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This page was generated on 2025-10-02 11:40 -0400 (Thu, 02 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4831
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4612
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4584
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: 2025-09-29 13:40 -0400 (Mon, 29 Sep 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  YES
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for BulkSignalR on kjohnson1

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.

raw results


Summary

Package: BulkSignalR
Version: 1.0.5
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BulkSignalR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BulkSignalR_1.0.5.tar.gz
StartedAt: 2025-09-30 14:45:21 -0400 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 14:53:20 -0400 (Tue, 30 Sep 2025)
EllapsedTime: 479.1 seconds
RetCode: 0
Status:   OK  
CheckDir: BulkSignalR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BulkSignalR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BulkSignalR_1.0.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BulkSignalR.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* 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 13.7.5
* 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 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 8.337  0.588   9.232
cacheClear    4.226  0.211   6.001
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BulkSignalR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
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(BulkSignalR)
Local "resources" are up to date.

> test_check("BulkSignalR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 17.244   0.875  18.844 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0030.0000.004
BSRClusterComp0.4190.0210.442
BSRDataModel-class0.0600.0070.068
BSRDataModel0.2860.0060.295
BSRDataModelComp-class0.0050.0000.006
BSRDataModelComp0.3190.0100.336
BSRInference-class0.0050.0010.005
BSRInference3.2360.1063.425
BSRInferenceComp-class0.0080.0000.008
BSRInferenceComp1.2840.1641.477
BSRSignature-class0.0020.0000.002
BSRSignature0.0260.0030.029
BSRSignatureComp-class0.0050.0010.006
BSRSignatureComp0.0150.0030.019
LRinter0.0020.0000.001
LRinterScore0.0040.0020.006
LRinterShort0.0040.0010.006
addClusterComp0.3680.0300.400
alluvialPlot0.6360.0200.660
assignCellTypesToInteractions0.7460.0510.814
bubblePlotPathwaysLR0.4890.0160.511
cacheClear4.2260.2116.001
cacheInfo0.1140.0080.123
cacheVersion0.3460.0340.518
cellTypeFrequency0.7050.0400.749
cellularNetwork0.6250.0410.683
cellularNetworkTable0.6210.0340.668
chordDiagramLR1.1640.0231.206
coerce0.0010.0000.002
colClusterA0.0000.0000.001
colClusterB000
comparison000
comparisonName000
convertToHuman0.2470.0140.917
createResources0.3060.0340.485
differentialStats0.0010.0000.001
findOrthoGenes0.1650.0050.307
generateSpatialPlots1.8620.0541.944
getLRIntracellNetwork2.1850.3692.683
getLRNetwork0.0300.0020.032
getPathwayStats0.0150.0020.017
getResource0.2800.0150.316
inferenceParameters0.0000.0010.000
initialOrganism0.0010.0000.002
initialOrthologs0.0020.0010.002
learnParameters2.5250.0282.733
ligands000
logTransformed0.0020.0000.002
maxLigandSpatialCounts0.0660.0050.076
mu0.0000.0000.001
ncounts0.0010.0010.002
normalization0.0010.0000.002
parameters0.0010.0000.001
pathways0.0000.0010.000
receptors000
reduceToBestPathway0.0840.0060.093
reduceToLigand0.0350.0040.038
reduceToPathway0.1130.0090.156
reduceToReceptor0.0150.0040.022
relateToGeneSet0.0850.0070.105
removeClusterComp0.4500.0310.489
rescoreInference0.0440.0050.049
resetLRdb0.0120.0000.013
resetNetwork0.0060.0000.006
resetPathways0.3280.0190.370
resetToInitialOrganism0.1730.0110.219
scoreLRGeneSignatures1.6490.0541.853
scoreSignatures0.5090.0160.529
separatedLRPlot1.8180.0631.900
signatureHeatmaps0.0300.0060.037
simpleHeatmap8.3370.5889.232
smoothSpatialCounts0.0570.0110.069
sourceComparisonName0.0000.0000.001
spatialAssociation0.0670.0190.087
spatialAssociationPlot4.0560.0934.212
spatialDiversityPlot0.9840.0511.056
spatialIndexPlot1.5060.0591.588
spatialPlot1.2540.0501.346
summarizedCellularNetwork0.6290.0280.662
tgCorr000
tgExpr0.0000.0010.001
tgGenes0.0010.0000.000
tgLogFC000
tgPval0.0000.0010.001
updateInference0.1100.0100.121