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This page was generated on 2025-09-23 12:05 -0400 (Tue, 23 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4816
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4605
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4549
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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: 2025-09-22 13:45 -0400 (Mon, 22 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 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: 1.1.4
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: 2025-09-22 18:30:35 -0400 (Mon, 22 Sep 2025)
EndedAt: 2025-09-22 18:33:34 -0400 (Mon, 22 Sep 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_1.1.4.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: 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 ‘1.1.4’
* 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
cacheClear 1.386   0.08   5.063
* 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 ‘1.1.4’
** 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: 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 
  5.645   0.245   6.912 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0000.0000.001
BSRClusterComp0.1000.0060.105
BSRDataModel-class0.0210.0020.023
BSRDataModel0.0680.0030.072
BSRDataModelComp-class0.0020.0000.002
BSRDataModelComp0.0690.0020.072
BSRInference-class0.0010.0000.001
BSRInference1.0180.0271.047
BSRInferenceComp-class0.0020.0000.002
BSRInferenceComp0.3900.0510.450
BSRSignature-class0.0000.0000.001
BSRSignature0.0090.0010.009
BSRSignatureComp-class0.0010.0000.001
BSRSignatureComp0.0050.0010.004
LRinter000
LRinterScore0.0010.0000.002
LRinterShort0.0010.0010.001
addClusterComp0.0880.0040.096
alluvialPlot0.1970.0070.203
assignCellTypesToInteractions0.2240.0150.239
bubblePlotPathwaysLR0.1510.0010.153
cacheClear1.3860.0805.063
cacheInfo0.0290.0020.032
cacheVersion0.1000.0140.459
cellTypeFrequency0.2170.0110.233
cellularNetwork0.1900.0130.203
cellularNetworkTable0.1870.0110.198
chordDiagramLR0.3440.0070.363
coerce0.0000.0000.001
colClusterA000
colClusterB000
comparison000
comparisonName000
convertToHuman0.0680.0032.161
createResources0.0900.0130.448
differentialStats0.0000.0000.001
findOrthoGenes0.0550.0020.207
generateSpatialPlots0.5720.0230.598
getLRIntracellNetwork0.6420.1040.770
getLRNetwork0.0100.0010.011
getPathwayStats0.0050.0000.005
getResource0.0930.0030.095
inferenceParameters000
initialOrganism0.0010.0000.001
initialOrthologs0.0000.0000.001
learnParameters0.7190.0080.730
ligands0.0010.0000.001
logTransformed000
maxLigandSpatialCounts0.0200.0010.021
mu000
ncounts0.0000.0000.001
normalization0.0000.0000.001
parameters000
pathways000
receptors000
reduceToBestPathway0.0260.0010.027
reduceToLigand0.0110.0000.012
reduceToPathway0.0230.0010.024
reduceToReceptor0.0040.0010.005
relateToGeneSet0.0360.0040.041
removeClusterComp0.0900.0080.108
rescoreInference0.0140.0010.015
resetLRdb0.0040.0000.004
resetNetwork0.0020.0000.002
resetPathways0.0950.0040.099
resetToInitialOrganism0.0470.0030.051
scoreLRGeneSignatures0.5660.0140.587
scoreSignatures0.1100.0020.112
separatedLRPlot0.5390.0170.568
signatureHeatmaps0.0110.0000.011
simpleHeatmap2.8250.0862.998
smoothSpatialCounts0.0180.0020.019
sourceComparisonName000
spatialAssociation0.0210.0010.022
spatialAssociationPlot1.2600.0261.299
spatialDiversityPlot0.3070.0240.349
spatialIndexPlot0.4540.0170.471
spatialPlot0.3770.0250.402
summarizedCellularNetwork0.1940.0100.204
tgCorr0.0010.0010.000
tgExpr000
tgGenes000
tgLogFC0.0000.0000.001
tgPval000
updateInference0.0330.0040.036