Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 280/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CatsCradle 1.0.0  (landing page)
Michael Shapiro
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/CatsCradle
git_branch: RELEASE_3_20
git_last_commit: df3ef22
git_last_commit_date: 2024-10-29 11:33:50 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


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: 1.0.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CatsCradle.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CatsCradle_1.0.0.tar.gz
StartedAt: 2024-12-19 21:03:41 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 21:21:08 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 1046.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CatsCradle.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CatsCradle.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CatsCradle_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CatsCradle.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘CatsCradle/DESCRIPTION’ ... OK
* this is package ‘CatsCradle’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* 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 ... WARNING
Undocumented arguments in Rd file 'getFeatureZScores.Rd'
  ‘features’
Documented arguments not in \usage in Rd file 'getFeatureZScores.Rd':
  ‘featurs’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
computeNBHDVsCTObject           16.422  0.276  16.702
randomiseNodeIndices            13.230  0.051  13.281
getObjectSubsetClusteringPValue 12.073  0.095  12.169
aggregateGeneExpression         10.001  0.498  10.434
computeGraphEmbedding            8.316  0.194   8.513
transposeObject                  8.463  0.007   8.474
predictAnnotation                7.320  0.016   7.338
predictAnnotationAllGenes        6.192  0.041   6.235
predictGeneAnnotationImpl        5.392  0.037   5.431
* 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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/CatsCradle.Rcheck/00check.log’
for details.


Installation output

CatsCradle.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL CatsCradle
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘CatsCradle’ ...
** 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
aggregateGeneExpression10.001 0.49810.434
annotateGeneAsVector4.0080.3364.343
annotateGenesByGeneSet1.4860.0551.541
cellTypesPerCellTypeGraphFromCellMatrix0.4490.0020.452
collapseExtendedNBHDs2.2650.0092.205
combinatorialSpheres4.5210.0794.602
computeCellTypesPerCellTypeMatrix0.3480.0010.349
computeEdgeGraph0.4060.0110.388
computeEdgeObject0.9440.0070.951
computeGraphEmbedding8.3160.1948.513
computeNBHDByCTMatrix0.3880.0170.405
computeNBHDVsCTObject16.422 0.27616.702
computeNeighbourEnrichment1.6410.0721.713
computeNeighboursDelaunay0.3280.0010.329
computeNeighboursEuclidean1.8850.0261.414
cullEdges3.0430.0083.051
desymmetriseNN4.3300.1394.470
directedHausdorfDistance0.0000.0010.001
edgeCutoffsByClustering2.7040.1532.857
edgeCutoffsByPercentile2.6940.0092.703
edgeCutoffsByWatershed2.7080.1432.850
edgeCutoffsByZScore2.6790.1722.851
edgeLengthPlot2.7490.0922.840
edgeLengthsAndCellTypePairs2.6770.0742.751
exampleObjects0.0010.0000.000
geneSetsVsGeneClustersPValueMatrix4.5590.0234.583
getAverageExpressionDF4.3380.0054.343
getAverageExpressionMatrix4.3090.0054.315
getClusterOrder4.1660.0704.237
getExtendedNBHDs1.2450.0011.072
getFeatureZScores0.1870.0010.188
getGeneClusterAveragesPerCell4.1830.0314.215
getGeneNeighbors4.1570.0304.188
getLigandReceptorNetwork0.0150.0000.015
getLigandReceptorPairsInPanel0.2590.0000.259
getNearbyGenes4.7760.0814.858
getNearestNeighbourLists4.2200.0024.224
getObjectSubsetClusteringPValue12.073 0.09512.169
getObjectSubsetClusteringStatistics4.7460.0334.780
make.getExample0.3530.0010.352
makeLRInteractionHeatmap0.4460.0010.448
makeSummedLRInteractionHeatmap0.3420.0000.342
meanGeneClusterOnCellUMAP4.2460.0004.247
meanZPerCluster4.3430.0024.347
meanZPerClusterOnUMAP4.3880.0024.391
medianComplementDistance0.0010.0000.000
medianComplementPValue4.7730.0294.802
nbhdsAsEdgesToNbhdsAsList1.0980.0001.097
neighbourhoodDiameter1.1300.0011.131
performLigandReceptorAnalysis2.4450.1432.587
predictAnnotation7.3200.0167.338
predictAnnotationAllGenes6.1920.0416.235
predictGeneAnnotationImpl5.3920.0375.431
randomiseNodeIndices13.230 0.05113.281
runGeometricClusteringTrials4.4980.0274.527
runMoransI1.4210.0071.427
sankeyFromMatrix0.0020.0010.003
symmetriseNN4.0770.0014.079
symmetryCheckNN4.1880.0024.191
tagRowAndColNames4.3790.0004.380
transposeObject8.4630.0078.474