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This page was generated on 2025-10-09 11:41 -0400 (Thu, 09 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4832
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4613
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4554
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4585
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: 2025-10-06 13:40 -0400 (Mon, 06 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 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 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: 2025-10-07 07:18:20 -0000 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 07:28:02 -0000 (Tue, 07 Oct 2025)
EllapsedTime: 582.4 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          8.367  0.423   8.811
spatialAssociationPlot 5.756  0.072   5.841
cacheClear             4.728  0.226  20.851
* 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 
 18.322   1.473  21.685 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0040.0000.004
BSRClusterComp0.4390.0000.440
BSRDataModel-class0.0060.0000.006
BSRDataModel0.2840.0080.292
BSRDataModelComp-class0.0080.0000.007
BSRDataModelComp0.2900.0040.294
BSRInference-class0.0060.0000.006
BSRInference3.8210.1003.929
BSRInferenceComp-class0.0100.0000.011
BSRInferenceComp2.0650.0602.130
BSRSignature-class0.0020.0000.002
BSRSignature0.0470.0000.048
BSRSignatureComp-class0.0040.0000.005
BSRSignatureComp0.0210.0000.020
LRinter0.0020.0000.002
LRinterScore0.0050.0000.005
LRinterShort0.0040.0000.005
addClusterComp0.4060.0000.407
alluvialPlot1.5270.0801.611
assignCellTypesToInteractions0.9700.0160.990
bubblePlotPathwaysLR0.4920.0120.505
cacheClear 4.728 0.22620.851
cacheInfo0.1240.0120.137
cacheVersion0.3820.0161.037
cellTypeFrequency1.0370.0281.068
cellularNetwork0.9090.0040.915
cellularNetworkTable0.9400.0280.970
chordDiagramLR1.8770.0201.902
coerce0.0020.0000.001
colClusterA000
colClusterB000
comparison0.0000.0010.001
comparisonName000
convertToHuman0.2550.0252.872
createResources0.4070.0401.578
differentialStats0.0020.0000.002
findOrthoGenes0.1650.0840.647
generateSpatialPlots2.0970.2552.357
getLRIntracellNetwork3.2910.1363.436
getLRNetwork0.0510.0040.054
getPathwayStats0.0190.0040.023
getResource0.3260.0360.367
inferenceParameters0.0010.0000.001
initialOrganism0.0020.0000.002
initialOrthologs0.0010.0000.001
learnParameters3.8870.1003.996
ligands000
logTransformed0.0010.0000.002
maxLigandSpatialCounts0.0680.0000.068
mu0.0010.0000.000
ncounts0.0020.0000.002
normalization0.0000.0010.002
parameters0.0000.0010.002
pathways000
receptors000
reduceToBestPathway0.1230.0040.128
reduceToLigand0.0540.0000.054
reduceToPathway0.1140.0000.114
reduceToReceptor0.0230.0000.023
relateToGeneSet0.0980.0000.098
removeClusterComp0.3790.0040.384
rescoreInference0.0380.0040.042
resetLRdb0.0160.0040.020
resetNetwork0.0090.0000.009
resetPathways0.3380.0120.350
resetToInitialOrganism0.2060.0110.218
scoreLRGeneSignatures0.6590.0200.680
scoreSignatures0.5050.0070.514
separatedLRPlot1.8980.0681.969
signatureHeatmaps0.0170.0040.022
simpleHeatmap8.3670.4238.811
smoothSpatialCounts0.0670.0000.068
sourceComparisonName000
spatialAssociation0.0500.0080.058
spatialAssociationPlot5.7560.0725.841
spatialDiversityPlot1.2820.0201.305
spatialIndexPlot1.6550.0121.670
spatialPlot1.4060.0001.408
summarizedCellularNetwork0.9330.0350.971
tgCorr000
tgExpr0.0000.0000.001
tgGenes000
tgLogFC0.0010.0000.000
tgPval000
updateInference0.1060.0000.107