Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-27 11:39:04 -0400 (Wed, 27 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4698 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4436 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4461 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4376 |
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 274/2264 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CATALYST 1.27.1 (landing page) Helena L. Crowell
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
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: 1.27.1 |
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_1.27.1.tar.gz |
StartedAt: 2024-03-26 19:23:06 -0400 (Tue, 26 Mar 2024) |
EndedAt: 2024-03-26 19:35:25 -0400 (Tue, 26 Mar 2024) |
EllapsedTime: 739.5 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_1.27.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CATALYST.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * 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 ‘1.27.1’ * 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 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 ... NOTE checkRd: (-1) assignPrelim.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) assignPrelim.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) assignPrelim.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly 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 plotMultiHeatmap 15.516 1.176 16.903 plotPbExprs 15.119 1.184 16.454 plotDiffHeatmap 14.049 1.301 15.532 sce2fcs 12.619 1.260 14.096 plotDR 12.674 1.168 13.990 plotExprHeatmap 10.673 1.190 12.002 plotAbundances 7.502 1.089 8.710 plotFreqHeatmap 7.141 1.187 8.451 plotClusterExprs 7.203 0.848 8.147 pbMDS 6.867 1.149 8.160 SCE-accessors 6.922 1.050 8.038 plotCodes 6.942 0.990 8.028 clrDR 6.555 0.932 7.584 mergeClusters 6.566 0.834 7.481 cluster 6.081 0.973 7.186 filterSCE 6.041 0.969 7.074 compCytof 6.439 0.329 6.833 extractClusters 5.402 1.141 6.607 plotMahal 5.902 0.104 6.070 runDR 5.217 0.130 5.404 plotSpillmat 5.035 0.278 5.372 * 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: The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > > test_check("CATALYST") [ FAIL 1 | WARN 3 | SKIP 0 | PASS 741 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_plotScatter.R:39:5'): plotScatter() - color_by ─────────────── p$guides$colour inherits from `'NULL'` not `'character'`. [ FAIL 1 | WARN 3 | SKIP 0 | PASS 741 ] 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, 2 NOTEs 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.fail
R Under development (unstable) (2024-03-18 r86148) -- "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 1 | WARN 3 | SKIP 0 | PASS 741 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_plotScatter.R:39:5'): plotScatter() - color_by ─────────────── p$guides$colour inherits from `'NULL'` not `'character'`. [ FAIL 1 | WARN 3 | SKIP 0 | PASS 741 ] Error: Test failures Execution halted
CATALYST.Rcheck/CATALYST-Ex.timings
name | user | system | elapsed | |
SCE-accessors | 6.922 | 1.050 | 8.038 | |
adaptSpillmat | 4.119 | 0.180 | 4.319 | |
applyCutoffs | 3.599 | 0.113 | 3.743 | |
assignPrelim | 1.830 | 0.023 | 1.871 | |
clrDR | 6.555 | 0.932 | 7.584 | |
cluster | 6.081 | 0.973 | 7.186 | |
compCytof | 6.439 | 0.329 | 6.833 | |
computeSpillmat | 3.942 | 0.189 | 4.167 | |
data | 0.008 | 0.014 | 0.023 | |
estCutoffs | 4.592 | 0.132 | 4.764 | |
extractClusters | 5.402 | 1.141 | 6.607 | |
filterSCE | 6.041 | 0.969 | 7.074 | |
guessPanel | 0.024 | 0.005 | 0.029 | |
mergeClusters | 6.566 | 0.834 | 7.481 | |
normCytof | 3.594 | 0.181 | 3.811 | |
pbMDS | 6.867 | 1.149 | 8.160 | |
plotAbundances | 7.502 | 1.089 | 8.710 | |
plotClusterExprs | 7.203 | 0.848 | 8.147 | |
plotCodes | 6.942 | 0.990 | 8.028 | |
plotCounts | 1.233 | 0.016 | 1.265 | |
plotDR | 12.674 | 1.168 | 13.990 | |
plotDiffHeatmap | 14.049 | 1.301 | 15.532 | |
plotEvents | 2.290 | 0.040 | 2.352 | |
plotExprHeatmap | 10.673 | 1.190 | 12.002 | |
plotExprs | 3.682 | 0.162 | 3.878 | |
plotFreqHeatmap | 7.141 | 1.187 | 8.451 | |
plotMahal | 5.902 | 0.104 | 6.070 | |
plotMultiHeatmap | 15.516 | 1.176 | 16.903 | |
plotNRS | 1.476 | 0.028 | 1.522 | |
plotPbExprs | 15.119 | 1.184 | 16.454 | |
plotScatter | 4.769 | 0.129 | 4.951 | |
plotSpillmat | 5.035 | 0.278 | 5.372 | |
plotYields | 4.711 | 0.161 | 4.938 | |
prepData | 2.159 | 0.058 | 2.242 | |
runDR | 5.217 | 0.130 | 5.404 | |
sce2fcs | 12.619 | 1.260 | 14.096 | |