Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:39 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the MutationalPatterns package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MutationalPatterns.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 1333/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MutationalPatterns 3.9.1 (landing page) Mark van Roosmalen
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
Package: MutationalPatterns |
Version: 3.9.1 |
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 |
StartedAt: 2023-04-12 07:48:13 -0400 (Wed, 12 Apr 2023) |
EndedAt: 2023-04-12 08:13:12 -0400 (Wed, 12 Apr 2023) |
EllapsedTime: 1498.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: MutationalPatterns.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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.
MutationalPatterns.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MutationalPatterns ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘MutationalPatterns’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (MutationalPatterns)
MutationalPatterns.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(MutationalPatterns) Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: NMF Loading required package: registry Loading required package: rngtools Loading required package: cluster NMF - BioConductor layer [OK] | Shared memory capabilities [NO: bigmemory] | Cores 2/2 To enable shared memory capabilities, try: install.extras(' NMF ') Attaching package: 'NMF' The following object is masked from 'package:S4Vectors': nrun The following object is masked from 'package:testthat': compare > > test_check("MutationalPatterns") [ FAIL 0 | WARN 5 | SKIP 0 | PASS 474 ] [ FAIL 0 | WARN 5 | SKIP 0 | PASS 474 ] > > proc.time() user system elapsed 238.735 9.937 254.820
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
name | user | system | elapsed | |
bin_mutation_density | 10.350 | 0.620 | 10.971 | |
binomial_test | 0.010 | 0.000 | 0.009 | |
calculate_lesion_segregation | 10.517 | 0.212 | 10.730 | |
cluster_signatures | 0.047 | 0.000 | 0.047 | |
context_potential_damage_analysis | 27.247 | 0.584 | 27.832 | |
convert_sigs_to_ref | 0.041 | 0.000 | 0.045 | |
cos_sim | 0 | 0 | 0 | |
cos_sim_matrix | 0.02 | 0.00 | 0.02 | |
count_dbs_contexts | 0.110 | 0.000 | 0.111 | |
count_indel_contexts | 0.113 | 0.000 | 0.114 | |
count_mbs_contexts | 0.081 | 0.000 | 0.080 | |
determine_regional_similarity | 3.095 | 0.140 | 3.234 | |
enrichment_depletion_test | 0.149 | 0.000 | 0.149 | |
extract_signatures | 0.002 | 0.000 | 0.001 | |
fit_to_signatures | 0.097 | 0.000 | 0.097 | |
fit_to_signatures_bootstrapped | 5.923 | 0.092 | 6.014 | |
fit_to_signatures_strict | 3.345 | 0.004 | 3.350 | |
genomic_distribution | 11.416 | 0.228 | 11.646 | |
get_dbs_context | 0.316 | 0.008 | 0.325 | |
get_indel_context | 7.362 | 0.320 | 7.683 | |
get_known_signatures | 0.283 | 0.096 | 0.380 | |
get_mut_type | 13.852 | 0.063 | 13.915 | |
lengthen_mut_matrix | 0.012 | 0.001 | 0.012 | |
merge_signatures | 1.094 | 0.056 | 1.150 | |
mut_context | 1.244 | 0.052 | 1.296 | |
mut_matrix | 2.141 | 0.144 | 2.285 | |
mut_matrix_stranded | 4.464 | 0.156 | 4.621 | |
mut_strand | 1.138 | 0.024 | 1.162 | |
mut_type | 0.027 | 0.004 | 0.031 | |
mut_type_occurrences | 0.935 | 0.060 | 0.995 | |
mutations_from_vcf | 0.03 | 0.00 | 0.03 | |
plot_192_profile | 3.213 | 0.008 | 3.221 | |
plot_96_profile | 2.567 | 0.032 | 2.599 | |
plot_bootstrapped_contribution | 2.039 | 0.012 | 2.051 | |
plot_compare_dbs | 5.072 | 0.024 | 5.096 | |
plot_compare_indels | 9.088 | 0.052 | 9.140 | |
plot_compare_mbs | 0.901 | 0.000 | 0.901 | |
plot_compare_profiles | 2.33 | 0.00 | 2.33 | |
plot_contribution | 4.533 | 0.220 | 4.752 | |
plot_contribution_heatmap | 1.709 | 0.008 | 1.718 | |
plot_correlation_bootstrap | 0.521 | 0.000 | 0.521 | |
plot_cosine_heatmap | 2.015 | 0.015 | 2.031 | |
plot_dbs_contexts | 3.995 | 0.020 | 4.015 | |
plot_enrichment_depletion | 4.125 | 0.008 | 4.135 | |
plot_indel_contexts | 8.283 | 0.032 | 8.315 | |
plot_lesion_segregation | 15.146 | 0.028 | 15.175 | |
plot_main_dbs_contexts | 0.593 | 0.004 | 0.596 | |
plot_main_indel_contexts | 0.617 | 0.040 | 0.657 | |
plot_mbs_contexts | 0.605 | 0.008 | 0.613 | |
plot_original_vs_reconstructed | 0.599 | 0.000 | 0.599 | |
plot_profile_heatmap | 5.855 | 0.076 | 5.931 | |
plot_profile_region | 1.319 | 0.044 | 1.363 | |
plot_rainfall | 2.330 | 0.008 | 2.338 | |
plot_regional_similarity | 1.796 | 0.000 | 1.796 | |
plot_river | 6.272 | 0.191 | 6.467 | |
plot_signature_strand_bias | 0.885 | 0.005 | 0.890 | |
plot_spectrum | 5.070 | 0.063 | 5.134 | |
plot_spectrum_region | 6.333 | 0.033 | 6.365 | |
plot_strand | 0.277 | 0.000 | 0.277 | |
plot_strand_bias | 0.916 | 0.000 | 0.916 | |
pool_mut_mat | 0.04 | 0.00 | 0.04 | |
read_vcfs_as_granges | 27.950 | 3.120 | 33.388 | |
rename_nmf_signatures | 0.057 | 0.008 | 0.065 | |
signature_potential_damage_analysis | 0.169 | 0.016 | 0.185 | |
split_muts_region | 5.121 | 0.456 | 5.577 | |
strand_bias_test | 0.149 | 0.020 | 0.169 | |
strand_occurrences | 0.200 | 0.024 | 0.225 | |
type_context | 1.543 | 0.204 | 1.747 | |