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This page was generated on 2025-06-13 12:08 -0400 (Fri, 13 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4797
palomino8Windows Server 2022 Datacenterx644.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" 4538
lconwaymacOS 12.7.1 Montereyx86_644.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" 4571
kjohnson3macOS 13.7.1 Venturaarm644.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" 4515
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4483
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 253/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 1.1.2  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2025-06-12 13:25 -0400 (Thu, 12 Jun 2025)
git_url: https://git.bioconductor.org/packages/BulkSignalR
git_branch: devel
git_last_commit: bc0bbb1
git_last_commit_date: 2025-05-29 05:23:30 -0400 (Thu, 29 May 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 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: 1.1.2
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_1.1.2.tar.gz
StartedAt: 2025-06-12 19:33:54 -0400 (Thu, 12 Jun 2025)
EndedAt: 2025-06-12 19:41:56 -0400 (Thu, 12 Jun 2025)
EllapsedTime: 482.2 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_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BulkSignalR.Rcheck’
* using R version 4.5.0 Patched (2025-04-21 r88169)
* 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 ‘1.1.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 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
convertToHuman 0.226  0.012   7.873
* 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 ‘1.1.2’
** 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 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
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 "database" is up to date.

Local "resources" are up to date.

> test_check("BulkSignalR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 16.665   0.914  18.666 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0030.0010.004
BSRClusterComp0.3800.0190.400
BSRDataModel-class0.0040.0010.008
BSRDataModel0.2680.0080.282
BSRDataModelComp-class0.0070.0010.007
BSRInference-class0.0030.0000.004
BSRInference2.9120.0903.020
BSRInferenceComp-class0.0050.0000.006
BSRInferenceComp1.4910.0881.590
BSRSignature-class0.0020.0000.003
BSRSignature0.0310.0020.032
BSRSignatureComp-class0.0030.0010.003
BSRSignatureComp0.0150.0020.016
LRinter0.0010.0010.001
LRinterScore0.0040.0020.006
LRinterShort0.0040.0020.006
addClusterComp0.3480.0190.370
alluvialPlot0.4510.0150.471
assignCellTypesToInteractions1.5240.0261.558
bubblePlotPathwaysLR0.3980.0120.411
cacheClear2.1730.0843.773
cacheInfo0.2390.0180.257
cacheVersion0.4460.0460.843
cellTypeFrequency0.7510.0260.781
cellularNetwork0.6960.0270.730
cellularNetworkTable0.6930.0180.716
chordDiagramLR1.3740.0161.402
coerce0.0010.0000.001
colClusterA0.0000.0000.001
colClusterB0.0000.0010.000
comparison0.0000.0000.001
comparisonName0.0010.0000.000
convertToHuman0.2260.0127.873
createDatabase0.0010.0010.001
createResources0.2650.0340.835
differentialStats0.0010.0010.001
findOrthoGenes0.1540.0030.305
generateSpatialPlots1.4030.0401.452
getComplexes0.1330.0130.147
getInteractions1.1120.0181.137
getLRIntracellNetwork2.0220.1692.197
getLRNetwork0.0340.0020.036
getPathwayStats0.0170.0020.019
getResource0.2920.0170.310
inferenceParameters000
initialOrganism0.0000.0010.001
initialOrthologs0.0000.0000.001
learnParameters2.9370.0452.998
ligands0.0000.0000.001
logTransformed0.0000.0000.001
maxLigandSpatialCounts0.0570.0030.061
mu0.0010.0000.000
ncounts0.0010.0000.000
normalization0.0010.0000.001
parameters0.0010.0010.001
pathways000
receptors0.0000.0010.000
reduceToBestPathway0.1250.0050.131
reduceToLigand0.0410.0020.043
reduceToPathway0.0830.0020.086
reduceToReceptor0.0190.0020.020
relateToGeneSet0.0800.0040.084
removeClusterComp0.3590.0090.369
rescoreInference0.0300.0030.033
resetLRdb0.0100.0000.011
resetNetwork0.0080.0000.008
resetPathways0.2890.0150.307
resetToInitialOrganism0.1720.0050.177
scoreLRGeneSignatures0.4310.0380.472
scoreSignatures0.3830.0070.393
separatedLRPlot1.4260.0331.465
signatureHeatmaps0.0210.0020.023
simpleHeatmap1.1640.0521.260
smoothSpatialCounts0.0580.0030.062
sourceComparisonName0.0000.0010.000
spatialAssociation0.0670.0040.072
spatialAssociationPlot4.2080.0564.291
spatialDiversityPlot0.9410.0160.964
spatialIndexPlot1.1840.0321.221
spatialPlot0.9630.0270.995
summarizedCellularNetwork0.6480.0150.665
tgCorr0.0000.0000.001
tgExpr0.0010.0000.000
tgGenes000
tgLogFC0.0010.0000.000
tgPval000
updateInference0.0860.0020.090