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This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 255/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 1.0.5  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/BulkSignalR
git_branch: RELEASE_3_21
git_last_commit: 84707b3
git_last_commit_date: 2025-09-27 05:41:27 -0400 (Sat, 27 Sep 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for BulkSignalR on merida1

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: 1.0.5
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_1.0.5.tar.gz
StartedAt: 2025-10-14 00:57:44 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 01:11:17 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 812.3 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_1.0.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BulkSignalR.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.0.5’
* 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          11.371  0.657  12.408
spatialAssociationPlot  9.605  0.112   9.972
BSRInference            6.395  0.180   6.610
learnParameters         5.714  0.042   5.793
cacheClear              4.966  0.326   8.958
convertToHuman          0.417  0.015   7.117
* 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 ‘1.0.5’
** 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 RC (2025-06-05 r88288) -- "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 
 27.705   1.453  30.622 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0030.0010.003
BSRClusterComp0.4530.0340.488
BSRDataModel-class0.0580.0090.067
BSRDataModel0.3460.0090.356
BSRDataModelComp-class0.0100.0010.011
BSRDataModelComp0.3420.0120.354
BSRInference-class0.0090.0000.010
BSRInference6.3950.1806.610
BSRInferenceComp-class0.0160.0010.017
BSRInferenceComp2.7760.1702.987
BSRSignature-class0.0050.0000.004
BSRSignature0.0810.0070.089
BSRSignatureComp-class0.0080.0010.009
BSRSignatureComp0.0330.0070.040
LRinter0.0040.0010.005
LRinterScore0.0070.0080.015
LRinterShort0.0070.0070.015
addClusterComp0.4400.0170.459
alluvialPlot1.3180.0361.358
assignCellTypesToInteractions1.7200.0681.805
bubblePlotPathwaysLR1.2210.0171.241
cacheClear4.9660.3268.958
cacheInfo0.1980.0120.210
cacheVersion0.4750.0440.949
cellTypeFrequency1.7860.0331.829
cellularNetwork1.6420.0711.721
cellularNetworkTable1.6140.0401.680
chordDiagramLR3.0340.0273.087
coerce0.0020.0000.003
colClusterA000
colClusterB0.0010.0010.001
comparison0.0000.0010.001
comparisonName0.0000.0010.000
convertToHuman0.4170.0157.117
createResources0.4620.0501.300
differentialStats0.0020.0000.003
findOrthoGenes0.3320.0050.640
generateSpatialPlots4.6060.0984.728
getLRIntracellNetwork3.7310.2534.016
getLRNetwork0.0860.0070.094
getPathwayStats0.0340.0070.042
getResource0.5280.0230.553
inferenceParameters000
initialOrganism0.0030.0010.003
initialOrthologs0.0020.0010.003
learnParameters5.7140.0425.793
ligands0.0010.0000.001
logTransformed0.0020.0010.003
maxLigandSpatialCounts0.1070.0100.119
mu0.0000.0000.001
ncounts0.0030.0010.004
normalization0.0020.0010.003
parameters0.0030.0010.004
pathways0.0000.0010.001
receptors0.0010.0000.001
reduceToBestPathway0.2300.0190.252
reduceToLigand0.1020.0140.117
reduceToPathway0.2370.0180.256
reduceToReceptor0.0380.0140.051
relateToGeneSet0.1690.0160.187
removeClusterComp0.4350.0090.453
rescoreInference0.0560.0210.078
resetLRdb0.0270.0010.029
resetNetwork0.0160.0010.017
resetPathways0.5320.0230.561
resetToInitialOrganism0.3250.0070.334
scoreLRGeneSignatures2.1080.0792.206
scoreSignatures0.7200.0160.739
separatedLRPlot4.4530.0764.572
signatureHeatmaps0.0330.0150.047
simpleHeatmap11.371 0.65712.408
smoothSpatialCounts0.1180.0140.140
sourceComparisonName0.0000.0000.001
spatialAssociation0.1060.0230.133
spatialAssociationPlot9.6050.1129.972
spatialDiversityPlot2.5440.0582.613
spatialIndexPlot3.8160.0623.946
spatialPlot3.0880.0503.163
summarizedCellularNetwork1.6380.0331.688
tgCorr0.0010.0000.000
tgExpr0.0010.0000.001
tgGenes0.0000.0010.001
tgLogFC0.0000.0010.001
tgPval0.0000.0010.001
updateInference0.1650.0160.192