Roel Janssen
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/MutationalPatterns |
| Branch: RELEASE_3_9 |
| Last Commit: a161e30 |
| Last Changed Date: 2019-05-02 11:54:04 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:58:59 -0400 (Wed, 16 Oct 2019).
| Package 1074/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MutationalPatterns 1.10.0 Roel Janssen
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: MutationalPatterns |
| Version: 1.10.0 |
| 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_1.10.0.tar.gz |
| StartedAt: 2019-10-16 04:59:10 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:08:17 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 547.7 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_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MutationalPatterns.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.10.0’
* 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 31.430 18.861 8.153
read_vcfs_as_granges 16.615 14.595 4.803
genomic_distribution 25.350 2.625 27.985
mut_matrix 14.664 9.729 3.681
plot_spectrum 11.413 0.508 11.971
mut_type_occurrences 8.585 0.735 9.321
* 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’ ... ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MutationalPatterns)
MutationalPatterns.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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, 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
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 22/23
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 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
207.820 102.912 71.576
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
| name | user | system | elapsed | |
| binomial_test | 0.014 | 0.002 | 0.015 | |
| cluster_signatures | 0.055 | 0.009 | 0.066 | |
| cos_sim | 0.001 | 0.000 | 0.001 | |
| cos_sim_matrix | 0.025 | 0.008 | 0.034 | |
| enrichment_depletion_test | 0.211 | 0.036 | 0.247 | |
| explained_by_signatures | 0.028 | 0.010 | 0.038 | |
| extract_signatures | 0.002 | 0.001 | 0.003 | |
| fit_to_signatures | 0.092 | 0.023 | 0.115 | |
| genomic_distribution | 25.350 | 2.625 | 27.985 | |
| mut_context | 1.165 | 0.106 | 1.272 | |
| mut_matrix | 14.664 | 9.729 | 3.681 | |
| mut_matrix_stranded | 31.430 | 18.861 | 8.153 | |
| mut_strand | 0.495 | 0.112 | 0.607 | |
| mut_type | 0.058 | 0.010 | 0.067 | |
| mut_type_occurrences | 8.585 | 0.735 | 9.321 | |
| mutation_context | 0.998 | 0.068 | 1.066 | |
| mutation_types | 0.038 | 0.003 | 0.041 | |
| mutations_from_vcf | 0.046 | 0.002 | 0.048 | |
| plot_192_profile | 1.607 | 0.040 | 1.649 | |
| plot_96_profile | 1.469 | 0.008 | 1.477 | |
| plot_compare_profiles | 1.321 | 0.012 | 1.335 | |
| plot_contribution | 1.602 | 0.013 | 1.616 | |
| plot_contribution_heatmap | 0.952 | 0.008 | 0.961 | |
| plot_cosine_heatmap | 0.740 | 0.007 | 0.748 | |
| plot_enrichment_depletion | 3.806 | 0.018 | 3.825 | |
| plot_rainfall | 1.268 | 0.010 | 1.278 | |
| plot_signature_strand_bias | 0.840 | 0.004 | 0.845 | |
| plot_spectrum | 11.413 | 0.508 | 11.971 | |
| plot_strand | 0.282 | 0.010 | 0.292 | |
| plot_strand_bias | 1.083 | 0.017 | 1.100 | |
| read_vcfs_as_granges | 16.615 | 14.595 | 4.803 | |
| strand_bias_test | 0.377 | 0.061 | 0.438 | |
| strand_occurrences | 0.557 | 0.175 | 0.731 | |
| type_context | 1.115 | 0.100 | 1.217 | |