| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-04 11:35 -0400 (Mon, 04 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4989 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4719 |
| 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 295/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CatsCradle 1.6.0 (landing page) Michael Shapiro
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| See other builds for CatsCradle in R Universe. | ||||||||||||||
|
To the developers/maintainers of the CatsCradle package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CatsCradle.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: CatsCradle |
| Version: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CatsCradle.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CatsCradle_1.6.0.tar.gz |
| StartedAt: 2026-05-03 18:40:14 -0400 (Sun, 03 May 2026) |
| EndedAt: 2026-05-03 18:43:35 -0400 (Sun, 03 May 2026) |
| EllapsedTime: 201.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CatsCradle.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CatsCradle.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CatsCradle_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/CatsCradle.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-03 22:40:14 UTC
* using option ‘--no-vignettes’
* checking for file ‘CatsCradle/DESCRIPTION’ ... OK
* this is package ‘CatsCradle’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 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 ‘CatsCradle’ 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 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 ... NOTE
edgeLengthPlot: no visible binding for global variable ‘cellTypePair’
edgeLengthPlot: no visible binding for global variable ‘cutoff’
make.getExample : getExample: no visible binding for global variable
‘seuratGenes’
make.getExample : getExample: no visible binding for global variable
‘seuratCells’
make.getExample : getExample: no visible binding for global variable
‘xeniumCells’
make.getExample : getExample: no visible binding for global variable
‘moransI’
make.getExample : getExample: no visible binding for global variable
‘moransILigandReceptor’
make.getExample : getExample: no visible binding for global variable
‘humanLRN’
make.getExample : getExample: no visible binding for global variable
‘mouseLRN’
meanGeneClusterOnCellUMAP: no visible binding for global variable
‘UMAP_1’
meanGeneClusterOnCellUMAP: no visible binding for global variable
‘UMAP_2’
plotLRDotplot: no visible binding for global variable ‘sender’
plotLRDotplot: no visible binding for global variable ‘negLog10PValue’
plotLRDotplot: no visible binding for global variable ‘receiver’
Undefined global functions or variables:
UMAP_1 UMAP_2 cellTypePair cutoff humanLRN moransI
moransILigandReceptor mouseLRN negLog10PValue receiver sender
seuratCells seuratGenes xeniumCells
* 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
computeNBHDVsCTObject 8.172 0.021 8.212
randomiseNodeIndices 6.589 0.017 6.609
getObjectSubsetClusteringPValue 6.269 0.035 6.314
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/CatsCradle.Rcheck/00check.log’
for details.
CatsCradle.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CatsCradle ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘CatsCradle’ ... ** this is package ‘CatsCradle’ version ‘1.6.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (CatsCradle)
