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This page was generated on 2024-11-09 21:30 -0500 (Sat, 09 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4505
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4486
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: 2024-11-08 13:40 -0500 (Fri, 08 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
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
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  YES
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


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: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2024-11-08 22:12:21 -0500 (Fri, 08 Nov 2024)
EndedAt: 2024-11-08 22:19:14 -0500 (Fri, 08 Nov 2024)
EllapsedTime: 413.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CatsCradle.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CatsCradle.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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           8.350  0.061   8.411
randomiseNodeIndices            6.234  0.076   6.309
getObjectSubsetClusteringPValue 5.599  0.269   5.869
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-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/4.4-arm64/Resources/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
aggregateGeneExpression4.3580.0754.434
annotateGeneAsVector1.8240.0321.855
annotateGenesByGeneSet0.6260.0660.691
cellTypesPerCellTypeGraphFromCellMatrix0.1820.0120.194
collapseExtendedNBHDs0.8040.0200.825
combinatorialSpheres2.0060.0352.041
computeCellTypesPerCellTypeMatrix0.1360.0060.142
computeEdgeGraph0.1430.0110.154
computeEdgeObject0.3420.0180.360
computeGraphEmbedding4.2490.0264.274
computeNBHDByCTMatrix0.1650.0060.172
computeNBHDVsCTObject8.3500.0618.411
computeNeighbourEnrichment0.7280.0210.751
computeNeighboursDelaunay0.1230.0020.126
computeNeighboursEuclidean0.5350.0260.560
cullEdges1.1710.1621.333
desymmetriseNN1.9760.0352.011
directedHausdorfDistance000
edgeCutoffsByClustering0.9820.2121.195
edgeCutoffsByPercentile0.9800.2681.249
edgeCutoffsByWatershed0.9810.2631.244
edgeCutoffsByZScore0.9740.2151.189
edgeLengthPlot1.0220.1611.183
edgeLengthsAndCellTypePairs0.9890.1251.115
exampleObjects0.0000.0000.001
geneSetsVsGeneClustersPValueMatrix2.2220.0492.271
getAverageExpressionDF2.0170.0322.049
getAverageExpressionMatrix1.8960.0511.948
getClusterOrder1.8410.0501.891
getExtendedNBHDs0.4500.0270.478
getFeatureZScores0.0700.0020.073
getGeneClusterAveragesPerCell1.9570.0191.976
getGeneNeighbors1.9430.0271.971
getLigandReceptorNetwork0.0080.0010.008
getLigandReceptorPairsInPanel0.1080.0040.112
getNearbyGenes2.1120.0202.133
getNearestNeighbourLists1.8350.0231.858
getObjectSubsetClusteringPValue5.5990.2695.869
getObjectSubsetClusteringStatistics2.2140.0362.250
make.getExample0.1260.0030.129
makeLRInteractionHeatmap0.1550.0100.165
makeSummedLRInteractionHeatmap0.1250.0040.130
meanGeneClusterOnCellUMAP2.040.032.07
meanZPerCluster1.9730.0332.006
meanZPerClusterOnUMAP2.0210.0312.052
medianComplementDistance000
medianComplementPValue2.1570.0432.201
nbhdsAsEdgesToNbhdsAsList0.4610.0590.520
neighbourhoodDiameter0.4410.0460.487
performLigandReceptorAnalysis1.0620.2571.319
predictAnnotation3.6670.3033.970
predictAnnotationAllGenes2.6330.1672.800
predictGeneAnnotationImpl2.5820.1052.690
randomiseNodeIndices6.2340.0766.309
runGeometricClusteringTrials2.1530.0482.200
runMoransI0.5550.0820.638
sankeyFromMatrix0.0020.0000.002
symmetriseNN2.0050.0172.023
symmetryCheckNN1.9660.0151.981
tagRowAndColNames2.0470.0182.066
transposeObject3.7670.0633.830