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CHECK report for basecallQC on malbec1

This page was generated on 2021-01-25 11:48:04 -0500 (Mon, 25 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE basecallQC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 116/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basecallQC 1.14.0
Thomas Carroll
Snapshot Date: 2021-01-24 14:40:16 -0500 (Sun, 24 Jan 2021)
URL: https://git.bioconductor.org/packages/basecallQC
Branch: RELEASE_3_12
Last Commit: 0930609
Last Changed Date: 2020-10-27 11:23:18 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: basecallQC
Version: 1.14.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings basecallQC_1.14.0.tar.gz
StartedAt: 2021-01-24 23:39:22 -0500 (Sun, 24 Jan 2021)
EndedAt: 2021-01-24 23:46:24 -0500 (Sun, 24 Jan 2021)
EllapsedTime: 422.7 seconds
RetCode: 0
Status:  OK 
CheckDir: basecallQC.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings basecallQC_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/basecallQC.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.14.0’
* 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             13.880  0.392  14.820
summaryConvStatsTable  9.860  0.088   9.973
makeFQTable            9.320  0.008   9.352
passFilterTileplot     9.260  0.020   9.307
passFilterBar          9.012  0.012   9.105
summaryDemuxTable      8.896  0.012   8.938
passFilterBoxplot      8.800  0.016   8.825
baseCallMetrics        8.752  0.048   9.026
demuxBarplot           8.756  0.016   8.793
demuxBoxplot           8.432  0.016   8.456
basecallQC             7.628  0.016   7.686
* 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-3.12-bioc/R/bin/R CMD INSTALL basecallQC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
══ Warnings ════════════════════════════════════════════════════════════════════
── Warning (test_Run1.R:8:1): (code run outside of `test_that()`) ──────────────
`tbl_df()` is deprecated as of dplyr 1.0.0.
Please use `tibble::as_tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Backtrace:
 1. basecallQC::BCL2FastQparams(...) test_Run1.R:8:0
 5. dplyr::tbl_df(.)
── Warning (test_Run1.R:9:1): (code run outside of `test_that()`) ──────────────
appending column names to file
Backtrace:
 1. basecallQC::basecallQC(bcl2fastqparams, RunMetaData = NULL, sampleSheet) test_Run1.R:9:0
 2. basecallQC::createBCLcommand(...)
 3. utils::write.table(...)
── Warning (test_Run1.R:10:1): (code run outside of `test_that()`) ─────────────
`summarise_()` is deprecated as of dplyr 0.7.0.
Please use `summarise()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Backtrace:
  1. basecallQC::passFilterBoxplot(bclQC, groupBy = "Sample") test_Run1.R:10:0
 10. dplyr::summarise_(...)
 11. dplyr:::lazy_deprec("summarise", hint = FALSE)
── Warning (test_Run1.R:10:1): (code run outside of `test_that()`) ─────────────
`group_by_()` is deprecated as of dplyr 0.7.0.
Please use `group_by()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Backtrace:
  1. basecallQC::passFilterBoxplot(bclQC, groupBy = "Sample") test_Run1.R:10:0
 12. dplyr::group_by_(., .dots = as.list(groupByS))
 13. dplyr:::lazy_deprec("group_by")
── Warning (test_Run1.R:11:1): (code run outside of `test_that()`) ─────────────
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(class(plot)[2] == "ggplot", is_true()) test_Run1.R:11:0
 2. testthat:::condition(object)
── Warning (test_Run2.R:8:1): (code run outside of `test_that()`) ──────────────
appending column names to file
Backtrace:
 1. basecallQC::basecallQC(bcl2fastqparams, RunMetaData = NULL, sampleSheet) test_Run2.R:8:0
 2. basecallQC::createBCLcommand(...)
 3. utils::write.table(...)
── Warning (test_Run2.R:13:1): (code run outside of `test_that()`) ─────────────
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...) test_Run2.R:13:0
 2. testthat:::condition(object)
── Warning (test_Run3.R:9:1): (code run outside of `test_that()`) ──────────────
appending column names to file
Backtrace:
 1. basecallQC::basecallQC(bcl2fastqparams, RunMetaData = NULL, sampleSheet) test_Run3.R:9:0
 2. basecallQC::createBCLcommand(...)
 3. utils::write.table(...)
── Warning (test_Run3.R:14:1): (code run outside of `test_that()`) ─────────────
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...) test_Run3.R:14:0
 2. testthat:::condition(object)
── Warning (test_Run4.R:9:1): (code run outside of `test_that()`) ──────────────
appending column names to file
Backtrace:
 1. basecallQC::basecallQC(bcl2fastqparams, RunMetaData = NULL, sampleSheet) test_Run4.R:9:0
 2. basecallQC::createBCLcommand(...)
 3. utils::write.table(...)
── Warning (test_Run4.R:14:1): (code run outside of `test_that()`) ─────────────
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...) test_Run4.R:14:0
 2. testthat:::condition(object)
── Warning (test_Run5.R:9:1): (code run outside of `test_that()`) ──────────────
appending column names to file
Backtrace:
 1. basecallQC::basecallQC(bcl2fastqparams, RunMetaData = NULL, sampleSheet) test_Run5.R:9:0
 2. basecallQC::createBCLcommand(...)
 3. utils::write.table(...)
── Warning (test_Run5.R:14:1): (code run outside of `test_that()`) ─────────────
`is_true()` is deprecated. Please use `expect_true()` instead.
Backtrace:
 1. testthat::expect_that(...) test_Run5.R:14:0
 2. testthat:::condition(object)

[ FAIL 0 | WARN 13 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
 26.936   0.524  27.842 

Example timings

basecallQC.Rcheck/basecallQC-Ex.timings

nameusersystemelapsed
BCL2FastQparams0.3280.0321.079
baseCallMetrics8.7520.0489.026
basecallQC7.6280.0167.686
createBCLcommand0.6480.0040.653
createBasemasks0.6720.0040.678
demultiplexMetrics0.1160.0000.113
demuxBarplot8.7560.0168.793
demuxBoxplot8.4320.0168.456
indexlengths0.0520.0000.049
interOpsReport0.0400.0000.041
makeFQTable9.3200.0089.352
passFilterBar9.0120.0129.105
passFilterBoxplot8.8000.0168.825
passFilterTileplot9.2600.0209.307
readlengths0.0520.0000.055
reportBCL13.880 0.39214.820
summaryConvStatsTable9.8600.0889.973
summaryDemuxTable8.8960.0128.938
validateBCLSheet0.1680.0000.168