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This page was generated on 2026-05-02 11:35 -0400 (Sat, 02 May 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 RC (2026-04-17 r89917) -- "Because it was There" 4988
kjohnson3macOS 13.7.7 Venturaarm644.6.0 Patched (2026-04-24 r89963) -- "Because it was There" 4718
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 265/2418HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 1.4.0  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2026-05-01 13:40 -0400 (Fri, 01 May 2026)
git_url: https://git.bioconductor.org/packages/BulkSignalR
git_branch: RELEASE_3_23
git_last_commit: 7077d21
git_last_commit_date: 2026-04-28 09:04:07 -0400 (Tue, 28 Apr 2026)
nebbiolo1Linux (Ubuntu 24.04.4 LTS) / x86_64  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
See other builds for BulkSignalR in R Universe.


CHECK results for BulkSignalR on kjohnson3

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: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2026-05-01 18:37:23 -0400 (Fri, 01 May 2026)
EndedAt: 2026-05-01 18:40:31 -0400 (Fri, 01 May 2026)
EllapsedTime: 188.2 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BulkSignalR.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-01 22:37:23 UTC
* using option ‘--no-vignettes’
* checking for file ‘BulkSignalR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BulkSignalR’ version ‘1.4.0’
* 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
* 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/4.6/Resources/library’
* installing *source* package ‘BulkSignalR’ ...
** this is package ‘BulkSignalR’ version ‘1.4.0’
** 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 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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 
  5.804   0.285   7.429 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0010.0010.001
BSRClusterComp0.0990.0030.102
BSRDataModel-class0.0020.0000.002
BSRDataModel0.0690.0020.072
BSRDataModelComp-class0.0020.0000.003
BSRDataModelComp0.0690.0010.070
BSRInference-class0.0020.0000.002
BSRInference0.6680.0260.695
BSRInferenceComp-class0.0030.0000.002
BSRInferenceComp0.3860.0090.397
BSRSignature-class0.0010.0000.001
BSRSignature0.0090.0000.010
BSRSignatureComp-class0.0020.0000.001
BSRSignatureComp0.0040.0000.005
LRinter0.0010.0000.001
LRinterScore0.0010.0010.002
LRinterShort0.0010.0000.001
addClusterComp0.0910.0010.093
alluvialPlot0.5410.0040.546
assignCellTypesToInteractions0.2240.0050.229
bubblePlotPathwaysLR0.1740.0020.176
cacheClear1.3200.0744.454
cacheInfo0.0350.0030.038
cacheVersion0.1080.0140.818
cellTypeFrequency0.2200.0030.224
cellularNetwork0.2010.0030.203
cellularNetworkTable0.2030.0060.208
chordDiagramLR0.3540.0040.359
coerce0.0010.0000.001
colClusterA000
colClusterB000
comparison000
comparisonName000
convertToHuman0.2660.0080.276
createResources0.1170.0140.828
differentialStats0.0010.0000.000
findOrthoGenes0.1060.0010.108
generateSpatialPlots0.6120.0250.638
getLRIntracellNetwork1.1550.0251.181
getLRNetwork0.0110.0000.011
getPathwayStats0.0050.0000.005
getResource0.1020.0050.108
inferenceParameters000
initialOrganism0.0010.0000.001
initialOrthologs000
learnParameters0.7080.0040.714
ligands000
logTransformed0.0010.0000.000
maxLigandSpatialCounts0.0190.0020.020
mu000
ncounts000
normalization0.0010.0000.001
parameters0.0000.0000.001
pathways0.0000.0010.000
receptors000
reduceToBestPathway0.0250.0010.027
reduceToLigand0.0110.0010.012
reduceToPathway0.0250.0010.026
reduceToReceptor0.0050.0010.006
relateToGeneSet0.0250.0020.026
removeClusterComp0.0890.0010.091
rescoreInference0.0140.0010.015
resetLRdb0.0080.0000.008
resetNetwork0.0020.0000.002
resetPathways0.1030.0050.108
resetToInitialOrganism0.0490.0020.051
scoreLRGeneSignatures0.1550.0030.158
scoreSignatures0.1110.0020.113
separatedLRPlot0.5700.0070.578
signatureHeatmaps0.0100.0010.011
simpleHeatmap2.7630.0782.867
smoothSpatialCounts0.0180.0000.020
sourceComparisonName000
spatialAssociation0.0210.0010.022
spatialAssociationPlot1.2640.0401.304
spatialDiversityPlot0.3140.0180.338
spatialIndexPlot0.4640.0140.494
spatialPlot0.3780.0090.751
summarizedCellularNetwork0.2080.0050.224
tgCorr000
tgExpr000
tgGenes0.0000.0010.000
tgLogFC000
tgPval000
updateInference0.0320.0010.034