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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:qPLEXanalyzer.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings qPLEXanalyzer_1.28.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/qPLEXanalyzer.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘qPLEXanalyzer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qPLEXanalyzer’ version ‘1.28.1’
* 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 code 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
coefVar: no visible binding for global variable ‘SampleName’
coefVar: no visible binding for global variable ‘CV’
coefVar: no visible binding for global variable ‘cum_sum’
coefVar: no visible binding for global variable ‘fraction’
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 CV 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
  cum_sum fraction group logFC logInt logIntensity meanscaledIntensity
  medianLogInt sInt where x xend y yend
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  IRSnorm.Rd: MSnSet-class
  computeDiffStats.Rd: limma, MSnSet-class, eBayes
  convertToMSnset.Rd: MSnSet-class
  groupScaling.Rd: MSnSet-class
  mergePeptides.Rd: MSnSet-class
  mergeSites.Rd: MSnSet-class
  normalizeQuantiles.Rd: MSnSet-class
  normalizeScaling.Rd: MSnSet-class
  regressIntensity.Rd: MSnSet-class
  rowScaling.Rd: MSnSet-class
  summarizeIntensities.Rd: MSnSet-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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: getContrastResults
> ### Title: Get differential statistics results
> ### Aliases: getContrastResults
> 
> ### ** 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")
> diffstats <- computeDiffStats(MSnset_Pnorm, contrasts=contrasts)
Fitting linear model
Fitting contrasts

Computing empirical Bayes statistics for differential expression
> diffexp <- getContrastResults(diffstats=diffstats, contrast=contrasts)
Error: 'tam.24h - vehicle' is not a valid contrast. Available contrasts:
       tam.24h_vs_vehicle
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/qPLEXanalyzer.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL qPLEXanalyzer
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘qPLEXanalyzer’ ...
** this is package ‘qPLEXanalyzer’ version ‘1.28.1’
** 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)