Multiple platform build/check report for BioC 3.6 - CHECK report for MutationalPatterns on tokay1

Package: MutationalPatterns

Version: 1.4.3

Command: rm -rf MutationalPatterns.buildbin-libdir MutationalPatterns.Rcheck && mkdir MutationalPatterns.buildbin-libdir MutationalPatterns.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MutationalPatterns.buildbin-libdir MutationalPatterns_1.4.3.tar.gz >MutationalPatterns.Rcheck\00install.out 2>&1 && cp MutationalPatterns.Rcheck\00install.out MutationalPatterns-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MutationalPatterns.buildbin-libdir --install="check:MutationalPatterns-install.out" --force-multiarch --no-vignettes --timings MutationalPatterns_1.4.3.tar.gz

StartedAt: 2018-04-12 01:43:20 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:53:50 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 629.2 seconds

RetCode: 0

Status: OK

CheckDir: MutationalPatterns.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf MutationalPatterns.buildbin-libdir MutationalPatterns.Rcheck && mkdir MutationalPatterns.buildbin-libdir MutationalPatterns.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MutationalPatterns.buildbin-libdir MutationalPatterns_1.4.3.tar.gz >MutationalPatterns.Rcheck\00install.out 2>&1 && cp MutationalPatterns.Rcheck\00install.out MutationalPatterns-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MutationalPatterns.buildbin-libdir --install="check:MutationalPatterns-install.out" --force-multiarch --no-vignettes --timings MutationalPatterns_1.4.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/MutationalPatterns.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.4.3'
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
genomic_distribution 15.07   0.31   15.37
mut_matrix_stranded   9.33   0.53    9.86
read_vcfs_as_granges  7.12   0.15    7.28
plot_spectrum         5.95   0.21    6.15
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
genomic_distribution 15.68   0.52   16.19
mut_matrix_stranded  10.69   0.49   11.17
read_vcfs_as_granges 10.22   0.22   10.44
plot_spectrum         7.68   0.10    7.79
mut_matrix            4.92   0.23    5.16
* 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


install for i386

* installing *source* package 'MutationalPatterns' ...
** R
** inst
** preparing 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
In R CMD INSTALL

install for x64

* installing *source* package 'MutationalPatterns' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MutationalPatterns' as MutationalPatterns_1.4.3.zip
* DONE (MutationalPatterns)
In R CMD INSTALL
In R CMD INSTALL


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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
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

The following object is masked from 'package:base':

    isNamespaceLoaded

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 19/20

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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  78.95    2.21   81.81


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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
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

The following object is masked from 'package:base':

    isNamespaceLoaded

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 19/20

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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  94.96    2.17   97.12

name	user	system	elapsed
binomial_test	0	0	0
cluster_signatures	0.42	0.00	0.43
cos_sim	0	0	0
cos_sim_matrix	0.02	0.00	0.02
enrichment_depletion_test	0.14	0.00	0.14
explained_by_signatures	0.00	0.02	0.01
extract_signatures	0.01	0.00	0.02
fit_to_signatures	0.03	0.00	0.03
genomic_distribution	15.07	0.31	15.37
mut_context	0.75	0.10	0.85
mut_matrix	4.18	0.25	4.44
mut_matrix_stranded	9.33	0.53	9.86
mut_strand	0.67	0.00	0.67
mut_type	0.01	0.01	0.03
mut_type_occurrences	3.77	0.24	4.00
mutation_context	0.48	0.01	0.50
mutation_types	0.04	0.00	0.04
mutations_from_vcf	0.01	0.00	0.01
plot_192_profile	1.58	0.02	1.59
plot_96_profile	1.41	0.00	1.41
plot_compare_profiles	0.79	0.00	0.80
plot_contribution	1.05	0.00	1.04
plot_contribution_heatmap	1.33	0.00	1.33
plot_cosine_heatmap	0.53	0.01	0.55
plot_enrichment_depletion	1.76	0.00	1.77
plot_rainfall	0.81	0.00	0.81
plot_signature_strand_bias	0.47	0.00	0.47
plot_spectrum	5.95	0.21	6.15
plot_strand	0.17	0.00	0.17
plot_strand_bias	0.51	0.00	0.52
read_vcfs_as_granges	7.12	0.15	7.28
strand_bias_test	0.19	0.00	0.19
strand_occurrences	0.14	0.00	0.14
type_context	0.50	0.03	0.53

name	user	system	elapsed
binomial_test	0	0	0
cluster_signatures	0.05	0.00	0.05
cos_sim	0	0	0
cos_sim_matrix	0.5	0.0	0.5
enrichment_depletion_test	0.12	0.00	0.13
explained_by_signatures	0.01	0.00	0.02
extract_signatures	0	0	0
fit_to_signatures	0.03	0.00	0.03
genomic_distribution	15.68	0.52	16.19
mut_context	0.87	0.03	0.90
mut_matrix	4.92	0.23	5.16
mut_matrix_stranded	10.69	0.49	11.17
mut_strand	0.17	0.01	0.19
mut_type	0.03	0.00	0.03
mut_type_occurrences	4.46	0.22	4.67
mutation_context	0.57	0.00	0.58
mutation_types	0.05	0.00	0.05
mutations_from_vcf	0.03	0.00	0.03
plot_192_profile	1.97	0.00	1.97
plot_96_profile	1.84	0.02	1.86
plot_compare_profiles	1	0	1
plot_contribution	1.38	0.00	1.38
plot_contribution_heatmap	1.62	0.00	1.62
plot_cosine_heatmap	0.95	0.00	0.95
plot_enrichment_depletion	3.26	0.00	3.27
plot_rainfall	1.32	0.00	1.31
plot_signature_strand_bias	0.4	0.0	0.4
plot_spectrum	7.68	0.10	7.79
plot_strand	0.20	0.02	0.21
plot_strand_bias	0.58	0.00	0.58
read_vcfs_as_granges	10.22	0.22	10.44
strand_bias_test	0.21	0.01	0.23
strand_occurrences	0.16	0.02	0.18
type_context	0.61	0.06	0.67

CHECK report for MutationalPatterns on tokay1

Summary

Command output

Installation output

Tests output

Example timings