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CHECK report for NanoStringQCPro on merida1

This page was generated on 2021-02-22 12:44:00 -0500 (Mon, 22 Feb 2021).

To the developers/maintainers of the NanoStringQCPro package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1199/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoStringQCPro 1.22.0
Robert Ziman
Snapshot Date: 2021-02-21 14:52:07 -0500 (Sun, 21 Feb 2021)
URL: https://git.bioconductor.org/packages/NanoStringQCPro
Branch: RELEASE_3_12
Last Commit: 11526ca
Last Changed Date: 2020-10-27 11:04:32 -0500 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: NanoStringQCPro
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NanoStringQCPro.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NanoStringQCPro_1.22.0.tar.gz
StartedAt: 2021-02-22 04:20:02 -0500 (Mon, 22 Feb 2021)
EndedAt: 2021-02-22 04:22:42 -0500 (Mon, 22 Feb 2021)
EllapsedTime: 159.9 seconds
RetCode: 0
Status:   OK  
CheckDir: NanoStringQCPro.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NanoStringQCPro.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NanoStringQCPro_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/NanoStringQCPro.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NanoStringQCPro/DESCRIPTION’ ... OK
* this is package ‘NanoStringQCPro’ version ‘1.22.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
makeQCReport 15.347  0.544  19.019
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/NanoStringQCPro.Rcheck/00check.log’
for details.



Installation output

NanoStringQCPro.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘NanoStringQCPro’ ...
** using staged installation
** 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 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 (NanoStringQCPro)

Tests output


Example timings

NanoStringQCPro.Rcheck/NanoStringQCPro-Ex.timings

nameusersystemelapsed
RccSet-class0.4620.0060.468
addCodesetAnnotation0.3610.0090.373
buildCodesetAnnotation0.0110.0010.012
checkRccSet0.0680.0020.070
contentNorm0.1470.0020.149
copyRccSet0.0220.0010.023
getBackground0.1060.0020.109
getBlankLabel0.0020.0010.003
makeQCReport15.347 0.54419.019
newRccSet0.4140.0160.429
posCtrlNorm0.0260.0010.027
preprocRccSet0.2040.0030.207
presAbsCall0.0630.0020.065
readCdrDesignData0.0030.0000.003
readRcc0.0060.0010.007
readRlf0.0040.0000.004
subtractBackground0.0910.0010.093