Back to Multiple platform build/check report for BioC 3.21:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-03-14 11:39 -0400 (Fri, 14 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4781
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4537
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4567
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4519
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4451
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 251/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BulkSignalR 0.99.22  (landing page)
Jean-Philippe Villemin
Snapshot Date: 2025-03-13 13:40 -0400 (Thu, 13 Mar 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 -0400 (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  ERROR    ERROR  skippedskipped
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 24.03 LTS) / aarch64  ERROR    ERROR  skipped


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: 2025-03-13 20:22:50 -0400 (Thu, 13 Mar 2025)
EndedAt: 2025-03-13 20:32:40 -0400 (Thu, 13 Mar 2025)
EllapsedTime: 589.6 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) (2025-02-19 r87757)
* 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 24.04.2 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) (2025-02-19 r87757) -- "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 
 13.858   0.669  15.122 

Example timings

BulkSignalR.Rcheck/BulkSignalR-Ex.timings

nameusersystemelapsed
BSRClusterComp-class0.0030.0000.004
BSRClusterComp0.2310.0290.261
BSRDataModel-class0.0040.0000.005
BSRDataModel0.1510.0010.152
BSRDataModelComp-class0.0050.0000.005
BSRInference-class0.0030.0000.003
BSRInference2.4690.1632.633
BSRInferenceComp-class0.0050.0010.006
BSRInferenceComp1.1780.1181.296
BSRSignature-class0.0020.0000.002
BSRSignature0.0270.0010.028
BSRSignatureComp-class0.0040.0000.004
BSRSignatureComp0.0100.0030.013
LRinter0.0010.0000.001
LRinterScore0.0030.0000.003
LRinterShort0.0030.0000.003
addClusterComp0.9660.0981.064
alluvialPlot0.3240.0050.329
assignCellTypesToInteractions0.5930.0140.607
bubblePlotPathwaysLR0.3050.0020.307
cacheClear2.1100.0913.306
cacheInfo0.1910.0060.197
cacheVersion0.3660.0600.767
cellTypeFrequency0.6460.0520.698
cellularNetwork0.5810.0520.633
cellularNetworkTable0.5910.0360.626
chordDiagramLR1.1690.0851.255
coerce0.0000.0010.001
colClusterA000
colClusterB000
comparison0.0000.0010.000
comparisonName0.0000.0000.001
convertToHuman0.3310.0402.089
createDatabase000
createResources0.2170.0510.786
differentialStats0.0010.0000.001
findOrthoGenes0.1590.0180.429
generateSpatialPlots1.2900.0951.384
getComplexes0.1080.0120.120
getInteractions0.9680.0110.978
getLRIntracellNetwork1.6210.0841.704
getLRNetwork0.0300.0030.032
getPathwayStats0.0150.0010.016
getResource0.2540.0150.270
inferenceParameters0.0000.0000.001
initialOrganism0.0010.0000.001
initialOrthologs0.0000.0010.000
learnParameters2.5680.1562.724
ligands0.0010.0000.001
logTransformed0.0010.0000.001
maxLigandSpatialCounts0.0500.0040.054
mu000
ncounts0.0010.0000.001
normalization000
parameters0.0010.0000.001
pathways000
receptors000
reduceToBestPathway0.0840.0050.089
reduceToLigand0.1010.0080.109
reduceToPathway0.0730.0040.076
reduceToReceptor0.0130.0020.016
relateToGeneSet0.0710.0020.073
removeClusterComp0.2100.0090.219
rescoreInference0.0340.0010.035
resetLRdb0.0100.0010.012
resetNetwork0.0060.0000.006
resetPathways0.2590.0070.266
resetToInitialOrganism0.1530.0020.156
scoreLRGeneSignatures0.4060.0130.420
scoreSignatures0.2720.0020.274
separatedLRPlot1.2220.0101.232
signatureHeatmaps0.0220.0020.024
simpleHeatmap1.0250.0161.041
smoothSpatialCounts0.0480.0040.051
sourceComparisonName000
spatialAssociation0.0510.0010.053
spatialAssociationPlot3.4730.0613.535
spatialDiversityPlot0.8550.0210.877
spatialIndexPlot1.0780.0411.120
spatialPlot0.8930.0230.915
summarizedCellularNetwork0.6220.0060.628
tgCorr000
tgExpr0.0000.0010.000
tgGenes0.0010.0000.001
tgLogFC000
tgPval0.0000.0010.000
updateInference0.0810.0010.082