Back to Multiple platform build/check report for BioC 3.12
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

CHECK report for ngsReports on malbec1

This page was generated on 2021-05-06 12:28:24 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the ngsReports package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1226/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ngsReports 1.6.1  (landing page)
Steve Pederson
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/ngsReports
Branch: RELEASE_3_12
Last Commit: ef08d92
Last Changed Date: 2020-12-30 02:37:20 -0400 (Wed, 30 Dec 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: ngsReports
Version: 1.6.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ngsReports.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ngsReports_1.6.1.tar.gz
StartedAt: 2021-05-06 04:02:34 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:08:20 -0400 (Thu, 06 May 2021)
EllapsedTime: 345.9 seconds
RetCode: 0
Status:   OK  
CheckDir: ngsReports.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ngsReports.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ngsReports_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/ngsReports.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.6.1’
* 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 ‘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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL ngsReports
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-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
*** copying figures
** 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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.max, which.min

Loading required package: ggplot2
Loading required package: tibble
> 
> test_check("ngsReports")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 207 ]
> 
> proc.time()
   user  system elapsed 
 38.096   1.040  39.640 

Example timings

ngsReports.Rcheck/ngsReports-Ex.timings

nameusersystemelapsed
FastqcData0.1120.0040.153
FastqcDataList0.4640.0040.470
TheoreticalGC-class0.080.000.08
dot-FastqcFile-class0.0040.0000.002
dot-addPercent000
dot-emptyPlot0.0920.0080.101
dot-makeDendro0.3360.0040.337
dot-makeLabels0.0000.0000.001
dot-splitByTab0.0040.0000.004
estGcDistn0.0240.0000.022
extract-methods0.5360.0000.540
fqName-methods0.5560.0040.561
fqcVersion0.6800.0080.689
gcAvail0.0280.0000.030
gcTheoretical0.0560.0000.053
getColours-methods0.0000.0000.003
getGC0.0240.0000.024
getModule0.6360.0000.636
getSummary0.3520.0000.353
importNgsLogs0.0200.0000.023
importSJ0.0280.0000.039
isCompressed0.0000.0000.001
mData0.0160.0000.016
maxAdapterContent0.4880.0120.501
overRep2Fasta-methods0.6320.0000.632
path0.5560.0080.563
plotAdapterContent-methods1.9360.0401.978
plotAlignmentSummary0.2480.0000.246
plotAssemblyStats0.5240.0000.527
plotBaseQuals-methods1.1480.0081.154
plotDupLevels-methods1.3600.0041.364
plotFastqcPCA-methods1.0360.0041.043
plotGcContent-methods0.8480.0040.855
plotKmers-methods0.9240.0040.929
plotNContent-methods0.4760.0080.488
plotOverrep-methods0.6560.0000.655
plotReadTotals-methods0.9960.0000.995
plotSeqContent-methods0.8440.0080.853
plotSeqLengthDistn-methods1.2520.0001.255
plotSeqQuals-methods0.8880.0000.888
plotSummary-methods0.5360.0040.540
pwf0.0040.0000.004
readTotals0.3960.0000.395
runFastQC-methods0.0000.0000.001
writeHtmlReport000