Back to Multiple platform build/check report for BioC 3.15
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-10-19 13:22:35 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 merida1


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? 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 115/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basecallQC 1.20.0  (landing page)
Thomas Carroll
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/basecallQC
git_branch: RELEASE_3_15
git_last_commit: c233bf5
git_last_commit_date: 2022-04-26 11:40:14 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: basecallQC
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings basecallQC_1.20.0.tar.gz
StartedAt: 2022-10-18 23:26:32 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 23:39:09 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 756.8 seconds
RetCode: 0
Status:   OK  
CheckDir: basecallQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings basecallQC_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/basecallQC.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.20.0’
* 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             17.709  0.234  18.402
passFilterBoxplot     12.458  0.094  12.612
demuxBarplot          12.212  0.119  12.353
passFilterTileplot    11.602  0.047  11.718
baseCallMetrics       11.197  0.301  11.525
passFilterBar         11.371  0.057  11.599
summaryConvStatsTable 11.354  0.069  11.463
summaryDemuxTable     11.279  0.044  11.358
demuxBoxplot          11.017  0.040  11.069
basecallQC            10.942  0.061  11.023
makeFQTable           10.678  0.037  10.737
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL basecallQC
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 15 | SKIP 0 | PASS 5 ]

[ FAIL 0 | WARN 15 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
 49.031   1.294  50.614 

Example timings

basecallQC.Rcheck/basecallQC-Ex.timings

nameusersystemelapsed
BCL2FastQparams0.4900.0560.548
baseCallMetrics11.197 0.30111.525
basecallQC10.942 0.06111.023
createBCLcommand0.9500.0110.962
createBasemasks0.9030.0110.916
demultiplexMetrics0.1790.0030.183
demuxBarplot12.212 0.11912.353
demuxBoxplot11.017 0.04011.069
indexlengths0.0840.0020.085
interOpsReport0.0690.0010.071
makeFQTable10.678 0.03710.737
passFilterBar11.371 0.05711.599
passFilterBoxplot12.458 0.09412.612
passFilterTileplot11.602 0.04711.718
readlengths0.0910.0030.093
reportBCL17.709 0.23418.402
summaryConvStatsTable11.354 0.06911.463
summaryDemuxTable11.279 0.04411.358
validateBCLSheet0.2470.0020.250