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This page was generated on 2024-06-19 12:10 -0400 (Wed, 19 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4687
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4402
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4351
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 1682/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regioneR 1.37.0  (landing page)
Bernat Gel
Snapshot Date: 2024-06-18 14:00 -0400 (Tue, 18 Jun 2024)
git_url: https://git.bioconductor.org/packages/regioneR
git_branch: devel
git_last_commit: d6368f7
git_last_commit_date: 2024-04-30 10:42:51 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for regioneR on nebbiolo2

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.

raw results


Summary

Package: regioneR
Version: 1.37.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings regioneR_1.37.0.tar.gz
StartedAt: 2024-06-19 02:47:09 -0400 (Wed, 19 Jun 2024)
EndedAt: 2024-06-19 02:54:54 -0400 (Wed, 19 Jun 2024)
EllapsedTime: 464.9 seconds
RetCode: 0
Status:   OK  
CheckDir: regioneR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings regioneR_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/regioneR.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* 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 ‘1.37.0’
* 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 27.146  4.335  31.715
maskFromBSGenome         24.585  5.160  27.894
filterChromosomes        24.599  4.124  28.723
getMask                  21.580  3.944  25.524
resampleGenome            8.590  0.684   9.274
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/regioneR.Rcheck/00check.log’
for details.


Installation output

regioneR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL regioneR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-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)

Tests output

regioneR.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 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

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 
 39.723   4.992  44.706 

Example timings

regioneR.Rcheck/regioneR-Ex.timings

nameusersystemelapsed
characterToBSGenome0.2420.0080.253
circularRandomizeRegions27.146 4.33531.715
commonRegions0.2470.0000.247
createFunctionsList0.4290.0040.433
createRandomRegions0.1860.0000.186
emptyCacheRegioneR0.0010.0000.001
extendRegions0.1180.0000.118
filterChromosomes24.599 4.12428.723
getChromosomesByOrganism0.0010.0000.001
getGenome0.1800.0040.184
getGenomeAndMask0.0400.0040.044
getMask21.580 3.94425.524
joinRegions0.0940.0040.097
listChrTypes0.0060.0000.007
localZScore2.9850.3524.274
maskFromBSGenome24.585 5.16027.894
meanDistance0.0720.0080.080
meanInRegions0.1020.0040.107
mergeRegions0.0880.0040.092
numOverlaps0.1550.0000.155
overlapGraphicalSummary0.0880.0040.092
overlapPermTest1.4770.0361.513
overlapRegions0.040.000.04
permTest1.0500.0041.054
plot.localZScoreResults1.1320.0071.140
plot.localZScoreResultsList2.2940.0592.353
plot.permTestResults1.6320.0051.636
plot.permTestResultsList1.8400.0071.849
plotRegions0.0350.0000.035
print.permTestResults1.0390.0031.043
randomizeRegions0.2020.0070.210
recomputePermTest0.7490.0320.780
resampleGenome8.5900.6849.274
resampleRegions0.0380.0010.038
splitRegions0.0660.0000.066
subtractRegions0.1470.0070.154
toDataframe0.0160.0000.016
toGRanges0.5630.0280.591
uniqueRegions0.2930.0090.301