Back to Multiple platform build/check report for BioC 3.22:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-08-09 12:09 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 282/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CatsCradle 1.3.0  (landing page)
Michael Shapiro
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/CatsCradle
git_branch: devel
git_last_commit: ec233bd
git_last_commit_date: 2025-04-15 13:40:27 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 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: 1.3.0
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_1.3.0.tar.gz
StartedAt: 2025-08-08 18:29:37 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 18:33:20 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 222.8 seconds
RetCode: 0
Status:   OK  
CheckDir: CatsCradle.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/CatsCradle.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CatsCradle/DESCRIPTION’ ... OK
* this is package ‘CatsCradle’ version ‘1.3.0’
* 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’
Undefined global functions or variables:
  UMAP_1 UMAP_2 cellTypePair cutoff humanLRN moransI
  moransILigandReceptor mouseLRN 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            17.829  0.116  17.965
computeNBHDVsCTObject            9.205  0.072   9.281
randomiseNodeIndices             6.774  0.089   6.905
getObjectSubsetClusteringPValue  5.952  0.370   6.350
* 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

##############################################################################
##############################################################################
###
### 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 ‘1.3.0’
** 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)

Tests output


Example timings

CatsCradle.Rcheck/CatsCradle-Ex.timings

nameusersystemelapsed
aggregateGeneExpression4.7100.1344.856
annotateGeneAsVector17.829 0.11617.965
annotateGenesByGeneSet0.5750.1010.677
cellTypesPerCellTypeGraphFromCellMatrix0.1460.0050.151
collapseExtendedNBHDs0.9830.0371.021
combinatorialSpheres2.5750.0362.611
computeCellTypesPerCellTypeMatrix0.1240.0040.128
computeEdgeGraph0.1580.0060.152
computeEdgeObject0.3930.0200.414
computeGraphEmbedding4.7250.0354.765
computeNBHDByCTMatrix0.1180.0050.123
computeNBHDVsCTObject9.2050.0729.281
computeNeighbourEnrichment0.2050.0160.220
computeNeighboursDelaunay0.1530.0130.166
computeNeighboursEuclidean0.2840.0220.309
cullEdges0.2700.0160.293
desymmetriseNN2.3960.0432.442
directedHausdorfDistance0.0010.0000.000
edgeCutoffsByClustering0.6910.0180.710
edgeCutoffsByPercentile0.1800.0060.191
edgeCutoffsByWatershed0.1910.0050.196
edgeCutoffsByZScore0.2180.0120.231
edgeLengthPlot0.1970.0060.206
edgeLengthsAndCellTypePairs0.1740.0030.177
exampleObjects000
geneSetsVsGeneClustersPValueMatrix2.5680.0182.589
getAverageExpressionDF2.5260.0372.567
getAverageExpressionMatrix2.4280.0302.459
getClusterOrder2.3930.0222.441
getExtendedNBHDs0.4880.0300.450
getFeatureZScores0.0790.0020.082
getGeneClusterAveragesPerCell2.3800.0292.417
getGeneNeighbors2.3590.0332.395
getLigandReceptorNetwork0.0080.0010.010
getLigandReceptorPairsInPanel0.1170.0040.122
getNearbyGenes2.5410.0372.595
getNearestNeighbourLists2.4000.0322.448
getObjectSubsetClusteringPValue5.9520.3706.350
getObjectSubsetClusteringStatistics2.7300.0472.881
make.getExample0.1140.0070.121
makeLRInteractionHeatmap0.1850.0090.207
makeSummedLRInteractionHeatmap0.1510.0060.164
meanGeneClusterOnCellUMAP2.4180.0302.452
meanZPerCluster2.4170.0292.450
meanZPerClusterOnUMAP2.4370.0362.479
medianComplementDistance0.0000.0000.001
medianComplementPValue2.6530.0472.705
nbhdsAsEdgesToNbhdsAsList0.4150.0830.499
neighbourhoodDiameter0.4240.0690.501
performLigandReceptorAnalysis0.9710.3531.332
predictAnnotation3.7040.2743.990
predictAnnotationAllGenes3.2860.1623.461
predictGeneAnnotationImpl3.0590.1393.215
randomiseNodeIndices6.7740.0896.905
runGeometricClusteringTrials2.5840.0582.670
runMoransI0.5020.0690.571
sankeyFromMatrix0.0010.0000.001
symmetriseNN2.4040.0342.438
symmetryCheckNN2.3920.0262.448
tagRowAndColNames2.4750.0262.509
transposeObject4.7010.0544.781