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This page was generated on 2022-04-13 12:06:58 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 tokay2


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? 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 1256/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.4.1  (landing page)
Mark van Roosmalen
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/MutationalPatterns
git_branch: RELEASE_3_14
git_last_commit: 7ee7100
git_last_commit_date: 2022-02-14 05:44:44 -0400 (Mon, 14 Feb 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MutationalPatterns
Version: 3.4.1
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MutationalPatterns.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MutationalPatterns_3.4.1.tar.gz
StartedAt: 2022-04-12 23:30:51 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 23:52:35 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 1304.0 seconds
RetCode: 0
Status:   OK  
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MutationalPatterns.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MutationalPatterns_3.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MutationalPatterns.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '3.4.1'
* 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  5.1Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
read_vcfs_as_granges              28.73   0.98   60.06
context_potential_damage_analysis 26.33   0.33   26.65
get_mut_type                      22.06   0.00   22.11
calculate_lesion_segregation      15.52   0.39   15.91
genomic_distribution              14.06   0.53   52.16
plot_lesion_segregation           13.71   0.03   13.73
get_indel_context                  9.24   0.80   10.15
bin_mutation_density               8.29   0.99    9.41
fit_to_signatures_bootstrapped     7.58   0.36    7.93
plot_indel_contexts                6.76   0.00    6.77
plot_compare_indels                6.48   0.00    6.48
mut_matrix_stranded                5.45   0.26    5.73
plot_spectrum_region               4.63   0.14   14.36
plot_regional_similarity           1.64   0.02    7.49
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
read_vcfs_as_granges              28.27   1.06   31.50
context_potential_damage_analysis 28.09   0.47   28.57
get_mut_type                      22.39   0.00   22.39
calculate_lesion_segregation      17.61   0.18   17.80
plot_lesion_segregation           15.14   0.00   15.14
genomic_distribution              12.37   0.43   12.79
bin_mutation_density              11.78   0.29   12.06
get_indel_context                  8.73   0.67    9.40
mut_matrix_stranded                7.01   0.31    7.33
plot_indel_contexts                7.05   0.00    7.05
plot_compare_indels                6.62   0.00    6.63
fit_to_signatures_bootstrapped     5.71   0.01    5.71
plot_river                         5.33   0.03    5.36
plot_spectrum                      5.10   0.09    5.18
plot_spectrum_region               5.07   0.07    5.14
plot_profile_heatmap               5.03   0.01    5.04
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/MutationalPatterns.Rcheck/00check.log'
for details.



Installation output

MutationalPatterns.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MutationalPatterns_3.4.1.tar.gz && rm -rf MutationalPatterns.buildbin-libdir && mkdir MutationalPatterns.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MutationalPatterns.buildbin-libdir MutationalPatterns_3.4.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MutationalPatterns_3.4.1.zip && rm MutationalPatterns_3.4.1.tar.gz MutationalPatterns_3.4.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 43 2124k   43  925k    0     0  1362k      0  0:00:01 --:--:--  0:00:01 1362k
100 2124k  100 2124k    0     0  1709k      0  0:00:01  0:00:01 --:--:-- 1710k

install for i386

* 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

install for x64

* installing *source* package 'MutationalPatterns' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MutationalPatterns' as MutationalPatterns_3.4.1.zip
* DONE (MutationalPatterns)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MutationalPatterns' successfully unpacked and MD5 sums checked

