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This page was generated on 2022-01-24 11:07:54 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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

CHECK results for MutationalPatterns on riesling1


To the developers/maintainers of the MutationalPatterns package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1250/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.5.1  (landing page)
Mark van Roosmalen
Snapshot Date: 2022-01-23 13:55:15 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/MutationalPatterns
git_branch: master
git_last_commit: e3da76a
git_last_commit_date: 2021-11-03 09:56:47 -0500 (Wed, 03 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MutationalPatterns
Version: 3.5.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MutationalPatterns_3.5.1.tar.gz
StartedAt: 2022-01-23 19:32:27 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 19:40:40 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 493.1 seconds
RetCode: 0
Status:   OK  
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MutationalPatterns_3.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MutationalPatterns.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MutationalPatterns/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MutationalPatterns' version '3.5.1'
* 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 whether package 'MutationalPatterns' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   2.5Mb
    states    1.3Mb
* 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 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
context_potential_damage_analysis 22.13   0.44   22.56
read_vcfs_as_granges              17.87   0.95   27.83
get_mut_type                      10.66   0.00   10.66
plot_lesion_segregation           10.17   0.02   10.19
genomic_distribution               8.28   0.78    9.06
calculate_lesion_segregation       8.59   0.21    8.80
bin_mutation_density               7.36   0.34    7.70
get_indel_context                  6.28   0.68    6.95
plot_indel_contexts                5.31   0.00    5.31
plot_compare_indels                5.09   0.02    5.11
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/MutationalPatterns.Rcheck/00check.log'
for details.



Installation output

MutationalPatterns.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MutationalPatterns
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MutationalPatterns' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MutationalPatterns'
    finding HTML links ... done
    MutationalPatterns-defunct              html  
    MutationalPatterns-package              html  
    bin_mutation_density                    html  
    binomial_test                           html  
    calculate_lesion_segregation            html  
    cluster_signatures                      html  
    context_potential_damage_analysis       html  
    convert_sigs_to_ref                     html  
    cos_sim                                 html  
    cos_sim_matrix                          html  
    count_dbs_contexts                      html  
    count_indel_contexts                    html  
    count_mbs_contexts                      html  
    determine_regional_similarity           html  
    enrichment_depletion_test               html  
    extract_signatures                      html  
    fit_to_signatures                       html  
    fit_to_signatures_bootstrapped          html  
    fit_to_signatures_strict                html  
    genomic_distribution                    html  
    get_dbs_context                         html  
    get_indel_context                       html  
    get_known_signatures                    html  
    get_mut_type                            html  
    get_sim_tb                              html  
    lengthen_mut_matrix                     html  
    merge_signatures                        html  
    mut_192_occurrences                     html  
    mut_96_occurrences                      html  
    mut_context                             html  
    mut_matrix                              html  
    mut_matrix_stranded                     html  
    mut_strand                              html  
    mut_type                                html  
    mut_type_occurrences                    html  
    mutations_from_vcf                      html  
    plot_192_profile                        html  
    plot_96_profile                         html  
    plot_bootstrapped_contribution          html  
    plot_compare_dbs                        html  
    plot_compare_indels                     html  
    plot_compare_mbs                        html  
    plot_compare_profiles                   html  
    plot_contribution                       html  
    plot_contribution_heatmap               html  
    plot_correlation_bootstrap              html  
    plot_cosine_heatmap                     html  
    plot_dbs_contexts                       html  
    plot_enrichment_depletion               html  
    plot_indel_contexts                     html  
    plot_lesion_segregation                 html  
    plot_main_dbs_contexts                  html  
    plot_main_indel_contexts                html  
    plot_mbs_contexts                       html  
    plot_original_vs_reconstructed          html  
    plot_profile_heatmap                    html  
    plot_profile_region                     html  
    plot_rainfall                           html  
    plot_regional_similarity                html  
    plot_river                              html  
    plot_signature_strand_bias              html  
    plot_spectrum                           html  
    plot_spectrum_region                    html  
    plot_strand                             html  
    plot_strand_bias                        html  
    pool_mut_mat                            html  
    read_vcfs_as_granges                    html  
    region_cossim-class                     html  
    rename_nmf_signatures                   html  
    show-region_cossim-method               html  
    signature_potential_damage_analysis     html  
    split_muts_region                       html  
    strand_bias_test                        html  
    strand_occurrences                      html  
    type_context                            html  
** 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)
Making 'packages.html' ... done

Tests output

MutationalPatterns.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: NMF
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:S4Vectors':

    new2

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 79/80

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 0 | SKIP 0 | PASS 470 ]
> 
> proc.time()
   user  system elapsed 
 155.98   10.21  191.54 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density7.360.347.70
binomial_test000
calculate_lesion_segregation8.590.218.80
cluster_signatures0.050.000.05
context_potential_damage_analysis22.13 0.4422.56
convert_sigs_to_ref0.050.000.04
cos_sim000
cos_sim_matrix0.010.010.03
count_dbs_contexts0.070.000.07
count_indel_contexts0.070.000.07
count_mbs_contexts0.070.000.07
determine_regional_similarity2.120.342.47
enrichment_depletion_test0.110.000.10
extract_signatures000
fit_to_signatures0.060.020.08
fit_to_signatures_bootstrapped4.100.164.25
fit_to_signatures_strict2.840.012.86
genomic_distribution8.280.789.06
get_dbs_context0.220.030.25
get_indel_context6.280.686.95
get_known_signatures0.450.200.66
get_mut_type10.66 0.0010.66
lengthen_mut_matrix000
merge_signatures0.840.060.90
mut_context0.660.280.94
mut_matrix1.610.181.78
mut_matrix_stranded3.070.563.64
mut_strand0.830.030.86
mut_type0.030.000.03
mut_type_occurrences0.690.140.83
mutations_from_vcf0.020.000.02
plot_192_profile1.780.021.79
plot_96_profile1.560.001.57
plot_bootstrapped_contribution1.250.031.28
plot_compare_dbs2.940.012.95
plot_compare_indels5.090.025.11
plot_compare_mbs0.560.000.56
plot_compare_profiles1.250.001.25
plot_contribution1.830.001.83
plot_contribution_heatmap1.070.011.08
plot_correlation_bootstrap0.280.000.28
plot_cosine_heatmap1.260.021.28
plot_dbs_contexts2.240.002.23
plot_enrichment_depletion2.170.032.21
plot_indel_contexts5.310.005.31
plot_lesion_segregation10.17 0.0210.19
plot_main_dbs_contexts0.550.000.54
plot_main_indel_contexts0.370.000.38
plot_mbs_contexts0.410.000.41
plot_original_vs_reconstructed0.330.030.36
plot_profile_heatmap3.910.063.96
plot_profile_region0.760.000.77
plot_rainfall1.410.001.41
plot_regional_similarity1.140.001.14
plot_river4.200.094.30
plot_signature_strand_bias0.580.000.58
plot_spectrum3.810.143.95
plot_spectrum_region3.970.084.05
plot_strand0.170.020.19
plot_strand_bias0.690.000.69
pool_mut_mat0.050.000.04
read_vcfs_as_granges17.87 0.9527.83
rename_nmf_signatures0.050.020.07
signature_potential_damage_analysis0.120.000.12
split_muts_region4.500.014.52
strand_bias_test0.100.000.09
strand_occurrences0.230.000.23
type_context1.360.191.55