Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-09 17:41 -0400 (Tue, 09 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4709 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
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 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
To the developers/maintainers of the 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: 2024-07-08 01:36:09 -0400 (Mon, 08 Jul 2024) |
EndedAt: 2024-07-08 02:01:37 -0400 (Mon, 08 Jul 2024) |
EllapsedTime: 1527.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CATALYST.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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: x86_64-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 Monterey 12.7.4 * 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 plotPbExprs 32.600 0.926 38.022 plotMultiHeatmap 32.204 0.720 37.684 plotDiffHeatmap 29.821 1.100 35.201 sce2fcs 24.819 0.896 29.067 plotExprHeatmap 23.101 1.028 28.704 plotDR 22.536 0.717 26.514 plotClusterExprs 16.265 0.738 19.240 pbMDS 15.162 0.704 17.632 plotAbundances 14.647 0.688 17.258 plotFreqHeatmap 14.244 0.703 16.853 mergeClusters 14.018 0.554 17.394 plotCodes 13.863 0.625 16.553 plotMahal 14.131 0.180 16.136 clrDR 13.662 0.583 15.972 SCE-accessors 13.040 1.089 18.623 filterSCE 12.343 0.580 14.512 compCytof 12.330 0.415 14.717 estCutoffs 11.935 0.220 13.548 cluster 11.364 0.493 13.657 extractClusters 10.663 0.660 12.693 plotYields 10.546 0.176 12.125 plotScatter 10.440 0.199 11.929 plotSpillmat 10.268 0.166 11.699 adaptSpillmat 9.473 0.292 10.927 computeSpillmat 9.256 0.266 11.029 plotExprs 8.585 0.260 10.593 applyCutoffs 8.590 0.167 9.785 runDR 6.946 0.096 7.950 normCytof 6.021 0.118 7.117 plotEvents 5.711 0.062 6.746 assignPrelim 5.008 0.049 5.635 * 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: 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-x86_64/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
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 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. > 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 0 | WARN 1 | SKIP 0 | PASS 746 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 746 ] > > proc.time() user system elapsed 402.609 11.010 454.503
CATALYST.Rcheck/CATALYST-Ex.timings
name | user | system | elapsed | |
SCE-accessors | 13.040 | 1.089 | 18.623 | |
adaptSpillmat | 9.473 | 0.292 | 10.927 | |
applyCutoffs | 8.590 | 0.167 | 9.785 | |
assignPrelim | 5.008 | 0.049 | 5.635 | |
clrDR | 13.662 | 0.583 | 15.972 | |
cluster | 11.364 | 0.493 | 13.657 | |
compCytof | 12.330 | 0.415 | 14.717 | |
computeSpillmat | 9.256 | 0.266 | 11.029 | |
data | 0.016 | 0.029 | 0.055 | |
estCutoffs | 11.935 | 0.220 | 13.548 | |
extractClusters | 10.663 | 0.660 | 12.693 | |
filterSCE | 12.343 | 0.580 | 14.512 | |
guessPanel | 0.048 | 0.010 | 0.067 | |
mergeClusters | 14.018 | 0.554 | 17.394 | |
normCytof | 6.021 | 0.118 | 7.117 | |
pbMDS | 15.162 | 0.704 | 17.632 | |
plotAbundances | 14.647 | 0.688 | 17.258 | |
plotClusterExprs | 16.265 | 0.738 | 19.240 | |
plotCodes | 13.863 | 0.625 | 16.553 | |
plotCounts | 2.529 | 0.029 | 2.946 | |
plotDR | 22.536 | 0.717 | 26.514 | |
plotDiffHeatmap | 29.821 | 1.100 | 35.201 | |
plotEvents | 5.711 | 0.062 | 6.746 | |
plotExprHeatmap | 23.101 | 1.028 | 28.704 | |
plotExprs | 8.585 | 0.260 | 10.593 | |
plotFreqHeatmap | 14.244 | 0.703 | 16.853 | |
plotMahal | 14.131 | 0.180 | 16.136 | |
plotMultiHeatmap | 32.204 | 0.720 | 37.684 | |
plotNRS | 3.396 | 0.041 | 4.087 | |
plotPbExprs | 32.600 | 0.926 | 38.022 | |
plotScatter | 10.440 | 0.199 | 11.929 | |
plotSpillmat | 10.268 | 0.166 | 11.699 | |
plotYields | 10.546 | 0.176 | 12.125 | |
prepData | 4.303 | 0.053 | 4.905 | |
runDR | 6.946 | 0.096 | 7.950 | |
sce2fcs | 24.819 | 0.896 | 29.067 | |