Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-20 12:05 -0400 (Sat, 20 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4814 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
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 1897/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scDiagnostics 1.3.0 (landing page) Anthony Christidis
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the scDiagnostics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scDiagnostics.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: scDiagnostics |
Version: 1.3.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scDiagnostics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scDiagnostics_1.3.0.tar.gz |
StartedAt: 2025-09-19 23:47:05 -0400 (Fri, 19 Sep 2025) |
EndedAt: 2025-09-19 23:55:12 -0400 (Fri, 19 Sep 2025) |
EllapsedTime: 486.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scDiagnostics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scDiagnostics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scDiagnostics_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/scDiagnostics.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scDiagnostics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scDiagnostics’ version ‘1.3.0’ * 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 ‘scDiagnostics’ 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 ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: argumentCheck.Rd: SingleCellExperiment-class boxplotPCA.Rd: SingleCellExperiment-class calculateAveragePairwiseCorrelation.Rd: SingleCellExperiment-class calculateCellDistances.Rd: SingleCellExperiment-class calculateCellDistancesSimilarity.Rd: SingleCellExperiment-class calculateCellSimilarityPCA.Rd: SingleCellExperiment-class calculateCramerPValue.Rd: SingleCellExperiment-class calculateDiscriminantSpace.Rd: SingleCellExperiment-class calculateHotellingPValue.Rd: SingleCellExperiment-class calculateNearestNeighborProbabilities.Rd: SingleCellExperiment-class calculateSIRSpace.Rd: SingleCellExperiment-class calculateVarImpOverlap.Rd: SingleCellExperiment-class calculateWassersteinDistance.Rd: SingleCellExperiment-class compareCCA.Rd: SingleCellExperiment-class comparePCA.Rd: SingleCellExperiment-class comparePCASubspace.Rd: SingleCellExperiment-class detectAnomaly.Rd: SingleCellExperiment-class histQCvsAnnotation.Rd: SingleCellExperiment-class plotCellTypeMDS.Rd: SingleCellExperiment-class plotCellTypePCA.Rd: SingleCellExperiment-class plotGeneExpressionDimred.Rd: SingleCellExperiment-class plotGeneSetScores.Rd: SingleCellExperiment-class plotMarkerExpression.Rd: SingleCellExperiment-class plotPairwiseDistancesDensity.Rd: SingleCellExperiment-class plotQCvsAnnotation.Rd: SingleCellExperiment-class projectPCA.Rd: SingleCellExperiment-class projectSIR.Rd: SingleCellExperiment-class regressPC.Rd: SingleCellExperiment-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 LazyData ... NOTE 'LazyDataCompression' is specified without 'LazyData' * 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 plotCellTypeMDS 18.645 0.379 19.125 calculateCellDistances 17.761 0.718 18.712 calculateCramerPValue 12.578 2.236 14.928 calculateDiscriminantSpace 6.539 0.224 4.834 calculateCellDistancesSimilarity 6.419 0.311 6.909 calculateVarImpOverlap 6.049 0.396 3.656 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/scDiagnostics.Rcheck/00check.log’ for details.
scDiagnostics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scDiagnostics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘scDiagnostics’ ... ** this is package ‘scDiagnostics’ 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 (scDiagnostics)
scDiagnostics.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(scDiagnostics) > > test_check("scDiagnostics") [ FAIL 0 | WARN 27 | SKIP 0 | PASS 276 ] [ FAIL 0 | WARN 27 | SKIP 0 | PASS 276 ] > > proc.time() user system elapsed 156.105 9.722 159.239
scDiagnostics.Rcheck/scDiagnostics-Ex.timings
name | user | system | elapsed | |
boxplotPCA | 3.289 | 0.109 | 3.414 | |
calculateAveragePairwiseCorrelation | 3.892 | 0.138 | 4.054 | |
calculateCategorizationEntropy | 0.058 | 0.001 | 0.060 | |
calculateCellDistances | 17.761 | 0.718 | 18.712 | |
calculateCellDistancesSimilarity | 6.419 | 0.311 | 6.909 | |
calculateCellSimilarityPCA | 2.390 | 0.122 | 2.590 | |
calculateCramerPValue | 12.578 | 2.236 | 14.928 | |
calculateDiscriminantSpace | 6.539 | 0.224 | 4.834 | |
calculateHVGOverlap | 1.358 | 0.062 | 1.425 | |
calculateHotellingPValue | 1.746 | 0.083 | 1.844 | |
calculateNearestNeighborProbabilities | 2.080 | 0.064 | 2.160 | |
calculateSIRSpace | 3.958 | 0.065 | 4.085 | |
calculateVarImpOverlap | 6.049 | 0.396 | 3.656 | |
calculateWassersteinDistance | 2.987 | 0.156 | 3.183 | |
compareCCA | 1.513 | 0.050 | 1.573 | |
comparePCA | 1.536 | 0.055 | 1.602 | |
comparePCASubspace | 1.710 | 0.053 | 1.772 | |
detectAnomaly | 3.268 | 0.144 | 3.483 | |
histQCvsAnnotation | 1.012 | 0.015 | 1.035 | |
plot.calculateWassersteinDistanceObject | 2.151 | 0.101 | 2.265 | |
plotCellTypeMDS | 18.645 | 0.379 | 19.125 | |
plotCellTypePCA | 1.833 | 0.085 | 1.938 | |
plotGeneExpressionDimred | 1.808 | 0.032 | 1.851 | |
plotGeneSetScores | 1.520 | 0.025 | 1.555 | |
plotMarkerExpression | 0.740 | 0.021 | 0.766 | |
plotPairwiseDistancesDensity | 2.076 | 0.129 | 2.215 | |
plotQCvsAnnotation | 0.370 | 0.012 | 0.385 | |
projectPCA | 0.312 | 0.020 | 0.334 | |
projectSIR | 1.420 | 0.025 | 1.472 | |
qc_data | 0.024 | 0.007 | 0.033 | |
query_data | 0.022 | 0.006 | 0.028 | |
reference_data | 0.048 | 0.007 | 0.054 | |
regressPC | 2.433 | 0.157 | 2.613 | |