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

This page was generated on 2025-09-26 12:07 -0400 (Fri, 26 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4619
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4563
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 256/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 1.1.4  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2025-09-25 13:45 -0400 (Thu, 25 Sep 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 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: 1.1.4
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_1.1.4.tar.gz
StartedAt: 2025-09-26 05:55:50 -0000 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 06:05:05 -0000 (Fri, 26 Sep 2025)
EllapsedTime: 555.4 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_1.1.4.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 ‘1.1.4’
* 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          7.033  0.359   7.419
spatialAssociationPlot 5.459  0.138   5.623
cacheClear             4.167  0.382  20.581
* 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 ‘1.1.4’
** 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 4.5.0 (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 
 17.440   0.619  19.873 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0030.0000.003
BSRClusterComp0.3120.0120.325
BSRDataModel-class0.0450.0230.069
BSRDataModel0.1840.0010.185
BSRDataModelComp-class0.0080.0000.008
BSRDataModelComp0.2040.0070.214
BSRInference-class0.0060.0010.007
BSRInference4.3410.2034.559
BSRInferenceComp-class0.0100.0000.009
BSRInferenceComp1.7750.1111.896
BSRSignature-class0.0030.0000.003
BSRSignature0.0480.0000.049
BSRSignatureComp-class0.0050.0000.005
BSRSignatureComp0.0190.0040.023
LRinter0.0020.0000.002
LRinterScore0.0050.0000.005
LRinterShort0.0050.0000.005
addClusterComp0.2990.0000.300
alluvialPlot0.8100.0120.826
assignCellTypesToInteractions0.9580.0280.992
bubblePlotPathwaysLR0.7250.0040.732
cacheClear 4.167 0.38220.581
cacheInfo0.1520.0160.169
cacheVersion0.4360.0361.143
cellTypeFrequency1.0160.2391.260
cellularNetwork0.9920.1831.178
cellularNetworkTable0.9590.0531.015
chordDiagramLR1.8730.0871.967
coerce0.0020.0000.002
colClusterA0.0000.0000.001
colClusterB0.0010.0000.000
comparison000
comparisonName000
convertToHuman0.2340.1393.069
createResources0.3950.1031.632
differentialStats0.0000.0020.002
findOrthoGenes0.1640.0932.145
generateSpatialPlots2.6360.1992.844
getLRIntracellNetwork2.4440.0322.485
getLRNetwork0.0490.0000.049
getPathwayStats0.020.000.02
getResource0.3360.0080.346
inferenceParameters000
initialOrganism0.0020.0000.002
initialOrthologs0.0020.0000.002
learnParameters3.8280.2234.067
ligands000
logTransformed0.0030.0000.002
maxLigandSpatialCounts0.0740.0000.073
mu000
ncounts0.0020.0000.002
normalization0.0010.0000.001
parameters0.0010.0000.002
pathways0.0000.0000.001
receptors0.0010.0000.000
reduceToBestPathway0.1310.0000.131
reduceToLigand0.0560.0040.060
reduceToPathway0.1170.0120.129
reduceToReceptor0.0180.0080.025
relateToGeneSet0.1400.0160.157
removeClusterComp0.3910.0040.397
rescoreInference0.0350.0040.038
resetLRdb0.0220.0000.022
resetNetwork0.0070.0040.011
resetPathways0.3400.0240.365
resetToInitialOrganism0.2000.0120.212
scoreLRGeneSignatures1.5420.1511.699
scoreSignatures0.3710.0000.373
separatedLRPlot2.6010.0162.628
signatureHeatmaps0.0140.0070.021
simpleHeatmap7.0330.3597.419
smoothSpatialCounts0.0620.0120.074
sourceComparisonName000
spatialAssociation0.0570.0000.057
spatialAssociationPlot5.4590.1385.623
spatialDiversityPlot1.4080.0401.456
spatialIndexPlot2.1520.0282.190
spatialPlot1.8110.0231.846
summarizedCellularNetwork0.9250.0080.936
tgCorr0.0010.0000.000
tgExpr000
tgGenes000
tgLogFC000
tgPval0.0000.0000.001
updateInference0.0940.0040.099