Michael Shapiro
| Snapshot Date: 2025-11-04 13:40 -0500 (Tue, 04 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/CatsCradle |
| git_branch: devel |
| git_last_commit: 032f58b |
| git_last_commit_date: 2025-11-04 07:21:19 -0500 (Tue, 04 Nov 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-05 11:32 -0500 (Wed, 05 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4818 |
| 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 283/2323 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CatsCradle 1.5.1 (landing page) Michael Shapiro
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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: 1.5.1 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:CatsCradle.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings CatsCradle_1.5.1.tar.gz |
| StartedAt: 2025-11-04 21:36:58 -0500 (Tue, 04 Nov 2025) |
| EndedAt: 2025-11-04 21:54:52 -0500 (Tue, 04 Nov 2025) |
| EllapsedTime: 1073.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CatsCradle.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:CatsCradle.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings CatsCradle_1.5.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/CatsCradle.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘CatsCradle/DESCRIPTION’ ... OK
* this is package ‘CatsCradle’ version ‘1.5.1’
* 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 loading without being on the library search path ... 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 45.627 1.326 46.955
computeNBHDVsCTObject 18.545 0.215 18.762
randomiseNodeIndices 14.764 0.076 14.842
aggregateGeneExpression 11.942 1.345 13.220
getObjectSubsetClusteringPValue 12.554 0.177 12.731
transposeObject 10.560 0.054 10.614
computeGraphEmbedding 9.503 0.141 9.649
predictAnnotation 8.212 0.070 8.282
predictAnnotationAllGenes 7.447 0.060 7.508
predictGeneAnnotationImpl 6.551 0.083 6.634
getAverageExpressionMatrix 5.905 0.021 5.926
geneSetsVsGeneClustersPValueMatrix 5.783 0.101 5.885
getNearbyGenes 5.669 0.097 5.774
runGeometricClusteringTrials 5.728 0.037 5.764
medianComplementPValue 5.757 0.003 5.760
getAverageExpressionDF 5.662 0.064 5.727
combinatorialSpheres 5.653 0.042 5.695
getObjectSubsetClusteringStatistics 5.556 0.047 5.603
getGeneClusterAveragesPerCell 5.496 0.001 5.497
desymmetriseNN 5.386 0.109 5.495
tagRowAndColNames 5.417 0.003 5.420
symmetriseNN 5.333 0.063 5.396
meanZPerClusterOnUMAP 5.387 0.005 5.391
getClusterOrder 5.312 0.003 5.316
meanZPerCluster 5.311 0.003 5.315
getGeneNeighbors 5.248 0.064 5.312
symmetryCheckNN 5.247 0.017 5.265
meanGeneClusterOnCellUMAP 5.239 0.017 5.256
getNearestNeighbourLists 5.141 0.019 5.161
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/CatsCradle.Rcheck/00check.log’
for details.
CatsCradle.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL CatsCradle ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘CatsCradle’ ... ** this is package ‘CatsCradle’ version ‘1.5.1’ ** 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 | 11.942 | 1.345 | 13.220 | |
| annotateGeneAsVector | 45.627 | 1.326 | 46.955 | |
| annotateGenesByGeneSet | 1.534 | 0.210 | 1.744 | |
