Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-19 13:05:43 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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? here 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: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 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 -0500 (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: 2022-01-18 08:35:14 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 08:37:30 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 136.4 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 4.1.2 (2021-11-01)
* 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 4.1.2 (2021-11-01) -- "Bird Hippie"
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

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 
 16.261   0.699  16.967 

Example timings

ngsReports.Rcheck/ngsReports-Ex.timings

nameusersystemelapsed
FastqcData0.0760.0010.078
FastqcDataList0.3120.0000.322
TheoreticalGC-class0.1020.0000.103
dot-FastqcFile-class0.0020.0000.002
dot-addPercent000
dot-emptyPlot0.0920.0000.092
dot-makeDendro0.3150.0000.315
dot-makeLabels0.0010.0000.001
dot-splitByTab0.0030.0000.003
estGcDistn0.0180.0000.018
extract-methods0.3120.0040.316
fqName-methods0.3020.0000.302
fqcVersion0.3530.0070.361
gcAvail0.0180.0010.018
gcTheoretical0.0320.0000.032
getColours-methods0.0010.0000.002
getGC0.0160.0000.016
getModule0.3660.0040.370
getSummary0.3120.0000.312
importNgsLogs0.0180.0000.018
importSJ0.0260.0000.026
isCompressed0.0000.0000.001
mData0.0150.0020.017
maxAdapterContent0.3520.0000.352
overRep2Fasta-methods0.3410.0200.360
path0.2980.0150.313
plotAdapterContent-methods1.2950.0881.383
plotAlignmentSummary0.210.000.21
plotAssemblyStats0.4070.0000.407
plotBaseQuals-methods1.0010.0351.037
plotDupLevels-methods0.7510.0200.772
plotFastqcPCA-methods0.4210.0080.429
plotGcContent-methods0.5190.0000.519
plotKmers-methods0.4580.0080.466
plotNContent-methods0.3310.0030.335
plotOverrep-methods0.4290.0040.433
plotReadTotals-methods0.5660.0040.570
plotSeqContent-methods0.4020.0040.406
plotSeqLengthDistn-methods0.7230.0160.739
plotSeqQuals-methods0.6230.0170.639
plotSummary-methods0.4410.0000.441
pwf0.0040.0000.004
readTotals0.30.00.3
writeHtmlReport0.0010.0000.000