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### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:QFeatures.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings QFeatures_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/QFeatures.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QFeatures/DESCRIPTION’ ... OK
* this is package ‘QFeatures’ version ‘1.14.0’
* 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 ‘QFeatures’ 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 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::replaceSlots’
  ‘MultiAssayExperiment:::.sampleMapFromData’
  See the note in ?`:::` about the use of this operator.
* 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 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
readQFeaturesFromDIANN 246.948  2.976 257.495
* 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:
    6. │       ├─BiocGenerics (local) standardGeneric("mapply")
    7. │       │ ├─BiocGenerics::eval(mc, env)
    8. │       │ └─base::eval(mc, env)
    9. │       │   └─base::eval(mc, env)
   10. │       └─base::mapply(FUN = FUN, ..., SIMPLIFY = SIMPLIFY)
   11. │         └─MultiAssayExperiment (local) `<fn>`(obj = dots[[1L]][[1L]], obname = dots[[2L]][[1L]], idx = dots[[3L]][[1L]])
   12. │           ├─base::data.frame(...)
   13. │           └─MultiAssayExperiment:::.longFormatANY(obj, i = idx)
   14. │             └─base::stop("Package 'reshape2' is required for 'longFormat()' conversion")
   15. └─base::.handleSimpleError(...)
   16.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 756 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/QFeatures.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL QFeatures
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘QFeatures’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘sweep’ in package ‘QFeatures’
** 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 (QFeatures)

R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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.

> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> 
> library("testthat")
> library("QFeatures")
Loading required package: MultiAssayExperiment
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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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


Attaching package: 'QFeatures'

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

    longFormat

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

    sweep

> 
> test_check("QFeatures")
AssayLink for assay <foo>
[from:NA|fcol:NA|hits:0]
AssayLinks of length 0
names(0): 
A empty instance of class QFeatures 
An instance of class QFeatures containing 1 assays:
 [1] psms: SummarizedExperiment with 10 rows and 2 columns 
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 756 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_Features.R:829:5'): longFormat ─────────────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'args' in selecting a method for function 'do.call': Package 'reshape2' is required for 'longFormat()' conversion
Backtrace:
     ▆
  1. ├─QFeatures::longFormat(feat2, rowvars = "Prot", colvars = "X") at test_Features.R:829:5
  2. │ └─MultiAssayExperiment::longFormat(object, colvars, index)
  3. │   ├─BiocGenerics::do.call(...)
  4. │   └─MultiAssayExperiment:::.longFormatElist(...)
  5. │     └─BiocGenerics::mapply(...)
  6. │       ├─BiocGenerics (local) standardGeneric("mapply")
  7. │       │ ├─BiocGenerics::eval(mc, env)
  8. │       │ └─base::eval(mc, env)
  9. │       │   └─base::eval(mc, env)
 10. │       └─base::mapply(FUN = FUN, ..., SIMPLIFY = SIMPLIFY)
 11. │         └─MultiAssayExperiment (local) `<fn>`(obj = dots[[1L]][[1L]], obname = dots[[2L]][[1L]], idx = dots[[3L]][[1L]])
 12. │           ├─base::data.frame(...)
 13. │           └─MultiAssayExperiment:::.longFormatANY(obj, i = idx)
 14. │             └─base::stop("Package 'reshape2' is required for 'longFormat()' conversion")
 15. └─base::.handleSimpleError(...)
 16.   └─base (local) h(simpleError(msg, call))

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 756 ]
Error: Test failures
Execution halted