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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 255/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 1.0.5  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/BulkSignalR
git_branch: RELEASE_3_21
git_last_commit: 84707b3
git_last_commit_date: 2025-09-27 05:41:27 -0400 (Sat, 27 Sep 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for BulkSignalR on kunpeng2

To the developers/maintainers of the BulkSignalR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BulkSignalR.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: BulkSignalR
Version: 1.0.5
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BulkSignalR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BulkSignalR_1.0.5.tar.gz
StartedAt: 2025-10-14 07:04:46 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 07:14:35 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 589.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BulkSignalR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:BulkSignalR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BulkSignalR_1.0.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BulkSignalR.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BulkSignalR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BulkSignalR’ version ‘1.0.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘BulkSignalR’ 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* 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
simpleHeatmap          8.686  0.407   9.114
spatialAssociationPlot 5.733  0.116   5.864
cacheClear             4.679  0.072  20.302
* 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: OK


Installation output

BulkSignalR.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘BulkSignalR’ ...
** this is package ‘BulkSignalR’ version ‘1.0.5’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (BulkSignalR)

Tests output

BulkSignalR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 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(BulkSignalR)
Local "resources" are up to date.

> test_check("BulkSignalR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 18.950   1.076  21.922 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0030.0000.003
BSRClusterComp0.370.020.39
BSRDataModel-class0.0610.0080.069
BSRDataModel0.2140.0000.215
BSRDataModelComp-class0.0070.0000.006
BSRDataModelComp0.2010.0000.201
BSRInference-class0.0050.0000.006
BSRInference4.4670.1164.593
BSRInferenceComp-class0.0090.0000.010
BSRInferenceComp1.7900.0841.879
BSRSignature-class0.0020.0000.003
BSRSignature0.0440.0000.045
BSRSignatureComp-class0.0040.0000.005
BSRSignatureComp0.0190.0000.020
LRinter0.0020.0000.002
LRinterScore0.0040.0000.005
LRinterShort0.0010.0040.005
addClusterComp0.3680.0040.373
alluvialPlot0.8250.0080.835
assignCellTypesToInteractions0.9790.0000.982
bubblePlotPathwaysLR0.7280.0000.730
cacheClear 4.679 0.07220.302
cacheInfo0.1400.0080.148
cacheVersion0.4590.0161.121
cellTypeFrequency1.0670.0121.082
cellularNetwork0.9290.0640.996
cellularNetworkTable0.9730.0591.035
chordDiagramLR1.9260.0641.996
coerce0.0020.0000.002
colClusterA0.0010.0000.000
colClusterB000
comparison000
comparisonName0.0010.0000.000
convertToHuman0.2190.0442.327
createResources0.4150.0271.575
differentialStats0.0010.0000.001
findOrthoGenes0.1710.0080.580
generateSpatialPlots2.7430.1322.881
getLRIntracellNetwork3.1810.0763.264
getLRNetwork0.0550.0000.056
getPathwayStats0.0190.0040.023
getResource0.3600.0120.373
inferenceParameters0.0010.0000.000
initialOrganism0.0020.0000.002
initialOrthologs0.0020.0000.002
learnParameters3.8340.1153.959
ligands0.0010.0000.000
logTransformed0.0020.0000.001
maxLigandSpatialCounts0.0720.0040.077
mu000
ncounts0.0010.0000.002
normalization0.0020.0000.002
parameters0.0010.0000.002
pathways000
receptors0.0000.0000.001
reduceToBestPathway0.1340.0040.138
reduceToLigand0.0590.0000.059
reduceToPathway0.1480.0040.153
reduceToReceptor0.0250.0000.025
relateToGeneSet0.1030.0000.103
removeClusterComp0.3850.0040.390
rescoreInference0.0430.0000.044
resetLRdb0.0150.0040.019
resetNetwork0.0100.0000.009
resetPathways0.3470.0160.364
resetToInitialOrganism0.1990.0200.220
scoreLRGeneSignatures1.6890.1481.843
scoreSignatures0.4130.0080.421
separatedLRPlot2.6660.0162.687
signatureHeatmaps0.0210.0000.021
simpleHeatmap8.6860.4079.114
smoothSpatialCounts0.0720.0000.071
sourceComparisonName000
spatialAssociation0.0550.0040.059
spatialAssociationPlot5.7330.1165.864
spatialDiversityPlot1.5160.0281.548
spatialIndexPlot2.2110.0002.217
spatialPlot1.7830.0231.811
summarizedCellularNetwork0.9650.0080.976
tgCorr0.0000.0000.001
tgExpr000
tgGenes000
tgLogFC0.0010.0000.000
tgPval000
updateInference0.1000.0040.105