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This page was generated on 2025-01-23 11:44 -0500 (Thu, 23 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4435
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4374
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 3605
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 3835
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4407
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 1706/2286HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReducedExperiment 0.99.6  (landing page)
Jack Gisby
Snapshot Date: 2025-01-22 13:40 -0500 (Wed, 22 Jan 2025)
git_url: https://git.bioconductor.org/packages/ReducedExperiment
git_branch: devel
git_last_commit: d7ad3c7
git_last_commit_date: 2025-01-15 09:52:58 -0500 (Wed, 15 Jan 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for ReducedExperiment on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ReducedExperiment
Version: 0.99.6
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ReducedExperiment.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReducedExperiment_0.99.6.tar.gz
StartedAt: 2025-01-23 12:15:50 -0000 (Thu, 23 Jan 2025)
EndedAt: 2025-01-23 12:24:54 -0000 (Thu, 23 Jan 2025)
EllapsedTime: 544.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ReducedExperiment.Rcheck
Warnings: 5

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:ReducedExperiment.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReducedExperiment_0.99.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReducedExperiment.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReducedExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReducedExperiment’ version ‘0.99.6’
* 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 ... WARNING
Found the following significant warnings:
  Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/ReducedExperiment.Rcheck/00install.out’ for details.
* 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 ...Warning: program compiled against libxml 212 using older 211
 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 ... NOTE
Warning: program compiled against libxml 212 using older 211

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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
Warning: program compiled against libxml 212 using older 211
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 ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
identifyModules        21.167  0.191  22.299
runWGCNA               20.636  0.143  22.240
modulePreservation     10.841  0.044  12.288
plotModulePreservation 10.117  0.043  10.690
getMsigdbT2G            7.513  0.260   7.836
assessSoftThreshold     7.266  0.267   7.618
estimateStability       7.210  0.068   7.453
plotStability           6.984  0.136   7.300
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 WARNINGs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/ReducedExperiment.Rcheck/00check.log’
for details.


Installation output

ReducedExperiment.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ReducedExperiment
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘ReducedExperiment’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: program compiled against libxml 212 using older 211
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
Warning: program compiled against libxml 212 using older 211
** testing if installed package can be loaded from final location
Warning: program compiled against libxml 212 using older 211
** testing if installed package keeps a record of temporary installation path
* DONE (ReducedExperiment)

Tests output

ReducedExperiment.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
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.

> 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: 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

Warning: program compiled against libxml 212 using older 211

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

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 585 ]
> 
> proc.time()
   user  system elapsed 
123.978   1.544 135.515 

Example timings

ReducedExperiment.Rcheck/ReducedExperiment-Ex.timings

nameusersystemelapsed
assessSoftThreshold7.2660.2677.618
associateComponents1.5440.0641.614
calcEigengenes0.1160.0040.121
cbind_rbind0.3880.0080.396
component_names0.0370.0000.038
dim-ReducedExperiment-method0.0270.0000.027
enrichment3.5890.1433.886
estimateFactors0.2220.0080.231
estimateStability7.2100.0687.453
factorised_experiment0.0480.0000.048
feature_names0.0360.0030.039
getAlignedFeatures0.1680.0000.171
getCentrality0.1190.0000.119
getCommonFeatures0.1630.0120.176
getMsigdbT2G7.5130.2607.836
get_gene_ids3.7830.0793.884
identifyModules21.167 0.19122.299
individual_dims0.0730.0000.073
loadings0.0620.0000.062
modular_experiment0.0510.0000.051
modulePreservation10.841 0.04412.288
module_assignments0.0820.0080.090
module_dendrogram0.0870.0040.091
plotCommonFeatures0.2340.0000.235
plotDendro0.0610.0000.061
plotModulePreservation10.117 0.04310.690
plotStability6.9840.1367.300
projectData0.1110.0000.112
reduced0.0360.0000.036
reduced_experiment0.0340.0000.034
runICA0.1360.0000.135
runWGCNA20.636 0.14322.240
sample_names0.0380.0000.038
show0.0330.0000.032
slice0.1390.0000.139
stability0.680.000.68