Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:40:39 -0400 (Thu, 28 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" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 582/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
dittoSeq 1.15.6 (landing page) Daniel Bunis
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | 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 dittoSeq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dittoSeq.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: dittoSeq |
Version: 1.15.6 |
Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:dittoSeq.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings dittoSeq_1.15.6.tar.gz |
StartedAt: 2024-03-28 04:49:26 -0000 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 05:00:36 -0000 (Thu, 28 Mar 2024) |
EllapsedTime: 669.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: dittoSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:dittoSeq.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings dittoSeq_1.15.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/dittoSeq.Rcheck’ * using R Under development (unstable) (2024-03-19 r86153) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 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 ‘dittoSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘dittoSeq’ version ‘1.15.6’ * 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 ‘dittoSeq’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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) Darken.Rd:10: Lost braces 10 | \item{colors}{the color(s) input. Can be a list of colors, for example, /code{dittoColors()}.} | ^ checkRd: (-1) Lighten.Rd:10: Lost braces 10 | \item{colors}{the color(s) input. Can be a list of colors, for example, /code{dittoColors()}.} | ^ * 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 dittoPlot 16.313 0.139 16.485 multi_dittoDimPlotVaryCells 15.150 0.283 15.464 dittoHex 14.580 0.136 14.742 dittoDimPlot 12.580 0.207 12.811 dittoFreqPlot 10.697 0.064 10.780 multi_dittoPlot 9.473 0.108 9.601 dittoScatterPlot 9.502 0.048 9.569 dittoDotPlot 8.081 0.092 8.189 multi_dittoDimPlot 5.908 0.004 5.925 dittoPlotVarsAcrossGroups 5.660 0.020 5.688 gene 5.116 0.136 5.263 * 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 ‘/home/biocbuild/bbs-3.19-bioc/meat/dittoSeq.Rcheck/00check.log’ for details.
dittoSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL dittoSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’ * installing *source* package ‘dittoSeq’ ... ** 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 (dittoSeq)
dittoSeq.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 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) > test_check("dittoSeq") Loading required package: dittoSeq Loading required package: ggplot2 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 [ FAIL 0 | WARN 106 | SKIP 0 | PASS 838 ] [ FAIL 0 | WARN 106 | SKIP 0 | PASS 838 ] > > proc.time() user system elapsed 281.301 2.958 284.860
dittoSeq.Rcheck/dittoSeq-Ex.timings
name | user | system | elapsed | |
Darken | 0.011 | 0.000 | 0.011 | |
Lighten | 0.003 | 0.000 | 0.003 | |
Simulate | 3.331 | 0.124 | 3.461 | |
addDimReduction | 1.664 | 0.036 | 1.704 | |
addPrcomp | 1.630 | 0.012 | 1.646 | |
demux.SNP.summary | 2.498 | 0.008 | 2.511 | |
demux.calls.summary | 2.907 | 0.036 | 2.948 | |
dittoBarPlot | 4.475 | 0.088 | 4.572 | |
dittoColors | 0.007 | 0.012 | 0.019 | |
dittoDimPlot | 12.580 | 0.207 | 12.811 | |
dittoDotPlot | 8.081 | 0.092 | 8.189 | |
dittoFreqPlot | 10.697 | 0.064 | 10.780 | |
dittoHeatmap | 4.336 | 0.064 | 4.413 | |
dittoHex | 14.580 | 0.136 | 14.742 | |
dittoPlot | 16.313 | 0.139 | 16.485 | |
dittoPlotVarsAcrossGroups | 5.660 | 0.020 | 5.688 | |
dittoScatterPlot | 9.502 | 0.048 | 9.569 | |
gene | 5.116 | 0.136 | 5.263 | |
getGenes | 1.359 | 0.008 | 1.370 | |
getMetas | 1.213 | 0.000 | 1.216 | |
getReductions | 1.585 | 0.012 | 1.600 | |
importDemux | 3.189 | 0.012 | 3.207 | |
importDittoBulk | 1.277 | 0.008 | 1.287 | |
isBulk | 1.345 | 0.004 | 1.351 | |
isGene | 1.314 | 0.004 | 1.320 | |
isMeta | 1.170 | 0.000 | 1.173 | |
meta | 1.283 | 0.008 | 1.294 | |
metaLevels | 1.199 | 0.012 | 1.213 | |
multi_dittoDimPlot | 5.908 | 0.004 | 5.925 | |
multi_dittoDimPlotVaryCells | 15.150 | 0.283 | 15.464 | |
multi_dittoPlot | 9.473 | 0.108 | 9.601 | |
setBulk | 1.492 | 0.012 | 1.507 | |