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This page was generated on 2025-10-28 12:04 -0400 (Tue, 28 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
kjohnson3macOS 13.7.7 Venturaarm644.5.1 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 289/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CatsCradle 1.3.3  (landing page)
Michael Shapiro
Snapshot Date: 2025-10-27 13:45 -0400 (Mon, 27 Oct 2025)
git_url: https://git.bioconductor.org/packages/CatsCradle
git_branch: devel
git_last_commit: 00cf5a4
git_last_commit_date: 2025-10-25 15:46:54 -0400 (Sat, 25 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for CatsCradle on kjohnson3

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.

raw results


Summary

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: 2025-10-27 18:49:40 -0400 (Mon, 27 Oct 2025)
EndedAt: 2025-10-27 18:53:25 -0400 (Mon, 27 Oct 2025)
EllapsedTime: 225.8 seconds
RetCode: 0
Status:   OK  
CheckDir: CatsCradle.Rcheck
Warnings: 0

Command output

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### Running 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
###
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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            17.706  0.092  17.809
computeNBHDVsCTObject            9.346  0.063   9.471
randomiseNodeIndices             6.720  0.112   6.843
getObjectSubsetClusteringPValue  6.049  0.370   6.429
* 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.


Installation output

CatsCradle.Rcheck/00install.out

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###
### 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)

Tests output


Example timings

CatsCradle.Rcheck/CatsCradle-Ex.timings

nameusersystemelapsed
aggregateGeneExpression4.7150.0974.820
annotateGeneAsVector17.706 0.09217.809
annotateGenesByGeneSet0.6940.0900.785
cellTypesPerCellTypeGraphFromCellMatrix0.0750.0040.080
collapseExtendedNBHDs0.9480.0240.973
combinatorialSpheres2.6040.0272.639
computeCellTypesPerCellTypeMatrix0.0470.0040.051
computeEdgeGraph0.0810.0040.080
computeEdgeObject0.3280.0130.341
computeGraphEmbedding4.7320.0284.763
computeNBHDByCTMatrix0.0430.0030.046
computeNBHDVsCTObject9.3460.0639.471
computeNeighbourEnrichment0.0520.0060.058
computeNeighboursDelaunay0.0740.0070.080
computeNeighboursEuclidean0.2100.0160.226
cullEdges0.1930.0120.205
desymmetriseNN2.4560.0362.495
directedHausdorfDistance000
edgeCutoffsByClustering0.1460.0110.158
edgeCutoffsByPercentile0.1040.0030.107
edgeCutoffsByWatershed0.1140.0040.117
edgeCutoffsByZScore0.1320.0050.138
edgeLengthPlot0.1250.0060.130
edgeLengthsAndCellTypePairs0.1320.0050.136
exampleObjects000
geneSetsVsGeneClustersPValueMatrix2.5810.0302.619
getAverageExpressionDF2.4730.0472.536
getAverageExpressionMatrix2.4970.0392.537
getClusterOrder2.3670.0382.406
getExtendedNBHDs0.4280.0230.375
getFeatureZScores0.0810.0040.085
getGeneClusterAveragesPerCell2.4810.0362.531
getGeneNeighbors2.4230.0252.474
getLigandReceptorNetwork0.0080.0020.010
getLigandReceptorPairsInPanel0.0360.0030.038
getNearbyGenes2.5580.0322.591
getNearestNeighbourLists2.5260.0382.569
getObjectSubsetClusteringPValue6.0490.3706.429
getObjectSubsetClusteringStatistics2.6830.0462.759
make.getExample0.0380.0040.043
makeLRInteractionHeatmap0.0830.0050.088
makeSummedLRInteractionHeatmap0.0730.0030.076
meanGeneClusterOnCellUMAP2.6000.0432.650
meanZPerCluster2.5470.0252.611
meanZPerClusterOnUMAP2.6300.0222.740
medianComplementDistance0.0010.0000.000
medianComplementPValue2.7570.0372.838
nbhdsAsEdgesToNbhdsAsList0.3430.0720.430
neighbourhoodDiameter0.3480.0660.419
performLigandReceptorAnalysis0.4660.3390.821
performLigandReceptorAnalysisPermutation0.4250.3390.768
plotLRDotplot0.5280.0240.565
predictAnnotation3.7660.2384.054
predictAnnotationAllGenes3.4220.1653.643
predictGeneAnnotationImpl3.0810.1473.308
randomiseNodeIndices6.7200.1126.843
runGeometricClusteringTrials2.8030.0522.864
runMoransI0.4350.0540.502
sankeyFromMatrix0.0010.0000.001
symmetriseNN2.5000.0402.584
symmetryCheckNN2.3560.0222.399
tagRowAndColNames2.4710.0272.525
transposeObject4.8260.0544.934