############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MutationalPatterns_3.9.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck’ * using R Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 LTS * using session charset: UTF-8 * checking for file ‘MutationalPatterns/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MutationalPatterns’ version ‘3.9.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘MutationalPatterns’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed read_vcfs_as_granges 27.950 3.120 33.388 context_potential_damage_analysis 27.247 0.584 27.832 plot_lesion_segregation 15.146 0.028 15.175 get_mut_type 13.852 0.063 13.915 genomic_distribution 11.416 0.228 11.646 bin_mutation_density 10.350 0.620 10.971 calculate_lesion_segregation 10.517 0.212 10.730 plot_compare_indels 9.088 0.052 9.140 plot_indel_contexts 8.283 0.032 8.315 get_indel_context 7.362 0.320 7.683 plot_river 6.272 0.191 6.467 plot_spectrum_region 6.333 0.033 6.365 fit_to_signatures_bootstrapped 5.923 0.092 6.014 plot_profile_heatmap 5.855 0.076 5.931 split_muts_region 5.121 0.456 5.577 plot_spectrum 5.070 0.063 5.134 plot_compare_dbs 5.072 0.024 5.096 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘Introduction_to_MutationalPatterns.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘Introduction_to_MutationalPatterns.Rmd’ using rmarkdown The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/combine_plot_spectrum-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/combine_plot_spectrum_2-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_96_profile-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_profile_heatmap-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/riverplot-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/unnamed-chunk-4-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/unnamed-chunk-5-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_DBS_contexts-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_main_DBS_contexts-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_MBS_contexts-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/estimate_rank-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/use_bayesnmf-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_96_profile_signatures-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_contribution-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_contribution_heatmap_clust-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_contribution_heatmap_order-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_compare_profiles-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_ori_vs_rec-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_contribution_refit-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_ori_vs_rec_fit-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/strict_refit_decay-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_contribution_refit_strict-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_bootstrapped_refit-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_bootstrapped_refit_rel_boxtplot-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_correlation_signatures-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/Plot_cosine_heatmap-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_cosine_heatmap_samples-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_192_spectrum-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_strand_bias_combi-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/strand_bias_test_notstrict-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_strand_rep-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_rainfall-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_enrichment_depletion-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/extract_signatures_regions-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_spectrum_region-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_spectrum_region_yaxis-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_profile_region-1.png" but not available. Killed * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/00check.log’ for details.