Francis Blokzijl
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/MutationalPatterns |
| Branch: RELEASE_3_6 |
| Last Commit: 0427b4c |
| Last Changed Date: 2018-03-16 10:25:01 -0400 (Fri, 16 Mar 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:15:34 -0400 (Thu, 12 Apr 2018).
| Package 918/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MutationalPatterns 1.4.3 Francis Blokzijl
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: MutationalPatterns |
| Version: 1.4.3 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MutationalPatterns_1.4.3.tar.gz |
| StartedAt: 2018-04-12 01:23:41 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 01:28:41 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 299.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MutationalPatterns.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MutationalPatterns_1.4.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/MutationalPatterns.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.3’
* 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 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 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
mut_matrix_stranded 12.572 3.624 2.934
genomic_distribution 14.688 0.112 14.818
read_vcfs_as_granges 11.664 2.496 2.414
mut_matrix 5.088 1.644 8.812
plot_spectrum 6.420 0.088 6.512
* 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
* installing *source* package ‘MutationalPatterns’ ... ** R ** inst ** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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: synchronicity] | Cores 19/20
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
122.564 21.776 35.264
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
| name | user | system | elapsed | |
| binomial_test | 0.008 | 0.000 | 0.007 | |
| cluster_signatures | 0.020 | 0.004 | 0.026 | |
| cos_sim | 0.000 | 0.000 | 0.001 | |
| cos_sim_matrix | 0.016 | 0.012 | 0.024 | |
| enrichment_depletion_test | 0.144 | 0.000 | 0.145 | |
| explained_by_signatures | 0.008 | 0.000 | 0.010 | |
| extract_signatures | 0.000 | 0.000 | 0.002 | |
| fit_to_signatures | 0.028 | 0.000 | 0.029 | |
| genomic_distribution | 14.688 | 0.112 | 14.818 | |
| mut_context | 0.948 | 0.012 | 2.140 | |
| mut_matrix | 5.088 | 1.644 | 8.812 | |
| mut_matrix_stranded | 12.572 | 3.624 | 2.934 | |
| mut_strand | 0.348 | 0.016 | 0.362 | |
| mut_type | 0.024 | 0.000 | 0.026 | |
| mut_type_occurrences | 4.288 | 0.092 | 4.383 | |
| mutation_context | 0.56 | 0.02 | 0.58 | |
| mutation_types | 0.024 | 0.000 | 0.024 | |
| mutations_from_vcf | 0.024 | 0.000 | 0.023 | |
| plot_192_profile | 1.856 | 0.000 | 1.860 | |
| plot_96_profile | 1.508 | 0.004 | 1.513 | |
| plot_compare_profiles | 0.792 | 0.008 | 0.801 | |
| plot_contribution | 1.132 | 0.000 | 1.130 | |
| plot_contribution_heatmap | 1.304 | 0.000 | 1.304 | |
| plot_cosine_heatmap | 0.56 | 0.00 | 0.56 | |
| plot_enrichment_depletion | 1.976 | 0.000 | 1.978 | |
| plot_rainfall | 0.920 | 0.000 | 0.923 | |
| plot_signature_strand_bias | 0.388 | 0.000 | 0.390 | |
| plot_spectrum | 6.420 | 0.088 | 6.512 | |
| plot_strand | 0.208 | 0.000 | 0.208 | |
| plot_strand_bias | 0.588 | 0.000 | 0.587 | |
| read_vcfs_as_granges | 11.664 | 2.496 | 2.414 | |
| strand_bias_test | 0.372 | 0.040 | 0.414 | |
| strand_occurrences | 0.168 | 0.008 | 0.175 | |
| type_context | 0.828 | 0.032 | 0.862 | |