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This page was generated on 2021-10-15 15:06:34 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the dittoSeq package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 511/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
dittoSeq 1.4.4 (landing page) Daniel Bunis
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: dittoSeq |
Version: 1.4.4 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dittoSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dittoSeq_1.4.4.tar.gz |
StartedAt: 2021-10-14 18:27:59 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 18:39:51 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 711.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: dittoSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dittoSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dittoSeq_1.4.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/dittoSeq.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘dittoSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘dittoSeq’ version ‘1.4.4’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 ... 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 multi_dittoDimPlotVaryCells 14.903 0.052 14.968 dittoHex 12.090 0.085 12.189 dittoFreqPlot 11.902 0.157 12.070 dittoPlot 11.426 0.095 11.532 dittoDimPlot 11.310 0.102 11.426 dittoHeatmap 10.243 0.115 10.378 multi_dittoPlot 9.230 0.079 9.321 multi_dittoDimPlot 8.137 0.034 8.177 dittoScatterPlot 7.714 0.055 7.782 dittoPlotVarsAcrossGroups 5.193 0.086 5.287 dittoBarPlot 5.124 0.088 5.219 gene 5.092 0.112 5.210 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.13-bioc/meat/dittoSeq.Rcheck/00check.log’ for details.
dittoSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL dittoSeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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) > 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 Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, 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 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 716 ] > > proc.time() user system elapsed 322.087 2.348 324.853
dittoSeq.Rcheck/dittoSeq-Ex.timings
name | user | system | elapsed | |
Darken | 0.012 | 0.001 | 0.013 | |
Lighten | 0.002 | 0.000 | 0.004 | |
Simulate | 4.355 | 0.088 | 4.449 | |
addDimReduction | 2.485 | 0.035 | 2.526 | |
addPrcomp | 2.317 | 0.025 | 2.343 | |
demux.SNP.summary | 3.280 | 0.033 | 3.319 | |
demux.calls.summary | 3.861 | 0.032 | 3.902 | |
dittoBarPlot | 5.124 | 0.088 | 5.219 | |
dittoColors | 0.052 | 0.100 | 0.151 | |
dittoDimPlot | 11.310 | 0.102 | 11.426 | |
dittoDotPlot | 4.788 | 0.034 | 4.828 | |
dittoFreqPlot | 11.902 | 0.157 | 12.070 | |
dittoHeatmap | 10.243 | 0.115 | 10.378 | |
dittoHex | 12.090 | 0.085 | 12.189 | |
dittoPlot | 11.426 | 0.095 | 11.532 | |
dittoPlotVarsAcrossGroups | 5.193 | 0.086 | 5.287 | |
dittoScatterPlot | 7.714 | 0.055 | 7.782 | |
gene | 5.092 | 0.112 | 5.210 | |
getGenes | 2.726 | 0.065 | 2.792 | |
getMetas | 1.964 | 0.021 | 1.986 | |
getReductions | 2.693 | 0.024 | 2.718 | |
importDemux | 3.981 | 0.024 | 4.008 | |
importDittoBulk | 2.181 | 0.020 | 2.202 | |
isBulk | 2.084 | 0.017 | 2.102 | |
isGene | 2.097 | 0.020 | 2.117 | |
isMeta | 2.044 | 0.020 | 2.066 | |
meta | 2.405 | 0.029 | 2.436 | |
metaLevels | 2.195 | 0.018 | 2.214 | |
multi_dittoDimPlot | 8.137 | 0.034 | 8.177 | |
multi_dittoDimPlotVaryCells | 14.903 | 0.052 | 14.968 | |
multi_dittoPlot | 9.230 | 0.079 | 9.321 | |
setBulk | 2.480 | 0.023 | 2.504 | |