Multiple platform build/check report for BioC 3.14 - CHECK results for regioneR on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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: regioneR

Version: 1.26.1

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:regioneR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings regioneR_1.26.1.tar.gz

StartedAt: 2022-04-13 01:26:21 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 01:47:16 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 1255.1 seconds

RetCode: 0

Status: OK

CheckDir: regioneR.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:regioneR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings regioneR_1.26.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/regioneR.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.26.1'
* 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
circularRandomizeRegions 96.13   4.84  101.11
getMask                  94.52   4.43   99.39
filterChromosomes        91.15   4.04   95.49
maskFromBSGenome         90.69   4.28   95.05
localZScore               6.36   0.08    6.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
filterChromosomes        79.61   4.18   83.87
circularRandomizeRegions 78.64   4.38   83.01
getMask                  74.14   4.38   78.60
maskFromBSGenome         73.37   4.12   77.52
localZScore               5.83   0.00    5.82
* 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-3.14-bioc/meat/regioneR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/regioneR_1.26.1.tar.gz && rm -rf regioneR.buildbin-libdir && mkdir regioneR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=regioneR.buildbin-libdir regioneR_1.26.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL regioneR_1.26.1.zip && rm regioneR_1.26.1.tar.gz regioneR_1.26.1.zip
###
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  % 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  995k  100  995k    0     0  1473k      0 --:--:-- --:--:-- --:--:-- 1476k

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_1.26.1.zip
* DONE (regioneR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'regioneR' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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

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, 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 objects are masked from 'package:base':

    I, expand.grid, unname

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 
 103.62    6.89  110.54


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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

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, 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 objects are masked from 'package:base':

    I, expand.grid, unname

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 
 100.73    5.73  106.48

name	user	system	elapsed
characterToBSGenome	1.78	1.36	3.14
circularRandomizeRegions	96.13	4.84	101.11
commonRegions	0.3	0.0	0.3
createFunctionsList	0.54	0.00	0.55
createRandomRegions	0.27	0.00	0.26
emptyCacheRegioneR	0	0	0
extendRegions	0.18	0.00	0.17
filterChromosomes	91.15	4.04	95.49
getChromosomesByOrganism	0.02	0.00	0.01
getGenome	0.29	0.00	0.30
getGenomeAndMask	0.16	0.00	0.15
getMask	94.52	4.43	99.39
joinRegions	0.14	0.00	0.15
listChrTypes	0	0	0
localZScore	6.36	0.08	6.44
maskFromBSGenome	90.69	4.28	95.05
meanDistance	0.08	0.00	0.07
meanInRegions	0.14	0.00	0.14
mergeRegions	0.12	0.00	0.13
numOverlaps	0.24	0.00	0.23
overlapGraphicalSummary	0.11	0.00	0.11
overlapPermTest	2.47	0.00	2.47
overlapRegions	0.06	0.00	0.06
permTest	1.61	0.00	1.61
plot.localZScoreResults	1.78	0.00	1.78
plot.localZScoreResultsList	3.20	0.02	3.22
plot.permTestResults	2.64	0.00	2.64
plot.permTestResultsList	2.36	0.01	2.38
plotRegions	0.05	0.00	0.05
print.permTestResults	1.34	0.00	1.34
randomizeRegions	0.28	0.00	0.28
recomputePermTest	0.85	0.00	0.84
resampleRegions	0.04	0.00	0.05
splitRegions	0.08	0.00	0.08
subtractRegions	0.21	0.00	0.20
toDataframe	0.01	0.00	0.02
toGRanges	0.61	0.05	0.65
uniqueRegions	0.41	0.00	0.41

name	user	system	elapsed
characterToBSGenome	2.91	0.84	3.75
circularRandomizeRegions	78.64	4.38	83.01
commonRegions	0.38	0.00	0.37
createFunctionsList	0.62	0.00	0.63
createRandomRegions	0.3	0.0	0.3
emptyCacheRegioneR	0	0	0
extendRegions	0.2	0.0	0.2
filterChromosomes	79.61	4.18	83.87
getChromosomesByOrganism	0	0	0
getGenome	0.21	0.02	0.22
getGenomeAndMask	0.17	0.00	0.18
getMask	74.14	4.38	78.60
joinRegions	0.12	0.00	0.13
listChrTypes	0.02	0.00	0.02
localZScore	5.83	0.00	5.82
maskFromBSGenome	73.37	4.12	77.52
meanDistance	0.10	0.00	0.09
meanInRegions	0.14	0.00	0.14
mergeRegions	0.12	0.00	0.13
numOverlaps	0.24	0.00	0.23
overlapGraphicalSummary	0.09	0.00	0.10
overlapPermTest	2.12	0.00	2.12
overlapRegions	0.05	0.00	0.04
permTest	1.45	0.00	1.46
plot.localZScoreResults	1.7	0.0	1.7
plot.localZScoreResultsList	3.27	0.00	3.27
plot.permTestResults	3.03	0.05	3.07
plot.permTestResultsList	2.36	0.00	2.36
plotRegions	0.05	0.00	0.05
print.permTestResults	1.39	0.00	1.39
randomizeRegions	0.31	0.00	0.31
recomputePermTest	0.96	0.00	0.95
resampleRegions	0.06	0.00	0.06
splitRegions	0.08	0.00	0.08
subtractRegions	0.22	0.00	0.22
toDataframe	0.03	0.00	0.03
toGRanges	0.69	0.06	0.75
uniqueRegions	0.45	0.00	0.46

CHECK results for regioneR on tokay2

Summary

Command output

Installation output

Tests output

Example timings