Back to Multiple platform build/check report for BioC 3.22:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-09-01 12:03 -0400 (Mon, 01 Sep 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: 2025-08-31 13:45 -0400 (Sun, 31 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BulkSignalR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BulkSignalR_1.1.4.tar.gz
StartedAt: 2025-08-31 20:53:06 -0400 (Sun, 31 Aug 2025)
EndedAt: 2025-08-31 21:03:44 -0400 (Sun, 31 Aug 2025)
EllapsedTime: 638.6 seconds
RetCode: 0
Status:   OK  
CheckDir: BulkSignalR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BulkSignalR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BulkSignalR_1.1.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BulkSignalR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 6.604  0.612   7.217
cacheClear    3.336  0.068   5.525
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

BulkSignalR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BulkSignalR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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-pc-linux-gnu

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 
 13.793   0.761  15.507 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0030.0000.003
BSRClusterComp0.2280.0060.235
BSRDataModel-class0.0050.0000.005
BSRDataModel0.1460.0020.149
BSRDataModelComp-class0.0050.0000.005
BSRDataModelComp0.1560.0010.158
BSRInference-class0.0040.0000.005
BSRInference2.3830.0972.481
BSRInferenceComp-class0.0070.0000.007
BSRInferenceComp1.1550.0821.237
BSRSignature-class0.0010.0000.002
BSRSignature0.0270.0010.029
BSRSignatureComp-class0.0030.0000.003
BSRSignatureComp0.0130.0000.014
LRinter0.0010.0000.002
LRinterScore0.0030.0000.004
LRinterShort0.0040.0000.003
addClusterComp1.1110.0301.140
alluvialPlot0.3390.0040.343
assignCellTypesToInteractions0.6190.0080.627
bubblePlotPathwaysLR0.3080.0020.310
cacheClear3.3360.0685.525
cacheInfo0.0830.0040.087
cacheVersion0.2330.0040.578
cellTypeFrequency0.6040.0190.623
cellularNetwork0.5520.0020.554
cellularNetworkTable0.5250.0010.526
chordDiagramLR1.1480.0091.158
coerce0.0010.0000.001
colClusterA0.0000.0000.001
colClusterB000
comparison000
comparisonName0.0010.0000.000
convertToHuman0.2040.0142.033
createResources0.2840.0210.914
differentialStats0.0000.0000.001
findOrthoGenes0.1280.0010.281
generateSpatialPlots1.1960.0281.223
getLRIntracellNetwork1.6710.0341.704
getLRNetwork0.0320.0000.031
getPathwayStats0.0140.0000.014
getResource0.2650.0020.268
inferenceParameters000
initialOrganism0.0020.0000.001
initialOrthologs0.0010.0000.001
learnParameters2.5000.0072.508
ligands000
logTransformed0.0020.0000.001
maxLigandSpatialCounts0.0500.0020.052
mu000
ncounts0.0010.0000.001
normalization0.0010.0000.002
parameters0.0010.0000.001
pathways000
receptors000
reduceToBestPathway0.0860.0010.087
reduceToLigand0.0370.0000.037
reduceToPathway0.0920.0010.093
reduceToReceptor0.0170.0000.017
relateToGeneSet0.0740.0000.073
removeClusterComp0.1990.0020.201
rescoreInference0.0300.0010.031
resetLRdb0.0110.0010.011
resetNetwork0.0060.0000.006
resetPathways0.2680.0020.270
resetToInitialOrganism0.1430.0010.143
scoreLRGeneSignatures0.3800.0220.401
scoreSignatures0.2610.0020.263
separatedLRPlot1.2060.0031.209
signatureHeatmaps0.0220.0000.023
simpleHeatmap6.6040.6127.217
smoothSpatialCounts0.0470.0000.047
sourceComparisonName000
spatialAssociation0.0500.0020.052
spatialAssociationPlot3.4730.0243.497
spatialDiversityPlot0.7850.0040.789
spatialIndexPlot0.9930.0191.011
spatialPlot0.8750.0070.882
summarizedCellularNetwork0.5500.0000.551
tgCorr000
tgExpr000
tgGenes000
tgLogFC0.0000.0000.001
tgPval000
updateInference0.0850.0000.085