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This page was generated on 2025-08-30 12:05 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 255/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 1.1.4  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 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: 2025-08-29 19:35:25 -0400 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 19:43:13 -0400 (Fri, 29 Aug 2025)
EllapsedTime: 468.1 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 (2025-06-13)
* 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 7.162  0.422   8.036
cacheClear    3.659  0.240   6.816
* 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 (2025-06-13) -- "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 
 16.148   0.932  18.147 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0040.0000.005
BSRClusterComp0.4140.0220.438
BSRDataModel-class0.0070.0010.009
BSRDataModel0.2790.0070.287
BSRDataModelComp-class0.0050.0010.006
BSRDataModelComp0.2610.0070.267
BSRInference-class0.0050.0000.005
BSRInference2.6970.0812.791
BSRInferenceComp-class0.0070.0000.008
BSRInferenceComp1.3240.0971.426
BSRSignature-class0.0020.0000.002
BSRSignature0.0340.0010.035
BSRSignatureComp-class0.0050.0000.005
BSRSignatureComp0.0170.0010.018
LRinter0.0010.0000.002
LRinterScore0.0040.0010.003
LRinterShort0.0030.0010.004
addClusterComp0.3260.0220.349
alluvialPlot1.1640.0221.193
assignCellTypesToInteractions0.7020.0150.722
bubblePlotPathwaysLR0.3860.0230.411
cacheClear3.6590.2406.816
cacheInfo0.1220.0100.132
cacheVersion0.3160.0370.695
cellTypeFrequency0.7220.0250.749
cellularNetwork0.6490.0230.674
cellularNetworkTable0.6290.0080.640
chordDiagramLR1.3140.0211.341
coerce0.0010.0000.001
colClusterA000
colClusterB0.0000.0010.001
comparison000
comparisonName0.0000.0010.001
convertToHuman0.2110.0114.258
createResources0.3050.0420.960
differentialStats0.0010.0000.001
findOrthoGenes0.1460.0040.304
generateSpatialPlots1.4670.0361.509
getLRIntracellNetwork2.2550.1672.433
getLRNetwork0.0330.0010.036
getPathwayStats0.0140.0010.015
getResource0.3040.0170.323
inferenceParameters0.0000.0000.001
initialOrganism0.0020.0010.002
initialOrthologs0.0020.0000.002
learnParameters2.9450.0412.998
ligands000
logTransformed0.0010.0000.002
maxLigandSpatialCounts0.0600.0030.064
mu0.0000.0000.001
ncounts0.0020.0000.002
normalization0.0020.0000.002
parameters0.0020.0010.002
pathways000
receptors000
reduceToBestPathway0.1020.0040.106
reduceToLigand0.0430.0020.045
reduceToPathway0.1300.0070.139
reduceToReceptor0.0190.0020.021
relateToGeneSet0.0820.0030.086
removeClusterComp0.3580.0100.370
rescoreInference0.0320.0030.034
resetLRdb0.0110.0000.011
resetNetwork0.0070.0010.007
resetPathways0.3340.0190.357
resetToInitialOrganism0.1740.0050.181
scoreLRGeneSignatures0.4280.0380.470
scoreSignatures0.3930.0100.406
separatedLRPlot1.4150.0341.457
signatureHeatmaps0.0220.0020.024
simpleHeatmap7.1620.4228.036
smoothSpatialCounts0.0550.0100.065
sourceComparisonName0.0000.0010.000
spatialAssociation0.0550.0220.078
spatialAssociationPlot4.2140.0854.316
spatialDiversityPlot0.9620.0190.986
spatialIndexPlot1.2240.0241.254
spatialPlot1.0640.0321.101
summarizedCellularNetwork0.6290.0090.640
tgCorr000
tgExpr0.0000.0010.000
tgGenes0.0010.0000.000
tgLogFC0.0000.0000.001
tgPval000
updateInference0.0790.0020.081