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This page was generated on 2025-09-20 12:03 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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

Package 1446/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ngsReports 2.11.1  (landing page)
Stevie Pederson
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 2025)
git_url: https://git.bioconductor.org/packages/ngsReports
git_branch: devel
git_last_commit: 15ce45d
git_last_commit_date: 2025-09-13 11:58:00 -0400 (Sat, 13 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ngsReports on nebbiolo2

To the developers/maintainers of the ngsReports package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ngsReports
Version: 2.11.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ngsReports.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ngsReports_2.11.1.tar.gz
StartedAt: 2025-09-20 02:23:42 -0400 (Sat, 20 Sep 2025)
EndedAt: 2025-09-20 02:27:53 -0400 (Sat, 20 Sep 2025)
EllapsedTime: 250.3 seconds
RetCode: 0
Status:   OK  
CheckDir: ngsReports.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ngsReports.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ngsReports_2.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ngsReports.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ngsReports/DESCRIPTION’ ... OK
* this is package ‘ngsReports’ version ‘2.11.1’
* 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 code 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 loading without being on the library search path ... 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

ngsReports.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ngsReports
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ngsReports’ ...
** this is package ‘ngsReports’ version ‘2.11.1’
** 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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: ggplot2
Loading required package: patchwork
Loading required package: tibble
> 
> test_check("ngsReports")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 388 ]
> 
> proc.time()
   user  system elapsed 
 69.651   2.143  71.807 

Example timings

ngsReports.Rcheck/ngsReports-Ex.timings

nameusersystemelapsed
FastqcData0.0680.0030.074
FastqcDataList0.3080.0110.328
TheoreticalGC-class0.0630.0010.063
dot-FastqcFile-class0.0020.0000.003
dot-addPercent000
dot-emptyPlot0.2060.0000.206
dot-makeDendro0.3080.0050.313
dot-makeLabels0.0010.0000.001
dot-splitByTab0.0030.0000.002
estGcDistn0.0170.0010.017
extract-methods0.3020.0020.303
fqName-methods0.3100.0030.312
fqcVersion0.4970.0330.529
gcAvail0.0190.0010.020
gcTheoretical0.0320.0030.035
getColours-methods0.0020.0000.002
getGC0.0170.0000.017
getModule0.3640.0000.364
getSummary0.3290.0030.332
importNgsLogs0.020.000.02
importSJ0.0060.0000.006
isCompressed0.0010.0000.002
mData0.0290.0000.029
maxAdapterContent0.3530.0070.360
overRep2Fasta-methods0.3430.0010.344
path0.6310.0320.663
plotAdapterContent-methods2.8530.1142.968
plotAlignmentSummary0.3370.0120.349
plotAssemblyStats0.8450.0000.844
plotBaseQuals-methods1.7480.0581.806
plotDupLevels-methods1.2410.0081.249
plotFastqcPCA-methods0.6510.0050.657
plotGcContent-methods1.0390.0041.043
plotInsertSize-methods0.6210.0000.622
plotKmers-methods1.7690.0041.774
plotNContent-methods0.8940.0020.896
plotOverrep-methods0.8620.0020.865
plotReadTotals-methods0.8670.0300.896
plotSeqContent-methods3.4190.0663.484
plotSeqLengthDistn-methods1.3050.0041.309
plotSeqQuals-methods1.8380.0241.863
plotSummary-methods0.5410.0060.547
pwf0.0040.0000.004
readTotals0.3290.0040.333
summariseOverrep-methods0.5280.0010.529
writeHtmlReport000