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CHECK report for chromswitch on tokay1

This page was generated on 2019-04-13 11:28:33 -0400 (Sat, 13 Apr 2019).

Package 260/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromswitch 1.4.1
Selin Jessa
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/chromswitch
Branch: RELEASE_3_8
Last Commit: 0f4b655
Last Changed Date: 2019-01-04 13:25:32 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chromswitch
Version: 1.4.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chromswitch.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings chromswitch_1.4.1.tar.gz
StartedAt: 2019-04-13 01:13:10 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:18:21 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 311.3 seconds
RetCode: 0
Status:  OK  
CheckDir: chromswitch.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chromswitch.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings chromswitch_1.4.1.tar.gz
###
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##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/chromswitch.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chromswitch/DESCRIPTION' ... OK
* this is package 'chromswitch' version '1.4.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'chromswitch' 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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

chromswitch.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/chromswitch_1.4.1.tar.gz && rm -rf chromswitch.buildbin-libdir && mkdir chromswitch.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chromswitch.buildbin-libdir chromswitch_1.4.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL chromswitch_1.4.1.zip && rm chromswitch_1.4.1.tar.gz chromswitch_1.4.1.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 1569k  100 1569k    0     0  27.5M      0 --:--:-- --:--:-- --:--:-- 29.4M

install for i386

* installing *source* package 'chromswitch' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'chromswitch'
    finding HTML links ... done
    GRangesToCoord                          html  
    H3K4me3                                 html  
    LocalPeaks-class                        html  
    NMI                                     html  
    binarizePeaks                           html  
    callBinary                              html  
    callSummary                             html  
    chromswitch                             html  
    classEntropy                            html  
    cluster                                 html  
    clusterEntropy                          html  
    completeness                            html  
    conditionalClassEntropy                 html  
    conditionalClusterEntropy               html  
    coordToGRanges                          html  
    filterPeaks                             html  
    homogeneity                             html  
    makeBrowserCoord                        html  
    normalizePeaks                          html  
    pReciprocalOverlap                      html  
    purity                                  html  
    readNarrowPeak                          html  
    reducePeaks                             html  
    retrievePeaks                           html  
    summarizePeaks                          html  
    vMeasure                                html  
    winsorNorm                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'chromswitch' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chromswitch' as chromswitch_1.4.1.zip
* DONE (chromswitch)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'chromswitch' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

chromswitch.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(chromswitch)
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, lengths, 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("chromswitch")
== testthat results  ===========================================================
OK: 55 SKIPPED: 10 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   9.67    0.71   10.37 

chromswitch.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(chromswitch)
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, lengths, 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("chromswitch")
== testthat results  ===========================================================
OK: 55 SKIPPED: 10 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  10.87    0.50   11.37 

Example timings

chromswitch.Rcheck/examples_i386/chromswitch-Ex.timings

nameusersystemelapsed
GRangesToCoord0.050.020.06
LocalPeaks-class0.280.120.40
NMI000
binarizePeaks1.260.021.28
callBinary2.520.052.56
callSummary0.980.061.25
classEntropy000
cluster0.550.020.57
clusterEntropy000
completeness000
conditionalClassEntropy0.010.000.01
conditionalClusterEntropy000
coordToGRanges0.020.000.02
filterPeaks0.230.000.23
homogeneity0.020.000.02
makeBrowserCoord000
normalizePeaks0.20.00.2
pReciprocalOverlap0.050.000.05
purity000
readNarrowPeak0.500.000.64
reducePeaks1.150.001.16
retrievePeaks0.190.000.19
summarizePeaks0.280.100.39
vMeasure000
winsorNorm000

chromswitch.Rcheck/examples_x64/chromswitch-Ex.timings

nameusersystemelapsed
GRangesToCoord0.050.000.05
LocalPeaks-class0.260.030.29
NMI000
binarizePeaks1.090.051.14
callBinary2.770.052.81
callSummary1.480.031.52
classEntropy000
cluster0.360.050.40
clusterEntropy000
completeness000
conditionalClassEntropy000
conditionalClusterEntropy000
coordToGRanges0.020.000.02
filterPeaks0.150.000.16
homogeneity000
makeBrowserCoord000
normalizePeaks0.140.000.14
pReciprocalOverlap0.030.000.03
purity000
readNarrowPeak0.320.000.31
reducePeaks0.210.000.22
retrievePeaks0.190.000.19
summarizePeaks0.300.000.29
vMeasure000
winsorNorm000