Multiple platform build/check report for BioC 3.14 - CHECK results for MutationalPatterns on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (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*

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

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###
### 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
###
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* 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.

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


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 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


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


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

name	user	system	elapsed
bin_mutation_density	8.29	0.99	9.41
binomial_test	0.02	0.00	0.02
calculate_lesion_segregation	15.52	0.39	15.91
cluster_signatures	0.09	0.00	0.10
context_potential_damage_analysis	26.33	0.33	26.65
convert_sigs_to_ref	0.09	0.00	0.19
cos_sim	0.02	0.00	0.02
cos_sim_matrix	0.03	0.01	0.04
count_dbs_contexts	0.23	0.00	0.25
count_indel_contexts	0.27	0.00	0.29
count_mbs_contexts	0.17	0.00	0.18
determine_regional_similarity	4.56	0.27	4.83
enrichment_depletion_test	0.22	0.00	0.22
extract_signatures	0	0	0
fit_to_signatures	0.14	0.12	0.27
fit_to_signatures_bootstrapped	7.58	0.36	7.93
fit_to_signatures_strict	3.33	0.00	3.33
genomic_distribution	14.06	0.53	52.16
get_dbs_context	0.42	0.02	0.43
get_indel_context	9.24	0.80	10.15
get_known_signatures	0.72	0.15	1.46
get_mut_type	22.06	0.00	22.11
lengthen_mut_matrix	0.01	0.00	0.02
merge_signatures	1.52	0.05	1.56
mut_context	1.33	0.16	1.48
mut_matrix	2.60	0.17	2.77
mut_matrix_stranded	5.45	0.26	5.73
mut_strand	1.22	0.00	1.22
mut_type	0.05	0.00	0.04
mut_type_occurrences	1.30	0.05	1.35
mutations_from_vcf	0.06	0.00	0.06
plot_192_profile	2.66	0.00	2.69
plot_96_profile	2.09	0.00	2.09
plot_bootstrapped_contribution	1.63	0.02	1.64
plot_compare_dbs	4.25	0.01	4.27
plot_compare_indels	6.48	0.00	6.48
plot_compare_mbs	0.69	0.00	0.69
plot_compare_profiles	1.56	0.02	1.58
plot_contribution	2.48	0.00	2.68
plot_contribution_heatmap	1.82	0.00	2.05
plot_correlation_bootstrap	0.42	0.00	0.42
plot_cosine_heatmap	1.89	0.01	1.90
plot_dbs_contexts	3.13	0.00	3.13
plot_enrichment_depletion	2.94	0.02	2.95
plot_indel_contexts	6.76	0.00	6.77
plot_lesion_segregation	13.71	0.03	13.73
plot_main_dbs_contexts	0.40	0.00	0.41
plot_main_indel_contexts	0.46	0.00	0.46
plot_mbs_contexts	0.37	0.00	0.37
plot_original_vs_reconstructed	0.38	0.00	0.38
plot_profile_heatmap	4.12	0.00	4.44
plot_profile_region	0.83	0.01	0.84
plot_rainfall	2.09	0.00	2.09
plot_regional_similarity	1.64	0.02	7.49
plot_river	4.24	0.01	4.25
plot_signature_strand_bias	0.56	0.00	0.56
plot_spectrum	3.73	0.14	3.87
plot_spectrum_region	4.63	0.14	14.36
plot_strand	0.25	0.00	0.25
plot_strand_bias	0.84	0.02	0.86
pool_mut_mat	0.05	0.00	0.05
read_vcfs_as_granges	28.73	0.98	60.06
rename_nmf_signatures	0.05	0.00	0.05
signature_potential_damage_analysis	0.13	0.00	0.12
split_muts_region	4.54	0.02	4.57
strand_bias_test	0.19	0.00	0.18
strand_occurrences	0.16	0.00	0.16
type_context	1.57	0.14	1.72

name	user	system	elapsed
bin_mutation_density	11.78	0.29	12.06
binomial_test	0.01	0.00	0.01
calculate_lesion_segregation	17.61	0.18	17.80
cluster_signatures	0.05	0.00	0.05
context_potential_damage_analysis	28.09	0.47	28.57
convert_sigs_to_ref	0.05	0.00	0.04
cos_sim	0	0	0
cos_sim_matrix	0.01	0.00	0.02
count_dbs_contexts	0.13	0.00	0.12
count_indel_contexts	0.15	0.00	0.16
count_mbs_contexts	0.11	0.00	0.11
determine_regional_similarity	4.27	0.25	4.52
enrichment_depletion_test	0.16	0.00	0.15
extract_signatures	0	0	0
fit_to_signatures	0.07	0.02	0.10
fit_to_signatures_bootstrapped	5.71	0.01	5.71
fit_to_signatures_strict	3.03	0.00	3.04
genomic_distribution	12.37	0.43	12.79
get_dbs_context	0.44	0.00	0.44
get_indel_context	8.73	0.67	9.40
get_known_signatures	0.38	0.11	0.49
get_mut_type	22.39	0.00	22.39
lengthen_mut_matrix	0.02	0.00	0.02
merge_signatures	1.23	0.04	1.28
mut_context	1.44	0.14	1.58
mut_matrix	2.91	0.27	3.17
mut_matrix_stranded	7.01	0.31	7.33
mut_strand	1.17	0.02	1.18
mut_type	0.05	0.00	0.05
mut_type_occurrences	1.16	0.11	1.27
mutations_from_vcf	0.05	0.00	0.05
plot_192_profile	2.55	0.00	2.55
plot_96_profile	2.45	0.03	2.48
plot_bootstrapped_contribution	1.67	0.00	1.67
plot_compare_dbs	4.22	0.00	4.22
plot_compare_indels	6.62	0.00	6.63
plot_compare_mbs	0.74	0.00	0.73
plot_compare_profiles	2.28	0.00	2.28
plot_contribution	2.84	0.00	2.85
plot_contribution_heatmap	1.57	0.03	1.59
plot_correlation_bootstrap	0.42	0.02	0.44
plot_cosine_heatmap	1.89	0.01	1.90
plot_dbs_contexts	3.39	0.00	3.39
plot_enrichment_depletion	3.11	0.02	3.13
plot_indel_contexts	7.05	0.00	7.05
plot_lesion_segregation	15.14	0.00	15.14
plot_main_dbs_contexts	0.54	0.00	0.54
plot_main_indel_contexts	0.58	0.00	0.58
plot_mbs_contexts	0.47	0.00	0.47
plot_original_vs_reconstructed	0.44	0.00	0.44
plot_profile_heatmap	5.03	0.01	5.04
plot_profile_region	1.01	0.00	1.02
plot_rainfall	2.54	0.02	2.55
plot_regional_similarity	1.43	0.00	1.43
plot_river	5.33	0.03	5.36
plot_signature_strand_bias	0.78	0.00	0.79
plot_spectrum	5.10	0.09	5.18
plot_spectrum_region	5.07	0.07	5.14
plot_strand	0.22	0.00	0.22
plot_strand_bias	0.69	0.00	0.69
pool_mut_mat	0.03	0.00	0.03
read_vcfs_as_granges	28.27	1.06	31.50
rename_nmf_signatures	0.03	0.01	0.05
signature_potential_damage_analysis	0.12	0.00	0.12
split_muts_region	4.47	0.02	4.48
strand_bias_test	0.15	0.00	0.16
strand_occurrences	0.16	0.01	0.17
type_context	1.86	0.15	2.00

CHECK results for MutationalPatterns on tokay2

Summary

Command output

Installation output

Tests output

Example timings