Multiple platform build/check report for BioC 3.13 - CHECK results for MutationalPatterns on tokay2

Package: MutationalPatterns

Version: 3.2.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MutationalPatterns.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MutationalPatterns_3.2.0.tar.gz

StartedAt: 2021-10-15 02:31:44 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 02:52:23 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 1238.6 seconds

RetCode: 0

Status: OK

CheckDir: MutationalPatterns.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MutationalPatterns.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MutationalPatterns_3.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MutationalPatterns.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '3.2.0'
* 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 ... 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
* 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              26.02   0.90   29.44
context_potential_damage_analysis 24.62   0.29   24.90
get_mut_type                      19.91   0.00   19.94
plot_lesion_segregation           14.33   0.00   14.33
genomic_distribution              12.75   0.51   14.75
calculate_lesion_segregation      12.68   0.21   67.70
get_indel_context                  9.31   0.63   10.14
bin_mutation_density               7.88   0.88   10.12
mut_matrix_stranded                6.50   0.52    7.02
plot_compare_indels                6.14   0.00    6.14
fit_to_signatures_bootstrapped     5.80   0.18    5.98
plot_indel_contexts                5.89   0.02    5.91
plot_profile_heatmap               5.18   0.00    5.21
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
read_vcfs_as_granges              27.08   1.09   30.36
context_potential_damage_analysis 23.82   0.39   24.20
get_mut_type                      22.84   0.00   22.85
plot_lesion_segregation           17.10   0.04   17.18
calculate_lesion_segregation      14.75   0.16   14.91
genomic_distribution              12.35   0.44   12.78
get_indel_context                 10.95   0.84   11.81
bin_mutation_density              10.11   0.27   10.38
plot_indel_contexts                7.04   0.00    7.04
plot_compare_indels                6.95   0.02    6.97
plot_river                         6.87   0.03    6.91
fit_to_signatures_bootstrapped     6.28   0.02    6.30
plot_spectrum                      6.14   0.11    6.25
mut_matrix_stranded                5.80   0.41    6.21
plot_spectrum_region               5.59   0.18    5.78
split_muts_region                  5.50   0.00    5.50
* 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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MutationalPatterns_3.2.0.tar.gz && rm -rf MutationalPatterns.buildbin-libdir && mkdir MutationalPatterns.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MutationalPatterns.buildbin-libdir MutationalPatterns_3.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MutationalPatterns_3.2.0.zip && rm MutationalPatterns_3.2.0.tar.gz MutationalPatterns_3.2.0.zip
###
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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_3.2.0.zip
* DONE (MutationalPatterns)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'MutationalPatterns' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 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 17 | SKIP 0 | PASS 434 ]
> 
> proc.time()
   user  system elapsed 
 236.29    8.23  250.25


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 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 17 | SKIP 0 | PASS 434 ]
> 
> proc.time()
   user  system elapsed 
 272.01    7.32  285.81

name	user	system	elapsed
bin_mutation_density	7.88	0.88	10.12
binomial_test	0.02	0.00	0.02
calculate_lesion_segregation	12.68	0.21	67.70
cluster_signatures	0.09	0.00	1.12
context_potential_damage_analysis	24.62	0.29	24.90
convert_sigs_to_ref	0.10	0.00	0.75
cos_sim	0	0	0
cos_sim_matrix	0.04	0.00	0.05
count_dbs_contexts	0.21	0.00	0.24
count_indel_contexts	0.27	0.00	0.33
count_mbs_contexts	0.14	0.00	0.14
enrichment_depletion_test	0.17	0.00	0.17
extract_signatures	0	0	0
fit_to_signatures	0.14	0.13	0.44
fit_to_signatures_bootstrapped	5.80	0.18	5.98
fit_to_signatures_strict	3.69	0.00	3.68
genomic_distribution	12.75	0.51	14.75
get_dbs_context	0.65	0.00	0.74
get_indel_context	9.31	0.63	10.14
get_known_signatures	0.63	0.14	1.06
get_mut_type	19.91	0.00	19.94
lengthen_mut_matrix	0.00	0.02	0.01
merge_signatures	1.06	0.00	1.07
mut_context	1.64	0.15	1.79
mut_matrix	3.03	0.28	3.32
mut_matrix_stranded	6.50	0.52	7.02
mut_strand	1.20	0.08	1.28
mut_type	0.05	0.00	0.05
mut_type_occurrences	1.03	0.11	1.14
mutations_from_vcf	0.05	0.00	0.05
plot_192_profile	2.56	0.00	2.56
plot_96_profile	2.44	0.01	2.52
plot_bootstrapped_contribution	1.69	0.00	1.68
plot_compare_dbs	3.86	0.00	3.86
plot_compare_indels	6.14	0.00	6.14
plot_compare_mbs	0.61	0.00	0.61
plot_compare_profiles	1.54	0.00	1.55
plot_contribution	2.42	0.02	2.48
plot_contribution_heatmap	1.32	0.01	1.33
plot_correlation_bootstrap	0.30	0.00	0.29
plot_cosine_heatmap	1.47	0.00	1.47
plot_dbs_contexts	2.83	0.00	2.83
plot_enrichment_depletion	2.5	0.0	2.5
plot_indel_contexts	5.89	0.02	5.91
plot_lesion_segregation	14.33	0.00	14.33
plot_main_dbs_contexts	0.5	0.0	0.5
plot_main_indel_contexts	0.46	0.00	0.46
plot_mbs_contexts	0.44	0.00	0.44
plot_original_vs_reconstructed	0.42	0.00	0.42
plot_profile_heatmap	5.18	0.00	5.21
plot_profile_region	0.79	0.00	0.79
plot_rainfall	1.24	0.00	1.24
plot_river	4.72	0.08	4.80
plot_signature_strand_bias	0.57	0.00	0.57
plot_spectrum	4.38	0.22	4.60
plot_spectrum_region	4.28	0.12	4.45
plot_strand	0.12	0.02	0.14
plot_strand_bias	0.58	0.00	0.58
pool_mut_mat	0.03	0.00	0.03
read_vcfs_as_granges	26.02	0.90	29.44
rename_nmf_signatures	0.05	0.00	0.04
signature_potential_damage_analysis	0.11	0.00	0.11
split_muts_region	4.64	0.05	4.69
strand_bias_test	0.09	0.00	0.10
strand_occurrences	0.09	0.03	0.13
type_context	1.52	0.14	1.65

