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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_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ReducedExperiment.Rcheck’
* using R version 4.5.2 Patched (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 ‘1.2.0’
* 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           59.025  0.741  85.808
runWGCNA               28.699  0.293  42.766
identifyModules        28.482  0.334  42.354
modulePreservation     14.496  0.104  20.125
plotModulePreservation 13.667  0.081  21.082
assessSoftThreshold     8.352  0.222  12.877
estimateStability       5.276  0.162   8.155
enrichment              4.287  0.183   6.735
plotStability           3.379  0.308   5.838
* 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:
  Differences:
  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 ──────────────────────────────────
  Expected `loadings(airway_fe_bootstrap)[1, ]` to equal `c(factor_1 = -0.6539, factor_2 = -0.0837)`.
  Differences:
  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-3.22-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/4.5-arm64/Resources/library’
* installing *source* package ‘ReducedExperiment’ ...
** this is package ‘ReducedExperiment’ version ‘1.2.0’
** 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 version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
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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Saving _problems/test_factors-56.R
Saving _problems/test_factors-57.R
[ 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 ──────────────────────────────────
Expected `reduced(airway_fe_bootstrap)[1, ]` to equal `c(factor_1 = -0.6462, factor_2 = -1.2427)`.
Differences:
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 ──────────────────────────────────
Expected `loadings(airway_fe_bootstrap)[1, ]` to equal `c(factor_1 = -0.6539, factor_2 = -0.0837)`.
Differences:
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