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This page was generated on 2025-10-04 12:07 -0400 (Sat, 04 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 258/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 1.1.5  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2025-10-03 13:45 -0400 (Fri, 03 Oct 2025)
git_url: https://git.bioconductor.org/packages/BulkSignalR
git_branch: devel
git_last_commit: dd2021f
git_last_commit_date: 2025-09-27 04:43:00 -0400 (Sat, 27 Sep 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: BulkSignalR
Version: 1.1.5
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BulkSignalR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BulkSignalR_1.1.5.tar.gz
StartedAt: 2025-10-03 05:19:36 -0000 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 05:28:44 -0000 (Fri, 03 Oct 2025)
EllapsedTime: 548.4 seconds
RetCode: 0
Status:   OK  
CheckDir: BulkSignalR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:BulkSignalR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BulkSignalR_1.1.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BulkSignalR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BulkSignalR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BulkSignalR’ version ‘1.1.5’
* 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 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          6.957  0.319   7.301
spatialAssociationPlot 5.547  0.077   5.644
cacheClear             4.193  0.362  10.166
* 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL BulkSignalR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘BulkSignalR’ ...
** this is package ‘BulkSignalR’ version ‘1.1.5’
** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
 18.063   0.888  20.776 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0030.0000.003
BSRClusterComp0.3470.0040.352
BSRDataModel-class0.0500.0040.053
BSRDataModel0.2080.0000.210
BSRDataModelComp-class0.0070.0000.007
BSRDataModelComp0.2230.0000.223
BSRInference-class0.0060.0000.006
BSRInference4.3550.2674.639
BSRInferenceComp-class0.0100.0000.009
BSRInferenceComp1.8250.1001.931
BSRSignature-class0.0030.0000.003
BSRSignature0.0450.0000.046
BSRSignatureComp-class0.0020.0030.005
BSRSignatureComp0.0170.0040.021
LRinter0.0020.0000.002
LRinterScore0.0050.0000.005
LRinterShort0.0050.0000.005
addClusterComp0.3110.0040.317
alluvialPlot0.8400.0000.843
assignCellTypesToInteractions0.9900.0281.023
bubblePlotPathwaysLR0.7140.0080.724
cacheClear 4.193 0.36210.166
cacheInfo0.1410.0400.182
cacheVersion0.4030.0641.110
cellTypeFrequency1.0590.2671.329
cellularNetwork0.9730.1871.164
cellularNetworkTable0.9080.0800.990
chordDiagramLR1.8600.0481.914
coerce0.0020.0000.001
colClusterA000
colClusterB000
comparison0.0010.0000.000
comparisonName000
convertToHuman0.2660.0273.092
createResources0.3700.0761.629
differentialStats0.0020.0000.002
findOrthoGenes0.1710.0521.739
generateSpatialPlots2.7420.4373.232
getLRIntracellNetwork2.4770.0682.553
getLRNetwork0.0490.0030.054
getPathwayStats0.0180.0080.026
getResource0.3580.0200.379
inferenceParameters000
initialOrganism0.0020.0000.002
initialOrthologs0.0020.0000.001
learnParameters3.8840.2124.110
ligands000
logTransformed0.0020.0000.002
maxLigandSpatialCounts0.0690.0080.078
mu000
ncounts0.0010.0000.002
normalization0.0010.0000.001
parameters0.0020.0000.001
pathways000
receptors000
reduceToBestPathway0.1380.0150.153
reduceToLigand0.0560.0080.065
reduceToPathway0.1100.0190.130
reduceToReceptor0.0180.0080.026
relateToGeneSet0.1280.0240.152
removeClusterComp0.2980.0080.307
rescoreInference0.0380.0000.038
resetLRdb0.0360.0040.041
resetNetwork0.0110.0000.012
resetPathways0.3470.0240.373
resetToInitialOrganism0.2240.0160.241
scoreLRGeneSignatures1.4340.1641.603
scoreSignatures0.4020.0000.403
separatedLRPlot2.5500.0072.568
signatureHeatmaps0.0210.0010.021
simpleHeatmap6.9570.3197.301
smoothSpatialCounts0.0670.0000.067
sourceComparisonName000
spatialAssociation0.0550.0010.057
spatialAssociationPlot5.5470.0775.644
spatialDiversityPlot1.4340.0081.447
spatialIndexPlot2.1570.0402.206
spatialPlot1.7970.0161.819
summarizedCellularNetwork0.9110.0200.935
tgCorr0.0000.0000.001
tgExpr000
tgGenes000
tgLogFC000
tgPval0.0010.0000.000
updateInference0.1030.0040.106