Multiple platform build/check report for BioC 3.11 - CHECK report for MutationalPatterns on tokay2

Package: MutationalPatterns

Version: 2.0.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MutationalPatterns.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MutationalPatterns_2.0.0.tar.gz

StartedAt: 2020-10-17 06:22:15 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 06:36:05 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 829.6 seconds

RetCode: 0

Status: OK

CheckDir: MutationalPatterns.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MutationalPatterns.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MutationalPatterns_2.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/MutationalPatterns.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '2.0.0'
* 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
genomic_distribution 18.50   0.62   19.65
mut_matrix_stranded  15.14   1.67   17.14
plot_spectrum         8.62   0.78    9.42
mut_matrix            6.11   0.66    6.77
mut_type_occurrences  5.99   0.72    6.71
read_vcfs_as_granges  5.31   0.16    5.64
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
genomic_distribution 23.88   0.47   24.35
mut_matrix_stranded  18.91   1.56   20.47
plot_spectrum         9.86   0.61   10.47
mut_type_occurrences  8.66   0.96    9.61
mut_matrix            8.31   0.78    9.09
* 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 https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/MutationalPatterns_2.0.0.tar.gz && rm -rf MutationalPatterns.buildbin-libdir && mkdir MutationalPatterns.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MutationalPatterns.buildbin-libdir MutationalPatterns_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL MutationalPatterns_2.0.0.zip && rm MutationalPatterns_2.0.0.tar.gz MutationalPatterns_2.0.0.zip
###
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  % 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 3136k  100 3136k    0     0  23.2M      0 --:--:-- --:--:-- --:--:-- 24.5M

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-package              html  
    binomial_test                           html  
    cluster_signatures                      html  
    cos_sim                                 html  
    cos_sim_matrix                          html  
    enrichment_depletion_test               html  
    explained_by_signatures                 html  
    extract_signatures                      html  
    fit_to_signatures                       html  
    genomic_distribution                    html  
    mut_context                             html  
    mut_matrix                              html  
    mut_matrix_stranded                     html  
    mut_strand                              html  
    mut_type                                html  
    mut_type_occurrences                    html  
    mutation_context                        html  
    mutation_types                          html  
    mutations_from_vcf                      html  
    plot_192_profile                        html  
    plot_96_profile                         html  
    plot_compare_profiles                   html  
    plot_contribution                       html  
    plot_contribution_heatmap               html  
    plot_cosine_heatmap                     html  
    plot_enrichment_depletion               html  
    plot_rainfall                           html  
    plot_signature_strand_bias              html  
    plot_spectrum                           html  
    plot_strand                             html  
    plot_strand_bias                        html  
    read_vcfs_as_granges                    html  
    strand_bias_test                        html  
    strand_from_vcf                         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_2.0.0.zip
* DONE (MutationalPatterns)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'MutationalPatterns' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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, 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")
== testthat results  ===========================================================
[ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  87.60    6.98   98.18


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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, 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")
== testthat results  ===========================================================
[ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  87.20    6.25   96.71

name	user	system	elapsed
binomial_test	0	0	0
cluster_signatures	0.03	0.00	0.03
cos_sim	0	0	0
cos_sim_matrix	0.02	0.00	0.01
enrichment_depletion_test	0.06	0.08	0.14
explained_by_signatures	0.02	0.00	0.02
extract_signatures	0	0	0
fit_to_signatures	0.20	0.02	0.22
genomic_distribution	18.50	0.62	19.65
mut_context	1.03	0.48	1.52
mut_matrix	6.11	0.66	6.77
mut_matrix_stranded	15.14	1.67	17.14
mut_strand	0.2	0.0	0.2
mut_type	0.03	0.00	0.03
mut_type_occurrences	5.99	0.72	6.71
mutation_context	0.75	0.11	0.86
mutation_types	0.03	0.00	0.03
mutations_from_vcf	0.04	0.00	0.03
plot_192_profile	0.78	0.00	0.79
plot_96_profile	0.75	0.00	0.75
plot_compare_profiles	0.53	0.00	0.53
plot_contribution	0.54	0.00	0.53
plot_contribution_heatmap	0.42	0.00	0.43
plot_cosine_heatmap	0.28	0.00	0.28
plot_enrichment_depletion	1.56	0.00	1.56
plot_rainfall	0.77	0.00	0.76
plot_signature_strand_bias	0.31	0.00	0.32
plot_spectrum	8.62	0.78	9.42
plot_strand	0.16	0.01	0.17
plot_strand_bias	0.42	0.02	0.44
read_vcfs_as_granges	5.31	0.16	5.64
strand_bias_test	0.24	0.00	0.23
strand_occurrences	0.14	0.00	0.14
type_context	0.77	0.12	0.89

name	user	system	elapsed
binomial_test	0.02	0.00	0.02
cluster_signatures	0.03	0.00	0.03
cos_sim	0	0	0
cos_sim_matrix	0	0	0
enrichment_depletion_test	0.06	0.02	0.08
explained_by_signatures	0.01	0.00	0.02
extract_signatures	0	0	0
fit_to_signatures	0.15	0.00	0.14
genomic_distribution	23.88	0.47	24.35
mut_context	1.45	0.12	1.58
mut_matrix	8.31	0.78	9.09
mut_matrix_stranded	18.91	1.56	20.47
mut_strand	0.21	0.00	0.20
mut_type	0.03	0.00	0.03
mut_type_occurrences	8.66	0.96	9.61
mutation_context	1.05	0.12	1.18
mutation_types	0.03	0.00	0.03
mutations_from_vcf	0.03	0.00	0.03
plot_192_profile	0.91	0.02	0.92
plot_96_profile	1.56	0.00	1.56
plot_compare_profiles	1.03	0.00	1.03
plot_contribution	0.94	0.01	0.96
plot_contribution_heatmap	0.62	0.00	0.62
plot_cosine_heatmap	0.35	0.00	0.35
plot_enrichment_depletion	2.6	0.0	2.6
plot_rainfall	1.45	0.00	1.45
plot_signature_strand_bias	0.56	0.00	0.56
plot_spectrum	9.86	0.61	10.47
plot_strand	0.20	0.02	0.22
plot_strand_bias	0.54	0.01	0.55
read_vcfs_as_granges	4.59	0.22	4.81
strand_bias_test	0.14	0.02	0.15
strand_occurrences	0.14	0.01	0.16
type_context	0.88	0.11	0.99

CHECK report for MutationalPatterns on tokay2

Summary

Command output

Installation output

Tests output

Example timings