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CHECK report for basecallQC on malbec1

This page was generated on 2018-04-12 13:16:09 -0400 (Thu, 12 Apr 2018).

Package 90/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basecallQC 1.2.0
Thomas Carroll
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/basecallQC
Branch: RELEASE_3_6
Last Commit: 967a5d5
Last Changed Date: 2017-10-30 12:41:27 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: basecallQC
Version: 1.2.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings basecallQC_1.2.0.tar.gz
StartedAt: 2018-04-11 21:37:48 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 21:42:22 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 274.4 seconds
RetCode: 0
Status:  OK 
CheckDir: basecallQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings basecallQC_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/basecallQC.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.2.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
reportBCL             12.920  0.224  13.433
makeFQTable            7.280  0.000   7.287
passFilterBoxplot      7.176  0.020   7.209
basecallQC             6.296  0.016   6.348
baseCallMetrics        6.232  0.048   6.296
summaryConvStatsTable  6.016  0.104   6.136
passFilterBar          6.020  0.004   6.030
demuxBarplot           5.900  0.024   5.927
passFilterTileplot     5.908  0.004   5.915
demuxBoxplot           5.812  0.004   5.819
summaryDemuxTable      5.592  0.004   5.599
* 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

* installing *source* package ‘basecallQC’ ...
** R
** inst
** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
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 
 15.716   0.252  15.976 

Example timings

basecallQC.Rcheck/basecallQC-Ex.timings

nameusersystemelapsed
BCL2FastQparams0.9720.0241.028
baseCallMetrics6.2320.0486.296
basecallQC6.2960.0166.348
createBCLcommand0.2840.0000.283
createBasemasks0.20.00.2
demultiplexMetrics0.1400.0000.141
demuxBarplot5.9000.0245.927
demuxBoxplot5.8120.0045.819
indexlengths0.0240.0000.022
interOpsReport0.020.000.02
makeFQTable7.2800.0007.287
passFilterBar6.0200.0046.030
passFilterBoxplot7.1760.0207.209
passFilterTileplot5.9080.0045.915
readlengths0.0240.0000.024
reportBCL12.920 0.22413.433
summaryConvStatsTable6.0160.1046.136
summaryDemuxTable5.5920.0045.599
validateBCLSheet0.0480.0000.045