Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:36:18 -0400 (Wed, 17 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 1711/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
regioneR 1.34.0 (landing page) Bernat Gel
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 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: 1.34.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings regioneR_1.34.0.tar.gz |
StartedAt: 2024-04-16 02:52:08 -0400 (Tue, 16 Apr 2024) |
EndedAt: 2024-04-16 03:00:56 -0400 (Tue, 16 Apr 2024) |
EllapsedTime: 528.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: regioneR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings regioneR_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/regioneR.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘regioneR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘regioneR’ version ‘1.34.0’ * 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 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 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 ... 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 circularRandomizeRegions 27.964 4.009 32.113 maskFromBSGenome 25.994 5.408 29.573 filterChromosomes 26.313 4.012 30.326 getMask 23.637 4.036 27.674 resampleGenome 7.884 0.384 8.267 * 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 ... ‘regioneR.Rmd’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/regioneR.Rcheck/00check.log’ for details.
regioneR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL regioneR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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(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, sort, 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 41.572 4.984 46.547
regioneR.Rcheck/regioneR-Ex.timings
name | user | system | elapsed | |
characterToBSGenome | 0.119 | 0.016 | 0.137 | |
circularRandomizeRegions | 27.964 | 4.009 | 32.113 | |
commonRegions | 0.261 | 0.000 | 0.261 | |
createFunctionsList | 0.435 | 0.004 | 0.439 | |
createRandomRegions | 0.19 | 0.00 | 0.19 | |
emptyCacheRegioneR | 0 | 0 | 0 | |
extendRegions | 0.129 | 0.000 | 0.129 | |
filterChromosomes | 26.313 | 4.012 | 30.326 | |
getChromosomesByOrganism | 0.001 | 0.000 | 0.001 | |
getGenome | 0.191 | 0.004 | 0.195 | |
getGenomeAndMask | 0.045 | 0.000 | 0.045 | |
getMask | 23.637 | 4.036 | 27.674 | |
joinRegions | 0.101 | 0.000 | 0.101 | |
listChrTypes | 0.007 | 0.000 | 0.007 | |
localZScore | 2.927 | 0.372 | 4.217 | |
maskFromBSGenome | 25.994 | 5.408 | 29.573 | |
meanDistance | 0.071 | 0.004 | 0.074 | |
meanInRegions | 0.095 | 0.004 | 0.099 | |
mergeRegions | 0.088 | 0.000 | 0.088 | |
numOverlaps | 0.168 | 0.004 | 0.171 | |
overlapGraphicalSummary | 0.078 | 0.004 | 0.081 | |
overlapPermTest | 1.493 | 0.044 | 1.537 | |
overlapRegions | 0.043 | 0.000 | 0.044 | |
permTest | 1.099 | 0.052 | 1.151 | |
plot.localZScoreResults | 1.188 | 0.012 | 1.200 | |
plot.localZScoreResultsList | 2.409 | 0.024 | 2.432 | |
plot.permTestResults | 1.754 | 0.012 | 1.766 | |
plot.permTestResultsList | 1.943 | 0.060 | 2.003 | |
plotRegions | 0.042 | 0.000 | 0.043 | |
print.permTestResults | 1.143 | 0.012 | 1.156 | |
randomizeRegions | 0.201 | 0.000 | 0.201 | |
recomputePermTest | 0.778 | 0.000 | 0.777 | |
resampleGenome | 7.884 | 0.384 | 8.267 | |
resampleRegions | 0.037 | 0.000 | 0.037 | |
splitRegions | 0.066 | 0.000 | 0.067 | |
subtractRegions | 0.158 | 0.004 | 0.162 | |
toDataframe | 0.014 | 0.004 | 0.018 | |
toGRanges | 0.633 | 0.008 | 0.641 | |
uniqueRegions | 0.291 | 0.000 | 0.291 | |