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This page was generated on 2025-09-27 12:04 -0400 (Sat, 27 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4832
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4620
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 256/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 1.1.4  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2025-09-26 13:45 -0400 (Fri, 26 Sep 2025)
git_url: https://git.bioconductor.org/packages/BulkSignalR
git_branch: devel
git_last_commit: cd57706
git_last_commit_date: 2025-08-14 12:25:16 -0400 (Thu, 14 Aug 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 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: 1.1.4
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_1.1.4.tar.gz
StartedAt: 2025-09-26 19:54:04 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 20:02:11 -0400 (Fri, 26 Sep 2025)
EllapsedTime: 486.6 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_1.1.4.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 ‘1.1.4’
* 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 7.411  0.412   7.902
cacheClear    3.723  0.244   7.228
* 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 ‘1.1.4’
** 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 
 16.755   0.968  18.797 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0030.0010.003
BSRClusterComp0.3700.0230.396
BSRDataModel-class0.0490.0070.056
BSRDataModel0.2420.0080.251
BSRDataModelComp-class0.0060.0000.007
BSRDataModelComp0.2640.0080.276
BSRInference-class0.0060.0000.006
BSRInference3.6230.0953.740
BSRInferenceComp-class0.0060.0000.007
BSRInferenceComp1.3060.0991.414
BSRSignature-class0.0020.0010.002
BSRSignature0.0320.0020.034
BSRSignatureComp-class0.0050.0000.004
BSRSignatureComp0.0130.0010.015
LRinter0.0020.0000.002
LRinterScore0.0040.0020.006
LRinterShort0.0040.0010.005
addClusterComp0.3340.0110.347
alluvialPlot0.6670.0230.693
assignCellTypesToInteractions0.7120.0350.750
bubblePlotPathwaysLR0.5740.0080.584
cacheClear3.7230.2447.228
cacheInfo0.1140.0090.124
cacheVersion0.3500.0410.737
cellTypeFrequency0.7850.0210.810
cellularNetwork0.7110.0310.748
cellularNetworkTable0.6950.0160.714
chordDiagramLR1.4330.0181.458
coerce0.0010.0000.002
colClusterA0.0000.0010.000
colClusterB000
comparison0.0000.0010.001
comparisonName000
convertToHuman0.2070.0101.687
createResources0.3360.0440.998
differentialStats0.0010.0000.001
findOrthoGenes0.1650.0040.440
generateSpatialPlots2.1330.0402.183
getLRIntracellNetwork2.3180.1672.492
getLRNetwork0.0310.0020.033
getPathwayStats0.0170.0010.018
getResource0.3170.0210.340
inferenceParameters0.0000.0000.001
initialOrganism0.0010.0000.001
initialOrthologs0.0020.0010.001
learnParameters2.9100.0322.954
ligands000
logTransformed0.0020.0010.003
maxLigandSpatialCounts0.0620.0040.067
mu000
ncounts0.0020.0000.002
normalization0.0010.0000.002
parameters0.0020.0000.002
pathways0.0010.0000.000
receptors000
reduceToBestPathway0.1080.0050.115
reduceToLigand0.0480.0030.051
reduceToPathway0.1010.0030.104
reduceToReceptor0.0190.0020.021
relateToGeneSet0.1120.0070.119
removeClusterComp0.3300.0090.341
rescoreInference0.0320.0030.036
resetLRdb0.0130.0000.013
resetNetwork0.0080.0000.008
resetPathways0.3050.0130.321
resetToInitialOrganism0.1600.0050.166
scoreLRGeneSignatures1.2990.0291.333
scoreSignatures0.4040.0080.414
separatedLRPlot2.0650.0462.119
signatureHeatmaps0.0210.0030.024
simpleHeatmap7.4110.4127.902
smoothSpatialCounts0.0580.0110.069
sourceComparisonName000
spatialAssociation0.0550.0200.075
spatialAssociationPlot4.2990.0744.396
spatialDiversityPlot1.0470.0251.077
spatialIndexPlot1.6170.0251.648
spatialPlot1.3700.0271.404
summarizedCellularNetwork0.6920.0190.714
tgCorr0.0000.0010.001
tgExpr0.0010.0000.000
tgGenes000
tgLogFC0.0000.0010.001
tgPval000
updateInference0.0890.0020.091