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This page was generated on 2025-01-24 11:38 -0500 (Fri, 24 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4609
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4393
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 3839
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 3835
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4408
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 249/2286HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 0.99.22  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2025-01-23 13:40 -0500 (Thu, 23 Jan 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for BulkSignalR on nebbiolo1

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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BulkSignalR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BulkSignalR_0.99.22.tar.gz
StartedAt: 2025-01-23 20:27:06 -0500 (Thu, 23 Jan 2025)
EndedAt: 2025-01-23 20:37:13 -0500 (Thu, 23 Jan 2025)
EllapsedTime: 606.8 seconds
RetCode: 0
Status:   OK  
CheckDir: BulkSignalR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BulkSignalR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BulkSignalR_0.99.22.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BulkSignalR.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* 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 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
* 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-3.21-bioc/R/bin/R CMD INSTALL BulkSignalR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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) (2025-01-20 r87609) -- "Unsuffered Consequences"
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 "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 
 14.327   0.876  15.859 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0010.0020.003
BSRClusterComp0.2430.0220.265
BSRDataModel-class0.0030.0020.004
BSRDataModel0.1640.0020.166
BSRDataModelComp-class0.0050.0000.006
BSRInference-class0.0020.0010.003
BSRInference2.5320.1882.720
BSRInferenceComp-class0.0040.0010.007
BSRInferenceComp1.2030.0531.256
BSRSignature-class0.0010.0000.002
BSRSignature0.0270.0020.028
BSRSignatureComp-class0.0040.0000.004
BSRSignatureComp0.0140.0010.014
LRinter0.0020.0000.002
LRinterScore0.0020.0010.004
LRinterShort0.0020.0020.003
addClusterComp0.2250.0230.248
alluvialPlot0.3550.0140.370
assignCellTypesToInteractions1.4350.1691.605
bubblePlotPathwaysLR0.3280.0160.344
cacheClear2.1960.1263.543
cacheInfo0.2690.0020.271
cacheVersion0.4760.0120.863
cellTypeFrequency0.7230.0620.785
cellularNetwork0.5890.0200.609
cellularNetworkTable0.5520.0010.554
chordDiagramLR1.2120.0281.240
coerce0.0010.0000.002
colClusterA0.0000.0010.001
colClusterB000
comparison000
comparisonName0.0000.0000.001
convertToHuman0.3500.0264.335
createDatabase0.0000.0000.001
createResources0.2290.0170.817
differentialStats0.0010.0000.001
findOrthoGenes0.1360.0010.390
generateSpatialPlots1.2220.0131.233
getComplexes0.1120.0020.113
getInteractions0.9660.0040.970
getLRIntracellNetwork1.9340.0561.990
getLRNetwork0.0300.0020.032
getPathwayStats0.0140.0000.014
getResource0.2510.0020.253
inferenceParameters000
initialOrganism0.0000.0000.001
initialOrthologs000
learnParameters2.4800.0372.518
ligands0.0000.0000.001
logTransformed0.0010.0000.001
maxLigandSpatialCounts0.0500.0060.057
mu0.0000.0010.000
ncounts0.0000.0000.001
normalization0.0000.0010.001
parameters0.0010.0000.001
pathways000
receptors0.0000.0010.001
reduceToBestPathway0.0850.0020.087
reduceToLigand0.0360.0000.037
reduceToPathway0.0760.0000.076
reduceToReceptor0.0150.0000.015
relateToGeneSet0.0740.0030.077
removeClusterComp0.2370.0280.265
rescoreInference0.0400.0030.043
resetLRdb0.0120.0030.016
resetNetwork0.0060.0010.008
resetPathways0.2680.0210.289
resetToInitialOrganism0.1550.0150.170
scoreLRGeneSignatures0.4060.0510.457
scoreSignatures0.2770.0190.296
separatedLRPlot1.2370.1091.346
signatureHeatmaps0.0220.0040.026
simpleHeatmap0.9990.0921.092
smoothSpatialCounts0.0490.0050.054
sourceComparisonName0.0000.0000.001
spatialAssociation0.0530.0020.055
spatialAssociationPlot3.5040.1623.666
spatialDiversityPlot0.8490.0280.879
spatialIndexPlot1.0630.0711.136
spatialPlot0.9490.0420.990
summarizedCellularNetwork0.6560.0090.665
tgCorr0.0000.0010.000
tgExpr000
tgGenes0.0010.0000.000
tgLogFC000
tgPval000
updateInference0.0960.0090.105