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This page was generated on 2025-09-27 12:03 -0400 (Sat, 27 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4832
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4620
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4565
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: 2025-09-26 13:45 -0400 (Fri, 26 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 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: 2025-09-26 21:43:52 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 21:58:48 -0400 (Fri, 26 Sep 2025)
EllapsedTime: 896.3 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 Patched (2025-08-23 r88802)
* 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          7.839  1.001  10.032
spatialAssociationPlot 4.790  0.158   5.293
cacheClear             3.648  0.166   6.522
* 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 Patched (2025-08-23 r88802) -- "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 
 18.344   0.952  21.173 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0030.0000.004
BSRClusterComp0.3180.0270.345
BSRDataModel-class0.0520.0000.052
BSRDataModel0.1960.0020.197
BSRDataModelComp-class0.0080.0000.007
BSRDataModelComp0.2220.0010.222
BSRInference-class0.0060.0000.006
BSRInference4.3550.1114.495
BSRInferenceComp-class0.0110.0010.012
BSRInferenceComp1.7660.0991.866
BSRSignature-class0.0020.0000.002
BSRSignature0.0330.0010.034
BSRSignatureComp-class0.0030.0000.004
BSRSignatureComp0.0160.0000.016
LRinter0.0020.0000.001
LRinterScore0.0040.0000.004
LRinterShort0.0030.0000.004
addClusterComp0.2320.0020.258
alluvialPlot0.7410.0060.793
assignCellTypesToInteractions0.8370.0061.178
bubblePlotPathwaysLR0.7040.0000.759
cacheClear3.6480.1666.522
cacheInfo0.1160.0030.130
cacheVersion0.3080.0320.756
cellTypeFrequency0.8100.0720.917
cellularNetwork0.7020.0600.784
cellularNetworkTable0.7410.0580.872
chordDiagramLR1.4160.0521.480
coerce0.0010.0000.001
colClusterA000
colClusterB0.0000.0000.001
comparison000
comparisonName0.0000.0010.001
convertToHuman0.6260.0282.289
createResources0.2750.0251.006
differentialStats0.0000.0010.002
findOrthoGenes0.2590.0150.462
generateSpatialPlots2.6840.2122.938
getLRIntracellNetwork2.3000.0772.491
getLRNetwork0.0390.0020.041
getPathwayStats0.0160.0010.017
getResource0.3410.0140.384
inferenceParameters000
initialOrganism0.0020.0000.002
initialOrthologs0.0020.0000.002
learnParameters3.6250.0903.845
ligands0.0000.0010.001
logTransformed0.0020.0000.002
maxLigandSpatialCounts0.0760.0050.080
mu000
ncounts0.0020.0000.002
normalization0.0010.0010.002
parameters0.0010.0000.001
pathways000
receptors000
reduceToBestPathway0.1470.0110.158
reduceToLigand0.0580.0060.064
reduceToPathway0.1160.0120.147
reduceToReceptor0.0190.0020.021
relateToGeneSet0.1130.0110.129
removeClusterComp0.2470.0050.252
rescoreInference0.0360.0020.042
resetLRdb0.0150.0010.016
resetNetwork0.0080.0000.008
resetPathways0.3450.0080.420
resetToInitialOrganism0.1780.0010.180
scoreLRGeneSignatures1.5390.1021.690
scoreSignatures0.3950.0000.394
separatedLRPlot2.0080.0242.067
signatureHeatmaps0.0280.0010.058
simpleHeatmap 7.839 1.00110.032
smoothSpatialCounts0.0580.0020.060
sourceComparisonName000
spatialAssociation0.0620.0030.088
spatialAssociationPlot4.7900.1585.293
spatialDiversityPlot1.6410.0281.673
spatialIndexPlot1.9650.0042.117
spatialPlot1.5170.0041.640
summarizedCellularNetwork0.7170.0260.791
tgCorr0.0010.0000.000
tgExpr000
tgGenes000
tgLogFC000
tgPval000
updateInference0.1280.0000.128