Package: qPLEXanalyzer

Version: 1.4.0

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_1.4.0.tar.gz

StartedAt: 2020-04-15 04:52:50 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:56:06 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 195.1 seconds

RetCode: 0

Status:  OK

CheckDir: qPLEXanalyzer.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/qPLEXanalyzer.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.4.0’
* 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 ‘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’
mergePeptides: no visible binding for global variable ‘Accessions’
mergePeptides: no visible binding for global variable ‘Sequences’
mergePeptides: no visible binding for global variable ‘phosseqid’
mergePeptides: no visible binding for global variable ‘Count’
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 phosseqid 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
* 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-3.10-bioc/meat/qPLEXanalyzer.Rcheck/00check.log’
for details.

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


* 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	0.878	0.019	0.901
computeDiffStats	1.210	0.038	1.260
convertToMSnset	0.305	0.012	0.321
corrPlot	0.910	0.041	0.958
coveragePlot	1.164	0.110	1.281
getContrastResults	0.659	0.037	0.702
groupScaling	0.819	0.047	0.877
hierarchicalPlot	0.527	0.013	0.547
intensityBoxplot	2.319	0.110	2.443
intensityPlot	1.879	0.081	1.979
maVolPlot	1.523	0.058	1.608
mergePeptides	0.549	0.021	0.576
normalizeQuantiles	0.333	0.016	0.356
normalizeScaling	0.354	0.020	0.377
pcaPlot	1.241	0.033	1.296
peptideIntensityPlot	0.869	0.028	0.901
plotMeanVar	1.023	0.027	1.057
regressIntensity	3.388	0.028	3.457
rliPlot	4.100	0.131	4.278
rowScaling	1.006	0.025	1.039
summarizeIntensities	0.427	0.015	0.447