Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-06 11:44 -0400 (Sat, 06 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4643 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3833 |
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 272/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CATALYST 1.29.1 (landing page) Helena L. Crowell
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: CATALYST |
Version: 1.29.1 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CATALYST_1.29.1.tar.gz |
StartedAt: 2024-07-06 03:35:04 -0000 (Sat, 06 Jul 2024) |
EndedAt: 2024-07-06 03:48:50 -0000 (Sat, 06 Jul 2024) |
EllapsedTime: 825.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CATALYST.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CATALYST_1.29.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CATALYST.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CATALYST/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CATALYST’ version ‘1.29.1’ * 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 ‘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 loading without being on the library search path ... 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 18.775 0.116 18.927 plotMultiHeatmap 18.176 0.028 18.240 plotDiffHeatmap 17.440 0.100 17.580 plotDR 15.240 0.071 15.352 sce2fcs 15.100 0.076 15.209 plotExprHeatmap 13.182 0.095 13.302 plotClusterExprs 10.874 0.036 10.934 clrDR 10.595 0.180 10.805 pbMDS 10.242 0.096 10.358 plotAbundances 9.701 0.056 9.778 mergeClusters 9.327 0.060 9.414 plotFreqHeatmap 9.292 0.095 9.409 plotCodes 9.264 0.096 9.378 SCE-accessors 8.696 0.292 9.009 compCytof 8.521 0.079 8.621 filterSCE 7.985 0.080 8.084 extractClusters 7.487 0.028 7.534 plotMahal 7.442 0.027 7.488 cluster 6.686 0.080 6.782 computeSpillmat 6.561 0.136 6.713 runDR 6.152 0.024 6.184 plotSpillmat 6.069 0.044 6.126 estCutoffs 6.017 0.032 6.064 adaptSpillmat 5.881 0.107 6.003 plotYields 5.857 0.028 5.899 plotScatter 5.667 0.076 5.756 plotExprs 5.110 0.092 5.215 * 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/CATALYST.Rcheck/00check.log’ for details.
CATALYST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL CATALYST ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-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: aarch64-unknown-linux-gnu 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 242.764 2.167 245.423
CATALYST.Rcheck/CATALYST-Ex.timings
name | user | system | elapsed | |
SCE-accessors | 8.696 | 0.292 | 9.009 | |
adaptSpillmat | 5.881 | 0.107 | 6.003 | |
applyCutoffs | 4.488 | 0.040 | 4.537 | |
assignPrelim | 2.437 | 0.016 | 2.458 | |
clrDR | 10.595 | 0.180 | 10.805 | |
cluster | 6.686 | 0.080 | 6.782 | |
compCytof | 8.521 | 0.079 | 8.621 | |
computeSpillmat | 6.561 | 0.136 | 6.713 | |
data | 0.008 | 0.000 | 0.008 | |
estCutoffs | 6.017 | 0.032 | 6.064 | |
extractClusters | 7.487 | 0.028 | 7.534 | |
filterSCE | 7.985 | 0.080 | 8.084 | |
guessPanel | 0.029 | 0.008 | 0.038 | |
mergeClusters | 9.327 | 0.060 | 9.414 | |
normCytof | 3.230 | 0.027 | 3.265 | |
pbMDS | 10.242 | 0.096 | 10.358 | |
plotAbundances | 9.701 | 0.056 | 9.778 | |
plotClusterExprs | 10.874 | 0.036 | 10.934 | |
plotCodes | 9.264 | 0.096 | 9.378 | |
plotCounts | 1.407 | 0.000 | 1.409 | |
plotDR | 15.240 | 0.071 | 15.352 | |
plotDiffHeatmap | 17.44 | 0.10 | 17.58 | |
plotEvents | 2.788 | 0.016 | 2.810 | |
plotExprHeatmap | 13.182 | 0.095 | 13.302 | |
plotExprs | 5.110 | 0.092 | 5.215 | |
plotFreqHeatmap | 9.292 | 0.095 | 9.409 | |
plotMahal | 7.442 | 0.027 | 7.488 | |
plotMultiHeatmap | 18.176 | 0.028 | 18.240 | |
plotNRS | 1.835 | 0.020 | 1.859 | |
plotPbExprs | 18.775 | 0.116 | 18.927 | |
plotScatter | 5.667 | 0.076 | 5.756 | |
plotSpillmat | 6.069 | 0.044 | 6.126 | |
plotYields | 5.857 | 0.028 | 5.899 | |
prepData | 2.387 | 0.000 | 2.393 | |
runDR | 6.152 | 0.024 | 6.184 | |
sce2fcs | 15.100 | 0.076 | 15.209 | |