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CHECK report for MutationalPatterns on tokay1

This page was generated on 2021-05-06 12:32:25 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the MutationalPatterns package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1189/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.0.1  (landing page)
Rurika Oka
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/MutationalPatterns
Branch: RELEASE_3_12
Last Commit: 72983a7
Last Changed Date: 2020-11-12 05:21:39 -0400 (Thu, 12 Nov 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: MutationalPatterns
Version: 3.0.1
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MutationalPatterns.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MutationalPatterns_3.0.1.tar.gz
StartedAt: 2021-05-06 04:57:46 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:27:55 -0400 (Thu, 06 May 2021)
EllapsedTime: 1808.5 seconds
RetCode: 0
Status:   OK   
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MutationalPatterns.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MutationalPatterns_3.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MutationalPatterns.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '3.0.1'
* 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  5.4Mb
  sub-directories of 1Mb or more:
    extdata   3.2Mb
    states    1.2Mb
* 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
context_potential_damage_analysis 66.66   0.72   68.99
calculate_lesion_segregation      63.93   0.95   64.87
read_vcfs_as_granges              30.48   0.97   33.63
fit_to_signatures_bootstrapped    30.75   0.18   30.92
get_mut_type                      22.25   0.01   22.26
genomic_distribution              15.98   0.45   19.64
bin_mutation_density               8.31   0.97    9.28
mut_matrix_stranded                8.66   0.40    9.08
plot_indel_contexts                8.65   0.01    8.66
plot_compare_indels                7.34   0.00    7.34
split_muts_region                  6.14   0.08    6.22
plot_river                         6.11   0.07    6.19
get_indel_context                  5.33   0.50    5.83
plot_lesion_segregation            5.62   0.00    5.63
plot_spectrum_region               5.49   0.13    5.61
plot_profile_heatmap               5.28   0.00    5.29
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
calculate_lesion_segregation      70.97   0.89   71.86
context_potential_damage_analysis 63.65   0.45   65.84
read_vcfs_as_granges              28.69   1.15   31.70
fit_to_signatures_bootstrapped    26.20   0.02   26.22
get_mut_type                      21.08   0.00   21.07
genomic_distribution              14.95   0.48   15.44
plot_indel_contexts               11.43   0.00   11.44
bin_mutation_density              10.51   0.33   10.85
plot_lesion_segregation           10.28   0.02   10.30
plot_river                         8.09   0.01    8.11
plot_profile_heatmap               7.16   0.00    7.15
plot_compare_indels                7.11   0.00    7.11
plot_compare_dbs                   7.03   0.00    7.03
mut_matrix_stranded                6.61   0.36    6.97
plot_spectrum                      6.30   0.21    6.50
get_indel_context                  5.92   0.58    6.50
plot_spectrum_region               5.34   0.11    5.45
split_muts_region                  5.22   0.11    5.33
plot_enrichment_depletion          5.21   0.02    5.22
plot_dbs_contexts                  5.22   0.00    5.22
* 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-3.12-bioc/meat/MutationalPatterns.Rcheck/00check.log'
for details.



Installation output

MutationalPatterns.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/MutationalPatterns_3.0.1.tar.gz && rm -rf MutationalPatterns.buildbin-libdir && mkdir MutationalPatterns.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MutationalPatterns.buildbin-libdir MutationalPatterns_3.0.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL MutationalPatterns_3.0.1.zip && rm MutationalPatterns_3.0.1.tar.gz MutationalPatterns_3.0.1.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
100 2176k  100 2176k    0     0  46.3M      0 --:--:-- --:--:-- --:--:-- 47.2M

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  
    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  
    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_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  
    rename_nmf_signatures                   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_3.0.1.zip
* DONE (MutationalPatterns)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'MutationalPatterns' successfully unpacked and MD5 sums checked

Tests output

MutationalPatterns.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 object is masked from 'package:base':

    expand.grid

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 408 ]
> 
> proc.time()
   user  system elapsed 
 345.37    9.96  363.81 

MutationalPatterns.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 object is masked from 'package:base':

    expand.grid

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 408 ]
> 
> proc.time()
   user  system elapsed 
 413.84    8.92  456.48 

