Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:39 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 274/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CatsCradle 1.1.0 (landing page) Michael Shapiro
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. |
Package: CatsCradle |
Version: 1.1.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CatsCradle.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CatsCradle_1.1.0.tar.gz |
StartedAt: 2024-12-23 20:23:33 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 20:38:48 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 915.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: CatsCradle.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CatsCradle.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CatsCradle_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CatsCradle.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * 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 ‘1.1.0’ * 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 ... 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 17.629 0.231 17.866 randomiseNodeIndices 15.689 0.038 15.730 getObjectSubsetClusteringPValue 13.880 0.089 13.970 aggregateGeneExpression 10.208 0.238 10.381 transposeObject 10.271 0.002 10.276 computeGraphEmbedding 8.642 0.063 8.707 predictAnnotation 8.219 0.029 8.249 predictAnnotationAllGenes 7.578 0.029 7.610 predictGeneAnnotationImpl 6.785 0.021 6.808 medianComplementPValue 5.888 0.079 5.968 getObjectSubsetClusteringStatistics 5.733 0.038 5.773 runGeometricClusteringTrials 5.656 0.055 5.712 getAverageExpressionDF 5.365 0.001 5.368 meanGeneClusterOnCellUMAP 5.320 0.002 5.323 combinatorialSpheres 5.162 0.119 5.283 getAverageExpressionMatrix 5.163 0.056 5.220 geneSetsVsGeneClustersPValueMatrix 5.060 0.103 5.164 getNearbyGenes 5.076 0.085 5.165 tagRowAndColNames 5.024 0.002 5.029 * 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-3.21-bioc/meat/CatsCradle.Rcheck/00check.log’ for details.
CatsCradle.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL CatsCradle ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-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)
CatsCradle.Rcheck/CatsCradle-Ex.timings
name | user | system | elapsed | |
aggregateGeneExpression | 10.208 | 0.238 | 10.381 | |
annotateGeneAsVector | 4.355 | 0.268 | 4.622 | |
annotateGenesByGeneSet | 1.639 | 0.041 | 1.681 | |
cellTypesPerCellTypeGraphFromCellMatrix | 0.418 | 0.004 | 0.423 | |
collapseExtendedNBHDs | 2.441 | 0.059 | 2.423 | |
combinatorialSpheres | 5.162 | 0.119 | 5.283 | |
computeCellTypesPerCellTypeMatrix | 0.314 | 0.002 | 0.315 | |
computeEdgeGraph | 0.371 | 0.002 | 0.341 | |
computeEdgeObject | 1.069 | 0.026 | 1.095 | |
computeGraphEmbedding | 8.642 | 0.063 | 8.707 | |
computeNBHDByCTMatrix | 0.276 | 0.000 | 0.277 | |
computeNBHDVsCTObject | 17.629 | 0.231 | 17.866 | |
computeNeighbourEnrichment | 1.959 | 0.014 | 1.974 | |
computeNeighboursDelaunay | 0.306 | 0.002 | 0.308 | |
computeNeighboursEuclidean | 1.647 | 0.014 | 1.156 | |
cullEdges | 3.138 | 0.002 | 3.140 | |
desymmetriseNN | 4.863 | 0.005 | 4.870 | |
directedHausdorfDistance | 0.000 | 0.001 | 0.001 | |
edgeCutoffsByClustering | 2.922 | 0.128 | 3.049 | |
edgeCutoffsByPercentile | 2.985 | 0.017 | 3.002 | |
edgeCutoffsByWatershed | 2.948 | 0.001 | 2.950 | |
edgeCutoffsByZScore | 2.872 | 0.026 | 2.899 | |
edgeLengthPlot | 2.844 | 0.005 | 2.852 | |
edgeLengthsAndCellTypePairs | 2.885 | 0.012 | 2.897 | |
exampleObjects | 0 | 0 | 0 | |
geneSetsVsGeneClustersPValueMatrix | 5.060 | 0.103 | 5.164 | |
getAverageExpressionDF | 5.365 | 0.001 | 5.368 | |
getAverageExpressionMatrix | 5.163 | 0.056 | 5.220 | |
getClusterOrder | 4.643 | 0.057 | 4.702 | |
getExtendedNBHDs | 1.287 | 0.002 | 1.113 | |
getFeatureZScores | 0.201 | 0.002 | 0.203 | |
getGeneClusterAveragesPerCell | 4.917 | 0.065 | 4.985 | |
getGeneNeighbors | 4.724 | 0.009 | 4.738 | |
getLigandReceptorNetwork | 0.016 | 0.001 | 0.016 | |
getLigandReceptorPairsInPanel | 0.308 | 0.003 | 0.311 | |
getNearbyGenes | 5.076 | 0.085 | 5.165 | |
getNearestNeighbourLists | 4.819 | 0.002 | 4.822 | |
getObjectSubsetClusteringPValue | 13.880 | 0.089 | 13.970 | |
getObjectSubsetClusteringStatistics | 5.733 | 0.038 | 5.773 | |
make.getExample | 0.319 | 0.002 | 0.323 | |
makeLRInteractionHeatmap | 0.457 | 0.005 | 0.463 | |
makeSummedLRInteractionHeatmap | 0.362 | 0.001 | 0.362 | |
meanGeneClusterOnCellUMAP | 5.320 | 0.002 | 5.323 | |
meanZPerCluster | 4.966 | 0.002 | 4.970 | |
meanZPerClusterOnUMAP | 4.822 | 0.001 | 4.825 | |
medianComplementDistance | 0.001 | 0.000 | 0.001 | |
medianComplementPValue | 5.888 | 0.079 | 5.968 | |
nbhdsAsEdgesToNbhdsAsList | 1.181 | 0.002 | 1.183 | |
neighbourhoodDiameter | 1.155 | 0.002 | 1.157 | |
performLigandReceptorAnalysis | 2.804 | 0.812 | 3.617 | |
predictAnnotation | 8.219 | 0.029 | 8.249 | |
predictAnnotationAllGenes | 7.578 | 0.029 | 7.610 | |
predictGeneAnnotationImpl | 6.785 | 0.021 | 6.808 | |
randomiseNodeIndices | 15.689 | 0.038 | 15.730 | |
runGeometricClusteringTrials | 5.656 | 0.055 | 5.712 | |
runMoransI | 1.483 | 0.002 | 1.485 | |
sankeyFromMatrix | 0.003 | 0.000 | 0.003 | |
symmetriseNN | 4.975 | 0.003 | 4.979 | |
symmetryCheckNN | 4.989 | 0.001 | 4.992 | |
tagRowAndColNames | 5.024 | 0.002 | 5.029 | |
transposeObject | 10.271 | 0.002 | 10.276 | |