Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:31 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 UMI4Cats package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/UMI4Cats.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 2120/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
UMI4Cats 1.8.1 (landing page) Mireia Ramos-Rodriguez
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: UMI4Cats |
Version: 1.8.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:UMI4Cats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings UMI4Cats_1.8.1.tar.gz |
StartedAt: 2023-04-10 23:15:02 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 23:20:22 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 319.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: UMI4Cats.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:UMI4Cats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings UMI4Cats_1.8.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/UMI4Cats.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘UMI4Cats/DESCRIPTION’ ... OK * this is package ‘UMI4Cats’ version ‘1.8.1’ * 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 ‘UMI4Cats’ 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 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 UMI4C 4.806 0.185 5.005 * 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: OK
UMI4Cats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL UMI4Cats ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘UMI4Cats’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (UMI4Cats)
UMI4Cats.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 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) > library(UMI4Cats) 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 > library(BSgenome) Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: rtracklayer > > test_check("UMI4Cats") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 22 ] > > proc.time() user system elapsed 22.702 1.151 23.905
UMI4Cats.Rcheck/UMI4Cats-Ex.timings
name | user | system | elapsed | |
UMI4C-methods | 2.684 | 0.062 | 2.748 | |
UMI4C | 4.806 | 0.185 | 5.005 | |
addGrouping | 0.976 | 0.036 | 1.014 | |
alignmentUMI4C | 0 | 0 | 0 | |
callInteractions | 3.044 | 0.142 | 3.214 | |
combineUMI4C | 0.460 | 0.018 | 0.480 | |
contactsUMI4C | 0.002 | 0.000 | 0.002 | |
counterUMI4C | 0.001 | 0.000 | 0.001 | |
createGeneAnnotation | 1.204 | 0.049 | 1.259 | |
darken | 0.000 | 0.000 | 0.001 | |
demultiplexFastq | 0.000 | 0.000 | 0.001 | |
differentialNbinomWaldTestUMI4C | 0.001 | 0.000 | 0.001 | |
digestGenome | 2.601 | 0.132 | 2.738 | |
downloadUMI4CexampleData | 0.000 | 0.000 | 0.001 | |
fisherUMI4C | 1.288 | 0.043 | 1.333 | |
getSignInteractions | 2.767 | 0.128 | 2.900 | |
getViewpointCoordinates | 0.643 | 0.062 | 0.706 | |
makeWindowFragments | 0.360 | 0.009 | 0.370 | |
pipe | 0.005 | 0.002 | 0.006 | |
plotDifferential | 2.561 | 0.093 | 2.662 | |
plotDomainogram | 1.925 | 0.121 | 2.053 | |
plotGenes | 1.403 | 0.018 | 1.424 | |
plotTrend | 0.654 | 0.011 | 0.669 | |
plotUMI4C | 3.025 | 0.076 | 3.112 | |
prepUMI4C | 0 | 0 | 0 | |
splitUMI4C | 0.000 | 0.001 | 0.001 | |
statsUMI4C | 0.725 | 0.012 | 0.742 | |
theme | 0.120 | 0.002 | 0.122 | |
themeXYblank | 0.098 | 0.002 | 0.102 | |
themeXblank | 0.112 | 0.002 | 0.115 | |
themeYblank | 0.083 | 0.001 | 0.085 | |
waldUMI4C | 2.324 | 0.101 | 2.435 | |