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CHECK report for basecallQC on malbec2

This page was generated on 2018-10-17 08:30:08 -0400 (Wed, 17 Oct 2018).

Package 92/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basecallQC 1.4.0
Thomas Carroll
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/basecallQC
Branch: RELEASE_3_7
Last Commit: 91bb781
Last Changed Date: 2018-04-30 10:35:46 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: basecallQC
Version: 1.4.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings basecallQC_1.4.0.tar.gz
StartedAt: 2018-10-15 22:37:15 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 22:41:16 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 240.7 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-3.7-bioc/R/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings basecallQC_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/basecallQC.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.4.0’
* 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             8.756  0.336   9.162
basecallQC            5.860  0.008   5.872
makeFQTable           5.756  0.008   5.775
summaryConvStatsTable 5.480  0.072   5.559
summaryDemuxTable     5.520  0.020   5.543
demuxBoxplot          5.496  0.004   5.507
passFilterBoxplot     5.396  0.004   5.402
passFilterTileplot    5.288  0.016   5.304
demuxBarplot          5.228  0.016   5.246
baseCallMetrics       5.064  0.108   5.178
passFilterBar         5.000  0.000   5.007
* 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-3.7-bioc/R/bin/R CMD INSTALL basecallQC
###
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* installing to library ‘/home/biocbuild/bbs-3.7-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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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 
 15.452   0.428  15.932 

Example timings

basecallQC.Rcheck/basecallQC-Ex.timings

nameusersystemelapsed
BCL2FastQparams0.8360.0080.860
baseCallMetrics5.0640.1085.178
basecallQC5.8600.0085.872
createBCLcommand0.2760.0000.278
createBasemasks0.1800.0000.181
demultiplexMetrics0.0480.0000.050
demuxBarplot5.2280.0165.246
demuxBoxplot5.4960.0045.507
indexlengths0.0200.0000.022
interOpsReport0.0240.0000.024
makeFQTable5.7560.0085.775
passFilterBar5.0000.0005.007
passFilterBoxplot5.3960.0045.402
passFilterTileplot5.2880.0165.304
readlengths0.0240.0000.023
reportBCL8.7560.3369.162
summaryConvStatsTable5.4800.0725.559
summaryDemuxTable5.5200.0205.543
validateBCLSheet0.1280.0000.126