Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-08 12:05 -0400 (Mon, 08 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4618 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4565 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4544 |
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 1889/2322 | 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: 2025-09-07 23:36:05 -0400 (Sun, 07 Sep 2025) |
EndedAt: 2025-09-07 23:43:57 -0400 (Sun, 07 Sep 2025) |
EllapsedTime: 472.4 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 (2025-06-13) * 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 18.448 0.314 18.881 calculateCellDistances 17.440 0.707 18.306 calculateCramerPValue 12.581 2.334 15.029 calculateCellDistancesSimilarity 7.334 0.276 7.811 calculateDiscriminantSpace 5.648 0.214 4.058 calculateVarImpOverlap 5.600 0.153 3.270 * 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 (2025-06-13) -- "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 150.011 9.209 152.724
scDiagnostics.Rcheck/scDiagnostics-Ex.timings
name | user | system | elapsed | |
boxplotPCA | 2.797 | 0.052 | 2.861 | |
calculateAveragePairwiseCorrelation | 3.080 | 0.138 | 3.232 | |
calculateCategorizationEntropy | 0.011 | 0.001 | 0.012 | |
calculateCellDistances | 17.440 | 0.707 | 18.306 | |
calculateCellDistancesSimilarity | 7.334 | 0.276 | 7.811 | |
calculateCellSimilarityPCA | 2.190 | 0.080 | 2.401 | |
calculateCramerPValue | 12.581 | 2.334 | 15.029 | |
calculateDiscriminantSpace | 5.648 | 0.214 | 4.058 | |
calculateHVGOverlap | 1.516 | 0.075 | 1.603 | |
calculateHotellingPValue | 1.672 | 0.060 | 1.739 | |
calculateNearestNeighborProbabilities | 4.872 | 0.079 | 4.982 | |
calculateSIRSpace | 3.449 | 0.073 | 3.533 | |
calculateVarImpOverlap | 5.600 | 0.153 | 3.270 | |
calculateWassersteinDistance | 2.780 | 0.156 | 2.946 | |
compareCCA | 1.511 | 0.082 | 1.598 | |
comparePCA | 1.516 | 0.051 | 1.574 | |
comparePCASubspace | 1.813 | 0.049 | 1.868 | |
detectAnomaly | 2.974 | 0.085 | 3.131 | |
histQCvsAnnotation | 0.729 | 0.012 | 0.747 | |
plot.calculateWassersteinDistanceObject | 2.238 | 0.110 | 2.364 | |
plotCellTypeMDS | 18.448 | 0.314 | 18.881 | |
plotCellTypePCA | 1.531 | 0.091 | 1.640 | |
plotGeneExpressionDimred | 1.465 | 0.031 | 1.505 | |
plotGeneSetScores | 1.151 | 0.030 | 1.228 | |
plotMarkerExpression | 0.539 | 0.020 | 0.563 | |
plotPairwiseDistancesDensity | 1.963 | 0.175 | 2.153 | |
plotQCvsAnnotation | 0.236 | 0.010 | 0.248 | |
projectPCA | 0.292 | 0.016 | 0.312 | |
projectSIR | 1.347 | 0.023 | 1.378 | |
qc_data | 0.022 | 0.005 | 0.027 | |
query_data | 0.021 | 0.006 | 0.027 | |
reference_data | 0.043 | 0.008 | 0.051 | |
regressPC | 1.937 | 0.132 | 2.087 | |