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This page was generated on 2026-04-04 11:35 -0400 (Sat, 04 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.6.0 alpha (2026-03-30 r89742) 4900
kjohnson3macOS 13.7.7 Venturaarm644.6.0 alpha (2026-03-28 r89739) 4634
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 261/2381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 1.3.2  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2026-04-03 13:40 -0400 (Fri, 03 Apr 2026)
git_url: https://git.bioconductor.org/packages/BulkSignalR
git_branch: devel
git_last_commit: 8559355
git_last_commit_date: 2026-04-01 10:35:44 -0400 (Wed, 01 Apr 2026)
nebbiolo1Linux (Ubuntu 24.04.3 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: 1.3.2
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_1.3.2.tar.gz
StartedAt: 2026-04-03 18:44:21 -0400 (Fri, 03 Apr 2026)
EndedAt: 2026-04-03 18:47:42 -0400 (Fri, 03 Apr 2026)
EllapsedTime: 201.1 seconds
RetCode: 0
Status:   OK  
CheckDir: BulkSignalR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BulkSignalR.Rcheck’
* using R version 4.6.0 alpha (2026-03-28 r89739)
* 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: 2026-04-03 22:44:21 UTC
* using option ‘--no-vignettes’
* checking for file ‘BulkSignalR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BulkSignalR’ version ‘1.3.2’
* 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 ‘1.3.2’
** 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 alpha (2026-03-28 r89739)
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 
  5.801   0.265   7.399 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0010.0000.001
BSRClusterComp0.1030.0030.106
BSRDataModel-class0.0030.0010.003
BSRDataModel0.0700.0010.072
BSRDataModelComp-class0.0020.0000.002
BSRDataModelComp0.0750.0010.075
BSRInference-class0.0010.0000.001
BSRInference0.7140.0230.750
BSRInferenceComp-class0.0030.0000.003
BSRInferenceComp0.7260.0060.734
BSRSignature-class0.0010.0000.001
BSRSignature0.0090.0010.009
BSRSignatureComp-class0.0020.0000.001
BSRSignatureComp0.0040.0010.005
LRinter0.0010.0000.000
LRinterScore0.0010.0010.001
LRinterShort0.0020.0000.002
addClusterComp0.0950.0020.097
alluvialPlot0.1860.0040.191
assignCellTypesToInteractions0.2380.0020.241
bubblePlotPathwaysLR0.1700.0020.172
cacheClear1.3220.0804.383
cacheInfo0.0300.0030.033
cacheVersion0.0950.0130.800
cellTypeFrequency0.2230.0030.227
cellularNetwork0.1960.0030.199
cellularNetworkTable0.1900.0010.191
chordDiagramLR0.3440.0030.347
coerce000
colClusterA000
colClusterB000
comparison000
comparisonName000
convertToHuman0.0680.0052.775
createResources0.0920.0130.801
differentialStats000
findOrthoGenes0.0480.0020.310
generateSpatialPlots0.5610.0180.588
getLRIntracellNetwork1.0160.0391.075
getLRNetwork0.0100.0010.011
getPathwayStats0.0050.0010.006
getResource0.1000.0050.104
inferenceParameters000
initialOrganism0.0010.0000.001
initialOrthologs0.0000.0000.001
learnParameters0.7240.0050.732
ligands000
logTransformed0.0010.0000.000
maxLigandSpatialCounts0.0200.0010.021
mu0.0000.0000.001
ncounts000
normalization0.0010.0000.000
parameters0.0000.0000.001
pathways000
receptors0.0000.0010.001
reduceToBestPathway0.0350.0010.036
reduceToLigand0.0110.0010.012
reduceToPathway0.0240.0010.025
reduceToReceptor0.0040.0010.006
relateToGeneSet0.0260.0010.026
removeClusterComp0.0910.0020.094
rescoreInference0.0130.0010.014
resetLRdb0.0080.0000.008
resetNetwork0.0020.0000.002
resetPathways0.1000.0050.105
resetToInitialOrganism0.0500.0020.053
scoreLRGeneSignatures0.1460.0040.150
scoreSignatures0.1160.0020.119
separatedLRPlot0.5500.0100.561
signatureHeatmaps0.0110.0010.012
simpleHeatmap2.6530.0722.838
smoothSpatialCounts0.0170.0000.018
sourceComparisonName0.0000.0000.001
spatialAssociation0.0220.0010.023
spatialAssociationPlot1.2640.0271.302
spatialDiversityPlot0.3200.0220.342
spatialIndexPlot0.4660.0100.480
spatialPlot0.3770.0070.386
summarizedCellularNetwork0.2160.0020.218
tgCorr000
tgExpr0.0000.0010.000
tgGenes000
tgLogFC000
tgPval000
updateInference0.0340.0010.036