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This page was generated on 2023-04-12 10:55:39 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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CHECK results for MutationalPatterns on nebbiolo2


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.

raw results

Package 1333/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.9.1  (landing page)
Mark van Roosmalen
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/MutationalPatterns
git_branch: devel
git_last_commit: b8898d2
git_last_commit_date: 2023-01-11 01:57:43 -0400 (Wed, 11 Jan 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    ERROR  

Summary

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

Command output

##############################################################################
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###
### 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.


Installation output

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)

Tests output

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 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density10.350 0.62010.971
binomial_test0.0100.0000.009
calculate_lesion_segregation10.517 0.21210.730
cluster_signatures0.0470.0000.047
context_potential_damage_analysis27.247 0.58427.832
convert_sigs_to_ref0.0410.0000.045
cos_sim000
cos_sim_matrix0.020.000.02
count_dbs_contexts0.1100.0000.111
count_indel_contexts0.1130.0000.114
count_mbs_contexts0.0810.0000.080
determine_regional_similarity3.0950.1403.234
enrichment_depletion_test0.1490.0000.149
extract_signatures0.0020.0000.001
fit_to_signatures0.0970.0000.097
fit_to_signatures_bootstrapped5.9230.0926.014
fit_to_signatures_strict3.3450.0043.350
genomic_distribution11.416 0.22811.646
get_dbs_context0.3160.0080.325
get_indel_context7.3620.3207.683
get_known_signatures0.2830.0960.380
get_mut_type13.852 0.06313.915
lengthen_mut_matrix0.0120.0010.012
merge_signatures1.0940.0561.150
mut_context1.2440.0521.296
mut_matrix2.1410.1442.285
mut_matrix_stranded4.4640.1564.621
mut_strand1.1380.0241.162
mut_type0.0270.0040.031
mut_type_occurrences0.9350.0600.995
mutations_from_vcf0.030.000.03
plot_192_profile3.2130.0083.221
plot_96_profile2.5670.0322.599
plot_bootstrapped_contribution2.0390.0122.051
plot_compare_dbs5.0720.0245.096
plot_compare_indels9.0880.0529.140
plot_compare_mbs0.9010.0000.901
plot_compare_profiles2.330.002.33
plot_contribution4.5330.2204.752
plot_contribution_heatmap1.7090.0081.718
plot_correlation_bootstrap0.5210.0000.521
plot_cosine_heatmap2.0150.0152.031
plot_dbs_contexts3.9950.0204.015
plot_enrichment_depletion4.1250.0084.135
plot_indel_contexts8.2830.0328.315
plot_lesion_segregation15.146 0.02815.175
plot_main_dbs_contexts0.5930.0040.596
plot_main_indel_contexts0.6170.0400.657
plot_mbs_contexts0.6050.0080.613
plot_original_vs_reconstructed0.5990.0000.599
plot_profile_heatmap5.8550.0765.931
plot_profile_region1.3190.0441.363
plot_rainfall2.3300.0082.338
plot_regional_similarity1.7960.0001.796
plot_river6.2720.1916.467
plot_signature_strand_bias0.8850.0050.890
plot_spectrum5.0700.0635.134
plot_spectrum_region6.3330.0336.365
plot_strand0.2770.0000.277
plot_strand_bias0.9160.0000.916
pool_mut_mat0.040.000.04
read_vcfs_as_granges27.950 3.12033.388
rename_nmf_signatures0.0570.0080.065
signature_potential_damage_analysis0.1690.0160.185
split_muts_region5.1210.4565.577
strand_bias_test0.1490.0200.169
strand_occurrences0.2000.0240.225
type_context1.5430.2041.747