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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReducedExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReducedExperiment_1.3.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/ReducedExperiment.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReducedExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReducedExperiment’ version ‘1.3.0’
* 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 ‘ReducedExperiment’ 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::replaceSlots’
  ‘SummarizedExperiment:::.SummarizedExperiment.charbound’
  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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
getMsigdbT2G           21.407  0.153  22.113
runWGCNA               10.332  0.056  10.963
identifyModules        10.146  0.064  11.015
modulePreservation      5.143  0.007   5.311
plotModulePreservation  4.943  0.010   5.180
* 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:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_factors.R:56:5'): Stability ──────────────────────────────────
  reduced(airway_fe_bootstrap)[1, ] not equal to c(factor_1 = -0.6462, factor_2 = -1.2427).
  2/2 mismatches (average diff: 0.82)
  [1] -1.24 - -0.646 == -0.597
  [2] -0.20 - -1.243 ==  1.043
  ── Failure ('test_factors.R:57:5'): Stability ──────────────────────────────────
  loadings(airway_fe_bootstrap)[1, ] not equal to c(factor_1 = -0.6539, factor_2 = -0.0837).
  2/2 mismatches (average diff: 0.523)
  [1] -0.0837 - -0.6539 ==  0.570
  [2] -0.5602 - -0.0837 == -0.476
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 577 ]
  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
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/ReducedExperiment.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReducedExperiment
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘ReducedExperiment’ ...
** this is package ‘ReducedExperiment’ version ‘1.3.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘loadings’ in package ‘ReducedExperiment’
** 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 (ReducedExperiment)

R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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(ReducedExperiment)
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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo
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: 'ReducedExperiment'

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

    featureNames, featureNames<-, sampleNames, sampleNames<-

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

    loadings

> 
> test_check("ReducedExperiment")
class: FactorisedExperiment 
dim: 300 100 10 
metadata(0):
assays(1): normal
rownames(300): gene_1 gene_2 ... gene_299 gene_300
rowData names(0):
colnames(100): sample_1 sample_2 ... sample_99 sample_100
colData names(0):
10 components
class: ModularExperiment 
dim: 300 100 10 
metadata(0):
assays(1): normal
rownames(300): gene_1 gene_2 ... gene_299 gene_300
rowData names(0):
colnames(100): sample_1 sample_2 ... sample_99 sample_100
colData names(0):
10 components
class: ReducedExperiment 
dim: 300 100 10 
metadata(0):
assays(1): normal
rownames(300): gene_1 gene_2 ... gene_299 gene_300
rowData names(0):
colnames(100): sample_1 sample_2 ... sample_99 sample_100
colData names(0):
10 components

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[ FAIL 2 | WARN 0 | SKIP 1 | PASS 577 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• {msigdbdf} is not installed (1): 'test_features.R:83:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_factors.R:56:5'): Stability ──────────────────────────────────
reduced(airway_fe_bootstrap)[1, ] not equal to c(factor_1 = -0.6462, factor_2 = -1.2427).
2/2 mismatches (average diff: 0.82)
[1] -1.24 - -0.646 == -0.597
[2] -0.20 - -1.243 ==  1.043
── Failure ('test_factors.R:57:5'): Stability ──────────────────────────────────
loadings(airway_fe_bootstrap)[1, ] not equal to c(factor_1 = -0.6539, factor_2 = -0.0837).
2/2 mismatches (average diff: 0.523)
[1] -0.0837 - -0.6539 ==  0.570
[2] -0.5602 - -0.0837 == -0.476

[ FAIL 2 | WARN 0 | SKIP 1 | PASS 577 ]
Error: Test failures
Execution halted