Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 1822/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scater 1.33.1 (landing page) Alan O'Callaghan
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 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: 1.33.1 |
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_1.33.1.tar.gz |
StartedAt: 2024-06-11 07:20:12 -0400 (Tue, 11 Jun 2024) |
EndedAt: 2024-06-11 07:29:19 -0400 (Tue, 11 Jun 2024) |
EllapsedTime: 547.0 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_1.33.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scater.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scater/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scater’ version ‘1.33.1’ * 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 ... NOTE checkRd: (-1) plotHeatmap.Rd:87: Lost braces; missing escapes or markup? 87 | \item{by_exprs_values}{Alias to {by.assay.type}.} | ^ * 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 10.865 0.444 10.130 plotRLE 8.198 0.240 8.473 runMultiUMAP 7.168 0.057 7.284 projectReducedDim 6.443 0.072 6.534 * 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 795 ] 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, 1 NOTE 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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 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, 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 795 ] ══ 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 795 ] Error: Test failures Execution halted
scater.Rcheck/scater-Ex.timings
name | user | system | elapsed | |
accessors | 2.000 | 0.034 | 2.040 | |
annotateBMFeatures | 0.000 | 0.001 | 0.000 | |
bootstraps | 0.481 | 0.007 | 0.489 | |
defunct | 0.000 | 0.000 | 0.001 | |
getExplanatoryPCs | 1.926 | 0.050 | 1.986 | |
getVarianceExplained | 0.645 | 0.010 | 0.657 | |
ggsce | 2.172 | 0.075 | 2.260 | |
nexprs | 0.469 | 0.007 | 0.495 | |
plotColData | 4.551 | 0.103 | 4.621 | |
plotDots | 1.905 | 0.031 | 1.946 | |
plotExplanatoryPCs | 1.328 | 0.018 | 1.350 | |
plotExplanatoryVariables | 1.743 | 0.020 | 1.773 | |
plotExpression | 4.410 | 0.096 | 4.481 | |
plotGroupedHeatmap | 0.854 | 0.017 | 0.877 | |
plotHeatmap | 0.786 | 0.016 | 0.806 | |
plotHighestExprs | 1.268 | 0.030 | 1.312 | |
plotPlatePosition | 1.204 | 0.031 | 1.239 | |
plotRLE | 8.198 | 0.240 | 8.473 | |
plotReducedDim | 10.865 | 0.444 | 10.130 | |
plotRowData | 0.787 | 0.021 | 0.812 | |
plotScater | 3.038 | 0.203 | 3.259 | |
plot_reddim | 3.320 | 0.082 | 3.457 | |
projectReducedDim | 6.443 | 0.072 | 6.534 | |
retrieveCellInfo | 0.654 | 0.017 | 0.673 | |
retrieveFeatureInfo | 0.596 | 0.008 | 0.606 | |
runColDataPCA | 0.910 | 0.014 | 0.926 | |
runMDS | 0.764 | 0.013 | 0.780 | |
runMultiUMAP | 7.168 | 0.057 | 7.284 | |
runNMF | 0.748 | 0.015 | 0.766 | |
runPCA | 1.016 | 0.021 | 1.044 | |
runTSNE | 1.562 | 0.019 | 1.587 | |
runUMAP | 4.898 | 0.037 | 4.952 | |
toSingleCellExperiment | 0 | 0 | 0 | |