| Back to Multiple platform build/check report for BioC 3.22: simplified long | 
 | 
This page was generated on 2025-10-25 12:05 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs | 
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 | 
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 | 
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 | 
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 | 
| 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 260/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BulkSignalR 1.1.5  (landing page) Jean-Philippe Villemin 
 | nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK |  | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK |  | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
| 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. | 
| 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: 2025-10-24 18:47:32 -0400 (Fri, 24 Oct 2025) | 
| EndedAt: 2025-10-24 18:50:32 -0400 (Fri, 24 Oct 2025) | 
| EllapsedTime: 180.1 seconds | 
| RetCode: 0 | 
| Status: OK | 
| CheckDir: BulkSignalR.Rcheck | 
| Warnings: 0 | 
##############################################################################
##############################################################################
###
### 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: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* 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
* 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
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-arm64/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)
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: aarch64-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 
  5.697   0.294   7.013 
BulkSignalR.Rcheck/BulkSignalR-Ex.timings
| name | user | system | elapsed | |
| BSRClusterComp-class | 0.001 | 0.000 | 0.001 | |
| BSRClusterComp | 0.100 | 0.007 | 0.108 | |
| BSRDataModel-class | 0.020 | 0.002 | 0.022 | |
| BSRDataModel | 0.072 | 0.003 | 0.076 | |
| BSRDataModelComp-class | 0.002 | 0.001 | 0.002 | |
| BSRDataModelComp | 0.070 | 0.002 | 0.072 | |
| BSRInference-class | 0.002 | 0.000 | 0.002 | |
| BSRInference | 1.032 | 0.032 | 1.064 | |
| BSRInferenceComp-class | 0.002 | 0.000 | 0.002 | |
| BSRInferenceComp | 0.406 | 0.056 | 0.463 | |
| BSRSignature-class | 0.001 | 0.000 | 0.001 | |
| BSRSignature | 0.008 | 0.000 | 0.009 | |
| BSRSignatureComp-class | 0.002 | 0.000 | 0.002 | |
| BSRSignatureComp | 0.004 | 0.001 | 0.004 | |
| LRinter | 0 | 0 | 0 | |
| LRinterScore | 0.001 | 0.000 | 0.002 | |
| LRinterShort | 0.001 | 0.001 | 0.001 | |
| addClusterComp | 0.090 | 0.005 | 0.096 | |
| alluvialPlot | 0.188 | 0.007 | 0.194 | |
| assignCellTypesToInteractions | 0.227 | 0.015 | 0.242 | |
| bubblePlotPathwaysLR | 0.155 | 0.002 | 0.156 | |
| cacheClear | 1.391 | 0.083 | 4.874 | |
| cacheInfo | 0.029 | 0.002 | 0.031 | |
| cacheVersion | 0.090 | 0.009 | 0.442 | |
| cellTypeFrequency | 0.211 | 0.010 | 0.222 | |
| cellularNetwork | 0.191 | 0.012 | 0.204 | |
| cellularNetworkTable | 0.186 | 0.010 | 0.195 | |
| chordDiagramLR | 0.342 | 0.005 | 0.348 | |
| coerce | 0.000 | 0.001 | 0.000 | |
| colClusterA | 0 | 0 | 0 | |
| colClusterB | 0 | 0 | 0 | |
| comparison | 0 | 0 | 0 | |
| comparisonName | 0.000 | 0.000 | 0.001 | |
| convertToHuman | 0.077 | 0.005 | 2.293 | |
| createResources | 0.078 | 0.009 | 0.430 | |
| differentialStats | 0 | 0 | 0 | |
| findOrthoGenes | 0.050 | 0.002 | 0.314 | |
| generateSpatialPlots | 0.551 | 0.018 | 0.570 | |
| getLRIntracellNetwork | 0.619 | 0.099 | 0.720 | |
| getLRNetwork | 0.009 | 0.001 | 0.010 | |
| getPathwayStats | 0.005 | 0.000 | 0.005 | |
| getResource | 0.093 | 0.006 | 0.099 | |
| inferenceParameters | 0 | 0 | 0 | |
| initialOrganism | 0 | 0 | 0 | |
| initialOrthologs | 0.001 | 0.000 | 0.001 | |
| learnParameters | 0.717 | 0.009 | 0.727 | |
| ligands | 0 | 0 | 0 | |
| logTransformed | 0.000 | 0.000 | 0.001 | |
| maxLigandSpatialCounts | 0.019 | 0.001 | 0.021 | |
| mu | 0 | 0 | 0 | |
| ncounts | 0.001 | 0.000 | 0.001 | |
| normalization | 0 | 0 | 0 | |
| parameters | 0.001 | 0.000 | 0.000 | |
| pathways | 0 | 0 | 0 | |
| receptors | 0 | 0 | 0 | |
| reduceToBestPathway | 0.027 | 0.001 | 0.027 | |
| reduceToLigand | 0.011 | 0.000 | 0.012 | |
| reduceToPathway | 0.025 | 0.000 | 0.025 | |
| reduceToReceptor | 0.004 | 0.001 | 0.006 | |
| relateToGeneSet | 0.034 | 0.001 | 0.036 | |
| removeClusterComp | 0.090 | 0.005 | 0.095 | |
| rescoreInference | 0.014 | 0.001 | 0.015 | |
| resetLRdb | 0.008 | 0.000 | 0.008 | |
| resetNetwork | 0.002 | 0.000 | 0.002 | |
| resetPathways | 0.088 | 0.004 | 0.092 | |
| resetToInitialOrganism | 0.045 | 0.003 | 0.048 | |
| scoreLRGeneSignatures | 0.549 | 0.014 | 0.563 | |
| scoreSignatures | 0.110 | 0.004 | 0.113 | |
| separatedLRPlot | 0.538 | 0.012 | 0.553 | |
| signatureHeatmaps | 0.010 | 0.001 | 0.011 | |
| simpleHeatmap | 2.749 | 0.114 | 2.870 | |
| smoothSpatialCounts | 0.019 | 0.001 | 0.019 | |
| sourceComparisonName | 0 | 0 | 0 | |
| spatialAssociation | 0.022 | 0.001 | 0.023 | |
| spatialAssociationPlot | 1.256 | 0.022 | 1.278 | |
| spatialDiversityPlot | 0.311 | 0.026 | 0.340 | |
| spatialIndexPlot | 0.455 | 0.023 | 0.477 | |
| spatialPlot | 0.375 | 0.014 | 0.395 | |
| summarizedCellularNetwork | 0.196 | 0.011 | 0.207 | |
| tgCorr | 0 | 0 | 0 | |
| tgExpr | 0 | 0 | 0 | |
| tgGenes | 0 | 0 | 0 | |
| tgLogFC | 0 | 0 | 0 | |
| tgPval | 0 | 0 | 0 | |
| updateInference | 0.032 | 0.003 | 0.036 | |