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CHECK report for NanoStringQCPro on malbec1

This page was generated on 2020-04-15 12:09:59 -0400 (Wed, 15 Apr 2020).

Package 1131/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoStringQCPro 1.18.0
Robert Ziman
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/NanoStringQCPro
Branch: RELEASE_3_10
Last Commit: f862b69
Last Changed Date: 2019-10-29 13:09:16 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: NanoStringQCPro
Version: 1.18.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:NanoStringQCPro.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings NanoStringQCPro_1.18.0.tar.gz
StartedAt: 2020-04-15 02:58:02 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 03:00:10 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 127.3 seconds
RetCode: 0
Status:  OK 
CheckDir: NanoStringQCPro.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:NanoStringQCPro.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings NanoStringQCPro_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/NanoStringQCPro.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.18.0’
* 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 13.372  0.284  13.737
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/NanoStringQCPro.Rcheck/00check.log’
for details.



Installation output

NanoStringQCPro.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL NanoStringQCPro
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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-class0.5960.0040.599
addCodesetAnnotation0.3200.0000.591
buildCodesetAnnotation0.0120.0000.018
checkRccSet0.0920.0000.091
contentNorm0.1560.0000.157
copyRccSet0.0200.0000.017
getBackground0.1040.0000.103
getBlankLabel0.0000.0000.002
makeQCReport13.372 0.28413.737
newRccSet0.3640.0000.368
posCtrlNorm0.0240.0000.025
preprocRccSet0.1880.0000.188
presAbsCall0.0640.0000.064
readCdrDesignData0.0040.0000.003
readRcc0.0080.0000.005
readRlf0.0040.0000.006
subtractBackground0.0920.0000.095