Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-23 12:03 -0400 (Tue, 23 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4816 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4605 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4549 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
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 256/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BulkSignalR 1.1.4 (landing page) Jean-Philippe Villemin
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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. |
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: 2025-09-22 21:41:32 -0400 (Mon, 22 Sep 2025) |
EndedAt: 2025-09-22 21:56:09 -0400 (Mon, 22 Sep 2025) |
EllapsedTime: 877.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BulkSignalR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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 Patched (2025-08-23 r88802) * 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 7.605 0.701 8.734 cacheClear 3.795 0.370 6.512 * 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
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)
BulkSignalR.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "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 17.529 1.265 20.323
BulkSignalR.Rcheck/BulkSignalR-Ex.timings
name | user | system | elapsed | |
BSRClusterComp-class | 0.003 | 0.000 | 0.002 | |
BSRClusterComp | 0.276 | 0.019 | 0.321 | |
BSRDataModel-class | 0.048 | 0.001 | 0.049 | |
BSRDataModel | 0.180 | 0.001 | 0.184 | |
BSRDataModelComp-class | 0.007 | 0.001 | 0.008 | |
BSRDataModelComp | 0.207 | 0.000 | 0.207 | |
BSRInference-class | 0.007 | 0.000 | 0.006 | |
BSRInference | 3.848 | 0.329 | 4.325 | |
BSRInferenceComp-class | 0.009 | 0.000 | 0.009 | |
BSRInferenceComp | 1.421 | 0.080 | 1.594 | |
BSRSignature-class | 0.002 | 0.000 | 0.002 | |
BSRSignature | 0.046 | 0.002 | 0.047 | |
BSRSignatureComp-class | 0.005 | 0.000 | 0.006 | |
BSRSignatureComp | 0.021 | 0.000 | 0.022 | |
LRinter | 0.002 | 0.000 | 0.003 | |
LRinterScore | 0.004 | 0.001 | 0.005 | |
LRinterShort | 0.005 | 0.000 | 0.005 | |
addClusterComp | 0.279 | 0.000 | 0.278 | |
alluvialPlot | 0.888 | 0.002 | 0.891 | |
assignCellTypesToInteractions | 1.049 | 0.043 | 1.098 | |
bubblePlotPathwaysLR | 0.701 | 0.029 | 0.754 | |
cacheClear | 3.795 | 0.370 | 6.512 | |
cacheInfo | 0.114 | 0.007 | 0.121 | |
cacheVersion | 0.335 | 0.020 | 0.781 | |
cellTypeFrequency | 1.064 | 0.069 | 1.135 | |
cellularNetwork | 0.991 | 0.102 | 1.093 | |
cellularNetworkTable | 0.705 | 0.034 | 0.740 | |
chordDiagramLR | 1.394 | 0.036 | 1.431 | |
coerce | 0.001 | 0.000 | 0.001 | |
colClusterA | 0 | 0 | 0 | |
colClusterB | 0 | 0 | 0 | |
comparison | 0 | 0 | 0 | |
comparisonName | 0 | 0 | 0 | |
convertToHuman | 0.697 | 0.040 | 2.047 | |
createResources | 0.295 | 0.031 | 0.995 | |
differentialStats | 0.001 | 0.000 | 0.001 | |
findOrthoGenes | 0.280 | 0.012 | 0.506 | |
generateSpatialPlots | 2.129 | 0.192 | 2.326 | |
getLRIntracellNetwork | 2.124 | 0.067 | 2.225 | |
getLRNetwork | 0.038 | 0.000 | 0.038 | |
getPathwayStats | 0.017 | 0.000 | 0.017 | |
getResource | 0.319 | 0.010 | 0.329 | |
inferenceParameters | 0 | 0 | 0 | |
initialOrganism | 0.003 | 0.000 | 0.003 | |
initialOrthologs | 0.002 | 0.000 | 0.002 | |
learnParameters | 2.923 | 0.039 | 2.994 | |
ligands | 0.001 | 0.000 | 0.000 | |
logTransformed | 0.002 | 0.000 | 0.002 | |
maxLigandSpatialCounts | 0.059 | 0.003 | 0.063 | |
mu | 0 | 0 | 0 | |
ncounts | 0.001 | 0.001 | 0.001 | |
normalization | 0.002 | 0.000 | 0.001 | |
parameters | 0.000 | 0.001 | 0.002 | |
pathways | 0 | 0 | 0 | |
receptors | 0 | 0 | 0 | |
reduceToBestPathway | 0.100 | 0.001 | 0.105 | |
reduceToLigand | 0.042 | 0.002 | 0.044 | |
reduceToPathway | 0.091 | 0.000 | 0.091 | |
reduceToReceptor | 0.016 | 0.009 | 0.026 | |
relateToGeneSet | 0.132 | 0.027 | 0.172 | |
removeClusterComp | 0.282 | 0.001 | 0.283 | |
rescoreInference | 0.044 | 0.001 | 0.045 | |
resetLRdb | 0.019 | 0.000 | 0.019 | |
resetNetwork | 0.009 | 0.000 | 0.009 | |
resetPathways | 0.416 | 0.006 | 0.422 | |
resetToInitialOrganism | 0.221 | 0.009 | 0.230 | |
scoreLRGeneSignatures | 1.419 | 0.188 | 1.736 | |
scoreSignatures | 0.310 | 0.003 | 0.314 | |
separatedLRPlot | 2.007 | 0.007 | 2.131 | |
signatureHeatmaps | 0.025 | 0.000 | 0.025 | |
simpleHeatmap | 7.605 | 0.701 | 8.734 | |
smoothSpatialCounts | 0.059 | 0.008 | 0.095 | |
sourceComparisonName | 0.000 | 0.000 | 0.001 | |
spatialAssociation | 0.064 | 0.001 | 0.065 | |
spatialAssociationPlot | 4.627 | 0.088 | 4.914 | |
spatialDiversityPlot | 1.110 | 0.006 | 1.120 | |
spatialIndexPlot | 1.960 | 0.057 | 2.107 | |
spatialPlot | 1.868 | 0.023 | 1.895 | |
summarizedCellularNetwork | 0.731 | 0.003 | 0.758 | |
tgCorr | 0 | 0 | 0 | |
tgExpr | 0 | 0 | 0 | |
tgGenes | 0 | 0 | 0 | |
tgLogFC | 0 | 0 | 0 | |
tgPval | 0 | 0 | 0 | |
updateInference | 0.094 | 0.003 | 0.096 | |