Back to Multiple platform build/check report for BioC 3.9
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for basecallQC on celaya2

This page was generated on 2019-04-09 13:18:10 -0400 (Tue, 09 Apr 2019).

Package 102/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basecallQC 1.7.0
Thomas Carroll
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/basecallQC
Branch: master
Last Commit: 33f4312
Last Changed Date: 2018-10-30 11:54:37 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  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 

Summary

Package: basecallQC
Version: 1.7.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings basecallQC_1.7.0.tar.gz
StartedAt: 2019-04-09 00:00:24 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:08:03 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 459.4 seconds
RetCode: 0
Status:  OK 
CheckDir: basecallQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings basecallQC_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/basecallQC.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.7.0’
* 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             15.705  0.983  17.002
baseCallMetrics       11.295  0.412  11.709
demuxBoxplot          10.512  0.155  10.668
demuxBarplot          10.438  0.173  10.611
summaryDemuxTable     10.518  0.079  10.595
basecallQC            10.461  0.090  10.554
passFilterBoxplot     10.431  0.077  10.509
passFilterTileplot    10.074  0.069  10.146
passFilterBar          9.735  0.050   9.788
makeFQTable            9.674  0.051   9.724
summaryConvStatsTable  9.069  0.049   9.115
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL basecallQC
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 
 29.293   1.929  31.180 

Example timings

basecallQC.Rcheck/basecallQC-Ex.timings

nameusersystemelapsed
BCL2FastQparams0.8310.0980.932
baseCallMetrics11.295 0.41211.709
basecallQC10.461 0.09010.554
createBCLcommand0.2910.0040.296
createBasemasks0.2800.0050.285
demultiplexMetrics0.0920.0030.095
demuxBarplot10.438 0.17310.611
demuxBoxplot10.512 0.15510.668
indexlengths0.0780.0080.087
interOpsReport0.0370.0010.038
makeFQTable9.6740.0519.724
passFilterBar9.7350.0509.788
passFilterBoxplot10.431 0.07710.509
passFilterTileplot10.074 0.06910.146
readlengths0.0260.0000.027
reportBCL15.705 0.98317.002
summaryConvStatsTable9.0690.0499.115
summaryDemuxTable10.518 0.07910.595
validateBCLSheet0.0770.0020.078