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This page was generated on 2025-09-22 12:04 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 256/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 1.1.4  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2025-09-21 13:45 -0400 (Sun, 21 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: 2025-09-21 19:47:35 -0400 (Sun, 21 Sep 2025)
EndedAt: 2025-09-21 19:55:40 -0400 (Sun, 21 Sep 2025)
EllapsedTime: 485.4 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 7.426  0.421   7.928
cacheClear    3.701  0.241   7.285
* 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 
 16.706   0.958  18.742 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0030.0010.003
BSRClusterComp0.4130.0160.431
BSRDataModel-class0.0580.0070.066
BSRDataModel0.2730.0050.279
BSRDataModelComp-class0.0050.0000.005
BSRDataModelComp0.2900.0110.309
BSRInference-class0.0050.0000.005
BSRInference3.7190.0853.822
BSRInferenceComp-class0.010.000.01
BSRInferenceComp1.4210.0931.528
BSRSignature-class0.0020.0000.002
BSRSignature0.0350.0010.036
BSRSignatureComp-class0.0060.0010.007
BSRSignatureComp0.0140.0020.017
LRinter0.0020.0010.002
LRinterScore0.0040.0010.005
LRinterShort0.0030.0010.005
addClusterComp0.3500.0120.365
alluvialPlot0.6920.0250.720
assignCellTypesToInteractions0.7650.0350.806
bubblePlotPathwaysLR0.6110.0070.620
cacheClear3.7010.2417.285
cacheInfo0.1240.0090.134
cacheVersion0.3410.0390.723
cellTypeFrequency0.7910.0190.815
cellularNetwork0.6740.0190.697
cellularNetworkTable0.6560.0150.675
chordDiagramLR1.3700.0201.397
coerce0.0020.0000.002
colClusterA0.0010.0000.000
colClusterB0.0000.0000.001
comparison0.0000.0000.001
comparisonName000
convertToHuman0.2040.0112.833
createResources0.3280.0390.985
differentialStats0.0010.0000.002
findOrthoGenes0.1700.0040.324
generateSpatialPlots2.1530.0432.209
getLRIntracellNetwork2.3370.1602.511
getLRNetwork0.0380.0020.040
getPathwayStats0.0190.0010.021
getResource0.3350.0210.358
inferenceParameters0.0000.0010.000
initialOrganism0.0020.0000.002
initialOrthologs0.0020.0000.002
learnParameters2.9750.0393.039
ligands0.0010.0000.000
logTransformed0.0020.0000.003
maxLigandSpatialCounts0.0590.0020.062
mu0.0010.0000.001
ncounts0.0020.0010.002
normalization0.0010.0000.002
parameters0.0010.0000.002
pathways0.0000.0010.001
receptors000
reduceToBestPathway0.0950.0030.099
reduceToLigand0.0450.0030.048
reduceToPathway0.0900.0030.093
reduceToReceptor0.0160.0020.019
relateToGeneSet0.1080.0050.114
removeClusterComp0.3610.0110.373
rescoreInference0.0330.0030.035
resetLRdb0.0180.0000.017
resetNetwork0.0100.0000.009
resetPathways0.3330.0180.352
resetToInitialOrganism0.1570.0050.162
scoreLRGeneSignatures1.3500.0341.388
scoreSignatures0.3970.0090.407
separatedLRPlot1.9940.0432.044
signatureHeatmaps0.0230.0020.025
simpleHeatmap7.4260.4217.928
smoothSpatialCounts0.0640.0120.076
sourceComparisonName0.0000.0000.001
spatialAssociation0.0650.0290.095
spatialAssociationPlot4.3450.0774.447
spatialDiversityPlot1.1170.0221.144
spatialIndexPlot1.6630.0301.698
spatialPlot1.3100.0241.340
summarizedCellularNetwork0.6940.0190.717
tgCorr000
tgExpr0.0000.0010.001
tgGenes000
tgLogFC000
tgPval0.0000.0000.001
updateInference0.0920.0030.096