Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:07 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 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 277/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CATALYST 1.28.0 (landing page) Helena L. Crowell
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | 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 CATALYST package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CATALYST.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: CATALYST |
Version: 1.28.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CATALYST_1.28.0.tar.gz |
StartedAt: 2024-07-22 14:20:39 -0400 (Mon, 22 Jul 2024) |
EndedAt: 2024-07-22 14:32:50 -0400 (Mon, 22 Jul 2024) |
EllapsedTime: 730.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: CATALYST.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CATALYST_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CATALYST.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 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CATALYST/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CATALYST’ version ‘1.28.0’ * 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 ‘CATALYST’ 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) plotDiffHeatmap.Rd:87: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotDiffHeatmap.Rd:88: Lost braces in \itemize; meant \describe ? * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... 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 plotDR 15.028 1.092 16.211 plotMultiHeatmap 14.135 0.929 15.123 plotPbExprs 12.827 0.689 13.808 plotDiffHeatmap 12.272 0.864 13.292 sce2fcs 11.210 0.895 12.355 plotExprHeatmap 10.551 0.878 11.493 plotAbundances 8.290 0.639 8.969 SCE-accessors 7.772 0.819 8.733 mergeClusters 6.979 0.723 7.754 clrDR 6.696 0.876 7.605 runDR 7.479 0.067 7.674 plotClusterExprs 6.838 0.595 7.468 plotFreqHeatmap 6.066 0.855 6.978 plotCodes 6.280 0.487 6.825 pbMDS 6.002 0.624 6.659 cluster 5.842 0.570 6.443 compCytof 5.987 0.214 6.238 plotYields 5.563 0.202 5.977 filterSCE 5.077 0.572 5.670 plotMahal 5.569 0.080 5.692 estCutoffs 5.429 0.113 5.576 plotSpillmat 5.222 0.161 5.668 plotExprs 4.921 0.159 5.097 extractClusters 4.329 0.685 5.039 plotScatter 4.899 0.107 5.311 * 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: c(y) not identical to c(ms). Objects equal but not identical ── Failure ('test_plotMultiHeatmap.R:58:9'): plotMultiHeatmap() - hm2 = specific state markers ── p@ht_list[[i + 1]]@matrix not identical to meds[[i]]. Objects equal but not identical ── Failure ('test_plotMultiHeatmap.R:58:9'): plotMultiHeatmap() - hm2 = specific state markers ── p@ht_list[[i + 1]]@matrix not identical to meds[[i]]. Objects equal but not identical ── Failure ('test_plotMultiHeatmap.R:58:9'): plotMultiHeatmap() - hm2 = specific state markers ── p@ht_list[[i + 1]]@matrix not identical to meds[[i]]. Objects equal but not identical [ FAIL 6 | WARN 1 | SKIP 0 | PASS 740 ] 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-3.19-bioc/meat/CATALYST.Rcheck/00check.log’ for details.
CATALYST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CATALYST ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘CATALYST’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (CATALYST)
CATALYST.Rcheck/tests/testthat.Rout.fail
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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. > library(testthat) > library(CATALYST) 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 > > test_check("CATALYST") [ FAIL 6 | WARN 1 | SKIP 0 | PASS 740 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_plotDiffHeatmap.R:36:5'): plotDiffHeatmap() - DA ───────────── all(colSums(y) == 1) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test_plotMultiHeatmap.R:26:5'): plotMultiHeatmap() - hm2 = 'abundances' ── all(colSums(y) == 1) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test_plotMultiHeatmap.R:43:5'): plotMultiHeatmap() - hm2 = 'state' ── c(y) not identical to c(ms). Objects equal but not identical ── Failure ('test_plotMultiHeatmap.R:58:9'): plotMultiHeatmap() - hm2 = specific state markers ── p@ht_list[[i + 1]]@matrix not identical to meds[[i]]. Objects equal but not identical ── Failure ('test_plotMultiHeatmap.R:58:9'): plotMultiHeatmap() - hm2 = specific state markers ── p@ht_list[[i + 1]]@matrix not identical to meds[[i]]. Objects equal but not identical ── Failure ('test_plotMultiHeatmap.R:58:9'): plotMultiHeatmap() - hm2 = specific state markers ── p@ht_list[[i + 1]]@matrix not identical to meds[[i]]. Objects equal but not identical [ FAIL 6 | WARN 1 | SKIP 0 | PASS 740 ] Error: Test failures Execution halted
CATALYST.Rcheck/CATALYST-Ex.timings
name | user | system | elapsed | |
SCE-accessors | 7.772 | 0.819 | 8.733 | |
adaptSpillmat | 3.740 | 0.167 | 3.949 | |
applyCutoffs | 3.278 | 0.101 | 3.395 | |
assignPrelim | 1.712 | 0.023 | 1.743 | |
clrDR | 6.696 | 0.876 | 7.605 | |
cluster | 5.842 | 0.570 | 6.443 | |
compCytof | 5.987 | 0.214 | 6.238 | |
computeSpillmat | 4.042 | 0.144 | 4.206 | |
data | 0.008 | 0.018 | 0.028 | |
estCutoffs | 5.429 | 0.113 | 5.576 | |
extractClusters | 4.329 | 0.685 | 5.039 | |
filterSCE | 5.077 | 0.572 | 5.670 | |
guessPanel | 0.039 | 0.005 | 0.045 | |
mergeClusters | 6.979 | 0.723 | 7.754 | |
normCytof | 2.764 | 0.063 | 2.842 | |
pbMDS | 6.002 | 0.624 | 6.659 | |
plotAbundances | 8.290 | 0.639 | 8.969 | |
plotClusterExprs | 6.838 | 0.595 | 7.468 | |
plotCodes | 6.280 | 0.487 | 6.825 | |
plotCounts | 1.089 | 0.014 | 1.114 | |
plotDR | 15.028 | 1.092 | 16.211 | |
plotDiffHeatmap | 12.272 | 0.864 | 13.292 | |
plotEvents | 2.039 | 0.023 | 2.070 | |
plotExprHeatmap | 10.551 | 0.878 | 11.493 | |
plotExprs | 4.921 | 0.159 | 5.097 | |
plotFreqHeatmap | 6.066 | 0.855 | 6.978 | |
plotMahal | 5.569 | 0.080 | 5.692 | |
plotMultiHeatmap | 14.135 | 0.929 | 15.123 | |
plotNRS | 1.381 | 0.021 | 1.407 | |
plotPbExprs | 12.827 | 0.689 | 13.808 | |
plotScatter | 4.899 | 0.107 | 5.311 | |
plotSpillmat | 5.222 | 0.161 | 5.668 | |
plotYields | 5.563 | 0.202 | 5.977 | |
prepData | 2.005 | 0.055 | 2.116 | |
runDR | 7.479 | 0.067 | 7.674 | |
sce2fcs | 11.210 | 0.895 | 12.355 | |