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CHECK report for regioneR on tokay2

This page was generated on 2019-04-09 12:23:33 -0400 (Tue, 09 Apr 2019).

Package 1325/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regioneR 1.15.2
Bernat Gel
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/regioneR
Branch: master
Last Commit: debe68a
Last Changed Date: 2019-02-12 11:30:59 -0400 (Tue, 12 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: regioneR
Version: 1.15.2
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:regioneR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings regioneR_1.15.2.tar.gz
StartedAt: 2019-04-09 05:19:23 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 05:39:27 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 1204.2 seconds
RetCode: 0
Status:  OK  
CheckDir: regioneR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:regioneR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings regioneR_1.15.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/regioneR.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.15.2'
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  print.permTestResults
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* 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 or elapsed time > 5s
                          user system elapsed
circularRandomizeRegions 88.16   3.89   92.06
filterChromosomes        68.14   4.17   72.31
maskFromBSGenome         62.72   2.89   65.63
getMask                  58.03   2.67   60.70
localZScore               3.45   0.08   42.31
plot.localZScoreResults   0.97   0.00    8.58
toGRanges                 0.78   0.13    8.48
permTest                  0.61   0.00   20.81
uniqueRegions             0.25   0.00   13.49
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
maskFromBSGenome         73.12   4.41   77.54
getMask                  66.49   4.42   70.93
filterChromosomes        61.72   4.26   66.00
circularRandomizeRegions 59.98   3.27   63.25
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/regioneR.Rcheck/00check.log'
for details.



Installation output

regioneR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/regioneR_1.15.2.tar.gz && rm -rf regioneR.buildbin-libdir && mkdir regioneR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=regioneR.buildbin-libdir regioneR_1.15.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL regioneR_1.15.2.zip && rm regioneR_1.15.2.tar.gz regioneR_1.15.2.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  995k  100  995k    0     0  7855k      0 --:--:-- --:--:-- --:--:-- 8295k

install for i386

* installing *source* package 'regioneR' ...
** 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_1.15.2.zip
* DONE (regioneR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'regioneR' successfully unpacked and MD5 sums checked

Tests output

regioneR.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, 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")
== testthat results  ===========================================================
OK: 24 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 102.35    5.98  109.12 

regioneR.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, 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")
== testthat results  ===========================================================
OK: 24 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  83.23    5.20   88.51 

Example timings

regioneR.Rcheck/examples_i386/regioneR-Ex.timings

nameusersystemelapsed
characterToBSGenome1.641.172.82
circularRandomizeRegions88.16 3.8992.06
commonRegions0.170.000.18
createFunctionsList1.280.151.43
createRandomRegions0.110.000.11
emptyCacheRegioneR000
extendRegions0.050.000.05
filterChromosomes68.14 4.1772.31
getChromosomesByOrganism000
getGenome0.050.000.04
getGenomeAndMask0.760.110.88
getMask58.03 2.6760.70
joinRegions0.070.002.34
listChrTypes000
localZScore 3.45 0.0842.31
maskFromBSGenome62.72 2.8965.63
meanDistance0.030.000.03
meanInRegions0.060.000.06
mergeRegions0.050.000.69
numOverlaps0.190.000.19
overlapGraphicalSummary0.080.010.09
overlapPermTest0.570.000.58
overlapRegions0.030.000.03
permTest 0.61 0.0020.81
plot.localZScoreResults0.970.008.58
plot.localZScoreResultsList1.770.001.77
plot.permTestResults1.230.001.36
plot.permTestResultsList1.100.001.09
plotRegions0.010.000.02
print.permTestResults0.530.000.53
randomizeRegions0.100.000.09
recomputePermTest0.340.000.41
resampleRegions0.050.000.04
splitRegions0.060.000.07
subtractRegions0.190.000.18
toDataframe000
toGRanges0.780.138.48
uniqueRegions 0.25 0.0013.49

regioneR.Rcheck/examples_x64/regioneR-Ex.timings

nameusersystemelapsed
characterToBSGenome1.890.532.42
circularRandomizeRegions59.98 3.2763.25
commonRegions0.160.000.16
createFunctionsList0.500.150.65
createRandomRegions0.090.000.09
emptyCacheRegioneR000
extendRegions0.060.000.07
filterChromosomes61.72 4.2666.00
getChromosomesByOrganism000
getGenome0.030.020.04
getGenomeAndMask0.810.361.17
getMask66.49 4.4270.93
joinRegions0.080.000.07
listChrTypes0.010.000.02
localZScore3.940.003.94
maskFromBSGenome73.12 4.4177.54
meanDistance0.10.00.1
meanInRegions0.090.000.09
mergeRegions0.050.000.05
numOverlaps0.120.000.12
overlapGraphicalSummary0.050.010.07
overlapPermTest0.530.000.53
overlapRegions0.030.000.03
permTest1.110.001.11
plot.localZScoreResults1.460.001.45
plot.localZScoreResultsList2.170.002.17
plot.permTestResults2.360.312.68
plot.permTestResultsList1.920.001.92
plotRegions0.030.000.03
print.permTestResults1.050.001.05
randomizeRegions0.220.000.21
recomputePermTest0.610.020.62
resampleRegions0.020.000.02
splitRegions0.030.000.03
subtractRegions0.120.000.13
toDataframe0.020.000.01
toGRanges0.690.220.93
uniqueRegions0.470.000.46