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This page was generated on 2023-06-06 11:00:26 -0000 (Tue, 06 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4366
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 kunpeng2


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 124/2199HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basecallQC 1.25.0  (landing page)
Thomas Carroll
Snapshot Date: 2023-06-05 06:35:06 -0000 (Mon, 05 Jun 2023)
git_url: https://git.bioconductor.org/packages/basecallQC
git_branch: devel
git_last_commit: 04dfd76
git_last_commit_date: 2023-04-25 14:53:38 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

Summary

Package: basecallQC
Version: 1.25.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings basecallQC_1.25.0.tar.gz
StartedAt: 2023-06-05 17:42:55 -0000 (Mon, 05 Jun 2023)
EndedAt: 2023-06-05 17:53:27 -0000 (Mon, 05 Jun 2023)
EllapsedTime: 631.9 seconds
RetCode: 0
Status:   OK  
CheckDir: basecallQC.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings basecallQC_1.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/basecallQC.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘basecallQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘basecallQC’ version ‘1.25.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
reportBCL             11.700  0.234  11.969
demuxBarplot           8.741  0.268   9.023
baseCallMetrics        7.736  0.160   7.919
passFilterTileplot     7.360  0.024   7.396
passFilterBoxplot      7.189  0.151   7.354
summaryDemuxTable      7.229  0.060   7.301
summaryConvStatsTable  7.067  0.131   7.214
demuxBoxplot           7.096  0.064   7.176
basecallQC             7.085  0.016   7.118
passFilterBar          6.969  0.024   7.006
makeFQTable            6.857  0.031   6.904
* 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 ...
  ‘basecallQC.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

basecallQC.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL basecallQC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
The legacy packages maptools, rgdal, and rgeos, underpinning this package
will retire shortly. Please refer to R-spatial evolution reports on
https://r-spatial.org/r/2023/05/15/evolution4.html for details.
This package is now running under evolution status 0 
> 
> test_check("basecallQC")
[ FAIL 0 | WARN 47 | SKIP 0 | PASS 5 ]

[ FAIL 0 | WARN 47 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
 35.263   1.948  37.316 

Example timings

basecallQC.Rcheck/basecallQC-Ex.timings

nameusersystemelapsed
BCL2FastQparams0.3280.0440.375
baseCallMetrics7.7360.1607.919
basecallQC7.0850.0167.118
createBCLcommand0.5990.0080.609
createBasemasks0.5520.0160.569
demultiplexMetrics0.1030.0000.103
demuxBarplot8.7410.2689.023
demuxBoxplot7.0960.0647.176
indexlengths0.0510.0040.056
interOpsReport0.0400.0040.044
makeFQTable6.8570.0316.904
passFilterBar6.9690.0247.006
passFilterBoxplot7.1890.1517.354
passFilterTileplot7.3600.0247.396
readlengths0.0530.0000.053
reportBCL11.700 0.23411.969
summaryConvStatsTable7.0670.1317.214
summaryDemuxTable7.2290.0607.301
validateBCLSheet0.1380.0040.143