Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2025-09-01 12:04 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1726/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReducedExperiment 1.1.2  (landing page)
Jack Gisby
Snapshot Date: 2025-08-31 13:45 -0400 (Sun, 31 Aug 2025)
git_url: https://git.bioconductor.org/packages/ReducedExperiment
git_branch: devel
git_last_commit: 31e725b
git_last_commit_date: 2025-05-22 16:12:18 -0400 (Thu, 22 May 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ReducedExperiment on nebbiolo2

To the developers/maintainers of the ReducedExperiment package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReducedExperiment.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ReducedExperiment
Version: 1.1.2
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReducedExperiment.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReducedExperiment_1.1.2.tar.gz
StartedAt: 2025-09-01 02:11:52 -0400 (Mon, 01 Sep 2025)
EndedAt: 2025-09-01 02:21:12 -0400 (Mon, 01 Sep 2025)
EllapsedTime: 559.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ReducedExperiment.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReducedExperiment.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReducedExperiment_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReducedExperiment.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ReducedExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReducedExperiment’ version ‘1.1.2’
* 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 loading without being on the library search path ... 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           45.255  0.699  45.956
identifyModules        20.473  0.219  20.692
runWGCNA               20.019  0.152  20.174
modulePreservation     10.346  0.011  10.358
plotModulePreservation 10.029  0.007  10.037
estimateStability       6.015  0.066   6.082
assessSoftThreshold     5.461  0.153   5.614
plotStability           4.947  0.213   5.161
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/ReducedExperiment.Rcheck/00check.log’
for details.


Installation output

ReducedExperiment.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ReducedExperiment
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ReducedExperiment’ ...
** this is package ‘ReducedExperiment’ version ‘1.1.2’
** 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)

Tests output

ReducedExperiment.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> 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

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 579 ]

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

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 579 ]
> 
> proc.time()
   user  system elapsed 
 89.516   1.604  91.098 

Example timings

ReducedExperiment.Rcheck/ReducedExperiment-Ex.timings

nameusersystemelapsed
assessSoftThreshold5.4610.1535.614
associateComponents1.0240.0001.025
calcEigengenes0.0680.0000.067
cbind_rbind0.2730.0010.273
component_names0.0260.0000.026
dim-ReducedExperiment-method0.0180.0000.018
enrichment2.8090.0912.900
estimateFactors0.1500.0030.153
estimateStability6.0150.0666.082
factorised_experiment0.0340.0000.034
feature_names0.0270.0010.027
getAlignedFeatures0.1170.0000.116
getCentrality0.0610.0000.060
getCommonFeatures0.1090.0000.109
getMsigdbT2G45.255 0.69945.956
get_gene_ids2.2370.0492.287
identifyModules20.473 0.21920.692
individual_dims0.0460.0000.046
loadings0.0380.0000.039
modular_experiment0.0330.0000.032
modulePreservation10.346 0.01110.358
module_assignments0.0600.0010.062
module_dendrogram0.0630.0000.063
plotCommonFeatures0.1590.0020.160
plotDendro0.0440.0000.044
plotModulePreservation10.029 0.00710.037
plotStability4.9470.2135.161
projectData0.0790.0000.080
reduced0.0270.0000.027
reduced_experiment0.0270.0000.028
runICA0.0880.0000.089
runWGCNA20.019 0.15220.174
sample_names0.0260.0010.027
show0.0230.0000.023
slice0.1040.0010.106
stability0.3720.0000.372