Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:41 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for ngsReports on nebbiolo2


To the developers/maintainers of the ngsReports package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ngsReports.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1295/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ngsReports 1.10.0  (landing page)
Steve Pederson
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/ngsReports
git_branch: RELEASE_3_14
git_last_commit: b18d9df
git_last_commit_date: 2021-10-26 12:50:47 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ngsReports
Version: 1.10.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ngsReports.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ngsReports_1.10.0.tar.gz
StartedAt: 2022-04-12 08:29:00 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 08:31:13 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 133.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ngsReports.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ngsReports.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ngsReports_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/ngsReports.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.10.0’
* 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 LazyData ... 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-3.14-bioc/R/bin/R CMD INSTALL ngsReports
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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

Attaching package: 'BiocGenerics'

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 205 ]
> 
> proc.time()
   user  system elapsed 
 16.212   0.685  16.895 

Example timings

ngsReports.Rcheck/ngsReports-Ex.timings

nameusersystemelapsed
FastqcData0.0700.0000.071
FastqcDataList0.2950.0000.303
TheoreticalGC-class0.0640.0000.065
dot-FastqcFile-class0.0020.0000.002
dot-addPercent000
dot-emptyPlot0.1290.0000.129
dot-makeDendro0.3240.0030.327
dot-makeLabels0.0010.0000.001
dot-splitByTab0.0030.0000.003
estGcDistn0.0160.0000.016
extract-methods0.2850.0000.285
fqName-methods0.3060.0080.314
fqcVersion0.3170.0160.333
gcAvail0.0180.0000.018
gcTheoretical0.0290.0040.033
getColours-methods0.0020.0000.002
getGC0.0160.0000.015
getModule0.3200.0040.324
getSummary0.3220.0040.326
importNgsLogs0.020.000.02
importSJ0.0250.0000.024
isCompressed0.0010.0000.001
mData0.0180.0000.018
maxAdapterContent0.3420.0040.345
overRep2Fasta-methods0.3290.0000.328
path0.3120.0000.312
plotAdapterContent-methods1.3180.0401.358
plotAlignmentSummary0.2190.0040.222
plotAssemblyStats0.4270.0040.431
plotBaseQuals-methods0.6730.0000.673
plotDupLevels-methods0.8040.0000.804
plotFastqcPCA-methods0.4730.0000.473
plotGcContent-methods0.5700.0000.569
plotKmers-methods0.5180.0320.549
plotNContent-methods0.8160.0480.864
plotOverrep-methods0.4530.0000.453
plotReadTotals-methods0.5120.0040.516
plotSeqContent-methods0.3920.0200.412
plotSeqLengthDistn-methods0.6960.0240.720
plotSeqQuals-methods0.6430.0040.647
plotSummary-methods0.4670.0040.471
pwf0.0040.0000.004
readTotals0.2920.0000.291
writeHtmlReport000