Back to Multiple platform build/check report for BioC 3.23:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2026-04-11 11:37 -0400 (Sat, 11 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 alpha (2026-04-05 r89794) 4919
kjohnson3macOS 13.7.7 Venturaarm644.6.0 alpha (2026-04-08 r89818) 4631
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 262/2390HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 1.3.2  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2026-04-10 13:40 -0400 (Fri, 10 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 24.04.4 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: 1.3.2
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: 2026-04-10 19:05:53 -0400 (Fri, 10 Apr 2026)
EndedAt: 2026-04-10 19:09:09 -0400 (Fri, 10 Apr 2026)
EllapsedTime: 196.2 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_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BulkSignalR.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* 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: 2026-04-10 23:05:53 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 (2026-04-08 r89818)
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 
  5.805   0.264   7.448 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0010.0010.001
BSRClusterComp0.1020.0030.105
BSRDataModel-class0.0020.0000.003
BSRDataModel0.0700.0020.071
BSRDataModelComp-class0.0010.0000.002
BSRDataModelComp0.0700.0010.072
BSRInference-class0.0010.0000.002
BSRInference0.6880.0280.718
BSRInferenceComp-class0.0020.0010.002
BSRInferenceComp0.7290.0070.741
BSRSignature-class0.0010.0000.001
BSRSignature0.0090.0010.009
BSRSignatureComp-class0.0010.0000.001
BSRSignatureComp0.0040.0010.005
LRinter0.0000.0000.001
LRinterScore0.0010.0000.002
LRinterShort0.0010.0010.001
addClusterComp0.0930.0020.097
alluvialPlot0.1880.0040.192
assignCellTypesToInteractions0.2410.0020.244
bubblePlotPathwaysLR0.1600.0010.162
cacheClear1.4710.1104.943
cacheInfo0.0290.0020.032
cacheVersion0.1150.0180.839
cellTypeFrequency0.2370.0060.246
cellularNetwork0.1990.0030.202
cellularNetworkTable0.2080.0030.213
chordDiagramLR0.3480.0030.351
coerce0.0000.0000.001
colClusterA000
colClusterB000
comparison000
comparisonName000
convertToHuman0.0940.0083.870
createResources0.0900.0151.075
differentialStats0.0000.0000.001
findOrthoGenes0.0490.0020.314
generateSpatialPlots0.5690.0170.588
getLRIntracellNetwork1.0120.0171.030
getLRNetwork0.0100.0000.011
getPathwayStats0.0050.0010.005
getResource0.1000.0060.106
inferenceParameters000
initialOrganism0.0010.0000.001
initialOrthologs0.0000.0010.001
learnParameters0.7100.0030.721
ligands0.0000.0010.000
logTransformed000
maxLigandSpatialCounts0.0180.0010.019
mu000
ncounts0.0000.0000.001
normalization0.0010.0000.000
parameters000
pathways000
receptors000
reduceToBestPathway0.0260.0010.027
reduceToLigand0.0110.0010.012
reduceToPathway0.0230.0010.024
reduceToReceptor0.0050.0010.005
relateToGeneSet0.0250.0010.026
removeClusterComp0.0900.0020.092
rescoreInference0.0130.0010.014
resetLRdb0.0080.0010.008
resetNetwork0.0020.0000.002
resetPathways0.0950.0040.100
resetToInitialOrganism0.0490.0020.051
scoreLRGeneSignatures0.1470.0030.150
scoreSignatures0.1130.0040.123
separatedLRPlot0.5610.0120.576
signatureHeatmaps0.0110.0010.012
simpleHeatmap2.6390.0592.724
smoothSpatialCounts0.0190.0010.019
sourceComparisonName000
spatialAssociation0.0220.0010.023
spatialAssociationPlot1.2600.0231.296
spatialDiversityPlot0.3120.0150.329
spatialIndexPlot0.4610.0030.466
spatialPlot0.3910.0030.394
summarizedCellularNetwork0.2010.0080.210
tgCorr000
tgExpr0.0000.0000.001
tgGenes000
tgLogFC000
tgPval0.0000.0000.001
updateInference0.0330.0010.034