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This page was generated on 2025-10-13 11:38 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 255/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 1.0.5  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2025-10-09 13:40 -0400 (Thu, 09 Oct 2025)
git_url: https://git.bioconductor.org/packages/BulkSignalR
git_branch: RELEASE_3_21
git_last_commit: 84707b3
git_last_commit_date: 2025-09-27 05:41:27 -0400 (Sat, 27 Sep 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for BulkSignalR on merida1

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: 1.0.5
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_1.0.5.tar.gz
StartedAt: 2025-10-10 00:59:48 -0400 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 01:13:25 -0400 (Fri, 10 Oct 2025)
EllapsedTime: 816.5 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_1.0.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BulkSignalR.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.0.5’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
simpleHeatmap          11.315  0.630  12.092
spatialAssociationPlot  9.503  0.114   9.735
BSRInference            6.274  0.181   6.516
learnParameters         5.716  0.045   5.818
cacheClear              4.862  0.314   8.911
* 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 ‘1.0.5’
** 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 RC (2025-06-05 r88288) -- "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 
 28.087   1.523  31.226 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0040.0010.006
BSRClusterComp0.5150.0310.573
BSRDataModel-class0.0600.0060.067
BSRDataModel0.3270.0120.340
BSRDataModelComp-class0.0100.0010.011
BSRDataModelComp0.3440.0090.359
BSRInference-class0.0090.0010.009
BSRInference6.2740.1816.516
BSRInferenceComp-class0.0160.0010.016
BSRInferenceComp2.5330.2132.766
BSRSignature-class0.0040.0010.005
BSRSignature0.0790.0030.082
BSRSignatureComp-class0.0060.0000.007
BSRSignatureComp0.0320.0030.035
LRinter0.0040.0010.004
LRinterScore0.0070.0030.010
LRinterShort0.0070.0030.010
addClusterComp0.4350.0280.464
alluvialPlot1.2230.0141.240
assignCellTypesToInteractions1.7050.0511.809
bubblePlotPathwaysLR1.2730.0241.385
cacheClear4.8620.3148.911
cacheInfo0.2070.0110.221
cacheVersion0.490.050.97
cellTypeFrequency1.8020.0271.843
cellularNetwork1.6140.0421.669
cellularNetworkTable1.6070.0291.647
chordDiagramLR3.0280.0263.076
coerce0.0020.0000.003
colClusterA0.0010.0000.000
colClusterB0.0010.0000.000
comparison0.0000.0010.000
comparisonName0.0000.0010.000
convertToHuman0.4290.0151.366
createResources0.4530.0481.272
differentialStats0.0020.0000.003
findOrthoGenes0.3260.0050.644
generateSpatialPlots4.5470.0954.666
getLRIntracellNetwork3.6640.2453.940
getLRNetwork0.0900.0040.095
getPathwayStats0.0340.0030.038
getResource0.5460.0280.576
inferenceParameters0.0000.0010.001
initialOrganism0.0030.0010.004
initialOrthologs0.0030.0010.004
learnParameters5.7160.0455.818
ligands0.0000.0010.001
logTransformed0.0030.0010.004
maxLigandSpatialCounts0.1030.0070.111
mu0.0000.0000.001
ncounts0.0030.0010.003
normalization0.0030.0010.004
parameters0.0030.0010.003
pathways0.0000.0000.001
receptors0.0000.0000.001
reduceToBestPathway0.2280.0120.242
reduceToLigand0.1030.0070.111
reduceToPathway0.2880.0310.320
reduceToReceptor0.0380.0070.045
relateToGeneSet0.1720.0090.186
removeClusterComp0.4300.0100.444
rescoreInference0.0540.0100.063
resetLRdb0.0270.0000.027
resetNetwork0.0160.0010.017
resetPathways0.5340.0220.559
resetToInitialOrganism0.3110.0060.319
scoreLRGeneSignatures1.0990.0491.155
scoreSignatures0.6990.0130.715
separatedLRPlot4.4470.0694.553
signatureHeatmaps0.0330.0070.040
simpleHeatmap11.315 0.63012.092
smoothSpatialCounts0.1150.0120.129
sourceComparisonName0.0000.0000.001
spatialAssociation0.1020.0220.127
spatialAssociationPlot9.5030.1149.735
spatialDiversityPlot2.4930.0442.672
spatialIndexPlot3.6970.0453.929
spatialPlot3.0080.0493.167
summarizedCellularNetwork1.6350.0301.722
tgCorr000
tgExpr000
tgGenes0.0000.0010.001
tgLogFC0.0000.0010.001
tgPval0.0010.0000.000
updateInference0.1590.0160.174