##############################################################################
##############################################################################
###
### Running command:
###
###   /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/library --timings qPLEXanalyzer_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/qPLEXanalyzer.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘qPLEXanalyzer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qPLEXanalyzer’ version ‘1.17.0’
* 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 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 6.103  0.132   6.235
* 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 ...
  ‘qPLEXanalyzer.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/qPLEXanalyzer.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL qPLEXanalyzer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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, aperm, 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 2.25.2 
  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 2 | WARN 34 | SKIP 11 | PASS 154 ]

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

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-getContrastResults.R:47'): argument checks - controlGroup ────
`getContrastResults(...)` threw an error with unexpected message.
Expected match: "controlGroup: 'Wibble' is not found in the diffstats object"
Actual message: "`..1` must be a vector, not a symbol."
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test-getContrastResults.R:47:4
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─qPLEXanalyzer::getContrastResults(...)
  7. │ └─qPLEXanalyzer:::checkArg_getContrastResults(...)
  8. │   └─assertthat::assert_that(is_validControlGroup(controlGroup, diffstats))
  9. │     └─assertthat::see_if(..., env = env, msg = msg)
 10. │       └─assertthat:::get_message(res, assertion, env)
 11. │         └─qPLEXanalyzer (local) fail(call, env)
 12. │           └─stringr::str_c(...)
 13. │             └─vctrs::vec_size_common(!!!dots)
 14. └─vctrs:::stop_scalar_type(`<fn>`(controlGroup), "..1", `<env>`)
 15.   └─vctrs:::stop_vctrs(...)
 16.     └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))
── Failure ('test-maVolPlot.R:66'): argument checks - controlGroup ─────────────
`maVolPlot(diffstats = diffstats, contrast = contrasts[1], controlGroup = "Wibble")` threw an error with unexpected message.
Expected match: "controlGroup: 'Wibble' is not found in .* diffstats"
Actual message: "`..1` must be a vector, not a symbol."
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test-maVolPlot.R:66:4
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─qPLEXanalyzer::maVolPlot(...)
  7. │ └─qPLEXanalyzer:::checkArg_maVolPlot(...)
  8. │   └─assertthat::assert_that(is_validControlGroup(controlGroup, diffstats))
  9. │     └─assertthat::see_if(..., env = env, msg = msg)
 10. │       └─assertthat:::get_message(res, assertion, env)
 11. │         └─qPLEXanalyzer (local) fail(call, env)
 12. │           └─stringr::str_c(...)
 13. │             └─vctrs::vec_size_common(!!!dots)
 14. └─vctrs:::stop_scalar_type(`<fn>`(controlGroup), "..1", `<env>`)
 15.   └─vctrs:::stop_vctrs(...)
 16.     └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))

[ FAIL 2 | WARN 34 | SKIP 11 | PASS 154 ]
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