rywbp85cy-gcc-7.5.0/bin:/gnu/store/z4li262il798hbl0l1h1k3a5g7r6bffa-glibc-2.31/bin:/gnu/store/z4li262il798hbl0l1h1k3a5g7r6bffa-glibc-2.31/sbin:/gnu/store/xddwdqcic57d2jprlkr6j1kdy9g8979c-curl-7.74.0/bin'
environment variable `R_LIBS_SITE' set to 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YAPSA/CONTRIBUTORS
YAPSA/DESCRIPTION
YAPSA/LICENSE.txt
YAPSA/NAMESPACE
YAPSA/NEWS
YAPSA/R/
YAPSA/R/LCD.R
YAPSA/R/SMC.R
YAPSA/R/basic_functions.R
YAPSA/R/compare_SMCs.R
YAPSA/R/complex_functions.R
YAPSA/R/confidence.R
YAPSA/R/data.R
YAPSA/R/global.R
YAPSA/R/indel_functions.R
YAPSA/R/indels.R
YAPSA/R/interact_foreign.R
YAPSA/R/io_functions.R
YAPSA/R/pkgname.R
YAPSA/R/plot_functions.R
YAPSA/README.md
YAPSA/README_files/
YAPSA/README_files/figure-html/
YAPSA/README_files/figure-html/SMC_mut_density-1.png
YAPSA/README_files/figure-html/apply_heatmap_exposures-1.png
YAPSA/README_files/figure-html/cluster_PIDs_sig_info-1.png
YAPSA/README_files/figure-html/exposures_barplot_LCD-1.png
YAPSA/README_files/figure-html/exposures_barplot_LCD_sig_ind-1.png
YAPSA/README_files/figure-html/exposures_barplot_abs_cutoffGen-1.png
YAPSA/README_files/figure-html/exposures_barplot_abs_cutoffSpec-1.png
YAPSA/README_files/figure-html/exposures_barplot_abs_cutoffZero-1.png
YAPSA/README_files/figure-html/exposures_barplot_rel_cutoffGen-1.png
YAPSA/README_files/figure-html/exposures_barplot_rel_cutoffSpec-1.png
YAPSA/README_files/figure-html/exposures_barplot_rel_cutoffZero-1.png
YAPSA/README_files/figure-html/make_rainfall_plot-1.png
YAPSA/build/
YAPSA/build/vignette.rds
YAPSA/data/
YAPSA/data/GenomeOfNl_MutCat.rda
YAPSA/data/GenomeOfNl_raw.rda
YAPSA/data/cutoffs.rda
YAPSA/data/cutoffs_pcawg.rda
YAPSA/data/exchange_colour_vector.rda
YAPSA/data/lymphomaNature2013_mutCat_df.rda
YAPSA/data/lymphoma_Nature2013_raw.rda
YAPSA/data/lymphoma_PID.rda
YAPSA/data/lymphoma_cohort_LCD_results.rda
YAPSA/data/lymphoma_test.rda
YAPSA/data/sigs.rda
YAPSA/data/sigs_pcawg.rda
YAPSA/data/smallCellLungCancerMutCat_NatureGenetics2012.rda
YAPSA/data/targetCapture_cor_factors.rda
YAPSA/inst/
YAPSA/inst/YAPSA_datasets/
YAPSA/inst/YAPSA_datasets/cutoffs.rda
YAPSA/inst/YAPSA_datasets/cutoffs_pcawg.rda
YAPSA/inst/YAPSA_datasets/sigs.rda
YAPSA/inst/YAPSA_datasets/sigs_pcawg.rda
YAPSA/inst/doc/
YAPSA/inst/doc/YAPSA.R
YAPSA/inst/doc/YAPSA.Rmd
YAPSA/inst/doc/YAPSA.html
YAPSA/inst/doc/index.html
YAPSA/inst/doc/vignette_confidenceIntervals.R
YAPSA/inst/doc/vignette_confidenceIntervals.Rmd