Tests output

MutationalPatterns.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 39/40

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 
 247.68   10.04  264.35 

MutationalPatterns.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 39/40

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 
 264.14    7.67  278.23 

Example timings

MutationalPatterns.Rcheck/examples_i386/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density8.290.999.41
binomial_test0.020.000.02
calculate_lesion_segregation15.52 0.3915.91
cluster_signatures0.090.000.10
context_potential_damage_analysis26.33 0.3326.65
convert_sigs_to_ref0.090.000.19
cos_sim0.020.000.02
cos_sim_matrix0.030.010.04
count_dbs_contexts0.230.000.25
count_indel_contexts0.270.000.29
count_mbs_contexts0.170.000.18
determine_regional_similarity4.560.274.83
enrichment_depletion_test0.220.000.22
extract_signatures000
fit_to_signatures0.140.120.27
fit_to_signatures_bootstrapped7.580.367.93
fit_to_signatures_strict3.330.003.33
genomic_distribution14.06 0.5352.16
get_dbs_context0.420.020.43
get_indel_context 9.24 0.8010.15
get_known_signatures0.720.151.46
get_mut_type22.06 0.0022.11
lengthen_mut_matrix0.010.000.02
merge_signatures1.520.051.56
mut_context1.330.161.48
mut_matrix2.600.172.77
mut_matrix_stranded5.450.265.73
mut_strand1.220.001.22
mut_type0.050.000.04
mut_type_occurrences1.300.051.35
mutations_from_vcf0.060.000.06
plot_192_profile2.660.002.69
plot_96_profile2.090.002.09
plot_bootstrapped_contribution1.630.021.64
plot_compare_dbs4.250.014.27
plot_compare_indels6.480.006.48
plot_compare_mbs0.690.000.69
plot_compare_profiles1.560.021.58
plot_contribution2.480.002.68
plot_contribution_heatmap1.820.002.05
plot_correlation_bootstrap0.420.000.42
plot_cosine_heatmap1.890.011.90
plot_dbs_contexts3.130.003.13
plot_enrichment_depletion2.940.022.95
plot_indel_contexts6.760.006.77
plot_lesion_segregation13.71 0.0313.73
plot_main_dbs_contexts0.400.000.41
plot_main_indel_contexts0.460.000.46
plot_mbs_contexts0.370.000.37
plot_original_vs_reconstructed0.380.000.38
plot_profile_heatmap4.120.004.44
plot_profile_region0.830.010.84
plot_rainfall2.090.002.09
plot_regional_similarity1.640.027.49
plot_river4.240.014.25
plot_signature_strand_bias0.560.000.56
plot_spectrum3.730.143.87
plot_spectrum_region 4.63 0.1414.36
plot_strand0.250.000.25
plot_strand_bias0.840.020.86
pool_mut_mat0.050.000.05
read_vcfs_as_granges28.73 0.9860.06
rename_nmf_signatures0.050.000.05
signature_potential_damage_analysis0.130.000.12
split_muts_region4.540.024.57
strand_bias_test0.190.000.18
strand_occurrences0.160.000.16
type_context1.570.141.72

MutationalPatterns.Rcheck/examples_x64/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density11.78 0.2912.06
binomial_test0.010.000.01
calculate_lesion_segregation17.61 0.1817.80
cluster_signatures0.050.000.05
context_potential_damage_analysis28.09 0.4728.57
convert_sigs_to_ref0.050.000.04
cos_sim000
cos_sim_matrix0.010.000.02
count_dbs_contexts0.130.000.12
count_indel_contexts0.150.000.16
count_mbs_contexts0.110.000.11
determine_regional_similarity4.270.254.52
enrichment_depletion_test0.160.000.15
extract_signatures000
fit_to_signatures0.070.020.10
fit_to_signatures_bootstrapped5.710.015.71
fit_to_signatures_strict3.030.003.04
genomic_distribution12.37 0.4312.79
get_dbs_context0.440.000.44
get_indel_context8.730.679.40
get_known_signatures0.380.110.49
get_mut_type22.39 0.0022.39
lengthen_mut_matrix0.020.000.02
merge_signatures1.230.041.28
mut_context1.440.141.58
mut_matrix2.910.273.17
mut_matrix_stranded7.010.317.33
mut_strand1.170.021.18
mut_type0.050.000.05
mut_type_occurrences1.160.111.27
mutations_from_vcf0.050.000.05
plot_192_profile2.550.002.55
plot_96_profile2.450.032.48
plot_bootstrapped_contribution1.670.001.67
plot_compare_dbs4.220.004.22
plot_compare_indels6.620.006.63
plot_compare_mbs0.740.000.73
plot_compare_profiles2.280.002.28
plot_contribution2.840.002.85
plot_contribution_heatmap1.570.031.59
plot_correlation_bootstrap0.420.020.44
plot_cosine_heatmap1.890.011.90
plot_dbs_contexts3.390.003.39
plot_enrichment_depletion3.110.023.13
plot_indel_contexts7.050.007.05
plot_lesion_segregation15.14 0.0015.14
plot_main_dbs_contexts0.540.000.54
plot_main_indel_contexts0.580.000.58
plot_mbs_contexts0.470.000.47
plot_original_vs_reconstructed0.440.000.44
plot_profile_heatmap5.030.015.04
plot_profile_region1.010.001.02
plot_rainfall2.540.022.55
plot_regional_similarity1.430.001.43
plot_river5.330.035.36
plot_signature_strand_bias0.780.000.79
plot_spectrum5.100.095.18
plot_spectrum_region5.070.075.14
plot_strand0.220.000.22
plot_strand_bias0.690.000.69
pool_mut_mat0.030.000.03
read_vcfs_as_granges28.27 1.0631.50
rename_nmf_signatures0.030.010.05
signature_potential_damage_analysis0.120.000.12
split_muts_region4.470.024.48
strand_bias_test0.150.000.16
strand_occurrences0.160.010.17
type_context1.860.152.00