Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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: 2024-11-19 13:40 -0500 (Tue, 19 Nov 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)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for CatsCradle on teran2

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: 2024-11-19 23:54:29 -0500 (Tue, 19 Nov 2024)
EndedAt: 2024-11-20 00:07:58 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 808.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CatsCradle.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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 ‘/media/volume/teran2_disk/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 ... 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               14.802  0.006  14.824
randomiseNodeIndices                12.745  0.083  12.837
getObjectSubsetClusteringPValue     10.924  0.108  11.043
aggregateGeneExpression             10.714  0.246  10.900
transposeObject                      9.412  0.010   9.424
computeGraphEmbedding                7.957  0.000   7.962
predictAnnotation                    7.303  0.023   7.331
predictAnnotationAllGenes            6.237  0.046   6.286
predictGeneAnnotationImpl            5.624  0.031   5.659
getAverageExpressionMatrix           5.273  0.002   5.278
geneSetsVsGeneClustersPValueMatrix   5.127  0.039   5.170
medianComplementPValue               5.094  0.040   5.138
getObjectSubsetClusteringStatistics  5.058  0.045   5.109
runGeometricClusteringTrials         5.027  0.039   5.076
* 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
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/CatsCradle.Rcheck/00check.log’
for details.


Installation output

CatsCradle.Rcheck/00install.out

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


* installing to library ‘/media/volume/teran2_disk/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
aggregateGeneExpression10.714 0.24610.900
annotateGeneAsVector3.8630.2814.169
annotateGenesByGeneSet1.1830.0501.233
cellTypesPerCellTypeGraphFromCellMatrix0.3750.0000.375
collapseExtendedNBHDs1.9110.0031.846
combinatorialSpheres4.9780.0144.992
computeCellTypesPerCellTypeMatrix0.2750.0010.275
computeEdgeGraph0.3300.0010.303
computeEdgeObject1.1790.0041.180
computeGraphEmbedding7.9570.0007.962
computeNBHDByCTMatrix0.3210.0160.338
computeNBHDVsCTObject14.802 0.00614.824
computeNeighbourEnrichment1.6130.0121.625
computeNeighboursDelaunay0.2580.0000.260
computeNeighboursEuclidean1.5220.0121.085
cullEdges2.8010.0052.807
desymmetriseNN4.5830.0014.586
directedHausdorfDistance0.0000.0000.001
edgeCutoffsByClustering2.3610.1632.526
edgeCutoffsByPercentile2.2520.0062.259
edgeCutoffsByWatershed2.4840.1712.657
edgeCutoffsByZScore2.2390.2062.446
edgeLengthPlot2.3770.1432.520
edgeLengthsAndCellTypePairs2.4640.1002.565
exampleObjects000
geneSetsVsGeneClustersPValueMatrix5.1270.0395.170
getAverageExpressionDF4.7270.0014.735
getAverageExpressionMatrix5.2730.0025.278
getClusterOrder4.7470.0014.753
getExtendedNBHDs0.9570.0010.788
getFeatureZScores0.1540.0010.155
getGeneClusterAveragesPerCell4.8610.0024.866
getGeneNeighbors4.5380.0034.545
getLigandReceptorNetwork0.0100.0010.011
getLigandReceptorPairsInPanel0.1970.0020.199
getNearbyGenes4.8380.0234.863
getNearestNeighbourLists4.4330.0014.437
getObjectSubsetClusteringPValue10.924 0.10811.043
getObjectSubsetClusteringStatistics5.0580.0455.109
make.getExample0.2610.0010.262
makeLRInteractionHeatmap0.3040.0030.310
makeSummedLRInteractionHeatmap0.2360.0010.237
meanGeneClusterOnCellUMAP4.9050.0044.920
meanZPerCluster4.7560.0014.762
meanZPerClusterOnUMAP4.6880.0054.695
medianComplementDistance0.0010.0000.000
medianComplementPValue5.0940.0405.138
nbhdsAsEdgesToNbhdsAsList0.7850.0020.788
neighbourhoodDiameter1.2200.0081.230
performLigandReceptorAnalysis1.7310.2031.934
predictAnnotation7.3030.0237.331
predictAnnotationAllGenes6.2370.0466.286
predictGeneAnnotationImpl5.6240.0315.659
randomiseNodeIndices12.745 0.08312.837
runGeometricClusteringTrials5.0270.0395.076
runMoransI1.120.001.12
sankeyFromMatrix0.0030.0010.003
symmetriseNN4.8180.0064.828
symmetryCheckNN4.4840.0024.489
tagRowAndColNames4.7110.0004.712
transposeObject9.4120.0109.424