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This page was generated on 2025-04-17 11:43 -0400 (Thu, 17 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4667
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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 255/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 1.0.0  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2025-04-16 13:40 -0400 (Wed, 16 Apr 2025)
git_url: https://git.bioconductor.org/packages/BulkSignalR
git_branch: RELEASE_3_21
git_last_commit: a7b59e6
git_last_commit_date: 2025-04-15 13:44:41 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    ERROR  
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  ERROR    ERROR  skipped


CHECK results for BulkSignalR on lconway

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: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BulkSignalR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BulkSignalR_1.0.0.tar.gz
StartedAt: 2025-04-16 20:02:49 -0400 (Wed, 16 Apr 2025)
EndedAt: 2025-04-16 20:10:30 -0400 (Wed, 16 Apr 2025)
EllapsedTime: 461.2 seconds
RetCode: 0
Status:   OK  
CheckDir: BulkSignalR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BulkSignalR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BulkSignalR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BulkSignalR.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BulkSignalR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BulkSignalR’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 28 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 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
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BulkSignalR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘BulkSignalR’ ...
** this is package ‘BulkSignalR’ version ‘1.0.0’
** 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 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 "database" is up to date.

Local "resources" are up to date.

> test_check("BulkSignalR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 16.357   0.933  17.987 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0030.0000.004
BSRClusterComp0.3640.0240.390
BSRDataModel-class0.0050.0000.006
BSRDataModel0.2480.0080.263
BSRDataModelComp-class0.0060.0010.007
BSRInference-class0.0040.0000.004
BSRInference2.8240.0902.936
BSRInferenceComp-class0.0050.0000.006
BSRInferenceComp2.1370.0932.245
BSRSignature-class0.0020.0000.002
BSRSignature0.0350.0010.037
BSRSignatureComp-class0.0040.0010.004
BSRSignatureComp0.0170.0020.018
LRinter0.0020.0010.003
LRinterScore0.0030.0010.004
LRinterShort0.0050.0020.005
addClusterComp0.3490.0250.379
alluvialPlot0.4010.0110.414
assignCellTypesToInteractions0.7340.0390.784
bubblePlotPathwaysLR0.3690.0040.375
cacheClear2.0920.0723.552
cacheInfo0.2290.0150.246
cacheVersion0.4340.0480.831
cellTypeFrequency0.7170.0240.745
cellularNetwork0.6650.0260.695
cellularNetworkTable0.6980.0220.725
chordDiagramLR1.4060.0201.437
coerce0.0010.0000.001
colClusterA0.0000.0000.001
colClusterB0.0000.0010.000
comparison000
comparisonName000
convertToHuman0.3410.0252.030
createDatabase000
createResources0.2620.0350.818
differentialStats0.0010.0010.001
findOrthoGenes0.1480.0030.296
generateSpatialPlots1.3580.0381.401
getComplexes0.1360.0150.151
getInteractions1.1360.0161.155
getLRIntracellNetwork2.0930.1672.268
getLRNetwork0.0340.0020.035
getPathwayStats0.0160.0010.017
getResource0.2810.0240.306
inferenceParameters0.0000.0010.001
initialOrganism0.0030.0000.003
initialOrthologs0.0010.0000.001
learnParameters2.7670.0182.795
ligands000
logTransformed0.0010.0000.002
maxLigandSpatialCounts0.0590.0020.062
mu000
ncounts0.0000.0010.001
normalization0.0000.0000.001
parameters0.0000.0010.001
pathways0.0000.0000.001
receptors0.0000.0010.000
reduceToBestPathway0.0850.0040.090
reduceToLigand0.0430.0020.045
reduceToPathway0.1500.0150.167
reduceToReceptor0.0220.0020.024
relateToGeneSet0.0860.0030.088
removeClusterComp0.3060.0090.314
rescoreInference0.0290.0030.031
resetLRdb0.0130.0000.013
resetNetwork0.0070.0010.006
resetPathways0.2840.0190.304
resetToInitialOrganism0.1570.0050.162
scoreLRGeneSignatures0.4310.0390.471
scoreSignatures0.3650.0100.377
separatedLRPlot1.4000.0341.439
signatureHeatmaps0.0200.0020.023
simpleHeatmap1.2400.0622.110
smoothSpatialCounts0.0590.0030.062
sourceComparisonName000
spatialAssociation0.0630.0040.067
spatialAssociationPlot4.1270.0504.196
spatialDiversityPlot0.8950.0170.916
spatialIndexPlot1.2120.0421.261
spatialPlot1.0360.0161.057
summarizedCellularNetwork0.6950.0200.719
tgCorr000
tgExpr000
tgGenes0.0000.0010.000
tgLogFC0.0000.0000.001
tgPval0.0000.0000.001
updateInference0.0740.0020.077