CatsCradle.Rcheck/CatsCradle-Ex.timings
| name | user | system | elapsed | |
| aggregateGeneExpression | 4.786 | 0.068 | 4.868 | |
| annotateGeneAsVector | 1.045 | 0.021 | 1.068 | |
| annotateGenesByGeneSet | 0.647 | 0.031 | 0.678 | |
| cellTypesPerCellTypeGraphFromCellMatrix | 0.168 | 0.003 | 0.176 | |
| collapseExtendedNBHDs | 0.890 | 0.005 | 0.878 | |
| combinatorialSpheres | 2.027 | 0.015 | 2.043 | |
| computeCellTypesPerCellTypeMatrix | 0.125 | 0.004 | 0.136 | |
| computeEdgeGraph | 0.157 | 0.004 | 0.149 | |
| computeEdgeObject | 0.382 | 0.007 | 0.390 | |
| computeGraphEmbedding | 4.307 | 0.030 | 4.338 | |
| computeNBHDByCTMatrix | 0.120 | 0.004 | 0.122 | |
| computeNBHDVsCTObject | 8.172 | 0.021 | 8.212 | |
| computeNeighbourEnrichment | 0.126 | 0.008 | 0.134 | |
| computeNeighboursDelaunay | 0.114 | 0.002 | 0.117 | |
| computeNeighboursEuclidean | 0.321 | 0.008 | 0.330 | |
| cullEdges | 0.299 | 0.011 | 0.311 | |
| desymmetriseNN | 2.059 | 0.005 | 2.066 | |
| directedHausdorfDistance | 0 | 0 | 0 | |
| edgeCutoffsByClustering | 0.189 | 0.002 | 0.190 | |
| edgeCutoffsByPercentile | 0.186 | 0.002 | 0.188 | |
| edgeCutoffsByWatershed | 0.212 | 0.001 | 0.214 | |
| edgeCutoffsByZScore | 0.179 | 0.001 | 0.181 | |
| edgeLengthPlot | 0.205 | 0.002 | 0.207 | |
| edgeLengthsAndCellTypePairs | 0.195 | 0.002 | 0.197 | |
| exampleObjects | 0 | 0 | 0 | |
| geneSetsVsGeneClustersPValueMatrix | 2.088 | 0.004 | 2.094 | |
| getAverageExpressionDF | 2.076 | 0.004 | 2.081 | |
| getAverageExpressionMatrix | 2.106 | 0.004 | 2.112 | |
| getClusterOrder | 1.965 | 0.004 | 1.969 | |
| getExtendedNBHDs | 0.544 | 0.012 | 0.482 | |
| getFeatureZScores | 0.083 | 0.002 | 0.084 | |
| getGeneClusterAveragesPerCell | 2.049 | 0.004 | 2.057 | |
| getGeneNeighbors | 1.985 | 0.005 | 1.992 | |
| getLigandReceptorNetwork | 0.009 | 0.000 | 0.009 | |
| getLigandReceptorPairsInPanel | 0.112 | 0.001 | 0.112 | |
| getNearbyGenes | 2.024 | 0.004 | 2.031 | |
| getNearestNeighbourLists | 1.927 | 0.003 | 1.939 | |
| getObjectSubsetClusteringPValue | 6.269 | 0.035 | 6.314 | |
| getObjectSubsetClusteringStatistics | 2.008 | 0.009 | 2.023 | |
| make.getExample | 0.114 | 0.001 | 0.116 | |
| makeLRInteractionHeatmap | 0.163 | 0.002 | 0.165 | |
| makeSummedLRInteractionHeatmap | 0.157 | 0.002 | 0.160 | |
| meanGeneClusterOnCellUMAP | 2.044 | 0.004 | 2.051 | |
| meanZPerCluster | 1.990 | 0.020 | 2.025 | |
| meanZPerClusterOnUMAP | 2.089 | 0.004 | 2.096 | |
| medianComplementDistance | 0.000 | 0.001 | 0.001 | |
| medianComplementPValue | 2.064 | 0.007 | 2.083 | |
| nbhdsAsEdgesToNbhdsAsList | 0.442 | 0.021 | 0.464 | |
| neighbourhoodDiameter | 0.466 | 0.010 | 0.480 | |
| performLigandReceptorAnalysis | 0.520 | 0.361 | 0.887 | |
| performLigandReceptorAnalysisPermutation | 0.533 | 0.405 | 0.942 | |
| plotLRDotplot | 0.598 | 0.006 | 0.605 | |
| predictAnnotation | 3.559 | 0.076 | 3.638 | |
| predictAnnotationAllGenes | 3.053 | 0.021 | 3.079 | |
| predictGeneAnnotationImpl | 2.650 | 0.009 | 2.661 | |
| randomiseNodeIndices | 6.589 | 0.017 | 6.609 | |
| runGeometricClusteringTrials | 2.102 | 0.008 | 2.117 | |
| runMoransI | 0.602 | 0.013 | 0.615 | |
| sankeyFromMatrix | 0.002 | 0.000 | 0.001 | |
| symmetriseNN | 2.052 | 0.004 | 2.059 | |
| symmetryCheckNN | 2.097 | 0.004 | 2.104 | |
| tagRowAndColNames | 2.193 | 0.023 | 2.216 | |
| transposeObject | 4.140 | 0.008 | 4.155 | |