Package: qPLEXanalyzer

Version: 1.1.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qPLEXanalyzer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qPLEXanalyzer_1.1.3.tar.gz

StartedAt: 2019-04-09 04:40:12 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:44:02 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 229.8 seconds

RetCode: 0

Status:  OK

CheckDir: qPLEXanalyzer.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qPLEXanalyzer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qPLEXanalyzer_1.1.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/qPLEXanalyzer.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
rliPlot 4.837  0.231   5.069
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/qPLEXanalyzer.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL qPLEXanalyzer
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘qPLEXanalyzer’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (qPLEXanalyzer)

name	user	system	elapsed
assignColours	0.502	0.029	0.537
computeDiffStats	1.379	0.076	1.526
convertToMSnset	0.299	0.023	0.324
corrPlot	1.317	0.152	1.525
coveragePlot	1.302	0.041	1.453
getContrastResults	0.774	0.087	0.936
groupScaling	1.032	0.068	1.108
hierarchicalPlot	0.666	0.050	0.729
intensityBoxplot	2.043	0.219	2.350
intensityPlot	1.964	0.178	2.263
maVolPlot	1.838	0.088	1.977
normalizeQuantiles	0.319	0.037	0.422
normalizeScaling	0.325	0.037	0.365
pcaPlot	1.519	0.065	1.655
peptideIntensityPlot	0.989	0.064	1.070
plotMeanVar	1.278	0.041	1.398
regressIntensity	4.099	0.049	4.224
rliPlot	4.837	0.231	5.069
rowScaling	1.227	0.106	1.333
summarizeIntensities	0.354	0.023	0.377