YAPSA/inst/doc/vignette_confidenceIntervals.html
YAPSA/inst/doc/vignette_exomes.R
YAPSA/inst/doc/vignette_exomes.Rmd
YAPSA/inst/doc/vignette_exomes.html
YAPSA/inst/doc/vignette_signature_specific_cutoffs.R
YAPSA/inst/doc/vignette_signature_specific_cutoffs.Rmd
YAPSA/inst/doc/vignette_signature_specific_cutoffs.html
YAPSA/inst/doc/vignette_stratifiedAnalysis.R
YAPSA/inst/doc/vignette_stratifiedAnalysis.Rmd
YAPSA/inst/doc/vignette_stratifiedAnalysis.html
YAPSA/inst/doc/vignettes_Indel.R
YAPSA/inst/doc/vignettes_Indel.Rmd
YAPSA/inst/doc/vignettes_Indel.html
YAPSA/inst/foreign/
YAPSA/inst/foreign/annotate_vcf.pl
YAPSA/inst/foreign/kmer_frequencies.pl
YAPSA/man/
YAPSA/man/GenomeOfNl_raw.Rd
YAPSA/man/LCD.Rd
YAPSA/man/LCD_SMC.Rd
YAPSA/man/LCD_complex_cutoff.Rd
YAPSA/man/MutCat_indel_df.Rd
YAPSA/man/SMC.Rd
YAPSA/man/SMC_perPID.Rd
YAPSA/man/YAPSA.Rd
YAPSA/man/add_annotation.Rd
YAPSA/man/add_as_fist_to_list.Rd
YAPSA/man/aggregate_exposures_by_category.Rd
YAPSA/man/annotate_intermut_dist_PID.Rd
YAPSA/man/annotate_intermut_dist_cohort.Rd
YAPSA/man/annotation_exposures_barplot.Rd
YAPSA/man/annotation_exposures_list_barplot.Rd
YAPSA/man/annotation_heatmap_exposures.Rd
YAPSA/man/attribute_nucleotide_exchanges.Rd
YAPSA/man/attribute_sequence_contex_indel.Rd
YAPSA/man/attribution_of_indels.Rd
YAPSA/man/build_gene_list_for_pathway.Rd
YAPSA/man/classify_indels.Rd
YAPSA/man/compare_SMCs.Rd
YAPSA/man/compare_exposures.Rd
YAPSA/man/compare_expousre_sets.Rd
YAPSA/man/compare_sets.Rd
YAPSA/man/compare_to_catalogues.Rd
YAPSA/man/complex_heatmap_exposures.Rd
YAPSA/man/computeLogLik.Rd
YAPSA/man/compute_comparison_stat_df.Rd
YAPSA/man/confIntExp.Rd
YAPSA/man/confidence_indel_calulation.Rd
YAPSA/man/confidence_indel_only_calulation.Rd
YAPSA/man/correct_rounded.Rd
YAPSA/man/cosineDist.Rd
YAPSA/man/cosineMatchDist.Rd
YAPSA/man/create_indel_mut_cat_from_df.Rd
YAPSA/man/create_indel_mutation_catalogue_from_df.Rd
YAPSA/man/create_mutation_catalogue_from_VR.Rd
YAPSA/man/create_mutation_catalogue_from_df.Rd
YAPSA/man/cut_breaks_as_intervals.Rd
YAPSA/man/cutoffs.Rd
YAPSA/man/cutoffs_pcawg.Rd
YAPSA/man/deriveSigInd_df.Rd
YAPSA/man/disambiguateVector.Rd
YAPSA/man/enrichSigs.Rd
YAPSA/man/exampleINDEL_YAPSA.Rd
YAPSA/man/exampleYAPSA.Rd
YAPSA/man/exchange_colour_vector.Rd
YAPSA/man/exome_mutCatRaw_df.Rd
YAPSA/man/exposures_barplot.Rd
YAPSA/man/extract_names_from_gene_list.Rd
YAPSA/man/find_affected_PIDs.Rd
YAPSA/man/getSequenceContext.Rd
