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CHECK report for MutationalPatterns on merida2

This page was generated on 2019-04-09 13:34:09 -0400 (Tue, 09 Apr 2019).

Package 1056/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 1.9.0
Roel Janssen
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/MutationalPatterns
Branch: master
Last Commit: c50b5ed
Last Changed Date: 2018-10-30 11:54:36 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: MutationalPatterns
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MutationalPatterns_1.9.0.tar.gz
StartedAt: 2019-04-09 02:27:28 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:33:57 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 389.5 seconds
RetCode: 0
Status:  OK 
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MutationalPatterns_1.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MutationalPatterns.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MutationalPatterns/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MutationalPatterns’ version ‘1.9.0’
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mut_matrix_stranded  20.845  9.471   4.537
genomic_distribution 20.769  1.311  22.427
read_vcfs_as_granges  9.436  4.974   2.067
mut_matrix            9.274  3.997   1.995
plot_spectrum         9.044  0.248   9.368
mut_type_occurrences  6.277  0.324   6.666
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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


Installation output

MutationalPatterns.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MutationalPatterns
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MutationalPatterns’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MutationalPatterns)

Tests output

MutationalPatterns.Rcheck/tests/testthat.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, colMeans, colSums, 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, 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':

    isFALSE

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 23/24
  To enable shared memory capabilities, try: install.extras('
NMF
')

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 
141.004  54.941  42.484 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
binomial_test0.0070.0010.009
cluster_signatures0.0380.0060.044
cos_sim000
cos_sim_matrix0.0190.0040.022
enrichment_depletion_test0.1470.0190.167
explained_by_signatures0.0200.0040.024
extract_signatures0.0020.0000.001
fit_to_signatures0.0550.0100.065
genomic_distribution20.769 1.31122.427
mut_context0.9410.0390.992
mut_matrix9.2743.9971.995
mut_matrix_stranded20.845 9.471 4.537
mut_strand0.2540.0320.285
mut_type0.0300.0030.032
mut_type_occurrences6.2770.3246.666
mutation_context0.7690.0310.805
mutation_types0.0330.0010.034
mutations_from_vcf0.0270.0010.028
plot_192_profile1.2260.0131.258
plot_96_profile1.1790.0051.258
plot_compare_profiles0.9640.0050.982
plot_contribution1.2230.0061.239
plot_contribution_heatmap0.8080.0060.823
plot_cosine_heatmap0.6860.0100.699
plot_enrichment_depletion3.1030.0083.142
plot_rainfall1.1560.0041.178
plot_signature_strand_bias0.6490.0030.659
plot_spectrum9.0440.2489.368
plot_strand0.2240.0040.229
plot_strand_bias0.7220.0090.736
read_vcfs_as_granges9.4364.9742.067
strand_bias_test0.2420.0320.274
strand_occurrences0.2090.0220.233
type_context0.8280.0790.914