Back to Multiple platform build/check report for BioC 3.22:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-10-21 12:04 -0400 (Tue, 21 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4642
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 259/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 1.1.5  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2025-10-20 13:45 -0400 (Mon, 20 Oct 2025)
git_url: https://git.bioconductor.org/packages/BulkSignalR
git_branch: devel
git_last_commit: dd2021f
git_last_commit_date: 2025-09-27 04:43:00 -0400 (Sat, 27 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for BulkSignalR on lconway

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: 1.1.5
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_1.1.5.tar.gz
StartedAt: 2025-10-20 20:50:40 -0400 (Mon, 20 Oct 2025)
EndedAt: 2025-10-20 20:58:49 -0400 (Mon, 20 Oct 2025)
EllapsedTime: 488.6 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_1.1.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BulkSignalR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BulkSignalR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BulkSignalR’ version ‘1.1.5’
* 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
simpleHeatmap 7.147  0.446   7.685
cacheClear    3.794  0.255   7.311
* 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/4.5-x86_64/Resources/library’
* installing *source* package ‘BulkSignalR’ ...
** this is package ‘BulkSignalR’ version ‘1.1.5’
** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
 16.571   0.980  18.641 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0020.0010.003
BSRClusterComp0.3790.0220.403
BSRDataModel-class0.0500.0090.059
BSRDataModel0.2540.0130.278
BSRDataModelComp-class0.0060.0000.006
BSRDataModelComp0.2870.0110.302
BSRInference-class0.0050.0000.006
BSRInference3.4580.1023.591
BSRInferenceComp-class0.0090.0010.009
BSRInferenceComp1.3260.1091.453
BSRSignature-class0.0030.0010.002
BSRSignature0.0360.0020.037
BSRSignatureComp-class0.0050.0010.005
BSRSignatureComp0.0160.0010.017
LRinter0.0020.0000.002
LRinterScore0.0030.0010.004
LRinterShort0.0040.0010.005
addClusterComp0.3420.0160.362
alluvialPlot0.6260.0260.670
assignCellTypesToInteractions0.7070.0360.746
bubblePlotPathwaysLR0.5620.0060.570
cacheClear3.7940.2557.311
cacheInfo0.1200.0090.129
cacheVersion0.3460.0420.734
cellTypeFrequency0.7150.0180.736
cellularNetwork0.6280.0210.652
cellularNetworkTable0.6660.0210.691
chordDiagramLR1.3430.0161.366
coerce0.0010.0000.002
colClusterA0.0000.0010.000
colClusterB0.0000.0000.001
comparison0.0010.0000.000
comparisonName000
convertToHuman0.2190.0123.795
createResources0.2910.0420.944
differentialStats0.0010.0000.002
findOrthoGenes0.1400.0040.295
generateSpatialPlots1.9180.0471.975
getLRIntracellNetwork2.1930.1762.403
getLRNetwork0.0380.0020.042
getPathwayStats0.0170.0020.018
getResource0.3230.0180.346
inferenceParameters000
initialOrganism0.0020.0010.002
initialOrthologs0.0010.0000.001
learnParameters2.9000.0332.949
ligands0.0010.0000.001
logTransformed0.0020.0000.002
maxLigandSpatialCounts0.0620.0030.067
mu000
ncounts0.0010.0000.002
normalization0.0010.0000.001
parameters0.0010.0000.002
pathways000
receptors0.0000.0010.001
reduceToBestPathway0.0950.0040.100
reduceToLigand0.0410.0020.042
reduceToPathway0.0920.0020.094
reduceToReceptor0.0210.0020.022
relateToGeneSet0.0900.0090.101
removeClusterComp0.3100.0090.321
rescoreInference0.0310.0030.035
resetLRdb0.0260.0000.026
resetNetwork0.0070.0000.008
resetPathways0.3100.0150.326
resetToInitialOrganism0.1410.0040.146
scoreLRGeneSignatures1.3650.0451.419
scoreSignatures0.4060.0110.421
separatedLRPlot1.9240.0391.974
signatureHeatmaps0.0230.0030.026
simpleHeatmap7.1470.4467.685
smoothSpatialCounts0.0620.0130.076
sourceComparisonName0.0010.0000.000
spatialAssociation0.0630.0300.103
spatialAssociationPlot4.0960.1014.235
spatialDiversityPlot1.0280.0271.058
spatialIndexPlot1.6390.0271.673
spatialPlot1.4000.0301.439
summarizedCellularNetwork0.6730.0210.700
tgCorr000
tgExpr0.0000.0000.001
tgGenes0.0010.0010.000
tgLogFC000
tgPval0.0000.0000.001
updateInference0.0850.0030.088