Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-17 11:39 -0400 (Mon, 17 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
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 277/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CATALYST 1.31.2 (landing page) Helena L. Crowell
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | |||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | 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: 1.31.2 |
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_1.31.2.tar.gz |
StartedAt: 2025-03-16 18:29:50 -0400 (Sun, 16 Mar 2025) |
EndedAt: 2025-03-16 18:33:28 -0400 (Sun, 16 Mar 2025) |
EllapsedTime: 218.8 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_1.31.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/CATALYST.Rcheck’ * using R Under development (unstable) (2025-03-02 r87868) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CATALYST/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CATALYST’ version ‘1.31.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 24 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: SCE-accessors.Rd: SingleCellExperiment, FlowSOM, ConsensusClusterPlus cluster.Rd: ggplot compCytof.Rd: flowFrame data.Rd: flowSet, flowFrame plotClusterExprs.Rd: ggplot plotCounts.Rd: ggplot plotExprs.Rd: ggplot plotPbExprs.Rd: SingleCellExperiment prepData.Rd: read.FCS 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 ... 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 plotMultiHeatmap 5.23 0.45 4.537 * 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-3.21-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/4.5-arm64/Resources/library’ * installing *source* package ‘CATALYST’ ... ** this is package ‘CATALYST’ version ‘1.31.2’ ** 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 Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" Copyright (C) 2025 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 Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 58.204 4.370 57.007
CATALYST.Rcheck/CATALYST-Ex.timings
name | user | system | elapsed | |
SCE-accessors | 2.494 | 0.328 | 2.857 | |
adaptSpillmat | 1.100 | 0.092 | 1.225 | |
applyCutoffs | 0.864 | 0.043 | 0.909 | |
assignPrelim | 0.468 | 0.011 | 0.480 | |
clrDR | 2.012 | 0.226 | 2.279 | |
cluster | 1.410 | 0.182 | 1.650 | |
compCytof | 2.015 | 0.206 | 2.231 | |
computeSpillmat | 1.043 | 0.075 | 1.122 | |
data | 0.002 | 0.007 | 0.008 | |
estCutoffs | 1.069 | 0.062 | 1.180 | |
extractClusters | 1.390 | 0.338 | 1.782 | |
filterSCE | 1.736 | 0.490 | 2.252 | |
guessPanel | 0.008 | 0.002 | 0.010 | |
mergeClusters | 1.877 | 0.357 | 2.126 | |
normCytof | 0.719 | 0.022 | 0.744 | |
pbMDS | 2.489 | 0.418 | 2.557 | |
plotAbundances | 1.801 | 0.481 | 2.255 | |
plotClusterExprs | 2.226 | 0.381 | 2.456 | |
plotCodes | 2.201 | 0.384 | 2.646 | |
plotCounts | 0.284 | 0.005 | 0.291 | |
plotDR | 4.241 | 0.403 | 4.681 | |
plotDiffHeatmap | 3.771 | 0.507 | 4.021 | |
plotEvents | 0.638 | 0.020 | 0.581 | |
plotExprHeatmap | 3.843 | 0.508 | 3.441 | |
plotExprs | 1.037 | 0.073 | 1.130 | |
plotFreqHeatmap | 2.162 | 0.256 | 2.433 | |
plotMahal | 1.526 | 0.035 | 1.570 | |
plotMultiHeatmap | 5.230 | 0.450 | 4.537 | |
plotNRS | 0.363 | 0.008 | 0.388 | |
plotPbExprs | 4.272 | 0.431 | 4.030 | |
plotScatter | 1.304 | 0.046 | 1.359 | |
plotSpillmat | 1.348 | 0.080 | 1.433 | |
plotYields | 1.531 | 0.097 | 1.667 | |
prepData | 0.378 | 0.028 | 0.407 | |
runDR | 2.181 | 0.015 | 2.198 | |
sce2fcs | 3.164 | 0.394 | 3.572 | |