Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJKLMNOP[Q]RSTUVWXYZ

CHECK report for qPLEXanalyzer on merida1

This page was generated on 2019-04-16 12:10:51 -0400 (Tue, 16 Apr 2019).

Package 1225/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qPLEXanalyzer 1.0.4
Ashley Sawle
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/qPLEXanalyzer
Branch: RELEASE_3_8
Last Commit: dfcb3f9
Last Changed Date: 2019-04-15 07:03:27 -0400 (Mon, 15 Apr 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  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: qPLEXanalyzer
Version: 1.0.4
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_1.0.4.tar.gz
StartedAt: 2019-04-16 02:07:04 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:09:56 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 172.6 seconds
RetCode: 0
Status:  OK 
CheckDir: qPLEXanalyzer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.0.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/qPLEXanalyzer.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.0.4’
* 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
* 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-3.8-bioc/meat/qPLEXanalyzer.Rcheck/00check.log’
for details.



Installation output

qPLEXanalyzer.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘qPLEXanalyzer’ ...
** 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
* DONE (qPLEXanalyzer)

Tests output


Example timings

qPLEXanalyzer.Rcheck/qPLEXanalyzer-Ex.timings

nameusersystemelapsed
assignColours0.3980.0200.426
computeDiffStats0.6090.0340.645
convertToMSnset0.5790.0170.600
corrPlot0.8730.0640.941
coveragePlot1.0090.0451.061
getContrastResults0.5450.0350.590
groupScaling0.4150.0450.461
hierarchicalPlot0.4300.0160.451
intensityBoxplot1.7780.0991.884
intensityPlot1.3720.0901.487
maVolPlot1.2470.0571.310
normalizeQuantiles0.2910.0210.314
normalizeScaling0.2390.0150.256
pcaPlot1.4180.0281.452
peptideIntensityPlot0.5600.0190.580
plotMeanVar1.3390.0371.381
regressIntensity4.0110.0354.138
rliPlot3.8320.1394.049
rowScaling1.0840.0211.107
summarizeIntensities0.4100.0170.428