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CHECK report for NanoStringQCPro on tokay1

This page was generated on 2021-02-22 12:39:31 -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: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NanoStringQCPro.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings NanoStringQCPro_1.22.0.tar.gz
StartedAt: 2021-02-22 05:05:57 -0500 (Mon, 22 Feb 2021)
EndedAt: 2021-02-22 05:09:15 -0500 (Mon, 22 Feb 2021)
EllapsedTime: 197.6 seconds
RetCode: 0
Status:   OK   
CheckDir: NanoStringQCPro.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NanoStringQCPro.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings NanoStringQCPro_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/NanoStringQCPro.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
makeQCReport 9.53   2.63   12.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
makeQCReport 11.31   2.89   14.26
* checking PDF version of manual ... OK
* DONE

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



Installation output

NanoStringQCPro.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/NanoStringQCPro_1.22.0.tar.gz && rm -rf NanoStringQCPro.buildbin-libdir && mkdir NanoStringQCPro.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NanoStringQCPro.buildbin-libdir NanoStringQCPro_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL NanoStringQCPro_1.22.0.zip && rm NanoStringQCPro_1.22.0.tar.gz NanoStringQCPro_1.22.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  245k  100  245k    0     0  2811k      0 --:--:-- --:--:-- --:--:-- 2926k

install for i386

* 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
  converting help for package 'NanoStringQCPro'
    finding HTML links ... done
    NanoStringQCPro                         html  
    RccSet-class                            html  
    finding level-2 HTML links ... done

    RccSet                                  html  
    addCodesetAnnotation                    html  
    addQCFlags                              html  
    allSumPlot                              html  
    assessHousekeeping                      html  
    bdPlot                                  html  
    buildCodesetAnnotation                  html  
    checkRccSet                             html  
    colByCovar                              html  
    colByFun                                html  
    contentNorm                             html  
    copyRccSet                              html  
    countsInBlankSamples_verticalPlot       html  
    ctrlsOverviewPlot                       html  
    ctrlsZprimePlot                         html  
    cutoffByMMAD                            html  
    cutoffByVar                             html  
    dCoVar                                  html  
    densityPlot                             html  
    example_rccSet                          html  
    flagSamplesCount                        html  
    flagSamplesCtrl                         html  
    flagSamplesTech                         html  
    fovPlot                                 html  
    geneClustering                          html  
    getBackground                           html  
    getBlankLabel                           html  
    getSpikeInInput                         html  
    iqrPlot                                 html  
    lodAssess                               html  
    lodPlot                                 html  
    makeQCReport                            html  
    myCols                                  html  
    nSolverBackground                       html  
    nSolverCsv.to.pdata_fdata_adata         html  
    negCtrlsByLane                          html  
    negCtrlsByLane_verticalPlot             html  
    negCtrlsPairs                           html  
    negCtrlsPlot                            html  
    newRccSet                               html  
    panelCor                                html  
    pcaPlot                                 html  
    pdata_fdata_adata.to.rccSet             html  
    posCtrlNorm                             html  
    posNormFactPlot                         html  
    posR2Plot                               html  
    posRatioPlot                            html  
    posSlopePlot                            html  
    posSumVsAllSumPlot                      html  
    preprocRccSet                           html  
    presAbsCall                             html  
    previewPNG                              html  
    rccFiles.to.pdata_fdata_adata           html  
    readCdrDesignData                       html  
    readRcc                                 html  
    readRccBatch                            html  
    readRccCollectorToolExport              html  
    readRlf                                 html  
    sampleClustering                        html  
    scatterPair                             html  
    subtractBackground                      html  
    zfacFun                                 html  
** 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

install for x64

* installing *source* package 'NanoStringQCPro' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NanoStringQCPro' as NanoStringQCPro_1.22.0.zip
* DONE (NanoStringQCPro)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'NanoStringQCPro' successfully unpacked and MD5 sums checked

Tests output


Example timings

NanoStringQCPro.Rcheck/examples_i386/NanoStringQCPro-Ex.timings

nameusersystemelapsed
RccSet-class0.610.000.61
addCodesetAnnotation0.390.020.40
buildCodesetAnnotation0.020.000.02
checkRccSet0.080.000.07
contentNorm0.170.000.18
copyRccSet0.020.000.01
getBackground0.120.010.14
getBlankLabel000
makeQCReport 9.53 2.6312.16
newRccSet0.350.010.36
posCtrlNorm0.030.000.03
preprocRccSet0.210.000.21
presAbsCall0.060.000.06
readCdrDesignData000
readRcc000
readRlf000
subtractBackground0.070.000.06

NanoStringQCPro.Rcheck/examples_x64/NanoStringQCPro-Ex.timings

nameusersystemelapsed
RccSet-class0.720.000.72
addCodesetAnnotation0.450.030.48
buildCodesetAnnotation0.000.020.01
checkRccSet0.090.000.09
contentNorm0.210.000.21
copyRccSet0.030.000.03
getBackground0.150.000.15
getBlankLabel0.020.000.02
makeQCReport11.31 2.8914.26
newRccSet0.410.010.43
posCtrlNorm0.030.000.03
preprocRccSet0.20.00.2
presAbsCall0.060.000.07
readCdrDesignData000
readRcc000
readRlf000
subtractBackground0.130.000.12