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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MatrixQCvis.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MatrixQCvis_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MatrixQCvis.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘MatrixQCvis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MatrixQCvis’ version ‘1.9.0’
* 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 ‘MatrixQCvis’ 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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:
  Expected match: "no applicable method for"
  Actual message: "trying to get slot \"colData\" from an object of a basic class (\"NULL\") with no slots"
  Backtrace:
      ▆
   1. ├─testthat::expect_error(...) at test_tab_measuredvalues_missingvalues.R:161:4
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─MatrixQCvis::extractComb(...)
   7.   └─MatrixQCvis::measuredCategory(se = se, measured = measured, category = category)
  
  [ FAIL 4 | WARN 2 | SKIP 0 | PASS 459 ]
  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 ...
  ‘MatrixQCvis.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MatrixQCvis
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘MatrixQCvis’ ...
** using staged installation
** R
** 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 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 (MatrixQCvis)

R Under development (unstable) (2023-03-12 r83975) -- "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(MatrixQCvis)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

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


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

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

    slice

The following object is masked from 'package:S4Vectors':

    rename

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

    filter

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

    layout

Loading required package: shiny
> testthat::test_check("MatrixQCvis")
initial  value 0.091643 
final  value 0.091636 
converged
initial  value 0.091643 
final  value 0.091636 
converged
[1] 28.64894
[ FAIL 4 | WARN 2 | SKIP 0 | PASS 459 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_tab_dimensionreduction.R:142:5'): dimensionReductionPlot ─────
`dimensionReductionPlot(tbl = tbl, se = "foo")` threw an error with unexpected message.
Expected match: "no applicable method for"
Actual message: "trying to get slot \"colData\" from an object of a basic class (\"character\") with no slots"
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test_tab_dimensionreduction.R:142:4
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. └─MatrixQCvis::dimensionReductionPlot(tbl = tbl, se = "foo")
  7.   ├─base::match.arg(highlight)
  8.   │ └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
  9.   │   └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
 10.   └─base::colnames(se@colData)
 11.     └─base::is.data.frame(x)
── Failure ('test_tab_measuredvalues_missingvalues.R:88:5'): measuredCategory ──
`measuredCategory(se = NULL, measured = TRUE, category = "type")` threw an error with unexpected message.
Expected match: "no applicable method for"
Actual message: "trying to get slot \"colData\" from an object of a basic class (\"NULL\") with no slots"
Backtrace:
    ▆
 1. ├─testthat::expect_error(...) at test_tab_measuredvalues_missingvalues.R:88:4
 2. │ └─testthat:::quasi_capture(...)
 3. │   ├─testthat (local) .capture(...)
 4. │   │ └─base::withCallingHandlers(...)
 5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 6. └─MatrixQCvis::measuredCategory(se = NULL, measured = TRUE, category = "type")
── Failure ('test_tab_measuredvalues_missingvalues.R:100:5'): histFeatureCategory ──
`histFeatureCategory(...)` threw an error with unexpected message.
Expected match: "no applicable method for"
Actual message: "trying to get slot \"colData\" from an object of a basic class (\"NULL\") with no slots"
Backtrace:
    ▆
 1. ├─testthat::expect_error(...) at test_tab_measuredvalues_missingvalues.R:100:4
 2. │ └─testthat:::quasi_capture(...)
 3. │   ├─testthat (local) .capture(...)
 4. │   │ └─base::withCallingHandlers(...)
 5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 6. └─MatrixQCvis::histFeatureCategory(...)
 7.   └─MatrixQCvis::measuredCategory(se, measured = measured, category = category)
── Failure ('test_tab_measuredvalues_missingvalues.R:161:5'): extractComb ──────
`extractComb(se = NULL, combination = "1", measured = TRUE, category = "type")` threw an error with unexpected message.
Expected match: "no applicable method for"
Actual message: "trying to get slot \"colData\" from an object of a basic class (\"NULL\") with no slots"
Backtrace:
    ▆
 1. ├─testthat::expect_error(...) at test_tab_measuredvalues_missingvalues.R:161:4
 2. │ └─testthat:::quasi_capture(...)
 3. │   ├─testthat (local) .capture(...)
 4. │   │ └─base::withCallingHandlers(...)
 5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 6. └─MatrixQCvis::extractComb(...)
 7.   └─MatrixQCvis::measuredCategory(se = se, measured = measured, category = category)

[ FAIL 4 | WARN 2 | SKIP 0 | PASS 459 ]
Error: Test failures
Execution halted