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This page was generated on 2025-10-27 12:45 -0400 (Mon, 27 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 289/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CatsCradle 1.3.3 (landing page) Michael Shapiro
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ||||||||
|
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: 1.3.3 |
| 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_1.3.3.tar.gz |
| StartedAt: 2025-10-26 19:02:16 -0400 (Sun, 26 Oct 2025) |
| EndedAt: 2025-10-26 19:05:52 -0400 (Sun, 26 Oct 2025) |
| EllapsedTime: 215.6 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_1.3.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/CatsCradle.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CatsCradle/DESCRIPTION’ ... OK
* this is package ‘CatsCradle’ version ‘1.3.3’
* 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
annotateGeneAsVector 17.387 0.112 17.514
computeNBHDVsCTObject 8.829 0.062 8.936
randomiseNodeIndices 6.482 0.157 6.650
getObjectSubsetClusteringPValue 5.835 0.341 6.195
* 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-3.22-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/4.5-arm64/Resources/library’ * installing *source* package ‘CatsCradle’ ... ** this is package ‘CatsCradle’ version ‘1.3.3’ ** 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 | 4.522 | 0.111 | 4.622 | |
| annotateGeneAsVector | 17.387 | 0.112 | 17.514 | |
| annotateGenesByGeneSet | 0.706 | 0.087 | 0.793 | |
| cellTypesPerCellTypeGraphFromCellMatrix | 0.072 | 0.004 | 0.077 | |
| collapseExtendedNBHDs | 0.898 | 0.026 | 0.905 | |
| combinatorialSpheres | 2.460 | 0.025 | 2.485 | |
| computeCellTypesPerCellTypeMatrix | 0.046 | 0.004 | 0.049 | |
| computeEdgeGraph | 0.083 | 0.005 | 0.076 | |
| computeEdgeObject | 0.323 | 0.020 | 0.343 | |
| computeGraphEmbedding | 4.527 | 0.024 | 4.551 | |
| computeNBHDByCTMatrix | 0.042 | 0.003 | 0.044 | |
| computeNBHDVsCTObject | 8.829 | 0.062 | 8.936 | |
| computeNeighbourEnrichment | 0.048 | 0.005 | 0.053 | |
| computeNeighboursDelaunay | 0.071 | 0.009 | 0.081 | |
| computeNeighboursEuclidean | 0.206 | 0.015 | 0.222 | |
| cullEdges | 0.193 | 0.014 | 0.210 | |
| desymmetriseNN | 2.334 | 0.037 | 2.372 | |
| directedHausdorfDistance | 0.000 | 0.000 | 0.001 | |
| edgeCutoffsByClustering | 0.145 | 0.011 | 0.155 | |
| edgeCutoffsByPercentile | 0.102 | 0.004 | 0.105 | |
| edgeCutoffsByWatershed | 0.111 | 0.004 | 0.115 | |
| edgeCutoffsByZScore | 0.130 | 0.006 | 0.136 | |
| edgeLengthPlot | 0.123 | 0.004 | 0.128 | |
| edgeLengthsAndCellTypePairs | 0.128 | 0.005 | 0.134 | |
| exampleObjects | 0 | 0 | 0 | |
| geneSetsVsGeneClustersPValueMatrix | 2.401 | 0.021 | 2.424 | |
| getAverageExpressionDF | 2.374 | 0.035 | 2.413 | |
| getAverageExpressionMatrix | 2.428 | 0.027 | 2.463 | |
| getClusterOrder | 2.249 | 0.038 | 2.292 | |
| getExtendedNBHDs | 0.415 | 0.030 | 0.375 | |
| getFeatureZScores | 0.079 | 0.003 | 0.081 | |
| getGeneClusterAveragesPerCell | 2.281 | 0.044 | 2.332 | |
| getGeneNeighbors | 2.362 | 0.019 | 2.385 | |
| getLigandReceptorNetwork | 0.009 | 0.001 | 0.010 | |
| getLigandReceptorPairsInPanel | 0.037 | 0.002 | 0.039 | |
| getNearbyGenes | 2.453 | 0.016 | 2.488 | |
| getNearestNeighbourLists | 2.296 | 0.032 | 2.328 | |
| getObjectSubsetClusteringPValue | 5.835 | 0.341 | 6.195 | |
| getObjectSubsetClusteringStatistics | 2.463 | 0.044 | 2.507 | |
| make.getExample | 0.037 | 0.004 | 0.041 | |
| makeLRInteractionHeatmap | 0.080 | 0.004 | 0.085 | |
| makeSummedLRInteractionHeatmap | 0.069 | 0.003 | 0.073 | |
| meanGeneClusterOnCellUMAP | 2.195 | 0.048 | 2.244 | |
| meanZPerCluster | 2.247 | 0.019 | 2.271 | |
| meanZPerClusterOnUMAP | 2.322 | 0.032 | 2.353 | |
| medianComplementDistance | 0.000 | 0.000 | 0.001 | |
| medianComplementPValue | 2.455 | 0.040 | 2.497 | |
| nbhdsAsEdgesToNbhdsAsList | 0.335 | 0.065 | 0.403 | |
| neighbourhoodDiameter | 0.345 | 0.067 | 0.413 | |
| performLigandReceptorAnalysis | 0.451 | 0.398 | 0.876 | |
| performLigandReceptorAnalysisPermutation | 0.403 | 0.306 | 0.709 | |
| plotLRDotplot | 0.520 | 0.019 | 0.539 | |
| predictAnnotation | 3.490 | 0.213 | 3.705 | |
| predictAnnotationAllGenes | 3.045 | 0.126 | 3.172 | |
| predictGeneAnnotationImpl | 2.879 | 0.136 | 3.015 | |
| randomiseNodeIndices | 6.482 | 0.157 | 6.650 | |
| runGeometricClusteringTrials | 2.629 | 0.053 | 2.683 | |
| runMoransI | 0.425 | 0.078 | 0.503 | |
| sankeyFromMatrix | 0.002 | 0.000 | 0.001 | |
| symmetriseNN | 2.379 | 0.046 | 2.436 | |
| symmetryCheckNN | 2.331 | 0.028 | 2.363 | |
| tagRowAndColNames | 2.445 | 0.032 | 2.478 | |
| transposeObject | 4.702 | 0.048 | 4.768 | |