Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1857/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scater 1.34.0 (landing page) Alan O'Callaghan
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
To the developers/maintainers of the scater package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scater.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: scater |
Version: 1.34.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scater.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scater_1.34.0.tar.gz |
StartedAt: 2024-12-21 08:04:54 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 08:13:35 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 520.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: scater.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scater.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scater_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scater.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scater/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scater’ version ‘1.34.0’ * 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 ‘scater’ 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotReducedDim 9.404 0.446 8.701 plotRLE 9.046 0.224 9.389 runMultiUMAP 6.563 0.054 6.662 projectReducedDim 5.787 0.050 5.863 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: reducedDim(ref, "TSNE") not identical to reducedDim(alt, "TSNE"). Objects equal but not identical ── Failure ('test-red-dim.R:324:5'): runTSNE works with externally computed nearest neighbor results ── reducedDim(ref, "TSNE") not identical to reducedDim(alt, "TSNE"). Objects equal but not identical ── Failure ('test-red-dim.R:329:5'): runTSNE works with externally computed nearest neighbor results ── reducedDim(ref, "TSNE") not identical to reducedDim(alt, "TSNE"). Objects equal but not identical ── Failure ('test-red-dim.R:333:5'): runTSNE works with externally computed nearest neighbor results ── reducedDim(ref, "TSNE") not identical to reducedDim(alt, "TSNE"). Objects equal but not identical [ FAIL 6 | WARN 1 | SKIP 0 | PASS 796 ] Error: Test failures Execution halted * 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 ERROR See ‘/Users/biocbuild/bbs-3.20-bioc/meat/scater.Rcheck/00check.log’ for details.
scater.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scater ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘scater’ ... ** using staged installation ** R ** 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 (scater)
scater.Rcheck/tests/testthat.Rout.fail
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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. > Sys.setenv("R_TESTS" = "") > library(testthat) > library(scater) Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: scuttle Loading required package: ggplot2 > > test_check("scater") Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Loading required package: S4Arrays Loading required package: abind Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: SparseArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep [ FAIL 6 | WARN 1 | SKIP 0 | PASS 796 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-red-dim.R:312:5'): runTSNE works with externally computed nearest neighbor results ── reducedDim(ref, "TSNE") not identical to reducedDim(alt, "TSNE"). Objects equal but not identical ── Failure ('test-red-dim.R:316:5'): runTSNE works with externally computed nearest neighbor results ── reducedDim(ref, "TSNE") not identical to reducedDim(alt, "TSNE"). Objects equal but not identical ── Failure ('test-red-dim.R:320:5'): runTSNE works with externally computed nearest neighbor results ── reducedDim(ref, "TSNE") not identical to reducedDim(alt, "TSNE"). Objects equal but not identical ── Failure ('test-red-dim.R:324:5'): runTSNE works with externally computed nearest neighbor results ── reducedDim(ref, "TSNE") not identical to reducedDim(alt, "TSNE"). Objects equal but not identical ── Failure ('test-red-dim.R:329:5'): runTSNE works with externally computed nearest neighbor results ── reducedDim(ref, "TSNE") not identical to reducedDim(alt, "TSNE"). Objects equal but not identical ── Failure ('test-red-dim.R:333:5'): runTSNE works with externally computed nearest neighbor results ── reducedDim(ref, "TSNE") not identical to reducedDim(alt, "TSNE"). Objects equal but not identical [ FAIL 6 | WARN 1 | SKIP 0 | PASS 796 ] Error: Test failures Execution halted
scater.Rcheck/scater-Ex.timings
name | user | system | elapsed | |
accessors | 1.698 | 0.025 | 1.729 | |
annotateBMFeatures | 0 | 0 | 0 | |
bootstraps | 0.304 | 0.004 | 0.308 | |
defunct | 0.001 | 0.000 | 0.001 | |
getExplanatoryPCs | 0.839 | 0.015 | 0.856 | |
getVarianceExplained | 0.461 | 0.009 | 0.472 | |
ggsce | 1.967 | 0.050 | 2.031 | |
nexprs | 1.128 | 0.013 | 1.144 | |
plotColData | 3.304 | 0.100 | 3.370 | |
plotDots | 2.509 | 0.045 | 2.573 | |
plotExplanatoryPCs | 1.022 | 0.019 | 1.044 | |
plotExplanatoryVariables | 0.657 | 0.011 | 0.670 | |
plotExpression | 4.206 | 0.081 | 4.250 | |
plotGroupedHeatmap | 0.639 | 0.016 | 0.659 | |
plotHeatmap | 0.593 | 0.015 | 0.611 | |
plotHighestExprs | 1.043 | 0.038 | 1.095 | |
plotPlatePosition | 0.998 | 0.023 | 1.026 | |
plotRLE | 9.046 | 0.224 | 9.389 | |
plotReducedDim | 9.404 | 0.446 | 8.701 | |
plotRowData | 0.577 | 0.022 | 0.602 | |
plotScater | 3.767 | 0.208 | 3.986 | |
plot_reddim | 3.334 | 0.052 | 3.399 | |
projectReducedDim | 5.787 | 0.050 | 5.863 | |
retrieveCellInfo | 0.394 | 0.016 | 0.420 | |
retrieveFeatureInfo | 0.428 | 0.016 | 0.447 | |
runColDataPCA | 0.594 | 0.008 | 0.602 | |
runMDS | 0.499 | 0.015 | 0.515 | |
runMultiUMAP | 6.563 | 0.054 | 6.662 | |
runNMF | 0.481 | 0.011 | 0.493 | |
runPCA | 0.697 | 0.011 | 0.710 | |
runTSNE | 1.298 | 0.021 | 1.323 | |
runUMAP | 4.625 | 0.031 | 4.670 | |
toSingleCellExperiment | 0.000 | 0.001 | 0.000 | |