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CHECK report for ngsReports on malbec1

This page was generated on 2020-04-15 12:15:31 -0400 (Wed, 15 Apr 2020).

Package 1153/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ngsReports 1.2.0
Steve Pederson
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/ngsReports
Branch: RELEASE_3_10
Last Commit: 9fe5358
Last Changed Date: 2019-10-29 13:11:37 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ngsReports
Version: 1.2.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ngsReports.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ngsReports_1.2.0.tar.gz
StartedAt: 2020-04-15 06:26:48 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:32:19 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 330.8 seconds
RetCode: 0
Status:  OK 
CheckDir: ngsReports.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ngsReports.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ngsReports_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/ngsReports.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ngsReports/DESCRIPTION’ ... OK
* this is package ‘ngsReports’ version ‘1.2.0’
* 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 ‘ngsReports’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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


Installation output

ngsReports.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL ngsReports
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘ngsReports’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (ngsReports)

Tests output

ngsReports.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(ngsReports)
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: ggplot2
Loading required package: tibble
> 
> test_check("ngsReports")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 205 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 39.116   1.156  38.184 

Example timings

ngsReports.Rcheck/ngsReports-Ex.timings

nameusersystemelapsed
FastqcData0.1200.0000.145
FastqcDataList0.5720.0160.689
TheoreticalGC-class0.1600.0040.192
dot-FastqcFile-class0.0040.0000.002
dot-addPercent000
dot-emptyPlot0.1120.0000.113
dot-makeDendro0.5760.0080.585
dot-makeLabels0.0040.0000.002
dot-splitByTab0.0040.0000.006
estGcDistn0.0280.0000.025
extract-methods1.0800.0081.092
fqName-methods0.5520.0120.578
fqcVersion0.5760.0360.626
gcAvail0.2640.0520.317
gcTheoretical0.0440.0080.053
getColours-methods0.0040.0000.003
getGC0.0200.0000.022
getModule0.6600.0120.676
getSummary0.5800.0040.587
importNgsLogs0.0360.0000.047
isCompressed0.0000.0000.002
mData0.0240.0000.024
maxAdapterContent0.6400.0040.648
overRep2Fasta-methods0.5200.0000.521
path0.3800.0000.383
plotAdapterContent-methods1.8720.0401.912
plotAlignmentSummary0.4720.0080.629
plotAssemblyStats1.0320.0041.056
plotBaseQuals-methods1.3360.0001.344
plotDupLevels-methods1.1080.0121.131
plotFastqcPCA-methods1.2000.0041.205
plotGcContent-methods0.8320.0080.839
plotKmers-methods0.6080.0080.619
plotNContent-methods0.6640.0000.668
plotOverrep-methods0.9520.0080.961
plotReadTotals-methods1.0880.0001.090
plotSeqContent-methods0.7000.0120.711
plotSeqLengthDistn-methods1.1880.0001.191
plotSeqQuals-methods1.2760.0081.284
plotSummary-methods0.8800.0040.881
pwf0.0040.0000.006
readTotals0.5720.0040.588
runFastQC-methods0.0000.0000.001
writeHtmlReport0.0040.0000.001