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This page was generated on 2025-09-06 12:03 -0400 (Sat, 06 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
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 255/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 1.1.4  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2025-09-05 13:45 -0400 (Fri, 05 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: 2025-09-05 21:33:13 -0400 (Fri, 05 Sep 2025)
EndedAt: 2025-09-05 21:48:07 -0400 (Fri, 05 Sep 2025)
EllapsedTime: 893.2 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          8.978  0.802   9.834
spatialAssociationPlot 5.866  0.056   6.017
cacheClear             4.360  0.058   6.963
* 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 
 19.625   0.996  22.495 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0040.0000.004
BSRClusterComp0.2900.0130.382
BSRDataModel-class0.0080.0000.007
BSRDataModel0.1790.0010.180
BSRDataModelComp-class0.0070.0000.007
BSRDataModelComp0.1770.0010.178
BSRInference-class0.0060.0000.005
BSRInference3.4520.1313.597
BSRInferenceComp-class0.0110.0000.010
BSRInferenceComp1.7570.1011.858
BSRSignature-class0.0020.0000.002
BSRSignature0.0340.0010.035
BSRSignatureComp-class0.0040.0000.004
BSRSignatureComp0.0160.0000.016
LRinter0.0010.0000.002
LRinterScore0.0040.0000.004
LRinterShort0.0040.0000.004
addClusterComp1.0430.0431.354
alluvialPlot0.4920.0020.512
assignCellTypesToInteractions0.9880.0101.011
bubblePlotPathwaysLR0.5140.0000.515
cacheClear4.3600.0586.963
cacheInfo0.1330.0030.136
cacheVersion0.3360.0130.808
cellTypeFrequency1.0880.0201.108
cellularNetwork0.9680.0271.040
cellularNetworkTable0.9370.0040.942
chordDiagramLR2.0080.0082.020
coerce0.0020.0000.002
colClusterA000
colClusterB000
comparison000
comparisonName000
convertToHuman0.7530.0094.925
createResources0.2880.0080.973
differentialStats0.0010.0000.001
findOrthoGenes0.2510.0010.510
generateSpatialPlots2.0260.0582.122
getLRIntracellNetwork2.8140.0482.917
getLRNetwork0.0530.0000.052
getPathwayStats0.0230.0000.022
getResource0.4130.0050.418
inferenceParameters0.0000.0000.001
initialOrganism0.0020.0000.002
initialOrthologs0.0020.0000.002
learnParameters3.7350.0093.772
ligands000
logTransformed0.0020.0000.002
maxLigandSpatialCounts0.0780.0000.079
mu0.0000.0000.001
ncounts0.0010.0010.002
normalization0.0010.0000.002
parameters0.0020.0000.002
pathways000
receptors000
reduceToBestPathway0.1330.0000.133
reduceToLigand0.0580.0020.059
reduceToPathway0.1620.0010.163
reduceToReceptor0.0270.0000.027
relateToGeneSet0.1110.0030.115
removeClusterComp0.2810.0000.281
rescoreInference0.0360.0000.037
resetLRdb0.0140.0000.014
resetNetwork0.0070.0000.007
resetPathways0.3340.0030.338
resetToInitialOrganism0.2220.0000.221
scoreLRGeneSignatures0.6830.0260.712
scoreSignatures0.4200.0050.431
separatedLRPlot1.9570.0072.039
signatureHeatmaps0.030.000.03
simpleHeatmap8.9780.8029.834
smoothSpatialCounts0.0870.0000.088
sourceComparisonName0.0000.0000.001
spatialAssociation0.0920.0040.096
spatialAssociationPlot5.8660.0566.017
spatialDiversityPlot1.0240.0031.028
spatialIndexPlot1.4380.0031.453
spatialPlot1.1100.0011.112
summarizedCellularNetwork0.6860.0010.690
tgCorr000
tgExpr0.0000.0000.001
tgGenes000
tgLogFC0.0000.0000.001
tgPval000
updateInference0.0990.0010.100