name	user	system	elapsed
bin_mutation_density	10.11	0.27	10.38
binomial_test	0	0	0
calculate_lesion_segregation	14.75	0.16	14.91
cluster_signatures	0.06	0.00	0.06
context_potential_damage_analysis	23.82	0.39	24.20
convert_sigs_to_ref	0.03	0.00	0.03
cos_sim	0	0	0
cos_sim_matrix	0.08	0.00	0.08
count_dbs_contexts	0.11	0.00	0.11
count_indel_contexts	0.14	0.00	0.14
count_mbs_contexts	0.11	0.00	0.11
enrichment_depletion_test	0.13	0.00	0.12
extract_signatures	0	0	0
fit_to_signatures	0.07	0.01	0.09
fit_to_signatures_bootstrapped	6.28	0.02	6.30
fit_to_signatures_strict	2.8	0.0	2.8
genomic_distribution	12.35	0.44	12.78
get_dbs_context	0.41	0.00	0.40
get_indel_context	10.95	0.84	11.81
get_known_signatures	0.52	0.17	0.69
get_mut_type	22.84	0.00	22.85
lengthen_mut_matrix	0.02	0.00	0.01
merge_signatures	1.07	0.02	1.09
mut_context	1.39	0.22	1.61
mut_matrix	2.99	0.34	3.33
mut_matrix_stranded	5.80	0.41	6.21
mut_strand	1.06	0.06	1.12
mut_type	0.03	0.00	0.03
mut_type_occurrences	1.68	0.11	1.78
mutations_from_vcf	0.06	0.00	0.06
plot_192_profile	2.42	0.01	2.44
plot_96_profile	2.08	0.02	2.09
plot_bootstrapped_contribution	1.66	0.00	1.66
plot_compare_dbs	4.05	0.01	4.07
plot_compare_indels	6.95	0.02	6.97
plot_compare_mbs	0.7	0.0	0.7
plot_compare_profiles	1.58	0.00	1.58
plot_contribution	2.03	0.00	2.03
plot_contribution_heatmap	1.41	0.03	1.44
plot_correlation_bootstrap	0.44	0.00	0.43
plot_cosine_heatmap	1.76	0.00	1.77
plot_dbs_contexts	3.24	0.02	3.25
plot_enrichment_depletion	2.86	0.00	2.86
plot_indel_contexts	7.04	0.00	7.04
plot_lesion_segregation	17.10	0.04	17.18
plot_main_dbs_contexts	0.45	0.00	0.45
plot_main_indel_contexts	0.8	0.0	0.8
plot_mbs_contexts	0.47	0.00	0.47
plot_original_vs_reconstructed	0.48	0.02	0.50
plot_profile_heatmap	4.86	0.01	4.87
plot_profile_region	1.09	0.02	1.11
plot_rainfall	1.99	0.00	1.98
plot_river	6.87	0.03	6.91
plot_signature_strand_bias	0.69	0.02	0.70
plot_spectrum	6.14	0.11	6.25
plot_spectrum_region	5.59	0.18	5.78
plot_strand	0.32	0.00	0.32
plot_strand_bias	0.81	0.02	0.83
pool_mut_mat	0.03	0.00	0.03
read_vcfs_as_granges	27.08	1.09	30.36
rename_nmf_signatures	0.03	0.02	0.04
signature_potential_damage_analysis	0.11	0.00	0.11
split_muts_region	5.5	0.0	5.5
strand_bias_test	0.14	0.00	0.14
strand_occurrences	0.12	0.03	0.15
type_context	1.78	0.16	1.94

CHECK results for MutationalPatterns on tokay2

Summary

Command output

Installation output

Tests output

Example timings