Roel Janssen
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/MutationalPatterns |
| Branch: RELEASE_3_7 |
| Last Commit: 3254faa |
| Last Changed Date: 2018-10-11 04:00:18 -0400 (Thu, 11 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:57:19 -0400 (Wed, 17 Oct 2018).
| Package 970/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MutationalPatterns 1.6.1 Roel Janssen
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: MutationalPatterns |
| Version: 1.6.1 |
| 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_1.6.1.tar.gz |
| StartedAt: 2018-10-16 22:52:21 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 22:59:02 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 401.0 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_1.6.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/MutationalPatterns.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.6.1’
* 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 23.943 12.529 5.275
read_vcfs_as_granges 22.713 7.923 5.253
genomic_distribution 19.206 1.173 20.575
mut_matrix 10.678 5.380 2.321
plot_spectrum 9.814 0.222 10.148
mut_type_occurrences 6.433 0.315 6.801
* 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/3.5/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 version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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, 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':
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
258.333 99.395 71.861
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
| name | user | system | elapsed | |
| binomial_test | 0.671 | 0.002 | 0.678 | |
| cluster_signatures | 0.038 | 0.002 | 0.041 | |
| cos_sim | 0.002 | 0.000 | 0.002 | |
| cos_sim_matrix | 0.016 | 0.002 | 0.018 | |
| enrichment_depletion_test | 0.120 | 0.001 | 0.121 | |
| explained_by_signatures | 0.016 | 0.002 | 0.019 | |
| extract_signatures | 0.003 | 0.001 | 0.003 | |
| fit_to_signatures | 0.062 | 0.006 | 0.068 | |
| genomic_distribution | 19.206 | 1.173 | 20.575 | |
| mut_context | 1.060 | 0.069 | 1.151 | |
| mut_matrix | 10.678 | 5.380 | 2.321 | |
| mut_matrix_stranded | 23.943 | 12.529 | 5.275 | |
| mut_strand | 0.265 | 0.039 | 0.304 | |
| mut_type | 0.038 | 0.004 | 0.044 | |
| mut_type_occurrences | 6.433 | 0.315 | 6.801 | |
| mutation_context | 0.716 | 0.026 | 0.749 | |
| mutation_types | 0.027 | 0.001 | 0.028 | |
| mutations_from_vcf | 0.034 | 0.001 | 0.038 | |
| plot_192_profile | 1.300 | 0.024 | 1.335 | |
| plot_96_profile | 1.141 | 0.005 | 1.157 | |
| plot_compare_profiles | 0.948 | 0.005 | 0.960 | |
| plot_contribution | 1.296 | 0.005 | 1.317 | |
| plot_contribution_heatmap | 0.894 | 0.006 | 0.917 | |
| plot_cosine_heatmap | 0.701 | 0.004 | 0.723 | |
| plot_enrichment_depletion | 3.247 | 0.009 | 3.293 | |
| plot_rainfall | 1.377 | 0.004 | 1.400 | |
| plot_signature_strand_bias | 0.634 | 0.002 | 0.640 | |
| plot_spectrum | 9.814 | 0.222 | 10.148 | |
| plot_strand | 0.251 | 0.004 | 0.259 | |
| plot_strand_bias | 0.734 | 0.006 | 0.747 | |
| read_vcfs_as_granges | 22.713 | 7.923 | 5.253 | |
| strand_bias_test | 0.250 | 0.031 | 0.285 | |
| strand_occurrences | 0.254 | 0.047 | 0.303 | |
| type_context | 0.920 | 0.088 | 1.024 | |