Package: qPLEXanalyzer

Version: 1.1.3

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qPLEXanalyzer.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings qPLEXanalyzer_1.1.3.tar.gz

StartedAt: 2019-04-09 05:09:43 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:14:00 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 256.4 seconds

RetCode: 0

Status:  OK

CheckDir: qPLEXanalyzer.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qPLEXanalyzer.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings qPLEXanalyzer_1.1.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/qPLEXanalyzer.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'qPLEXanalyzer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'qPLEXanalyzer' version '1.1.3'
* 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 'qPLEXanalyzer' 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
* 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
convertToMSnset: no visible binding for global variable '.'
corrPlot: no visible binding for global variable 'Cor'
corrPlot: no visible binding for global variable 'X'
corrPlot: no visible binding for global variable 'Y'
corrPlot: no visible binding for global variable 'CorTxt'
coveragePlot: no visible binding for global variable 'Accessions'
coveragePlot: no visible binding for global variable 'Sequence'
coveragePlot: no visible binding for global variable '.'
getContrastResults: no visible binding for global variable 'B'
getContrastResults: no visible binding for global variable '.'
getContrastResults: no visible binding for global variable 'AveExpr'
getContrastResults: no visible binding for global variable 'logFC'
groupScaling: no visible binding for global variable 'PeptideID'
groupScaling: no visible binding for global variable 'SampleName'
groupScaling: no visible binding for global variable 'RawIntensity'
groupScaling: no visible binding for global variable 'Grouping_column'
groupScaling: no visible binding for global variable 'scaledIntensity'
groupScaling: no visible binding for global variable
  'meanscaledIntensity'
groupScaling: no visible binding for global variable 'scalingFactors'
groupScaling: no visible binding for global variable
  'normalizedIntensities'
hierarchicalPlot: no visible binding for global variable 'x'
hierarchicalPlot: no visible binding for global variable 'y'
hierarchicalPlot: no visible binding for global variable 'xend'
hierarchicalPlot: no visible binding for global variable 'yend'
intensityBoxplot: no visible binding for global variable 'Intensity'
intensityBoxplot: no visible binding for global variable 'logInt'
intensityPlot: no visible binding for global variable 'SampleName'
intensityPlot: no visible binding for global variable 'Intensity'
maVolPlot: no visible binding for global variable
  'controlLogFoldChange'
maVolPlot: no visible binding for global variable '.'
maVolPlot: no visible binding for global variable 'Accessions'
maVolPlot: no visible binding for global variable 'group'
maVolPlot: no visible binding for global variable 'adj.P.Val'
maVolPlot: no visible binding for global variable 'GeneSymbol'
peptideIntensityPlot: no visible binding for global variable
  'SampleName'
peptideIntensityPlot: no visible binding for global variable
  'Intensity'
peptideIntensityPlot: no visible binding for global variable
  'PeptideID'
peptideIntensityPlot: no visible binding for global variable
  'Accessions'
peptideIntensityPlot: no visible binding for global variable
  'Sequences'
peptideIntensityPlot: no visible binding for global variable
  'Modifications'
peptideIntensityPlot: no visible binding for global variable
  'logIntensity'
plotMeanVar: no visible binding for global variable 'x'
plotMeanVar: no visible binding for global variable 'y'
plotMeanVar: no visible binding for global variable 'Mean'
plotMeanVar: no visible binding for global variable 'Variance'
rliPlot: no visible binding for global variable 'RowID'
rliPlot: no visible binding for global variable 'Intensity'
rliPlot: no visible binding for global variable 'logInt'
rliPlot: no visible binding for global variable 'medianLogInt'
summarizeIntensities: no visible binding for global variable
  'Accessions'
summarizeIntensities: no visible binding for global variable
  'Sequences'
summarizeIntensities: no visible binding for global variable 'Count'
Undefined global functions or variables:
  . Accessions AveExpr B Cor CorTxt Count GeneSymbol Grouping_column
  Intensity Mean Modifications PeptideID RawIntensity RowID SampleName
  Sequence Sequences Variance X Y adj.P.Val controlLogFoldChange group
  logFC logInt logIntensity meanscaledIntensity medianLogInt
  normalizedIntensities scaledIntensity scalingFactors x xend y yend
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/qPLEXanalyzer.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/qPLEXanalyzer_1.1.3.tar.gz && rm -rf qPLEXanalyzer.buildbin-libdir && mkdir qPLEXanalyzer.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qPLEXanalyzer.buildbin-libdir qPLEXanalyzer_1.1.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL qPLEXanalyzer_1.1.3.zip && rm qPLEXanalyzer_1.1.3.tar.gz qPLEXanalyzer_1.1.3.zip
###
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100 1197k  100 1197k    0     0  16.4M      0 --:--:-- --:--:-- --:--:-- 18.2M

install for i386

* installing *source* package 'qPLEXanalyzer' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'qPLEXanalyzer'
    finding HTML links ... done
    assignColours                           html  
    computeDiffStats                        html  
    finding level-2 HTML links ... done

    convertToMSnset                         html  
    corrPlot                                html  
    coveragePlot                            html  
    exp2_Xlink                              html  
    exp3_OHT_ESR1                           html  
    getContrastResults                      html  
    groupScaling                            html  
    hierarchicalPlot                        html  
    human_anno                              html  
    intensityBoxplot                        html  
    intensityPlot                           html  
    maVolPlot                               html  
    normalizeQuantiles                      html  
    normalizeScaling                        html  
    pcaPlot                                 html  
    peptideIntensityPlot                    html  
    plotMeanVar                             html  
    qPLEXanalyzer-package                   html  
    regressIntensity                        html  
    rliPlot                                 html  
    rowScaling                              html  
    summarizeIntensities                    html  
** 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

install for x64

* installing *source* package 'qPLEXanalyzer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qPLEXanalyzer' as qPLEXanalyzer_1.1.3.zip
* DONE (qPLEXanalyzer)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'qPLEXanalyzer' successfully unpacked and MD5 sums checked