Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1715/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
regioneR 1.38.0 (landing page) Bernat Gel
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: regioneR |
Version: 1.38.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings regioneR_1.38.0.tar.gz |
StartedAt: 2024-11-20 11:32:50 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 11:42:14 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 564.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: regioneR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings regioneR_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/regioneR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘regioneR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘regioneR’ version ‘1.38.0’ * 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 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 43.045 2.781 45.971 filterChromosomes 41.623 2.821 44.588 maskFromBSGenome 40.212 3.362 40.869 getMask 38.843 2.279 41.206 resampleGenome 13.619 0.448 14.218 localZScore 4.597 0.355 6.647 * 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/regioneR.Rcheck/00check.log’ for details.
regioneR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL regioneR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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, saveRDS, 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 62.063 2.797 64.899
regioneR.Rcheck/regioneR-Ex.timings
name | user | system | elapsed | |
characterToBSGenome | 0.167 | 0.024 | 0.191 | |
circularRandomizeRegions | 43.045 | 2.781 | 45.971 | |
commonRegions | 0.368 | 0.004 | 0.372 | |
createFunctionsList | 0.644 | 0.028 | 0.674 | |
createRandomRegions | 0.272 | 0.016 | 0.288 | |
emptyCacheRegioneR | 0.000 | 0.000 | 0.001 | |
extendRegions | 0.183 | 0.008 | 0.192 | |
filterChromosomes | 41.623 | 2.821 | 44.588 | |
getChromosomesByOrganism | 0.002 | 0.000 | 0.001 | |
getGenome | 0.319 | 0.000 | 0.320 | |
getGenomeAndMask | 0.071 | 0.000 | 0.072 | |
getMask | 38.843 | 2.279 | 41.206 | |
joinRegions | 0.177 | 0.001 | 0.177 | |
listChrTypes | 0.01 | 0.00 | 0.01 | |
localZScore | 4.597 | 0.355 | 6.647 | |
maskFromBSGenome | 40.212 | 3.362 | 40.869 | |
meanDistance | 0.115 | 0.004 | 0.119 | |
meanInRegions | 0.169 | 0.000 | 0.169 | |
mergeRegions | 0.134 | 0.000 | 0.135 | |
numOverlaps | 0.228 | 0.012 | 0.240 | |
overlapGraphicalSummary | 0.127 | 0.000 | 0.128 | |
overlapPermTest | 2.334 | 0.008 | 2.347 | |
overlapRegions | 0.061 | 0.000 | 0.062 | |
permTest | 1.753 | 0.036 | 1.794 | |
plot.localZScoreResults | 1.851 | 0.012 | 1.869 | |
plot.localZScoreResultsList | 3.665 | 0.028 | 3.710 | |
plot.permTestResults | 2.704 | 0.027 | 2.765 | |
plot.permTestResultsList | 2.948 | 0.170 | 3.224 | |
plotRegions | 0.065 | 0.000 | 0.068 | |
print.permTestResults | 1.768 | 0.054 | 1.878 | |
randomizeRegions | 0.305 | 0.035 | 0.349 | |
recomputePermTest | 1.173 | 0.050 | 1.259 | |
resampleGenome | 13.619 | 0.448 | 14.218 | |
resampleRegions | 0.055 | 0.000 | 0.055 | |
splitRegions | 0.102 | 0.000 | 0.102 | |
subtractRegions | 0.233 | 0.004 | 0.238 | |
toDataframe | 0.025 | 0.000 | 0.025 | |
toGRanges | 0.902 | 0.008 | 0.914 | |
uniqueRegions | 0.457 | 0.000 | 0.458 | |