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CHECK report for NanoStringQCPro on malbec2

This page was generated on 2018-10-17 08:27:30 -0400 (Wed, 17 Oct 2018).

Package 979/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoStringQCPro 1.12.0
Robert Ziman
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/NanoStringQCPro
Branch: RELEASE_3_7
Last Commit: 009d557
Last Changed Date: 2018-04-30 10:35:36 -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: NanoStringQCPro
Version: 1.12.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:NanoStringQCPro.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings NanoStringQCPro_1.12.0.tar.gz
StartedAt: 2018-10-16 02:18:12 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 02:19:41 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 88.7 seconds
RetCode: 0
Status:  OK 
CheckDir: NanoStringQCPro.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:NanoStringQCPro.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings NanoStringQCPro_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/NanoStringQCPro.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 ‘NanoStringQCPro/DESCRIPTION’ ... OK
* this is package ‘NanoStringQCPro’ version ‘1.12.0’
* 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 ‘NanoStringQCPro’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘knitr’
A package should be listed in only one of these fields.
* 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 ... NOTE
centeredSampleClustering: no visible global function definition for
  ‘png’
centeredSampleClustering: no visible global function definition for
  ‘dev.off’
countsInBlankSamples_verticalPlot: no visible global function
  definition for ‘png’
countsInBlankSamples_verticalPlot: no visible global function
  definition for ‘dev.off’
geneClustering: no visible global function definition for ‘png’
geneClustering: no visible global function definition for ‘dev.off’
negCtrlsByLane_verticalPlot: no visible global function definition for
  ‘png’
negCtrlsByLane_verticalPlot: no visible global function definition for
  ‘dev.off’
previewPNG: no visible global function definition for ‘png’
previewPNG: no visible global function definition for ‘dev.off’
sampleClustering,RccSet: no visible global function definition for
  ‘png’
sampleClustering,RccSet: no visible global function definition for
  ‘dev.off’
Undefined global functions or variables:
  dev.off png
Consider adding
  importFrom("grDevices", "dev.off", "png")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
makeQCReport 10.668  0.372  11.087
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/NanoStringQCPro.Rcheck/00check.log’
for details.



Installation output

NanoStringQCPro.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL NanoStringQCPro
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘NanoStringQCPro’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (NanoStringQCPro)

Tests output


Example timings

NanoStringQCPro.Rcheck/NanoStringQCPro-Ex.timings

nameusersystemelapsed
RccSet-class0.3960.0000.395
addCodesetAnnotation0.3280.0000.345
buildCodesetAnnotation0.0120.0040.023
checkRccSet0.0720.0000.071
contentNorm0.1400.0040.146
copyRccSet0.0120.0000.012
getBackground0.0760.0000.075
getBlankLabel0.0000.0000.002
makeQCReport10.668 0.37211.087
newRccSet0.2200.0200.241
posCtrlNorm0.0120.0040.016
preprocRccSet0.1040.0000.105
presAbsCall0.0440.0000.045
readCdrDesignData0.0000.0000.002
readRcc0.0040.0000.003
readRlf0.0040.0000.003
subtractBackground0.0560.0000.055