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

This page was generated on 2026-04-09 11:36 -0400 (Thu, 09 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 alpha (2026-04-05 r89794) 4912
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2026-03-26 r89717) -- "Unsuffered Consequences" 4623
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 261/2388HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 1.3.2  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2026-04-08 13:40 -0400 (Wed, 08 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: 2026-04-08 18:48:37 -0400 (Wed, 08 Apr 2026)
EndedAt: 2026-04-08 18:52:05 -0400 (Wed, 08 Apr 2026)
EllapsedTime: 208.3 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 Under development (unstable) (2026-03-26 r89717)
* 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: 2026-04-08 22:48:37 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
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
cacheClear 1.391  0.087   5.106
* 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 Under development (unstable) (2026-03-26 r89717) -- "Unsuffered Consequences"
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 
  5.764   0.246   7.522 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0010.0000.001
BSRClusterComp0.1020.0030.104
BSRDataModel-class0.0020.0000.002
BSRDataModel0.0690.0010.070
BSRDataModelComp-class0.0020.0000.002
BSRDataModelComp0.0690.0010.070
BSRInference-class0.0020.0010.002
BSRInference0.6870.0140.707
BSRInferenceComp-class0.0030.0000.003
BSRInferenceComp0.7240.0110.740
BSRSignature-class000
BSRSignature0.0080.0010.009
BSRSignatureComp-class0.0020.0000.002
BSRSignatureComp0.0040.0010.005
LRinter0.0010.0000.001
LRinterScore0.0010.0000.001
LRinterShort0.0010.0000.001
addClusterComp0.0970.0010.098
alluvialPlot0.1860.0030.190
assignCellTypesToInteractions0.2410.0030.246
bubblePlotPathwaysLR0.1660.0020.168
cacheClear1.3910.0875.106
cacheInfo0.0340.0030.038
cacheVersion0.1040.0150.912
cellTypeFrequency0.2200.0020.223
cellularNetwork0.2230.0060.234
cellularNetworkTable0.2000.0020.202
chordDiagramLR0.3660.0060.375
coerce0.0000.0010.001
colClusterA000
colClusterB000
comparison000
comparisonName000
convertToHuman0.0800.0071.663
createResources0.1020.0160.914
differentialStats0.0010.0000.000
findOrthoGenes0.0500.0020.309
generateSpatialPlots0.5570.0120.571
getLRIntracellNetwork0.9950.0151.011
getLRNetwork0.0100.0000.011
getPathwayStats0.0050.0000.005
getResource0.1040.0060.110
inferenceParameters000
initialOrganism0.0010.0000.000
initialOrthologs0.0010.0000.000
learnParameters0.7200.0050.733
ligands0.0010.0000.000
logTransformed000
maxLigandSpatialCounts0.0210.0010.022
mu0.0000.0010.000
ncounts000
normalization0.0010.0000.000
parameters0.0000.0000.001
pathways000
receptors000
reduceToBestPathway0.0340.0010.036
reduceToLigand0.0120.0010.012
reduceToPathway0.0240.0010.025
reduceToReceptor0.0040.0010.005
relateToGeneSet0.0260.0010.028
removeClusterComp0.0910.0050.099
rescoreInference0.0140.0010.015
resetLRdb0.0080.0000.009
resetNetwork0.0020.0010.002
resetPathways0.1060.0060.117
resetToInitialOrganism0.0510.0030.054
scoreLRGeneSignatures0.1500.0040.155
scoreSignatures0.1140.0020.116
separatedLRPlot0.5590.0100.571
signatureHeatmaps0.0110.0010.011
simpleHeatmap2.6670.0592.838
smoothSpatialCounts0.0190.0010.020
sourceComparisonName000
spatialAssociation0.0220.0010.023
spatialAssociationPlot1.2590.0081.273
spatialDiversityPlot0.3140.0050.322
spatialIndexPlot0.4560.0070.472
spatialPlot0.3770.0040.389
summarizedCellularNetwork0.2200.0030.224
tgCorr0.0000.0000.001
tgExpr000
tgGenes000
tgLogFC0.0000.0000.001
tgPval0.0000.0010.000
updateInference0.0350.0010.036