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This page was generated on 2024-05-04 11:37:03 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1731/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regioneR 1.36.0  (landing page)
Bernat Gel
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/regioneR
git_branch: RELEASE_3_19
git_last_commit: 9563be5
git_last_commit_date: 2024-04-30 10:42:51 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for regioneR on nebbiolo1


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: 1.36.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings regioneR_1.36.0.tar.gz
StartedAt: 2024-05-04 02:51:23 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 02:59:27 -0400 (Sat, 04 May 2024)
EllapsedTime: 483.6 seconds
RetCode: 0
Status:   OK  
CheckDir: regioneR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings regioneR_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/regioneR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* 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 ‘1.36.0’
* 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 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 28.857  6.889  35.829
maskFromBSGenome         25.657  6.499  30.173
filterChromosomes        25.337  5.585  30.923
getMask                  22.229  5.527  27.756
resampleGenome            7.967  0.568   8.535
* 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-3.19-bioc/meat/regioneR.Rcheck/00check.log’
for details.


Installation output

regioneR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL regioneR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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 beta (2024-04-15 r86425) -- "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 
 41.755   6.642  48.396 

Example timings

regioneR.Rcheck/regioneR-Ex.timings

nameusersystemelapsed
characterToBSGenome0.2620.0280.292
circularRandomizeRegions28.857 6.88935.829
commonRegions0.2620.0000.262
createFunctionsList0.4630.0080.470
createRandomRegions0.2080.0000.207
emptyCacheRegioneR0.0010.0000.000
extendRegions0.1180.0000.118
filterChromosomes25.337 5.58530.923
getChromosomesByOrganism0.0010.0000.001
getGenome0.1730.0230.197
getGenomeAndMask0.0480.0000.049
getMask22.229 5.52727.756
joinRegions0.0940.0040.099
listChrTypes0.0070.0000.007
localZScore3.0430.3784.408
maskFromBSGenome25.657 6.49930.173
meanDistance0.0700.0000.071
meanInRegions0.0910.0000.091
mergeRegions0.0810.0000.082
numOverlaps0.1460.0000.146
overlapGraphicalSummary0.0810.0000.082
overlapPermTest1.4720.0201.491
overlapRegions0.0390.0030.042
permTest1.1090.0281.138
plot.localZScoreResults1.1970.0281.226
plot.localZScoreResultsList2.3790.0002.379
plot.permTestResults1.710.001.71
plot.permTestResultsList1.8820.0121.894
plotRegions0.0340.0030.038
print.permTestResults1.0930.0001.094
randomizeRegions0.2200.0040.223
recomputePermTest0.7780.0600.839
resampleGenome7.9670.5688.535
resampleRegions0.0370.0000.037
splitRegions0.0650.0000.065
subtractRegions0.1530.0000.153
toDataframe0.0220.0040.026
toGRanges0.5790.0270.606
uniqueRegions0.3390.0010.338