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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CNVMetrics.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CNVMetrics_0.99.3.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CNVMetrics.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNVMetrics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNVMetrics' version '0.99.3'
* 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 'CNVMetrics' 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
* 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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CNVMetrics
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'CNVMetrics' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CNVMetrics'
    finding HTML links ... done
    CNVMetrics-package                      html  
    calculateJaccard                        html  
    calculateLog2ratioMetric                html  
    calculateOneLog2valueMetricT            html  
    calculateOneOverlapMetricT              html  
    calculateOverlapMetric                  html  
    calculateSorensen                       html  
    calculateSzymkiewicz                    html  
    calculateWeightedEuclideanDistanceFor2Samples
                                            html  
    createDisjoinSegmentsForTwoSamples      html  
    is.CNVMetric                            html  
    plotMetric                              html  
    plotOneMetric                           html  
    print.CNVMetric                         html  
    validateCalculateOverlapMetricParameters
                                            html  
    validatecalculateLog2ratioMetricParameters
                                            html  
*** copying figures
** 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
* DONE (CNVMetrics)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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(CNVMetrics)
> 
> ## Run all unit tests
> test_check("CNVMetrics")
CNV Metrics
Metric:
sorensen

AMPLIFICATION:
           sample01 sample02 sample03
sample01         NA       NA       NA
sample02 0.04647582       NA       NA
sample03 0.05465532        0       NA


DELETION:
          sample01 sample02 sample03
sample01        NA       NA       NA
sample02 0.0541291       NA       NA
sample03 0.0000000        0       NA

CNV Metrics
Metric:
sorensen

AMPLIFICATION:
           sample01  sample02  sample03 sample04 sample05
sample01         NA        NA        NA       NA       NA
sample02 0.04647582        NA        NA       NA       NA
sample03 0.05465532 0.0000000        NA       NA       NA
sample04 0.05820635 0.0000000 0.9676239       NA       NA
sample05 0.14207052 0.3293641 0.0000000        0       NA
[ -- omitted 1 row/column ]

DELETION:
          sample01 sample02  sample03  sample04 sample05
sample01        NA       NA        NA        NA       NA
sample02 0.0541291       NA        NA        NA       NA
sample03 0.0000000        0        NA        NA       NA
sample04 0.0000000        0 0.9791909        NA       NA
sample05 0.0000000        0 0.9363260 0.9570782       NA
[ -- omitted 1 row/column ]
CNV Metrics
Metric:
szymkiewicz

AMPLIFICATION:
           sample01  sample02 sample03 sample04 sample05
sample01         NA        NA       NA       NA       NA
sample02 0.07796751        NA       NA       NA       NA
sample03 1.00000000 0.0000000       NA       NA       NA
sample04 1.00000000 0.0000000        1       NA       NA
sample05 0.64222246 0.7269269        0        0       NA
[ -- omitted 2 rows/columns ]

DELETION:
          sample01 sample02 sample03 sample04 sample05
sample01        NA       NA       NA       NA       NA
sample02 0.6477475       NA       NA       NA       NA
sample03 0.0000000        0       NA       NA       NA
sample04 0.0000000        0        1       NA       NA
sample05 0.0000000        0        1        1       NA
[ -- omitted 2 rows/columns ]
CNV Metrics
Metric:
weightedEuclideanDistance

LOG2RATIO:
           sample01 sample02 sample03
sample01         NA       NA       NA
sample02 0.06352523       NA       NA
sample03 0.11004168       NA       NA

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 68 ]
> 
> proc.time()
   user  system elapsed 
  33.82    0.39   34.20