Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-01 12:04 -0400 (Mon, 01 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 255/2320 | 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: /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_1.1.4.tar.gz |
StartedAt: 2025-08-31 19:35:23 -0400 (Sun, 31 Aug 2025) |
EndedAt: 2025-08-31 19:43:08 -0400 (Sun, 31 Aug 2025) |
EllapsedTime: 464.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BulkSignalR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.1.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BulkSignalR.Rcheck’ * using R version 4.5.1 (2025-06-13) * 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 ‘1.1.4’ * 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 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 7.140 0.424 7.630 cacheClear 3.666 0.239 6.855 convertToHuman 0.221 0.011 10.401 * 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
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 ‘1.1.4’ ** 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 (2025-06-13) -- "Great Square Root" 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 "resources" are up to date. > test_check("BulkSignalR") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] > > proc.time() user system elapsed 16.153 0.936 18.176
BulkSignalR.Rcheck/BulkSignalR-Ex.timings
name | user | system | elapsed | |
BSRClusterComp-class | 0.003 | 0.000 | 0.004 | |
BSRClusterComp | 0.356 | 0.020 | 0.377 | |
BSRDataModel-class | 0.005 | 0.001 | 0.005 | |
BSRDataModel | 0.275 | 0.008 | 0.284 | |
BSRDataModelComp-class | 0.007 | 0.001 | 0.007 | |
BSRDataModelComp | 0.285 | 0.009 | 0.295 | |
BSRInference-class | 0.004 | 0.000 | 0.006 | |
BSRInference | 2.712 | 0.080 | 2.806 | |
BSRInferenceComp-class | 0.007 | 0.000 | 0.007 | |
BSRInferenceComp | 1.359 | 0.077 | 1.444 | |
BSRSignature-class | 0.003 | 0.000 | 0.003 | |
BSRSignature | 0.036 | 0.001 | 0.038 | |
BSRSignatureComp-class | 0.005 | 0.001 | 0.005 | |
BSRSignatureComp | 0.015 | 0.002 | 0.017 | |
LRinter | 0.001 | 0.000 | 0.002 | |
LRinterScore | 0.003 | 0.001 | 0.004 | |
LRinterShort | 0.004 | 0.002 | 0.006 | |
addClusterComp | 0.389 | 0.021 | 0.414 | |
alluvialPlot | 1.185 | 0.022 | 1.214 | |
assignCellTypesToInteractions | 0.654 | 0.019 | 0.678 | |
bubblePlotPathwaysLR | 0.389 | 0.023 | 0.415 | |
cacheClear | 3.666 | 0.239 | 6.855 | |
cacheInfo | 0.122 | 0.009 | 0.131 | |
cacheVersion | 0.313 | 0.039 | 0.699 | |
cellTypeFrequency | 0.747 | 0.023 | 0.772 | |
cellularNetwork | 0.624 | 0.017 | 0.644 | |
cellularNetworkTable | 0.594 | 0.010 | 0.607 | |
chordDiagramLR | 1.356 | 0.027 | 1.390 | |
coerce | 0.001 | 0.000 | 0.002 | |
colClusterA | 0 | 0 | 0 | |
colClusterB | 0.000 | 0.001 | 0.000 | |
comparison | 0.000 | 0.000 | 0.001 | |
comparisonName | 0 | 0 | 0 | |
convertToHuman | 0.221 | 0.011 | 10.401 | |
createResources | 0.293 | 0.040 | 0.945 | |
differentialStats | 0.001 | 0.000 | 0.001 | |
findOrthoGenes | 0.151 | 0.003 | 0.334 | |
generateSpatialPlots | 1.426 | 0.035 | 1.466 | |
getLRIntracellNetwork | 2.190 | 0.176 | 2.376 | |
getLRNetwork | 0.041 | 0.002 | 0.042 | |
getPathwayStats | 0.019 | 0.001 | 0.020 | |
getResource | 0.307 | 0.019 | 0.327 | |
inferenceParameters | 0 | 0 | 0 | |
initialOrganism | 0.002 | 0.000 | 0.002 | |
initialOrthologs | 0.001 | 0.001 | 0.002 | |
learnParameters | 2.829 | 0.030 | 2.867 | |
ligands | 0 | 0 | 0 | |
logTransformed | 0.001 | 0.000 | 0.002 | |
maxLigandSpatialCounts | 0.051 | 0.002 | 0.054 | |
mu | 0.000 | 0.000 | 0.001 | |
ncounts | 0.002 | 0.000 | 0.002 | |
normalization | 0.002 | 0.000 | 0.002 | |
parameters | 0.001 | 0.001 | 0.002 | |
pathways | 0 | 0 | 0 | |
receptors | 0.000 | 0.001 | 0.000 | |
reduceToBestPathway | 0.098 | 0.004 | 0.102 | |
reduceToLigand | 0.038 | 0.002 | 0.039 | |
reduceToPathway | 0.115 | 0.005 | 0.119 | |
reduceToReceptor | 0.017 | 0.002 | 0.019 | |
relateToGeneSet | 0.075 | 0.003 | 0.078 | |
removeClusterComp | 0.344 | 0.008 | 0.353 | |
rescoreInference | 0.032 | 0.003 | 0.035 | |
resetLRdb | 0.014 | 0.000 | 0.014 | |
resetNetwork | 0.009 | 0.000 | 0.010 | |
resetPathways | 0.318 | 0.022 | 0.342 | |
resetToInitialOrganism | 0.155 | 0.004 | 0.159 | |
scoreLRGeneSignatures | 0.430 | 0.031 | 0.463 | |
scoreSignatures | 0.413 | 0.009 | 0.425 | |
separatedLRPlot | 1.434 | 0.028 | 1.469 | |
signatureHeatmaps | 0.017 | 0.001 | 0.019 | |
simpleHeatmap | 7.140 | 0.424 | 7.630 | |
smoothSpatialCounts | 0.047 | 0.010 | 0.058 | |
sourceComparisonName | 0 | 0 | 0 | |
spatialAssociation | 0.051 | 0.020 | 0.072 | |
spatialAssociationPlot | 4.106 | 0.080 | 4.206 | |
spatialDiversityPlot | 0.886 | 0.015 | 0.905 | |
spatialIndexPlot | 1.210 | 0.026 | 1.242 | |
spatialPlot | 1.085 | 0.035 | 1.128 | |
summarizedCellularNetwork | 0.696 | 0.009 | 0.709 | |
tgCorr | 0 | 0 | 0 | |
tgExpr | 0 | 0 | 0 | |
tgGenes | 0.000 | 0.001 | 0.000 | |
tgLogFC | 0.000 | 0.000 | 0.001 | |
tgPval | 0.000 | 0.000 | 0.001 | |
updateInference | 0.092 | 0.002 | 0.095 | |