Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:16 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (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

CHECK results for breakpointR on tokay2


To the developers/maintainers of the breakpointR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/breakpointR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 214/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
breakpointR 1.12.0  (landing page)
David Porubsky
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/breakpointR
git_branch: RELEASE_3_14
git_last_commit: 1624453
git_last_commit_date: 2021-10-26 12:46:54 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: breakpointR
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:breakpointR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings breakpointR_1.12.0.tar.gz
StartedAt: 2022-04-12 16:36:41 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 16:43:16 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 394.6 seconds
RetCode: 0
Status:   OK  
CheckDir: breakpointR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:breakpointR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings breakpointR_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/breakpointR.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 'breakpointR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'breakpointR' version '1.12.0'
* 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         13.22   1.03   14.25
hotspotter          8.41   0.33    8.74
synchronizeReadDir  5.79   0.12    5.93
exportRegions       3.18   0.12    8.62
breakSeekr          1.92   0.28    7.32
breakpointr2UCSC    1.22   0.03    7.52
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
genotyping         12.24   0.47   12.70
hotspotter          8.00   0.12    8.12
synchronizeReadDir  6.44   0.18    6.63
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/breakpointR_1.12.0.tar.gz && rm -rf breakpointR.buildbin-libdir && mkdir breakpointR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=breakpointR.buildbin-libdir breakpointR_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL breakpointR_1.12.0.zip && rm breakpointR_1.12.0.tar.gz breakpointR_1.12.0.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  736k  100  736k    0     0   585k      0  0:00:01  0:00:01 --:--:--  585k
100  736k  100  736k    0     0   585k      0  0:00:01  0:00:01 --:--:--  585k

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  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/breakpointR.buildbin-libdir/00LOCK-breakpointR/00new/breakpointR/help/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  
    removeReadPileupSpikes                  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_1.12.0.zip
* DONE (breakpointR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'breakpointR' successfully unpacked and MD5 sums checked

Tests output

breakpointR.Rcheck/tests_i386/testthat.Rout


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(breakpointR)
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
Loading required package: cowplot
Loading required package: breakpointRdata
> 
> test_check("breakpointR") 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
  18.76    0.70   19.43 

breakpointR.Rcheck/tests_x64/testthat.Rout


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(breakpointR)
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
Loading required package: cowplot
Loading required package: breakpointRdata
> 
> test_check("breakpointR") 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
  17.95    0.50   18.43 

Example timings

breakpointR.Rcheck/examples_i386/breakpointR-Ex.timings

nameusersystemelapsed
breakSeekr1.920.287.32
breakpointr000
breakpointr2UCSC1.220.037.52
confidenceInterval000
confidenceInterval.binomial000
deltaWCalculator1.270.021.28
exportRegions3.180.128.62
genotyping13.22 1.0314.25
hotspotter8.410.338.74
loadFromFiles1.660.081.73
plotBreakpoints2.150.282.44
plotBreakpointsPerChr2.960.083.03
plotHeatmap2.500.092.61
ranges2UCSC0.350.000.36
readBamFileAsGRanges0.210.020.22
removeReadPileupSpikes1.720.091.81
runBreakpointr3.230.083.31
summarizeBreaks0.270.020.28
synchronizeReadDir5.790.125.93

breakpointR.Rcheck/examples_x64/breakpointR-Ex.timings

nameusersystemelapsed
breakSeekr1.890.172.06
breakpointr000
breakpointr2UCSC0.840.000.84
confidenceInterval000
confidenceInterval.binomial000
deltaWCalculator0.530.020.55
exportRegions2.750.112.86
genotyping12.24 0.4712.70
hotspotter8.000.128.12
loadFromFiles1.560.081.64
plotBreakpoints2.550.092.65
plotBreakpointsPerChr2.140.072.20
plotHeatmap2.650.002.65
ranges2UCSC0.300.010.32
readBamFileAsGRanges0.170.020.18
removeReadPileupSpikes1.580.161.73
runBreakpointr3.280.033.32
summarizeBreaks0.220.050.26
synchronizeReadDir6.440.186.63