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CHECK report for breakpointR on tokay1

This page was generated on 2020-08-13 11:44:26 -0400 (Thu, 13 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE breakpointR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 196/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
breakpointR 1.7.1
David Porubsky
Snapshot Date: 2020-08-12 14:52:00 -0400 (Wed, 12 Aug 2020)
URL: https://git.bioconductor.org/packages/breakpointR
Branch: master
Last Commit: 30030d4
Last Changed Date: 2020-06-03 19:12:11 -0400 (Wed, 03 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: breakpointR
Version: 1.7.1
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:breakpointR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings breakpointR_1.7.1.tar.gz
StartedAt: 2020-08-13 05:17:56 -0400 (Thu, 13 Aug 2020)
EndedAt: 2020-08-13 05:25:07 -0400 (Thu, 13 Aug 2020)
EllapsedTime: 431.3 seconds
RetCode: 0
Status:  OK  
CheckDir: breakpointR.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:breakpointR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings breakpointR_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/breakpointR.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'breakpointR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'breakpointR' version '1.7.1'
* 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 'breakpointR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
genotyping         15.22   0.80   16.01
hotspotter          9.20   0.25    9.45
synchronizeReadDir  8.43   0.11    8.53
exportRegions       3.08   0.09    5.08
breakSeekr          2.21   0.23    5.05
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
genotyping         16.89   0.98   17.88
hotspotter         11.02   0.14   11.16
synchronizeReadDir  8.50   0.09    8.59
runBreakpointr      5.15   0.05    5.20
* 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: OK


Installation output

breakpointR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/breakpointR_1.7.1.tar.gz && rm -rf breakpointR.buildbin-libdir && mkdir breakpointR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=breakpointR.buildbin-libdir breakpointR_1.7.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL breakpointR_1.7.1.zip && rm breakpointR_1.7.1.tar.gz breakpointR_1.7.1.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  739k  100  739k    0     0  13.6M      0 --:--:-- --:--:-- --:--:-- 14.7M

install for i386

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

    breakSeekr                              html  
    breakpointR-package                     html  
    breakpointr                             html  
    breakpointr2UCSC                        html  
    collapseBins                            html  
    confidenceInterval                      html  
    confidenceInterval.binomial             html  
    createCompositeFile                     html  
    deltaWCalculator                        html  
    deltaWCalculatorVariousWindows          html  
    exportRegions                           html  
    genotype.binom                          html  
    genotype.fisher                         html  
    genotyping                              html  
    hotspotter                              html  
    insertchr                               html  
    loadFromFiles                           html  
    plotBreakpoints                         html  
    plotBreakpointsPerChr                   html  
    plotHeatmap                             html  
    ranges2UCSC                             html  
    readBamFileAsGRanges                    html  
    readConfig                              html  
    removeDoubleSCEs                        html  
    runBreakpointr                          html  
    summarizeBreaks                         html  
    synchronizeReadDir                      html  
    transCoord                              html  
    writeConfig                             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 'breakpointR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'breakpointR' as breakpointR_1.7.1.zip
* DONE (breakpointR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'breakpointR' successfully unpacked and MD5 sums checked

Tests output

breakpointR.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(breakpointR)
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
Loading required package: cowplot

********************************************************
Note: As of version 1.0.0, cowplot does not change the
  default ggplot2 theme anymore. To recover the previous
  behavior, execute:
  theme_set(theme_cowplot())
********************************************************

Loading required package: breakpointRdata
> 
> test_check("breakpointR") 
== testthat results  ===========================================================
[ OK: 5 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  16.60    0.84   17.43 

breakpointR.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(breakpointR)
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
Loading required package: cowplot

********************************************************
Note: As of version 1.0.0, cowplot does not change the
  default ggplot2 theme anymore. To recover the previous
  behavior, execute:
  theme_set(theme_cowplot())
********************************************************

Loading required package: breakpointRdata
> 
> test_check("breakpointR") 
== testthat results  ===========================================================
[ OK: 5 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  24.42    0.51   24.92 

Example timings

breakpointR.Rcheck/examples_i386/breakpointR-Ex.timings

nameusersystemelapsed
breakSeekr2.210.235.05
breakpointr000
breakpointr2UCSC1.280.052.16
confidenceInterval000
confidenceInterval.binomial000
deltaWCalculator1.390.051.44
exportRegions3.080.095.08
genotyping15.22 0.8016.01
hotspotter9.200.259.45
loadFromFiles1.790.051.84
plotBreakpoints2.690.152.85
plotBreakpointsPerChr2.710.032.73
plotHeatmap2.590.242.83
ranges2UCSC0.310.010.58
readBamFileAsGRanges0.270.030.29
runBreakpointr3.560.213.77
summarizeBreaks0.370.010.39
synchronizeReadDir8.430.118.53

breakpointR.Rcheck/examples_x64/breakpointR-Ex.timings

nameusersystemelapsed
breakSeekr3.190.033.38
breakpointr000
breakpointr2UCSC1.110.021.13
confidenceInterval000
confidenceInterval.binomial000
deltaWCalculator0.640.010.66
exportRegions3.160.053.20
genotyping16.89 0.9817.88
hotspotter11.02 0.1411.16
loadFromFiles1.700.071.76
plotBreakpoints2.660.042.71
plotBreakpointsPerChr3.550.053.59
plotHeatmap3.620.113.75
ranges2UCSC0.380.050.42
readBamFileAsGRanges0.280.010.30
runBreakpointr5.150.055.20
summarizeBreaks0.320.000.31
synchronizeReadDir8.500.098.59