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This page was generated on 2026-05-19 12:54 -0400 (Tue, 19 May 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 RC (2026-04-17 r89917) -- "Because it was There" 4898
kjohnson3macOS 13.7.7 Venturaarm644.6.0 Patched (2026-05-01 r89994) -- "Because it was There" 4617
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 262/2377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 1.5.0  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2026-05-18 13:45 -0400 (Mon, 18 May 2026)
git_url: https://git.bioconductor.org/packages/BulkSignalR
git_branch: devel
git_last_commit: ada5f63
git_last_commit_date: 2026-04-28 09:04:07 -0400 (Tue, 28 Apr 2026)
nebbiolo2Linux (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  YES
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: 1.5.0
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_1.5.0.tar.gz
StartedAt: 2026-05-18 20:37:07 -0400 (Mon, 18 May 2026)
EndedAt: 2026-05-18 20:40:13 -0400 (Mon, 18 May 2026)
EllapsedTime: 186.0 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/BulkSignalR.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* 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: 2026-05-19 00:37:07 UTC
* using option ‘--no-vignettes’
* checking for file ‘BulkSignalR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BulkSignalR’ version ‘1.5.0’
* 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

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###
### 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 ‘1.5.0’
** 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
ℹ /Users/biocbuild/Library/Caches/org.R-project.R/R/BulkSignalR first set up.

ℹ "GO-BP" added to cache with success.

ℹ "Reactome" added to cache with success.

ℹ "Network" added to cache with success.

ℹ "LRdb" added to cache with success.
** 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 (2026-05-01 r89994) -- "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 
  5.655   0.229   7.213 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0010.0000.001
BSRClusterComp0.0970.0030.100
BSRDataModel-class0.0020.0000.002
BSRDataModel0.0680.0010.069
BSRDataModelComp-class0.0020.0000.002
BSRDataModelComp0.0700.0010.071
BSRInference-class0.0020.0000.002
BSRInference0.6740.0100.685
BSRInferenceComp-class0.0030.0000.003
BSRInferenceComp0.3860.0040.391
BSRSignature-class0.0010.0000.001
BSRSignature0.0090.0000.009
BSRSignatureComp-class0.0010.0000.001
BSRSignatureComp0.0050.0000.005
LRinter0.0000.0000.001
LRinterScore0.0020.0000.002
LRinterShort0.0010.0010.002
addClusterComp0.0940.0020.096
alluvialPlot0.6180.0060.877
assignCellTypesToInteractions0.2170.0020.220
bubblePlotPathwaysLR0.1620.0020.165
cacheClear1.2960.0774.864
cacheInfo0.0310.0030.033
cacheVersion0.0920.0130.801
cellTypeFrequency0.2220.0040.226
cellularNetwork0.1980.0040.202
cellularNetworkTable0.1970.0030.198
chordDiagramLR0.3370.0030.339
coerce000
colClusterA000
colClusterB0.0000.0010.000
comparison000
comparisonName000
convertToHuman0.2590.0050.266
createResources0.1140.0130.825
differentialStats0.0000.0000.001
findOrthoGenes0.1050.0020.106
generateSpatialPlots0.6080.0190.628
getLRIntracellNetwork1.1350.0231.163
getLRNetwork0.0110.0010.011
getPathwayStats0.0050.0000.006
getResource0.0970.0050.102
inferenceParameters0.0010.0000.000
initialOrganism0.0000.0000.001
initialOrthologs0.0010.0000.000
learnParameters0.7450.0040.753
ligands000
logTransformed0.0000.0000.001
maxLigandSpatialCounts0.0180.0020.020
mu000
ncounts0.0010.0000.000
normalization0.0000.0000.001
parameters0.0000.0000.001
pathways0.0000.0010.000
receptors000
reduceToBestPathway0.0250.0010.026
reduceToLigand0.0110.0010.011
reduceToPathway0.0230.0010.024
reduceToReceptor0.0040.0000.006
relateToGeneSet0.0250.0010.025
removeClusterComp0.0880.0020.090
rescoreInference0.0130.0010.013
resetLRdb0.0080.0000.008
resetNetwork0.0020.0000.002
resetPathways0.0980.0050.103
resetToInitialOrganism0.0500.0020.053
scoreLRGeneSignatures0.1500.0020.152
scoreSignatures0.1110.0010.113
separatedLRPlot0.5640.0070.573
signatureHeatmaps0.0100.0010.011
simpleHeatmap2.7180.0552.778
smoothSpatialCounts0.0190.0010.019
sourceComparisonName000
spatialAssociation0.0210.0020.022
spatialAssociationPlot1.2380.0331.274
spatialDiversityPlot0.3120.0120.324
spatialIndexPlot0.4560.0090.465
spatialPlot0.3700.0090.380
summarizedCellularNetwork0.2060.0060.212
tgCorr000
tgExpr000
tgGenes0.0000.0010.001
tgLogFC000
tgPval000
updateInference0.0330.0010.035