Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-10 11:37:56 -0400 (Fri, 10 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4662 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4393 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4424 |
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 570/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
dittoSeq 1.17.0 (landing page) Daniel Bunis
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
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. |
Package: dittoSeq |
Version: 1.17.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dittoSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dittoSeq_1.17.0.tar.gz |
StartedAt: 2024-05-09 03:23:14 -0400 (Thu, 09 May 2024) |
EndedAt: 2024-05-09 03:44:40 -0400 (Thu, 09 May 2024) |
EllapsedTime: 1286.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: dittoSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dittoSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dittoSeq_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/dittoSeq.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘dittoSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘dittoSeq’ version ‘1.17.0’ * 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 ‘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 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 dittoHex 22.200 0.327 29.258 dittoPlot 21.261 0.300 27.813 multi_dittoDimPlotVaryCells 17.707 0.344 22.294 dittoDimPlot 15.990 0.287 20.591 dittoFreqPlot 15.316 0.250 19.721 dittoScatterPlot 13.732 0.184 17.429 dittoDotPlot 12.193 0.165 17.124 multi_dittoPlot 11.958 0.197 15.166 gene 8.720 0.396 11.441 multi_dittoDimPlot 8.987 0.103 11.707 dittoHeatmap 7.430 0.300 10.712 dittoPlotVarsAcrossGroups 7.017 0.179 9.407 dittoBarPlot 6.742 0.253 9.143 Simulate 5.079 0.298 6.728 demux.calls.summary 4.738 0.075 6.200 importDemux 4.395 0.074 5.776 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/dittoSeq.Rcheck/00check.log’ for details.
dittoSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL dittoSeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 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) > 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 846 ] [ FAIL 0 | WARN 106 | SKIP 0 | PASS 846 ] > > proc.time() user system elapsed 441.574 6.125 546.611
dittoSeq.Rcheck/dittoSeq-Ex.timings
name | user | system | elapsed | |
Darken | 0.015 | 0.003 | 0.026 | |
Lighten | 0.005 | 0.001 | 0.008 | |
Simulate | 5.079 | 0.298 | 6.728 | |
addDimReduction | 2.546 | 0.069 | 3.236 | |
addPrcomp | 2.526 | 0.055 | 3.221 | |
demux.SNP.summary | 3.719 | 0.069 | 4.911 | |
demux.calls.summary | 4.738 | 0.075 | 6.200 | |
dittoBarPlot | 6.742 | 0.253 | 9.143 | |
dittoColors | 0.065 | 0.161 | 0.274 | |
dittoDimPlot | 15.990 | 0.287 | 20.591 | |
dittoDotPlot | 12.193 | 0.165 | 17.124 | |
dittoFreqPlot | 15.316 | 0.250 | 19.721 | |
dittoHeatmap | 7.430 | 0.300 | 10.712 | |
dittoHex | 22.200 | 0.327 | 29.258 | |
dittoPlot | 21.261 | 0.300 | 27.813 | |
dittoPlotVarsAcrossGroups | 7.017 | 0.179 | 9.407 | |
dittoScatterPlot | 13.732 | 0.184 | 17.429 | |
gene | 8.720 | 0.396 | 11.441 | |
getGenes | 2.073 | 0.113 | 2.700 | |
getMetas | 1.893 | 0.045 | 2.398 | |
getReductions | 2.686 | 0.060 | 3.520 | |
importDemux | 4.395 | 0.074 | 5.776 | |
importDittoBulk | 1.994 | 0.043 | 2.643 | |
isBulk | 1.995 | 0.047 | 2.697 | |
isGene | 2.096 | 0.041 | 2.833 | |
isMeta | 1.883 | 0.040 | 2.515 | |
meta | 1.990 | 0.054 | 2.770 | |
metaLevels | 1.869 | 0.039 | 2.499 | |
multi_dittoDimPlot | 8.987 | 0.103 | 11.707 | |
multi_dittoDimPlotVaryCells | 17.707 | 0.344 | 22.294 | |
multi_dittoPlot | 11.958 | 0.197 | 15.166 | |
setBulk | 2.435 | 0.051 | 3.061 | |