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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qPLEXanalyzer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qPLEXanalyzer_1.14.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/qPLEXanalyzer.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.14.1’
* 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 ... 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 ‘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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
IRSnorm 9.082  0.185   9.476
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  • hierarchicalPlot/hierarchical-plot-custom-colour.svg
  • hierarchicalPlot/hierarchical-plot-veritcal.svg
  • intensityBoxplot/intensity-boxplot-colour-by-rep.svg
  • intensityBoxplot/intensity-boxplot-custom-colour.svg
  • intensityPlot/intensity-density-plot-colour-by-rep.svg
  • intensityPlot/intensity-density-plot-custom-colour.svg
  • pcaPlot/pca-plot-colour-by-biorep-omit-igg.svg
  • pcaPlot/pca-plot-custom-colours-and-pc2-v-pc3.svg
  • peptideIntensityPlot/no-combined-intensity.svg
  • peptideIntensityPlot/with-selected-modification.svg
  • peptideIntensityPlot/with-selected-sequence.svg
  • rliPlot/rli-plot-colour-by-biorep-include-igg.svg
  • rliPlot/rli-plot-custom-colours.svg
  Error: Test failures
  Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/qPLEXanalyzer.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL qPLEXanalyzer
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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)

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(vdiffr)
> library(qPLEXanalyzer)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: MSnbase
Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth


This is MSnbase version 2.22.0 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:base':

    trimws

> 
> options(lifecycle_verbosity = "warning")
> test_check("qPLEXanalyzer")
[ FAIL 3 | WARN 7 | SKIP 11 | PASS 153 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (11)

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-mergePeptides.R:50'): Merge peptides works ───────────────────
`protTestList` has changed from known value recorded in 'mergePeptides.rds'.
Component "Features": Attributes: < Component "row.names": 867 string mismatches >
Component "Features": Component "Accessions": 842 string mismatches
Component "Features": Component "Gene": 'is.NA' value mismatch: 1 in current 1 in target
Component "Features": Component "Description": 'is.NA' value mismatch: 1 in current 1 in target
Component "Features": Component "GeneSymbol": 'is.NA' value mismatch: 1 in current 1 in target
Component "Features": Component "Count": Mean relative difference: 0.7548387
Component "Features": Component "Seq_Acc": 867 string mismatches
Component "MergedIntensitied": Attributes: < Component "dimnames": Component 1: 867 string mismatches >
Component "MergedIntensitied": Mean relative difference: 1.364941
Backtrace:
    ▆
 1. └─testthat::expect_equal_to_reference(protTestList, file = "mergePeptides.rds") at test-mergePeptides.R:50:5
 2.   └─testthat::expect_known_value(..., update = update)
── Failure ('test-mergePeptides.R:52'): Merge peptides works ───────────────────
`phosProtTestList` has changed from known value recorded in 'mergePeptides_phos.rds'.
Component "Features": Attributes: < Component "row.names": 495 string mismatches >
Component "Features": Component "Accessions": 477 string mismatches
Component "Features": Component "Gene": 477 string mismatches
Component "Features": Component "Description": 477 string mismatches
Component "Features": Component "GeneSymbol": 477 string mismatches
Component "Features": Component "Count": Mean relative difference: 0.7159533
Component "Features": Component "Seq_Acc": 495 string mismatches
Component "Features": Component "Positions in Master Proteins": 495 string mismatches
Component "Features": Component "Modifications in Master Proteins": 'is.NA' value mismatch: 5 in current 5 in target
...
Backtrace:
    ▆
 1. └─testthat::expect_equal_to_reference(phosProtTestList, file = "mergePeptides_phos.rds") at test-mergePeptides.R:52:4
 2.   └─testthat::expect_known_value(..., update = update)
── Failure ('test-mergePeptides.R:54'): Merge peptides works ───────────────────
`phosProtColTestList` has changed from known value recorded in 'mergePeptides_phos.rds'.
Component "Features": Attributes: < Component "row.names": 495 string mismatches >
Component "Features": Component "Accessions": 477 string mismatches
Component "Features": Component "Gene": 477 string mismatches
Component "Features": Component "Description": 477 string mismatches
Component "Features": Component "GeneSymbol": 477 string mismatches
Component "Features": Component "Count": Mean relative difference: 0.7159533
Component "Features": Component "Seq_Acc": 495 string mismatches
Component "Features": Component "Positions in Master Proteins": 495 string mismatches
Component "Features": Component "Modifications in Master Proteins": 'is.NA' value mismatch: 5 in current 5 in target
...
Backtrace:
    ▆
 1. └─testthat::expect_equal_to_reference(phosProtColTestList, file = "mergePeptides_phos.rds") at test-mergePeptides.R:54:4
 2.   └─testthat::expect_known_value(..., update = update)

[ FAIL 3 | WARN 7 | SKIP 11 | PASS 153 ]
Deleting unused snapshots:
• corrPlot/correlation-plot-change-limit.svg
• corrPlot/correlation-plot-default-colour-no-numbers.svg
• corrPlot/correlation-plot-yellow-to-pink.svg
• hierarchicalPlot/hierarchical-plot-colour-by-rep.svg
• hierarchicalPlot/hierarchical-plot-custom-colour.svg
• hierarchicalPlot/hierarchical-plot-veritcal.svg
• intensityBoxplot/intensity-boxplot-colour-by-rep.svg
• intensityBoxplot/intensity-boxplot-custom-colour.svg
• intensityPlot/intensity-density-plot-colour-by-rep.svg
• intensityPlot/intensity-density-plot-custom-colour.svg
• pcaPlot/pca-plot-colour-by-biorep-omit-igg.svg
• pcaPlot/pca-plot-custom-colours-and-pc2-v-pc3.svg
• peptideIntensityPlot/no-combined-intensity.svg
• peptideIntensityPlot/with-selected-modification.svg
• peptideIntensityPlot/with-selected-sequence.svg
• rliPlot/rli-plot-colour-by-biorep-include-igg.svg
• rliPlot/rli-plot-custom-colours.svg
Error: Test failures
Execution halted