| cellTypesPerCellTypeGraphFromCellMatrix | 0.189 | 0.000 | 0.189 | |
| collapseExtendedNBHDs | 2.431 | 0.002 | 2.374 | |
| combinatorialSpheres | 5.653 | 0.042 | 5.695 | |
| computeCellTypesPerCellTypeMatrix | 0.117 | 0.021 | 0.138 | |
| computeEdgeGraph | 0.160 | 0.016 | 0.145 | |
| computeEdgeObject | 0.838 | 0.021 | 0.860 | |
| computeGraphEmbedding | 9.503 | 0.141 | 9.649 | |
| computeNBHDByCTMatrix | 0.100 | 0.002 | 0.102 | |
| computeNBHDVsCTObject | 18.545 | 0.215 | 18.762 | |
| computeNeighbourEnrichment | 0.124 | 0.010 | 0.134 | |
| computeNeighboursDelaunay | 0.097 | 0.005 | 0.102 | |
| computeNeighboursEuclidean | 1.070 | 0.039 | 0.682 | |
| cullEdges | 0.513 | 0.013 | 0.525 | |
| desymmetriseNN | 5.386 | 0.109 | 5.495 | |
| directedHausdorfDistance | 0.001 | 0.000 | 0.001 | |
| edgeCutoffsByClustering | 0.396 | 0.001 | 0.397 | |
| edgeCutoffsByPercentile | 0.274 | 0.000 | 0.274 | |
| edgeCutoffsByWatershed | 0.311 | 0.002 | 0.313 | |
| edgeCutoffsByZScore | 0.325 | 0.003 | 0.328 | |
| edgeLengthPlot | 0.330 | 0.003 | 0.333 | |
| edgeLengthsAndCellTypePairs | 0.326 | 0.001 | 0.328 | |
| exampleObjects | 0 | 0 | 0 | |
| geneSetsVsGeneClustersPValueMatrix | 5.783 | 0.101 | 5.885 | |
| getAverageExpressionDF | 5.662 | 0.064 | 5.727 | |
| getAverageExpressionMatrix | 5.905 | 0.021 | 5.926 | |
| getClusterOrder | 5.312 | 0.003 | 5.316 | |
| getExtendedNBHDs | 0.877 | 0.009 | 0.741 | |
| getFeatureZScores | 0.196 | 0.003 | 0.198 | |
| getGeneClusterAveragesPerCell | 5.496 | 0.001 | 5.497 | |
| getGeneNeighbors | 5.248 | 0.064 | 5.312 | |
| getLigandReceptorNetwork | 0.016 | 0.002 | 0.016 | |
| getLigandReceptorPairsInPanel | 0.079 | 0.002 | 0.081 | |
| getNearbyGenes | 5.669 | 0.097 | 5.774 | |
| getNearestNeighbourLists | 5.141 | 0.019 | 5.161 | |
| getObjectSubsetClusteringPValue | 12.554 | 0.177 | 12.731 | |
| getObjectSubsetClusteringStatistics | 5.556 | 0.047 | 5.603 | |
| make.getExample | 0.091 | 0.001 | 0.092 | |
| makeLRInteractionHeatmap | 0.176 | 0.002 | 0.178 | |
| makeSummedLRInteractionHeatmap | 0.154 | 0.002 | 0.157 | |
| meanGeneClusterOnCellUMAP | 5.239 | 0.017 | 5.256 | |
| meanZPerCluster | 5.311 | 0.003 | 5.315 | |
| meanZPerClusterOnUMAP | 5.387 | 0.005 | 5.391 | |
| medianComplementDistance | 0.000 | 0.001 | 0.000 | |
| medianComplementPValue | 5.757 | 0.003 | 5.760 | |
| nbhdsAsEdgesToNbhdsAsList | 0.684 | 0.007 | 0.691 | |
| neighbourhoodDiameter | 0.714 | 0.008 | 0.722 | |
| performLigandReceptorAnalysis | 0.995 | 1.203 | 2.199 | |
| performLigandReceptorAnalysisPermutation | 0.889 | 1.202 | 2.092 | |
| plotLRDotplot | 1.540 | 0.003 | 1.543 | |
| predictAnnotation | 8.212 | 0.070 | 8.282 | |
| predictAnnotationAllGenes | 7.447 | 0.060 | 7.508 | |
| predictGeneAnnotationImpl | 6.551 | 0.083 | 6.634 | |
| randomiseNodeIndices | 14.764 | 0.076 | 14.842 | |
| runGeometricClusteringTrials | 5.728 | 0.037 | 5.764 | |
| runMoransI | 1.069 | 0.015 | 1.085 | |
| sankeyFromMatrix | 0.003 | 0.001 | 0.004 | |
| symmetriseNN | 5.333 | 0.063 | 5.396 | |
| symmetryCheckNN | 5.247 | 0.017 | 5.265 | |
| tagRowAndColNames | 5.417 | 0.003 | 5.420 | |
| transposeObject | 10.560 | 0.054 | 10.614 | |