Example timings

MutationalPatterns.Rcheck/examples_i386/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density8.310.979.28
binomial_test000
calculate_lesion_segregation63.93 0.9564.87
cluster_signatures0.060.020.07
context_potential_damage_analysis66.66 0.7268.99
convert_sigs_to_ref0.040.000.07
cos_sim000
cos_sim_matrix0.020.000.01
count_dbs_contexts0.130.000.12
count_indel_contexts0.210.000.20
count_mbs_contexts0.110.000.11
enrichment_depletion_test0.170.000.17
extract_signatures000
fit_to_signatures0.140.120.27
fit_to_signatures_bootstrapped30.75 0.1830.92
fit_to_signatures_strict3.910.003.91
genomic_distribution15.98 0.4519.64
get_dbs_context0.390.000.39
get_indel_context5.330.505.83
get_known_signatures0.470.160.67
get_mut_type22.25 0.0122.26
lengthen_mut_matrix0.030.000.03
merge_signatures1.220.021.24
mut_context1.590.261.86
mut_matrix3.170.163.33
mut_matrix_stranded8.660.409.08
mut_strand1.170.041.20
mut_type0.030.000.03
mut_type_occurrences1.070.151.22
mutations_from_vcf0.050.000.05
plot_192_profile2.560.002.56
plot_96_profile2.140.002.14
plot_bootstrapped_contribution2.210.022.22
plot_compare_dbs4.340.004.35
plot_compare_indels7.340.007.34
plot_compare_mbs1.160.001.16
plot_compare_profiles2.310.012.33
plot_contribution3.330.003.32
plot_contribution_heatmap1.620.001.63
plot_correlation_bootstrap0.570.000.56
plot_cosine_heatmap2.180.022.20
plot_dbs_contexts4.630.004.63
plot_enrichment_depletion4.350.004.36
plot_indel_contexts8.650.018.66
plot_lesion_segregation5.620.005.63
plot_main_dbs_contexts0.440.020.45
plot_main_indel_contexts0.540.000.55
plot_mbs_contexts0.430.000.42
plot_original_vs_reconstructed0.530.000.53
plot_profile_heatmap5.280.005.29
plot_profile_region1.070.001.06
plot_rainfall1.000.021.01
plot_river6.110.076.19
plot_signature_strand_bias0.790.000.80
plot_spectrum4.280.114.39
plot_spectrum_region5.490.135.61
plot_strand0.190.010.20
plot_strand_bias0.720.000.72
pool_mut_mat0.030.000.03
read_vcfs_as_granges30.48 0.9733.63
rename_nmf_signatures0.060.000.06
signature_potential_damage_analysis0.180.000.17
split_muts_region6.140.086.22
strand_bias_test0.180.000.19
strand_occurrences0.320.000.31
type_context2.110.222.47

MutationalPatterns.Rcheck/examples_x64/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density10.51 0.3310.85
binomial_test000
calculate_lesion_segregation70.97 0.8971.86
cluster_signatures0.050.020.06
context_potential_damage_analysis63.65 0.4565.84
convert_sigs_to_ref0.050.000.05
cos_sim000
cos_sim_matrix0.030.000.03
count_dbs_contexts0.10.00.1
count_indel_contexts0.110.000.11
count_mbs_contexts0.110.000.10
enrichment_depletion_test0.140.000.15
extract_signatures000
fit_to_signatures0.100.000.09
fit_to_signatures_bootstrapped26.20 0.0226.22
fit_to_signatures_strict2.870.002.88
genomic_distribution14.95 0.4815.44
get_dbs_context0.520.000.52
get_indel_context5.920.586.50
get_known_signatures0.250.110.36
get_mut_type21.08 0.0021.07
lengthen_mut_matrix0.010.000.02
merge_signatures0.860.030.89
mut_context1.490.161.66
mut_matrix2.620.312.93
mut_matrix_stranded6.610.366.97
mut_strand1.200.011.22
mut_type0.040.000.03
mut_type_occurrences1.110.141.25
mutations_from_vcf0.020.000.01
plot_192_profile2.810.002.82
plot_96_profile2.410.002.40
plot_bootstrapped_contribution2.030.032.06
plot_compare_dbs7.030.007.03
plot_compare_indels7.110.007.11
plot_compare_mbs0.720.000.72
plot_compare_profiles2.50.02.5
plot_contribution3.360.003.36
plot_contribution_heatmap2.560.002.56
plot_correlation_bootstrap0.720.000.72
plot_cosine_heatmap2.90.02.9
plot_dbs_contexts5.220.005.22
plot_enrichment_depletion5.210.025.22
plot_indel_contexts11.43 0.0011.44
plot_lesion_segregation10.28 0.0210.30
plot_main_dbs_contexts0.830.000.82
plot_main_indel_contexts0.940.000.94
plot_mbs_contexts0.890.000.89
plot_original_vs_reconstructed0.890.010.91
plot_profile_heatmap7.160.007.15
plot_profile_region1.360.001.36
plot_rainfall1.340.021.36
plot_river8.090.018.11
plot_signature_strand_bias0.860.000.86
plot_spectrum6.300.216.50
plot_spectrum_region5.340.115.45
plot_strand0.230.000.23
plot_strand_bias0.880.000.88
pool_mut_mat0.030.000.03
read_vcfs_as_granges28.69 1.1531.70
rename_nmf_signatures0.060.000.07
signature_potential_damage_analysis0.140.020.15
split_muts_region5.220.115.33
strand_bias_test0.180.000.18
strand_occurrences0.220.000.22
type_context1.600.171.77