Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:04:54 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 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 basecallQC on nebbiolo2


To the developers/maintainers of the basecallQC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/basecallQC.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 115/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basecallQC 1.18.0  (landing page)
Thomas Carroll
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/basecallQC
git_branch: RELEASE_3_14
git_last_commit: 503470b
git_last_commit_date: 2021-10-26 12:34:33 -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: basecallQC
Version: 1.18.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings basecallQC_1.18.0.tar.gz
StartedAt: 2022-01-13 06:24:39 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 06:31:57 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 438.1 seconds
RetCode: 0
Status:   OK  
CheckDir: basecallQC.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings basecallQC_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/basecallQC.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 ‘basecallQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘basecallQC’ version ‘1.18.0’
* 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 ‘basecallQC’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
reportBCL          7.923  0.093   8.035
passFilterBar      6.838  0.072   6.911
baseCallMetrics    6.570  0.144   6.714
demuxBarplot       5.400  0.024   5.424
passFilterTileplot 5.237  0.008   5.245
basecallQC         5.213  0.024   5.236
demuxBoxplot       5.212  0.016   5.227
makeFQTable        5.135  0.004   5.139
* 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

basecallQC.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL basecallQC
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘basecallQC’ ...
** using staged installation
** R
** 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 (basecallQC)

Tests output

basecallQC.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(basecallQC)
Loading required package: rmarkdown
Loading required package: knitr
Loading required package: prettydoc
Loading required package: yaml
> 
> test_check("basecallQC")
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
 25.355   1.246  26.588 

Example timings

basecallQC.Rcheck/basecallQC-Ex.timings

nameusersystemelapsed
BCL2FastQparams0.1760.0440.221
baseCallMetrics6.5700.1446.714
basecallQC5.2130.0245.236
createBCLcommand0.5850.0000.585
createBasemasks0.5150.0000.514
demultiplexMetrics0.0800.0000.079
demuxBarplot5.4000.0245.424
demuxBoxplot5.2120.0165.227
indexlengths0.0410.0000.040
interOpsReport0.030.000.03
makeFQTable5.1350.0045.139
passFilterBar6.8380.0726.911
passFilterBoxplot4.8570.0404.896
passFilterTileplot5.2370.0085.245
readlengths0.0440.0000.044
reportBCL7.9230.0938.035
summaryConvStatsTable4.7940.0374.831
summaryDemuxTable4.6570.0044.661
validateBCLSheet0.1070.0000.107