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CHECK report for basecallQC on malbec1

This page was generated on 2019-04-16 11:52:44 -0400 (Tue, 16 Apr 2019).

Package 98/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basecallQC 1.6.0
Thomas Carroll
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/basecallQC
Branch: RELEASE_3_8
Last Commit: 2a64547
Last Changed Date: 2018-10-30 11:42:04 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: basecallQC
Version: 1.6.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings basecallQC_1.6.0.tar.gz
StartedAt: 2019-04-15 22:19:45 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:25:50 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 364.3 seconds
RetCode: 0
Status:  OK 
CheckDir: basecallQC.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings basecallQC_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/basecallQC.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.6.0’
* 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 or elapsed time > 5s
                        user system elapsed
reportBCL             14.988  0.452  15.763
demuxBarplot           9.572  0.020   9.633
baseCallMetrics        9.180  0.144   9.561
passFilterBoxplot      8.932  0.012   9.018
basecallQC             8.816  0.024   8.956
demuxBoxplot           8.804  0.000   8.852
makeFQTable            8.460  0.012   8.527
passFilterBar          8.456  0.000   8.541
summaryConvStatsTable  8.308  0.088   8.444
passFilterTileplot     8.280  0.008   8.422
summaryDemuxTable      8.208  0.020   8.352
* 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-3.8-bioc/R/bin/R CMD INSTALL basecallQC
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘basecallQC’ ...
** 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
* DONE (basecallQC)

Tests output

basecallQC.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 10 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 21.036   0.472  21.566 

Example timings

basecallQC.Rcheck/basecallQC-Ex.timings

nameusersystemelapsed
BCL2FastQparams0.5280.0160.572
baseCallMetrics9.1800.1449.561
basecallQC8.8160.0248.956
createBCLcommand0.2600.0000.261
createBasemasks0.2560.0000.257
demultiplexMetrics0.0840.0000.085
demuxBarplot9.5720.0209.633
demuxBoxplot8.8040.0008.852
indexlengths0.0360.0000.036
interOpsReport0.0280.0040.030
makeFQTable8.4600.0128.527
passFilterBar8.4560.0008.541
passFilterBoxplot8.9320.0129.018
passFilterTileplot8.2800.0088.422
readlengths0.0360.0000.037
reportBCL14.988 0.45215.763
summaryConvStatsTable8.3080.0888.444
summaryDemuxTable8.2080.0208.352
validateBCLSheet0.0600.0000.062