Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-21 11:38:24 -0400 (Tue, 21 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4515 |
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 1731/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
regioneR 1.36.0 (landing page) Bernat Gel
| 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 | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the regioneR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/regioneR.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: regioneR |
Version: 1.36.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:regioneR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings regioneR_1.36.0.tar.gz |
StartedAt: 2024-05-20 23:16:40 -0400 (Mon, 20 May 2024) |
EndedAt: 2024-05-20 23:25:30 -0400 (Mon, 20 May 2024) |
EllapsedTime: 530.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: regioneR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:regioneR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings regioneR_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/regioneR.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘regioneR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘regioneR’ version ‘1.36.0’ * 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 ‘regioneR’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘GenomicRanges’ A package should be listed in only one of these fields. * 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed maskFromBSGenome 39.187 5.416 42.233 circularRandomizeRegions 39.422 3.869 43.933 filterChromosomes 39.505 3.297 43.421 getMask 35.879 2.918 39.463 resampleGenome 9.991 1.203 11.328 localZScore 4.269 0.449 6.578 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.19-bioc/meat/regioneR.Rcheck/00check.log’ for details.
regioneR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL regioneR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘regioneR’ ... ** using staged installation ** R ** 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 (regioneR)
regioneR.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "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) > library(regioneR) 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 > > test_check("regioneR") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 89 ] > > proc.time() user system elapsed 58.307 5.493 64.577
regioneR.Rcheck/regioneR-Ex.timings
name | user | system | elapsed | |
characterToBSGenome | 1.690 | 0.986 | 2.783 | |
circularRandomizeRegions | 39.422 | 3.869 | 43.933 | |
commonRegions | 0.339 | 0.003 | 0.345 | |
createFunctionsList | 0.611 | 0.031 | 0.653 | |
createRandomRegions | 0.252 | 0.004 | 0.278 | |
emptyCacheRegioneR | 0.000 | 0.001 | 0.001 | |
extendRegions | 0.175 | 0.004 | 0.185 | |
filterChromosomes | 39.505 | 3.297 | 43.421 | |
getChromosomesByOrganism | 0.001 | 0.001 | 0.001 | |
getGenome | 0.249 | 0.022 | 0.274 | |
getGenomeAndMask | 0.069 | 0.001 | 0.072 | |
getMask | 35.879 | 2.918 | 39.463 | |
joinRegions | 0.149 | 0.002 | 0.152 | |
listChrTypes | 0.010 | 0.000 | 0.011 | |
localZScore | 4.269 | 0.449 | 6.578 | |
maskFromBSGenome | 39.187 | 5.416 | 42.233 | |
meanDistance | 0.107 | 0.002 | 0.110 | |
meanInRegions | 0.107 | 0.001 | 0.108 | |
mergeRegions | 0.127 | 0.002 | 0.131 | |
numOverlaps | 0.221 | 0.002 | 0.229 | |
overlapGraphicalSummary | 0.112 | 0.002 | 0.115 | |
overlapPermTest | 2.091 | 0.022 | 2.133 | |
overlapRegions | 0.056 | 0.001 | 0.060 | |
permTest | 1.478 | 0.018 | 1.512 | |
plot.localZScoreResults | 1.328 | 0.010 | 1.347 | |
plot.localZScoreResultsList | 3.191 | 0.034 | 3.260 | |
plot.permTestResults | 2.421 | 0.031 | 2.477 | |
plot.permTestResultsList | 2.656 | 0.031 | 2.713 | |
plotRegions | 0.052 | 0.002 | 0.054 | |
print.permTestResults | 1.524 | 0.018 | 1.559 | |
randomizeRegions | 0.283 | 0.003 | 0.288 | |
recomputePermTest | 0.997 | 0.012 | 1.019 | |
resampleGenome | 9.991 | 1.203 | 11.328 | |
resampleRegions | 0.052 | 0.001 | 0.053 | |
splitRegions | 0.102 | 0.003 | 0.107 | |
subtractRegions | 0.185 | 0.003 | 0.190 | |
toDataframe | 0.021 | 0.001 | 0.021 | |
toGRanges | 0.769 | 0.070 | 0.849 | |
uniqueRegions | 0.395 | 0.008 | 0.409 | |