Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:37 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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 |
To the developers/maintainers of the CATALYST package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 253/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CATALYST 1.23.5 (landing page) Helena L. Crowell
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: CATALYST |
Version: 1.23.5 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings CATALYST_1.23.5.tar.gz |
StartedAt: 2023-02-27 22:38:57 -0000 (Mon, 27 Feb 2023) |
EndedAt: 2023-02-27 22:56:08 -0000 (Mon, 27 Feb 2023) |
EllapsedTime: 1031.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CATALYST.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings CATALYST_1.23.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CATALYST.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘CATALYST/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CATALYST’ version ‘1.23.5’ * 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 ... 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 ... 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 plotMultiHeatmap 18.695 0.156 18.845 plotPbExprs 18.415 0.080 18.491 plotDiffHeatmap 17.265 0.104 17.371 plotExprHeatmap 15.613 0.168 15.779 plotDR 15.520 0.188 15.704 sce2fcs 14.448 0.120 14.569 plotClusterExprs 11.153 0.112 11.265 pbMDS 10.649 0.128 10.777 plotAbundances 10.327 0.164 10.491 SCE-accessors 9.953 0.372 10.325 plotCodes 9.929 0.064 9.993 clrDR 9.733 0.116 9.850 mergeClusters 9.675 0.140 9.815 plotFreqHeatmap 8.876 0.052 8.928 extractClusters 8.122 0.288 8.411 plotMahal 8.112 0.100 8.212 cluster 7.974 0.048 8.023 filterSCE 7.458 0.116 7.574 compCytof 7.289 0.116 7.405 plotSpillmat 7.215 0.073 7.287 computeSpillmat 6.516 0.448 6.963 plotScatter 5.903 0.028 5.931 adaptSpillmat 5.874 0.043 5.919 estCutoffs 5.617 0.194 5.811 runDR 5.666 0.100 5.760 plotYields 5.507 0.036 5.543 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘differential.Rmd’ using ‘UTF-8’... OK ‘preprocessing.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
CATALYST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CATALYST ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) 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, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' 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 240.675 4.201 244.857
CATALYST.Rcheck/CATALYST-Ex.timings
name | user | system | elapsed | |
SCE-accessors | 9.953 | 0.372 | 10.325 | |
adaptSpillmat | 5.874 | 0.043 | 5.919 | |
applyCutoffs | 4.589 | 0.027 | 4.618 | |
assignPrelim | 2.466 | 0.032 | 2.498 | |
clrDR | 9.733 | 0.116 | 9.850 | |
cluster | 7.974 | 0.048 | 8.023 | |
compCytof | 7.289 | 0.116 | 7.405 | |
computeSpillmat | 6.516 | 0.448 | 6.963 | |
data | 0.005 | 0.006 | 0.010 | |
estCutoffs | 5.617 | 0.194 | 5.811 | |
extractClusters | 8.122 | 0.288 | 8.411 | |
filterSCE | 7.458 | 0.116 | 7.574 | |
guessPanel | 0.042 | 0.000 | 0.042 | |
mergeClusters | 9.675 | 0.140 | 9.815 | |
normCytof | 3.390 | 0.068 | 3.457 | |
pbMDS | 10.649 | 0.128 | 10.777 | |
plotAbundances | 10.327 | 0.164 | 10.491 | |
plotClusterExprs | 11.153 | 0.112 | 11.265 | |
plotCodes | 9.929 | 0.064 | 9.993 | |
plotCounts | 1.521 | 0.028 | 1.549 | |
plotDR | 15.520 | 0.188 | 15.704 | |
plotDiffHeatmap | 17.265 | 0.104 | 17.371 | |
plotEvents | 2.898 | 0.011 | 2.910 | |
plotExprHeatmap | 15.613 | 0.168 | 15.779 | |
plotExprs | 4.734 | 0.060 | 4.794 | |
plotFreqHeatmap | 8.876 | 0.052 | 8.928 | |
plotMahal | 8.112 | 0.100 | 8.212 | |
plotMultiHeatmap | 18.695 | 0.156 | 18.845 | |
plotNRS | 1.967 | 0.012 | 1.979 | |
plotPbExprs | 18.415 | 0.080 | 18.491 | |
plotScatter | 5.903 | 0.028 | 5.931 | |
plotSpillmat | 7.215 | 0.073 | 7.287 | |
plotYields | 5.507 | 0.036 | 5.543 | |
prepData | 2.533 | 0.000 | 2.533 | |
runDR | 5.666 | 0.100 | 5.760 | |
sce2fcs | 14.448 | 0.120 | 14.569 | |