Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-02-18 02:28:16 -0500 (Sun, 18 Feb 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4657 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4397 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4424 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4400 |
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 273/2244 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CATALYST 1.27.0 (landing page) Helena L. Crowell
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.27.0 |
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_1.27.0.tar.gz |
StartedAt: 2024-02-17 01:09:12 -0500 (Sat, 17 Feb 2024) |
EndedAt: 2024-02-17 01:33:41 -0500 (Sat, 17 Feb 2024) |
EllapsedTime: 1469.1 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_1.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CATALYST.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CATALYST/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CATALYST’ version ‘1.27.0’ * 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 R 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 ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.cluster_cols’ * 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 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 29.704 0.819 34.003 plotMultiHeatmap 29.826 0.631 33.905 plotDiffHeatmap 26.577 0.713 31.215 sce2fcs 23.792 0.818 27.560 plotDR 21.719 0.603 25.168 plotExprHeatmap 21.195 0.676 25.253 pbMDS 15.696 0.749 18.713 plotAbundances 15.393 0.693 17.958 clrDR 14.301 0.675 16.872 plotClusterExprs 14.216 0.501 16.627 plotCodes 14.021 0.557 15.883 mergeClusters 13.885 0.574 16.228 plotFreqHeatmap 13.610 0.777 17.513 SCE-accessors 12.388 0.974 14.980 plotMahal 12.566 0.161 14.310 cluster 11.850 0.603 15.072 filterSCE 11.434 0.662 12.724 compCytof 11.513 0.287 13.172 extractClusters 10.404 0.583 12.170 plotScatter 10.005 0.201 11.458 plotSpillmat 9.727 0.204 11.381 estCutoffs 9.741 0.174 11.117 computeSpillmat 9.522 0.227 10.940 plotYields 9.476 0.150 10.901 adaptSpillmat 8.935 0.283 10.305 plotExprs 8.807 0.187 10.343 applyCutoffs 7.965 0.163 8.927 runDR 6.583 0.100 7.422 normCytof 5.756 0.140 7.384 plotEvents 5.497 0.061 6.475 assignPrelim 4.754 0.041 5.178 * 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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 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 741 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 741 ] > > proc.time() user system elapsed 382.256 9.681 439.765
CATALYST.Rcheck/CATALYST-Ex.timings
name | user | system | elapsed | |
SCE-accessors | 12.388 | 0.974 | 14.980 | |
adaptSpillmat | 8.935 | 0.283 | 10.305 | |
applyCutoffs | 7.965 | 0.163 | 8.927 | |
assignPrelim | 4.754 | 0.041 | 5.178 | |
clrDR | 14.301 | 0.675 | 16.872 | |
cluster | 11.850 | 0.603 | 15.072 | |
compCytof | 11.513 | 0.287 | 13.172 | |
computeSpillmat | 9.522 | 0.227 | 10.940 | |
data | 0.016 | 0.030 | 0.054 | |
estCutoffs | 9.741 | 0.174 | 11.117 | |
extractClusters | 10.404 | 0.583 | 12.170 | |
filterSCE | 11.434 | 0.662 | 12.724 | |
guessPanel | 0.048 | 0.009 | 0.061 | |
mergeClusters | 13.885 | 0.574 | 16.228 | |
normCytof | 5.756 | 0.140 | 7.384 | |
pbMDS | 15.696 | 0.749 | 18.713 | |
plotAbundances | 15.393 | 0.693 | 17.958 | |
plotClusterExprs | 14.216 | 0.501 | 16.627 | |
plotCodes | 14.021 | 0.557 | 15.883 | |
plotCounts | 2.642 | 0.027 | 2.992 | |
plotDR | 21.719 | 0.603 | 25.168 | |
plotDiffHeatmap | 26.577 | 0.713 | 31.215 | |
plotEvents | 5.497 | 0.061 | 6.475 | |
plotExprHeatmap | 21.195 | 0.676 | 25.253 | |
plotExprs | 8.807 | 0.187 | 10.343 | |
plotFreqHeatmap | 13.610 | 0.777 | 17.513 | |
plotMahal | 12.566 | 0.161 | 14.310 | |
plotMultiHeatmap | 29.826 | 0.631 | 33.905 | |
plotNRS | 3.153 | 0.031 | 3.613 | |
plotPbExprs | 29.704 | 0.819 | 34.003 | |
plotScatter | 10.005 | 0.201 | 11.458 | |
plotSpillmat | 9.727 | 0.204 | 11.381 | |
plotYields | 9.476 | 0.150 | 10.901 | |
prepData | 3.990 | 0.049 | 4.424 | |
runDR | 6.583 | 0.100 | 7.422 | |
sce2fcs | 23.792 | 0.818 | 27.560 | |