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This page was generated on 2025-08-12 12:05 -0400 (Tue, 12 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
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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: 2025-08-11 13:45 -0400 (Mon, 11 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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for CatsCradle on nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CatsCradle.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CatsCradle_1.3.0.tar.gz
StartedAt: 2025-08-11 23:30:25 -0400 (Mon, 11 Aug 2025)
EndedAt: 2025-08-11 23:48:14 -0400 (Mon, 11 Aug 2025)
EllapsedTime: 1068.2 seconds
RetCode: 0
Status:   OK  
CheckDir: CatsCradle.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CatsCradle.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CatsCradle_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CatsCradle.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* 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 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’
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                44.724  0.863  45.598
computeNBHDVsCTObject               18.430  0.155  18.589
randomiseNodeIndices                15.120  0.004  15.125
getObjectSubsetClusteringPValue     12.927  0.079  13.007
transposeObject                     11.337  0.004  11.342
aggregateGeneExpression             10.525  0.221  10.684
computeGraphEmbedding                9.628  0.120   9.750
predictAnnotation                    8.208  0.017   8.227
predictAnnotationAllGenes            7.680  0.050   7.731
predictGeneAnnotationImpl            6.986  0.073   7.061
runGeometricClusteringTrials         6.255  0.002   6.259
medianComplementPValue               6.184  0.018   6.205
tagRowAndColNames                    6.145  0.004   6.150
getNearbyGenes                       5.819  0.085   5.905
getObjectSubsetClusteringStatistics  5.850  0.009   5.860
getAverageExpressionDF               5.771  0.041   5.813
combinatorialSpheres                 5.775  0.035   5.811
symmetryCheckNN                      5.675  0.001   5.677
getAverageExpressionMatrix           5.600  0.035   5.636
geneSetsVsGeneClustersPValueMatrix   5.526  0.097   5.624
getGeneClusterAveragesPerCell        5.567  0.041   5.609
getGeneNeighbors                     5.566  0.038   5.605
meanZPerClusterOnUMAP                5.516  0.068   5.585
getNearestNeighbourLists             5.511  0.061   5.573
meanZPerCluster                      5.497  0.065   5.563
symmetriseNN                         5.541  0.008   5.549
desymmetriseNN                       5.456  0.029   5.485
getClusterOrder                      5.389  0.064   5.455
meanGeneClusterOnCellUMAP            5.402  0.002   5.406
* 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-3.22-bioc/meat/CatsCradle.Rcheck/00check.log’
for details.


Installation output

CatsCradle.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL CatsCradle
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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
aggregateGeneExpression10.525 0.22110.684
annotateGeneAsVector44.724 0.86345.598
annotateGenesByGeneSet1.5010.1781.680
cellTypesPerCellTypeGraphFromCellMatrix0.3720.0020.375
collapseExtendedNBHDs2.6180.0012.551
combinatorialSpheres5.7750.0355.811
computeCellTypesPerCellTypeMatrix0.3010.0170.318
computeEdgeGraph0.3540.0140.333
computeEdgeObject1.0120.0331.045
computeGraphEmbedding9.6280.1209.750
computeNBHDByCTMatrix0.3390.0000.339
computeNBHDVsCTObject18.430 0.15518.589
computeNeighbourEnrichment1.5420.0331.575
computeNeighboursDelaunay0.2720.0010.274
computeNeighboursEuclidean1.1600.0230.777
cullEdges0.6910.0490.740
desymmetriseNN5.4560.0295.485
directedHausdorfDistance0.0010.0000.001
edgeCutoffsByClustering0.5530.0110.564
edgeCutoffsByPercentile0.4530.0020.455
edgeCutoffsByWatershed0.4880.0020.490
edgeCutoffsByZScore0.5100.0020.512
edgeLengthPlot0.4920.0010.493
edgeLengthsAndCellTypePairs0.4460.0000.445
exampleObjects000
geneSetsVsGeneClustersPValueMatrix5.5260.0975.624
getAverageExpressionDF5.7710.0415.813
getAverageExpressionMatrix5.6000.0355.636
getClusterOrder5.3890.0645.455
getExtendedNBHDs1.0990.0070.958
getFeatureZScores0.1980.0000.199
getGeneClusterAveragesPerCell5.5670.0415.609
getGeneNeighbors5.5660.0385.605
getLigandReceptorNetwork0.0160.0000.017
getLigandReceptorPairsInPanel0.2980.0010.299
getNearbyGenes5.8190.0855.905
getNearestNeighbourLists5.5110.0615.573
getObjectSubsetClusteringPValue12.927 0.07913.007
getObjectSubsetClusteringStatistics5.8500.0095.860
make.getExample0.2750.0000.275
makeLRInteractionHeatmap0.4180.0020.420
makeSummedLRInteractionHeatmap0.3580.0010.359
meanGeneClusterOnCellUMAP5.4020.0025.406
meanZPerCluster5.4970.0655.563
meanZPerClusterOnUMAP5.5160.0685.585
medianComplementDistance000
medianComplementPValue6.1840.0186.205
nbhdsAsEdgesToNbhdsAsList0.8840.0230.907
neighbourhoodDiameter0.9340.0030.937
performLigandReceptorAnalysis2.3110.1102.421
predictAnnotation8.2080.0178.227
predictAnnotationAllGenes7.6800.0507.731
predictGeneAnnotationImpl6.9860.0737.061
randomiseNodeIndices15.120 0.00415.125
runGeometricClusteringTrials6.2550.0026.259
runMoransI1.3450.0021.347
sankeyFromMatrix0.0040.0000.003
symmetriseNN5.5410.0085.549
symmetryCheckNN5.6750.0015.677
tagRowAndColNames6.1450.0046.150
transposeObject11.337 0.00411.342