Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:46:57 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MutationalPatterns_1.9.0.tar.gz |
StartedAt: 2019-04-09 02:17:09 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 02:23:03 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 354.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MutationalPatterns.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MutationalPatterns_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MutationalPatterns.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * 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 ‘1.9.0’ * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed genomic_distribution 20.118 0.168 20.371 mut_matrix_stranded 13.930 4.643 3.573 read_vcfs_as_granges 6.186 2.523 1.950 plot_spectrum 7.033 0.072 7.106 mut_matrix 4.794 1.540 1.595 * 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: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL MutationalPatterns ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" Copyright (C) 2019 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, 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 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 97.955 25.024 38.286
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
name | user | system | elapsed | |
binomial_test | 0.011 | 0.000 | 0.011 | |
cluster_signatures | 0.034 | 0.004 | 0.051 | |
cos_sim | 0 | 0 | 0 | |
cos_sim_matrix | 0.016 | 0.000 | 0.016 | |
enrichment_depletion_test | 0.131 | 0.012 | 0.148 | |
explained_by_signatures | 0.017 | 0.000 | 0.017 | |
extract_signatures | 0.000 | 0.002 | 0.002 | |
fit_to_signatures | 0.057 | 0.001 | 0.059 | |
genomic_distribution | 20.118 | 0.168 | 20.371 | |
mut_context | 0.717 | 0.060 | 0.776 | |
mut_matrix | 4.794 | 1.540 | 1.595 | |
mut_matrix_stranded | 13.930 | 4.643 | 3.573 | |
mut_strand | 0.188 | 0.032 | 0.221 | |
mut_type | 0.024 | 0.000 | 0.025 | |
mut_type_occurrences | 4.633 | 0.124 | 4.760 | |
mutation_context | 0.784 | 0.004 | 0.788 | |
mutation_types | 0.054 | 0.000 | 0.054 | |
mutations_from_vcf | 0.037 | 0.000 | 0.037 | |
plot_192_profile | 1.188 | 0.004 | 1.191 | |
plot_96_profile | 1.246 | 0.000 | 1.247 | |
plot_compare_profiles | 0.973 | 0.004 | 0.976 | |
plot_contribution | 1.301 | 0.000 | 1.302 | |
plot_contribution_heatmap | 0.655 | 0.000 | 0.655 | |
plot_cosine_heatmap | 0.551 | 0.001 | 0.551 | |
plot_enrichment_depletion | 2.974 | 0.004 | 2.978 | |
plot_rainfall | 0.938 | 0.000 | 0.939 | |
plot_signature_strand_bias | 0.419 | 0.004 | 0.422 | |
plot_spectrum | 7.033 | 0.072 | 7.106 | |
plot_strand | 0.146 | 0.004 | 0.150 | |
plot_strand_bias | 0.694 | 0.004 | 0.698 | |
read_vcfs_as_granges | 6.186 | 2.523 | 1.950 | |
strand_bias_test | 0.218 | 0.017 | 0.236 | |
strand_occurrences | 0.212 | 0.008 | 0.220 | |
type_context | 0.794 | 0.036 | 0.831 | |