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CHECK report for regioneR on tokay1

This page was generated on 2021-05-06 12:33:10 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the regioneR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1497/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regioneR 1.22.0  (landing page)
Bernat Gel
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/regioneR
Branch: RELEASE_3_12
Last Commit: fb28e1a
Last Changed Date: 2020-10-27 11:04:09 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: regioneR
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:regioneR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings regioneR_1.22.0.tar.gz
StartedAt: 2021-05-06 06:04:55 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:27:58 -0400 (Thu, 06 May 2021)
EllapsedTime: 1383.4 seconds
RetCode: 0
Status:   OK   
CheckDir: regioneR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:regioneR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings regioneR_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/regioneR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'regioneR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'regioneR' version '1.22.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
maskFromBSGenome         115.20   5.24  120.45
circularRandomizeRegions 107.12   5.86  113.00
getMask                  100.18   5.11  105.33
filterChromosomes         95.57   4.59  100.22
localZScore                5.84   0.04    5.89
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
filterChromosomes        89.80   4.41   94.69
circularRandomizeRegions 88.27   4.49   92.97
maskFromBSGenome         83.18   4.47   87.80
getMask                  78.45   4.31   82.78
localZScore               5.91   0.00    5.91
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/regioneR.Rcheck/00check.log'
for details.



Installation output

regioneR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/regioneR_1.22.0.tar.gz && rm -rf regioneR.buildbin-libdir && mkdir regioneR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=regioneR.buildbin-libdir regioneR_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL regioneR_1.22.0.zip && rm regioneR_1.22.0.tar.gz regioneR_1.22.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  992k  100  992k    0     0  35.6M      0 --:--:-- --:--:-- --:--:-- 37.2M

install for i386

* installing *source* package 'regioneR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'regioneR'
    finding HTML links ... done
    characterToBSGenome                     html  
    finding level-2 HTML links ... done

    circularRandomizeRegions                html  
    commonRegions                           html  
    createFunctionsList                     html  
    createRandomRegions                     html  
    emptyCacheRegioneR                      html  
    extendRegions                           html  
    filterChromosomes                       html  
    getChromosomesByOrganism                html  
    getGenome                               html  
    getGenomeAndMask                        html  
    getMask                                 html  
    joinRegions                             html  
    listChrTypes                            html  
    localZScore                             html  
    maskFromBSGenome                        html  
    meanDistance                            html  
    meanInRegions                           html  
    mergeRegions                            html  
    numOverlaps                             html  
    overlapGraphicalSummary                 html  
    overlapPermTest                         html  
    overlapRegions                          html  
    permTest                                html  
    plot.localZScoreResults                 html  
    plot.localZScoreResultsList             html  
    plot.permTestResults                    html  
    plot.permTestResultsList                html  
    plotRegions                             html  
    print.permTestResults                   html  
    randomizeRegions                        html  
    recomputePermTest                       html  
    resampleRegions                         html  
    splitRegions                            html  
    subtractRegions                         html  
    summary.permTestResults                 html  
    summary.permTestResultsList             html  
    toDataframe                             html  
    toGRanges                               html  
    uniqueRegions                           html  
** 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

install for x64

* installing *source* package 'regioneR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'regioneR' as regioneR_1.22.0.zip
* DONE (regioneR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'regioneR' successfully unpacked and MD5 sums checked

Tests output

regioneR.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
> 
> test_check("regioneR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 89 ]
> 
> proc.time()
   user  system elapsed 
 136.25    8.29  144.64 

regioneR.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
> 
> test_check("regioneR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 89 ]
> 
> proc.time()
   user  system elapsed 
 100.12    5.79  105.93 

Example timings

regioneR.Rcheck/examples_i386/regioneR-Ex.timings

nameusersystemelapsed
characterToBSGenome2.081.513.59
circularRandomizeRegions107.12 5.86113.00
commonRegions0.290.000.29
createFunctionsList0.470.020.49
createRandomRegions0.190.000.18
emptyCacheRegioneR000
extendRegions0.130.000.13
filterChromosomes 95.57 4.59100.22
getChromosomesByOrganism000
getGenome0.210.000.20
getGenomeAndMask0.070.020.09
getMask100.18 5.11105.33
joinRegions0.140.000.14
listChrTypes000
localZScore5.840.045.89
maskFromBSGenome115.20 5.24120.45
meanDistance0.160.000.16
meanInRegions0.170.000.17
mergeRegions0.120.000.13
numOverlaps0.210.000.20
overlapGraphicalSummary0.090.000.09
overlapPermTest1.870.001.88
overlapRegions0.070.000.06
permTest2.150.002.16
plot.localZScoreResults1.820.001.81
plot.localZScoreResultsList2.870.032.91
plot.permTestResults2.550.002.54
plot.permTestResultsList2.830.002.83
plotRegions0.040.000.05
print.permTestResults1.360.001.36
randomizeRegions0.330.000.33
recomputePermTest0.970.000.97
resampleRegions0.050.000.05
splitRegions0.070.000.07
subtractRegions0.240.000.24
toDataframe0.010.000.01
toGRanges0.910.050.95
uniqueRegions0.480.000.49

regioneR.Rcheck/examples_x64/regioneR-Ex.timings

nameusersystemelapsed
characterToBSGenome1.430.792.23
circularRandomizeRegions88.27 4.4992.97
commonRegions0.280.000.28
createFunctionsList0.50.00.5
createRandomRegions0.20.00.2
emptyCacheRegioneR000
extendRegions0.140.000.14
filterChromosomes89.80 4.4194.69
getChromosomesByOrganism000
getGenome0.240.010.25
getGenomeAndMask0.110.000.11
getMask78.45 4.3182.78
joinRegions0.110.000.11
listChrTypes000
localZScore5.910.005.91
maskFromBSGenome83.18 4.4787.80
meanDistance0.100.000.09
meanInRegions0.110.000.11
mergeRegions0.090.000.09
numOverlaps0.190.000.19
overlapGraphicalSummary0.110.000.11
overlapPermTest1.820.001.83
overlapRegions0.050.000.04
permTest1.490.001.49
plot.localZScoreResults1.450.001.45
plot.localZScoreResultsList2.840.002.85
plot.permTestResults2.070.002.06
plot.permTestResultsList2.260.012.28
plotRegions0.050.000.05
print.permTestResults1.360.001.36
randomizeRegions0.270.000.27
recomputePermTest0.920.000.92
resampleRegions0.050.000.05
splitRegions0.080.000.07
subtractRegions0.210.000.22
toDataframe0.020.000.02
toGRanges0.700.030.75
uniqueRegions0.440.000.44