| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-22 12:04 -0400 (Wed, 22 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4890 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4680 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4625 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 1755/2355 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| regioneR 1.41.3 (landing page) Bernat Gel
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
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: 1.41.3 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings regioneR_1.41.3.tar.gz |
| StartedAt: 2025-10-22 03:52:38 -0400 (Wed, 22 Oct 2025) |
| EndedAt: 2025-10-22 04:00:47 -0400 (Wed, 22 Oct 2025) |
| EllapsedTime: 488.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: regioneR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings regioneR_1.41.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/regioneR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘regioneR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘regioneR’ version ‘1.41.3’
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
characterToBSGenome.Rd: BSgenome
circularRandomizeRegions.Rd: GenomicRanges, BSgenome
commonRegions.Rd: GenomicRanges
createRandomRegions.Rd: GenomicRanges, BSgenome
extendRegions.Rd: GenomicRanges
filterChromosomes.Rd: GenomicRanges, BSgenome, GRanges
getGenome.Rd: BSgenome, GRanges, memoise, forget
getGenomeAndMask.Rd: BSgenome, memoise, forget
getMask.Rd: BSgenome, GRanges, memoise, forget
joinRegions.Rd: GenomicRanges, reduce
localZScore.Rd: GenomicRanges
maskFromBSGenome.Rd: BSgenome, GRanges, memoise, forget
meanDistance.Rd: GenomicRanges
meanInRegions.Rd: GenomicRanges
mergeRegions.Rd: GenomicRanges, reduce
numOverlaps.Rd: GenomicRanges
overlapGraphicalSummary.Rd: GenomicRanges
overlapPermTest.Rd: GenomicRanges
overlapRegions.Rd: GenomicRanges, countOverlaps
permTest.Rd: GenomicRanges
randomizeRegions.Rd: GenomicRanges, BSgenome
resampleGenome.Rd: GenomicRanges
resampleRegions.Rd: GenomicRanges
splitRegions.Rd: GenomicRanges
subtractRegions.Rd: GenomicRanges
toDataframe.Rd: GRanges
toGRanges.Rd: GRanges, BSgenome
uniqueRegions.Rd: GenomicRanges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 31.116 4.618 35.796
maskFromBSGenome 29.191 5.757 32.949
filterChromosomes 29.005 4.215 33.221
getMask 27.037 4.136 31.174
resampleGenome 7.694 0.433 8.128
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/regioneR.Rcheck/00check.log’
for details.
regioneR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL regioneR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘regioneR’ ... ** this is package ‘regioneR’ version ‘1.41.3’ ** 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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo
>
> test_check("regioneR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 89 ]
>
> proc.time()
user system elapsed
44.825 5.435 50.251
regioneR.Rcheck/regioneR-Ex.timings
| name | user | system | elapsed | |
| characterToBSGenome | 0.119 | 0.009 | 0.130 | |
| circularRandomizeRegions | 31.116 | 4.618 | 35.796 | |
| commonRegions | 0.248 | 0.000 | 0.247 | |
| createFunctionsList | 0.412 | 0.003 | 0.415 | |
| createRandomRegions | 0.188 | 0.000 | 0.188 | |
| emptyCacheRegioneR | 0.001 | 0.000 | 0.001 | |
| extendRegions | 0.119 | 0.000 | 0.119 | |
| filterChromosomes | 29.005 | 4.215 | 33.221 | |
| getChromosomesByOrganism | 0.001 | 0.000 | 0.001 | |
| getGenome | 0.191 | 0.002 | 0.192 | |
| getGenomeAndMask | 0.045 | 0.000 | 0.045 | |
| getMask | 27.037 | 4.136 | 31.174 | |
| joinRegions | 0.112 | 0.001 | 0.113 | |
| listChrTypes | 0.005 | 0.002 | 0.007 | |
| localZScore | 2.994 | 0.412 | 4.442 | |
| maskFromBSGenome | 29.191 | 5.757 | 32.949 | |
| meanDistance | 0.075 | 0.004 | 0.080 | |
| meanInRegions | 0.113 | 0.000 | 0.113 | |
| mergeRegions | 0.086 | 0.001 | 0.086 | |
| numOverlaps | 0.153 | 0.002 | 0.154 | |
| overlapGraphicalSummary | 0.082 | 0.001 | 0.083 | |
| overlapPermTest | 1.563 | 0.054 | 1.618 | |
| overlapRegions | 0.04 | 0.00 | 0.04 | |
| permTest | 1.125 | 0.010 | 1.135 | |
| plot.localZScoreResults | 1.226 | 0.008 | 1.234 | |
| plot.localZScoreResultsList | 2.433 | 0.007 | 2.439 | |
| plot.permTestResults | 1.737 | 0.014 | 1.752 | |
| plot.permTestResultsList | 1.960 | 0.033 | 1.994 | |
| plotRegions | 0.037 | 0.001 | 0.038 | |
| print.permTestResults | 1.100 | 0.029 | 1.129 | |
| randomizeRegions | 0.217 | 0.006 | 0.223 | |
| recomputePermTest | 0.773 | 0.026 | 0.799 | |
| resampleGenome | 7.694 | 0.433 | 8.128 | |
| resampleRegions | 0.036 | 0.000 | 0.036 | |
| splitRegions | 0.071 | 0.000 | 0.072 | |
| subtractRegions | 0.180 | 0.001 | 0.181 | |
| toDataframe | 0.016 | 0.000 | 0.016 | |
| toGRanges | 0.617 | 0.042 | 0.659 | |
| uniqueRegions | 0.288 | 0.005 | 0.293 | |