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) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:34:09 -0400 (Tue, 09 Apr 2019).
| Package 1056/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MutationalPatterns 1.9.0 Roel Janssen
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| 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 |
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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
MutationalPatterns.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MutationalPatterns ### ############################################################################## ############################################################################## * 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)
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
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
| name | user | system | elapsed | |
| binomial_test | 0.007 | 0.001 | 0.009 | |
| cluster_signatures | 0.038 | 0.006 | 0.044 | |
| cos_sim | 0 | 0 | 0 | |
| cos_sim_matrix | 0.019 | 0.004 | 0.022 | |
| enrichment_depletion_test | 0.147 | 0.019 | 0.167 | |
| explained_by_signatures | 0.020 | 0.004 | 0.024 | |
| extract_signatures | 0.002 | 0.000 | 0.001 | |
| fit_to_signatures | 0.055 | 0.010 | 0.065 | |
| genomic_distribution | 20.769 | 1.311 | 22.427 | |
| mut_context | 0.941 | 0.039 | 0.992 | |
| mut_matrix | 9.274 | 3.997 | 1.995 | |
| mut_matrix_stranded | 20.845 | 9.471 | 4.537 | |
| mut_strand | 0.254 | 0.032 | 0.285 | |
| mut_type | 0.030 | 0.003 | 0.032 | |
| mut_type_occurrences | 6.277 | 0.324 | 6.666 | |
| mutation_context | 0.769 | 0.031 | 0.805 | |
| mutation_types | 0.033 | 0.001 | 0.034 | |
| mutations_from_vcf | 0.027 | 0.001 | 0.028 | |
| plot_192_profile | 1.226 | 0.013 | 1.258 | |
| plot_96_profile | 1.179 | 0.005 | 1.258 | |
| plot_compare_profiles | 0.964 | 0.005 | 0.982 | |
| plot_contribution | 1.223 | 0.006 | 1.239 | |
| plot_contribution_heatmap | 0.808 | 0.006 | 0.823 | |
| plot_cosine_heatmap | 0.686 | 0.010 | 0.699 | |
| plot_enrichment_depletion | 3.103 | 0.008 | 3.142 | |
| plot_rainfall | 1.156 | 0.004 | 1.178 | |
| plot_signature_strand_bias | 0.649 | 0.003 | 0.659 | |
| plot_spectrum | 9.044 | 0.248 | 9.368 | |
| plot_strand | 0.224 | 0.004 | 0.229 | |
| plot_strand_bias | 0.722 | 0.009 | 0.736 | |
| read_vcfs_as_granges | 9.436 | 4.974 | 2.067 | |
| strand_bias_test | 0.242 | 0.032 | 0.274 | |
| strand_occurrences | 0.209 | 0.022 | 0.233 | |
| type_context | 0.828 | 0.079 | 0.914 | |