YAPSA/man/get_extreme_PIDs.Rd
YAPSA/man/hclust_exposures.Rd
YAPSA/man/logLikelihood.Rd
YAPSA/man/lymphomaNature2013_mutCat_df.Rd
YAPSA/man/makeVRangesFromDataFrame.Rd
YAPSA/man/make_catalogue_strata_df.Rd
YAPSA/man/make_comparison_matrix.Rd
YAPSA/man/make_strata_df.Rd
YAPSA/man/make_subgroups_df.Rd
YAPSA/man/melt_exposures.Rd
YAPSA/man/merge_exposures.Rd
YAPSA/man/normalizeMotifs_otherRownames.Rd
YAPSA/man/normalize_df_per_dim.Rd
YAPSA/man/plotExchangeSpectra.Rd
YAPSA/man/plotExchangeSpectra_indel.Rd
YAPSA/man/plotExposuresConfidence.Rd
YAPSA/man/plotExposuresConfidence_indel.Rd
YAPSA/man/plot_SMC.Rd
YAPSA/man/plot_exposures.Rd
YAPSA/man/plot_strata.Rd
YAPSA/man/read_entry.Rd
YAPSA/man/relateSigs.Rd
YAPSA/man/repeat_df.Rd
YAPSA/man/round_precision.Rd
YAPSA/man/run_SMC.Rd
YAPSA/man/run_annotate_vcf_pl.Rd
YAPSA/man/run_comparison_catalogues.Rd
YAPSA/man/run_comparison_general.Rd
YAPSA/man/run_kmer_frequency_correction.Rd
YAPSA/man/run_kmer_frequency_normalization.Rd
YAPSA/man/run_plot_strata_general.Rd
YAPSA/man/shapiro_if_possible.Rd
YAPSA/man/sigs.Rd
YAPSA/man/sigs_pcawg.Rd
YAPSA/man/split_exposures_by_subgroups.Rd
YAPSA/man/stat_plot_subgroups.Rd
YAPSA/man/stat_test_SMC.Rd
YAPSA/man/stat_test_subgroups.Rd
YAPSA/man/stderrmean.Rd
YAPSA/man/sum_over_list_of_df.Rd
YAPSA/man/targetCapture_cor_factors.Rd
YAPSA/man/temp_trellis_rainfall_plot.Rd
YAPSA/man/testSigs.Rd
YAPSA/man/test_exposureAffected.Rd
YAPSA/man/test_gene_list_in_exposures.Rd
YAPSA/man/transform_rownames_R_to_MATLAB.Rd
YAPSA/man/translate_to_hg19.Rd
YAPSA/man/trellis_rainfall_plot.Rd
YAPSA/man/trellis_rainfall_plot_old.Rd
YAPSA/man/variateExp.Rd
YAPSA/man/variateExpSingle.Rd
YAPSA/tests/
YAPSA/tests/testthat/
YAPSA/tests/testthat.R
YAPSA/tests/testthat/test_LCD.R
YAPSA/tests/testthat/test_basic_functions.R
YAPSA/tests/testthat/test_complex_functions.R
YAPSA/vignettes/
YAPSA/vignettes/NMF.png
YAPSA/vignettes/YAPSA.Rmd
YAPSA/vignettes/vignette_confidenceIntervals.Rmd
YAPSA/vignettes/vignette_exomes.Rmd
YAPSA/vignettes/vignette_signature_specific_cutoffs.Rmd
YAPSA/vignettes/vignette_stratifiedAnalysis.Rmd
YAPSA/vignettes/vignettes_Indel.Rmd
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* installing *source* package ‘YAPSA’ ...
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** R
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** help
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* DONE (YAPSA)
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