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This page was generated on 2025-10-04 12:05 -0400 (Sat, 04 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 258/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 1.1.5  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2025-10-03 13:45 -0400 (Fri, 03 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 12.7.1 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 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: 1.1.5
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: 2025-10-03 18:31:37 -0400 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 18:34:36 -0400 (Fri, 03 Oct 2025)
EllapsedTime: 179.1 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: 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


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-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)

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: 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 
  5.639   0.241   6.951 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0010.0000.001
BSRClusterComp0.1020.0070.110
BSRDataModel-class0.0240.0020.026
BSRDataModel0.0710.0040.074
BSRDataModelComp-class0.0020.0000.002
BSRDataModelComp0.0700.0020.072
BSRInference-class0.0010.0000.001
BSRInference0.9990.0211.019
BSRInferenceComp-class0.0030.0000.002
BSRInferenceComp0.3960.0410.437
BSRSignature-class0.0010.0000.001
BSRSignature0.0090.0000.009
BSRSignatureComp-class0.0010.0000.001
BSRSignatureComp0.0050.0010.005
LRinter0.0000.0000.001
LRinterScore0.0010.0000.001
LRinterShort0.0010.0010.001
addClusterComp0.0890.0100.100
alluvialPlot0.1900.0070.196
assignCellTypesToInteractions0.2280.0110.239
bubblePlotPathwaysLR0.1570.0010.158
cacheClear1.3500.0704.905
cacheInfo0.0310.0030.033
cacheVersion0.0920.0090.443
cellTypeFrequency0.2170.0110.228
cellularNetwork0.1890.0080.197
cellularNetworkTable0.1940.0110.205
chordDiagramLR0.3360.0050.341
coerce0.0010.0000.000
colClusterA000
colClusterB000
comparison000
comparisonName000
convertToHuman0.0690.0032.272
createResources0.0900.0100.443
differentialStats0.0000.0000.001
findOrthoGenes0.0530.0020.216
generateSpatialPlots0.5510.0170.570
getLRIntracellNetwork0.6410.1200.761
getLRNetwork0.0090.0000.010
getPathwayStats0.0040.0010.005
getResource0.0960.0050.101
inferenceParameters000
initialOrganism0.0010.0000.001
initialOrthologs0.0000.0000.001
learnParameters1.0920.0101.114
ligands000
logTransformed0.0010.0000.000
maxLigandSpatialCounts0.0190.0010.020
mu000
ncounts0.0010.0000.001
normalization000
parameters0.0010.0000.000
pathways000
receptors0.0000.0000.001
reduceToBestPathway0.0260.0010.026
reduceToLigand0.0100.0000.011
reduceToPathway0.0240.0000.026
reduceToReceptor0.0050.0010.005
relateToGeneSet0.0260.0010.027
removeClusterComp0.0890.0090.101
rescoreInference0.0130.0010.014
resetLRdb0.0080.0000.008
resetNetwork0.0010.0000.001
resetPathways0.1040.0090.114
resetToInitialOrganism0.0500.0030.053
scoreLRGeneSignatures0.1350.0050.141
scoreSignatures0.1230.0080.134
separatedLRPlot0.5540.0220.577
signatureHeatmaps0.0120.0010.012
simpleHeatmap2.7140.0812.862
smoothSpatialCounts0.0180.0010.019
sourceComparisonName000
spatialAssociation0.0270.0020.027
spatialAssociationPlot1.3050.0271.417
spatialDiversityPlot0.3180.0170.337
spatialIndexPlot0.4750.0210.498
spatialPlot0.3740.0200.396
summarizedCellularNetwork0.1960.0120.209
tgCorr000
tgExpr000
tgGenes0.0000.0000.001
tgLogFC000
tgPval0.0010.0000.000
updateInference0.0320.0030.037