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This page was generated on 2025-09-27 12:04 -0400 (Sat, 27 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4832
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4620
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 134/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basecallQC 1.33.0  (landing page)
Thomas Carroll
Snapshot Date: 2025-09-26 13:45 -0400 (Fri, 26 Sep 2025)
git_url: https://git.bioconductor.org/packages/basecallQC
git_branch: devel
git_last_commit: 3b9d7e5
git_last_commit_date: 2025-04-15 11:10:19 -0400 (Tue, 15 Apr 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 basecallQC on lconway

To the developers/maintainers of the basecallQC package:
- 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 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: basecallQC
Version: 1.33.0
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_1.33.0.tar.gz
StartedAt: 2025-09-26 19:33:08 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 19:41:27 -0400 (Fri, 26 Sep 2025)
EllapsedTime: 499.4 seconds
RetCode: 0
Status:   OK  
CheckDir: basecallQC.Rcheck
Warnings: 0

Command output

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### 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_1.33.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/basecallQC.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘basecallQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘basecallQC’ version ‘1.33.0’
* 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 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 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 ... NOTE
checkRd: (-1) BCL2FastQparams.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BCL2FastQparams.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BCL2FastQparams.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:40-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:51-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) interOpsReport.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) interOpsReport.Rd:34-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) interOpsReport.Rd:38-41: Lost braces in \itemize; meant \describe ?
* 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             9.273  0.302   9.972
baseCallMetrics       6.338  0.186   6.558
passFilterTileplot    6.471  0.046   6.539
demuxBoxplot          5.666  0.067   5.757
makeFQTable           5.675  0.023   5.712
demuxBarplot          5.630  0.050   5.705
passFilterBoxplot     5.632  0.048   5.704
summaryDemuxTable     5.498  0.031   5.552
summaryConvStatsTable 5.462  0.025   5.501
passFilterBar         5.451  0.026   5.491
basecallQC            5.427  0.041   5.487
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/basecallQC.Rcheck/00check.log’
for details.


Installation output

basecallQC.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘basecallQC’ ...
** this is package ‘basecallQC’ version ‘1.33.0’
** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 47 | SKIP 0 | PASS 5 ]

[ FAIL 0 | WARN 47 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
 31.794   1.108  33.151 

Example timings

basecallQC.Rcheck/basecallQC-Ex.timings

nameusersystemelapsed
BCL2FastQparams0.2860.0360.328
baseCallMetrics6.3380.1866.558
basecallQC5.4270.0415.487
createBCLcommand0.3290.0040.334
createBasemasks0.3190.0030.323
demultiplexMetrics0.0680.0020.070
demuxBarplot5.6300.0505.705
demuxBoxplot5.6660.0675.757
indexlengths0.0340.0020.035
interOpsReport0.0180.0010.019
makeFQTable5.6750.0235.712
passFilterBar5.4510.0265.491
passFilterBoxplot5.6320.0485.704
passFilterTileplot6.4710.0466.539
readlengths0.0290.0020.031
reportBCL9.2730.3029.972
summaryConvStatsTable5.4620.0255.501
summaryDemuxTable5.4980.0315.552
validateBCLSheet0.0710.0020.073