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This page was generated on 2025-02-19 11:42 -0500 (Wed, 19 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4720
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4482
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4493
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4446
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 250/2295HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 0.99.22  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2025-02-18 13:40 -0500 (Tue, 18 Feb 2025)
git_url: https://git.bioconductor.org/packages/BulkSignalR
git_branch: devel
git_last_commit: a707d8a
git_last_commit_date: 2024-12-20 10:25:07 -0500 (Fri, 20 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 0.99.22
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_0.99.22.tar.gz
StartedAt: 2025-02-18 19:12:49 -0500 (Tue, 18 Feb 2025)
EndedAt: 2025-02-18 19:20:30 -0500 (Tue, 18 Feb 2025)
EllapsedTime: 461.0 seconds
RetCode: 0
Status:   OK  
CheckDir: BulkSignalR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_0.99.22.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BulkSignalR.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* 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 ‘0.99.22’
* 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 ‘0.99.22’
** 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 Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"
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 
 16.612   0.923  18.233 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0040.0000.004
BSRClusterComp0.3210.0170.340
BSRDataModel-class0.0040.0010.004
BSRDataModel0.2510.0080.261
BSRDataModelComp-class0.0050.0010.006
BSRInference-class0.0030.0000.003
BSRInference2.6780.0852.783
BSRInferenceComp-class0.0070.0000.007
BSRInferenceComp1.2860.0871.379
BSRSignature-class0.0020.0000.002
BSRSignature0.0290.0020.031
BSRSignatureComp-class0.0030.0000.003
BSRSignatureComp0.0170.0010.018
LRinter0.0020.0000.002
LRinterScore0.0040.0010.004
LRinterShort0.0040.0010.004
addClusterComp1.0790.0231.113
alluvialPlot0.3650.0100.378
assignCellTypesToInteractions0.6770.0200.701
bubblePlotPathwaysLR0.3650.0110.378
cacheClear2.1100.0793.743
cacheInfo0.2410.0160.259
cacheVersion0.4380.0470.829
cellTypeFrequency0.7130.0340.750
cellularNetwork0.6500.0230.676
cellularNetworkTable0.6350.0180.656
chordDiagramLR1.3070.0161.330
coerce0.0020.0000.001
colClusterA000
colClusterB0.0000.0010.001
comparison0.0000.0000.001
comparisonName000
convertToHuman0.3720.0273.765
createDatabase000
createResources0.2390.0320.819
differentialStats0.0010.0010.001
findOrthoGenes0.1810.0050.450
generateSpatialPlots1.4070.0361.452
getComplexes0.1350.0130.147
getInteractions1.1540.0191.178
getLRIntracellNetwork2.0100.1892.239
getLRNetwork0.0350.0020.036
getPathwayStats0.0170.0010.019
getResource0.3050.0180.326
inferenceParameters0.0000.0000.001
initialOrganism0.0000.0000.001
initialOrthologs0.0000.0000.001
learnParameters2.7060.0232.742
ligands000
logTransformed0.0010.0000.001
maxLigandSpatialCounts0.0540.0020.056
mu0.0000.0010.001
ncounts0.0010.0000.001
normalization0.0010.0010.001
parameters0.0010.0000.001
pathways000
receptors0.0010.0000.001
reduceToBestPathway0.1640.0180.184
reduceToLigand0.0450.0020.048
reduceToPathway0.0870.0020.089
reduceToReceptor0.0190.0020.022
relateToGeneSet0.0680.0030.071
removeClusterComp0.3140.0090.326
rescoreInference0.0340.0030.037
resetLRdb0.0120.0000.012
resetNetwork0.0070.0010.007
resetPathways0.2990.0160.316
resetToInitialOrganism0.1620.0050.167
scoreLRGeneSignatures0.4250.0410.468
scoreSignatures0.3450.0070.355
separatedLRPlot1.2800.0261.311
signatureHeatmaps0.0160.0020.019
simpleHeatmap1.0970.0561.200
smoothSpatialCounts0.0580.0010.060
sourceComparisonName000
spatialAssociation0.0560.0030.060
spatialAssociationPlot3.9840.0524.053
spatialDiversityPlot0.9330.0150.956
spatialIndexPlot1.2920.0341.334
spatialPlot0.9890.0191.012
summarizedCellularNetwork0.7320.0180.753
tgCorr000
tgExpr000
tgGenes0.0010.0000.000
tgLogFC000
tgPval0.0010.0000.001
updateInference0.0790.0030.082