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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:qPLEXanalyzer.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings qPLEXanalyzer_1.17.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/qPLEXanalyzer.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘qPLEXanalyzer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qPLEXanalyzer’ version ‘1.17.1’
* package encoding: UTF-8
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    Updates to vignette to avoid build errors when attempting to connect to Uniprot
* 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 loading without being on the library search path ... 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 ‘SampleName’
corrPlot: no visible binding for global variable ‘X’
corrPlot: no visible binding for global variable ‘AddValues’
corrPlot: no visible binding for global variable ‘Cor’
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 ‘Sequences’
getContrastResults: no visible binding for global variable ‘B’
getContrastResults: no visible binding for global variable ‘AveExpr’
getContrastResults: no visible binding for global variable ‘logFC’
groupScaling: no visible binding for global variable ‘sInt’
groupScaling: no visible binding for global variable
  ‘meanscaledIntensity’
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’
hierarchicalPlot: no visible binding for global variable ‘SampleName’
intensityBoxplot: no visible binding for global variable ‘Intensity’
intensityBoxplot: no visible binding for global variable ‘logInt’
intensityBoxplot: no visible binding for global variable ‘SampleName’
intensityPlot: no visible binding for global variable ‘Intensity’
intensityPlot: no visible binding for global variable ‘SampleName’
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’
maVolPlot: no visible binding for global variable ‘SymbolLab’
mergePeptides: no visible binding for global variable ‘Accessions’
mergePeptides: no visible binding for global variable ‘Sequences’
mergePeptides: no visible binding for global variable ‘Seq_Acc’
mergePeptides: no visible global function definition for ‘where’
mergePeptides: no visible binding for global variable ‘Count’
mergeSites: no visible binding for global variable ‘Accessions’
mergeSites: no visible binding for global variable ‘Sites’
mergeSites: no visible binding for global variable ‘Type’
mergeSites: no visible binding for global variable ‘Sites_Acc’
mergeSites: no visible global function definition for ‘where’
mergeSites: no visible binding for global variable ‘Count’
peptideIntensityPlot: no visible binding for global variable
  ‘PeptideID’
peptideIntensityPlot: no visible binding for global variable
  ‘Intensity’
peptideIntensityPlot: no visible binding for global variable
  ‘Accessions’
peptideIntensityPlot: no visible binding for global variable
  ‘SampleName’
peptideIntensityPlot: no visible binding for global variable
  ‘logIntensity’
peptideIntensityPlot: no visible binding for global variable
  ‘Sequences’
peptideIntensityPlot: no visible binding for global variable
  ‘Modifications’
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’
rliPlot: no visible binding for global variable ‘SampleName’
rliPlot: no visible binding for global variable ‘RLI’
summarizeIntensities: no visible binding for global variable
  ‘Accessions’
summarizeIntensities: no visible binding for global variable
  ‘Sequences’
summarizeIntensities: no visible global function definition for ‘where’
summarizeIntensities: no visible binding for global variable ‘Count’
Undefined global functions or variables:
  Accessions AddValues AveExpr B Cor CorTxt Count GeneSymbol Intensity
  Mean Modifications PeptideID RLI RowID SampleName Seq_Acc Sequences
  Sites Sites_Acc SymbolLab Type Variance X Y adj.P.Val group logFC
  logInt logIntensity meanscaledIntensity medianLogInt sInt where 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 ... ERROR
Running examples in ‘qPLEXanalyzer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: computeDiffStats
> ### Title: Compute differential statistics
> ### Aliases: computeDiffStats
> 
> ### ** Examples
> 
> 
> data(human_anno)
> data(exp3_OHT_ESR1)
> MSnSet_data <- convertToMSnset(exp3_OHT_ESR1$intensities_qPLEX1,
+                                metadata=exp3_OHT_ESR1$metadata_qPLEX1,
+                                indExpData=c(7:16), 
+                                Sequences=2, 
+                                Accessions=6)
> MSnset_norm <- groupScaling(MSnSet_data, scalingFunction=median)
> MSnset_Pnorm <- summarizeIntensities(MSnset_norm, sum, human_anno)
> contrasts <- c(tam.24h_vs_vehicle = "tam.24h - vehicle", 
+                tam.6h_vs_vehicle = "tam.6h - vehicle")
> diffstats <- computeDiffStats(MSnSetObj=MSnset_Pnorm, contrasts=contrasts)
Fitting linear model
Fitting contrasts

Computing empirical Bayes statistics for differential expression
Error in fitFDistRobustly(var, df1 = df, covariate = covariate, winsor.tail.p = winsor.tail.p) : 
  statmod package required but is not installed
Calls: computeDiffStats ... eBayes -> .ebayes -> squeezeVar -> fitFDistRobustly
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘qPLEXanalyzer.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘qPLEXanalyzer.Rmd’ using rmarkdown
Quitting from lines 429-434 (qPLEXanalyzer.Rmd) 
Error: processing vignette 'qPLEXanalyzer.Rmd' failed with diagnostics:
statmod package required but is not installed
--- failed re-building ‘qPLEXanalyzer.Rmd’

SUMMARY: processing the following file failed:
  ‘qPLEXanalyzer.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/qPLEXanalyzer.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL qPLEXanalyzer
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘qPLEXanalyzer’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '==' 
Note: wrong number of arguments to '==' 
** 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)