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CHECK report for MinimumDistance on tokay1

This page was generated on 2021-05-06 12:32:16 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the MinimumDistance package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1104/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MinimumDistance 1.34.0  (landing page)
Robert Scharpf
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/MinimumDistance
Branch: RELEASE_3_12
Last Commit: 50ebfdd
Last Changed Date: 2020-10-27 10:45:43 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: MinimumDistance
Version: 1.34.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MinimumDistance.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MinimumDistance_1.34.0.tar.gz
StartedAt: 2021-05-06 04:40:08 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:47:49 -0400 (Thu, 06 May 2021)
EllapsedTime: 461.3 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: MinimumDistance.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MinimumDistance.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MinimumDistance_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MinimumDistance.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MinimumDistance/DESCRIPTION' ... OK
* this is package 'MinimumDistance' version '1.34.0'
* 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 'MinimumDistance' 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 ... NOTE
Namespace in Imports field not imported from: 'MatrixGenerics'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
callDenovoSegments: no visible global function definition for
  'read.bsfiles'
combineRanges: no visible global function definition for 'RangedData'
getRefGene: no visible global function definition for 'RangedData'
overlapsCentromere: no visible global function definition for
  'RangedData'
pruneMD: no visible global function definition for 'RangedDataCBS'
pruneTrioSet: no visible global function definition for
  'RangedDataList'
read.bsfiles2: no visible binding for global variable 'read.bsfiles'
GenomeAnnotatedDataFrameFrom,character: no visible global function
  definition for 'read.bsfiles'
calculateMindist,list: no visible binding for global variable 'elt'
Undefined global functions or variables:
  RangedData RangedDataCBS RangedDataList elt read.bsfiles
* checking Rd files ... WARNING
checkRd: (5) MinimumDistance.Rd:0-7: Must have a \description
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'coerce' but not in code:
  'as'

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'coerce':
  'as'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... NOTE
Output for data("trioSetListExample", package = "MinimumDistance"):
  No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... 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
pedigreeGrid 4.89   0.12    5.03
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'doRUnit.R'
 OK
** running tests for arch 'x64' ...
  Running 'doRUnit.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: 3 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/MinimumDistance.Rcheck/00check.log'
for details.



Installation output

MinimumDistance.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/MinimumDistance_1.34.0.tar.gz && rm -rf MinimumDistance.buildbin-libdir && mkdir MinimumDistance.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MinimumDistance.buildbin-libdir MinimumDistance_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL MinimumDistance_1.34.0.zip && rm MinimumDistance_1.34.0.tar.gz MinimumDistance_1.34.0.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
100  928k  100  928k    0     0  38.5M      0 --:--:-- --:--:-- --:--:-- 41.2M

install for i386

* installing *source* package 'MinimumDistance' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
Creating a new generic function for 'allNames' in package 'MinimumDistance'
in method for 'coerce' with signature '"RangedDataCNV","GRanges"': no definition for class "RangedDataCNV"
in method for 'todf' with signature 'object="TrioSet",rangeData="RangedData"': no definition for class "RangedData"
in method for 'prune' with signature 'object="TrioSet",ranges="RangedDataCNV"': no definition for class "RangedDataCNV"
in method for 'prune' with signature 'object="TrioSetList",ranges="RangedDataCNV"': no definition for class "RangedDataCNV"
** help
*** installing help indices
  converting help for package 'MinimumDistance'
    finding HTML links ... done
    DNAcopyParam                            html  
    Defunct                                 html  
    Deprecated                              html  
    FilterParamMD-class                     html  
    FilterParamMD                           html  
    MAP                                     html  
    MAP2                                    html  
    MDRanges-class                          html  
    MinDistExperiment-class                 html  
    MinDistExperiment                       html  
    MinDistGRanges-class                    html  
    MinDistGRanges                          html  
    MinDistParam-class                      html  
    MinDistParam                            html  
    MinDistPosterior-class                  html  
    MinimumDistance                         html  
    ParentOffspring-class                   html  
    ParentOffspringList-class               html  
    Pedigree-class                          html  
    Pedigree                                html  
    PennParam                               html  
    TrioSet-class                           html  
    TrioSet                                 html  
    TrioSetList-class                       html  
    TrioSetList                             html  
    TrioSetListLD                           html  
    acf2                                    html  
    calculateMindist                        html  
    coercion-methods                        html  
    denovo                                  html  
    exampleTrioSetList                      html  
    filterExperiment                        html  
    mad2                                    html  
    mdLegend                                html  
    md_exp                                  html  
    md_gr                                   html  
    mindist                                 html  
    nMAD                                    html  
    pedigreeGrid                            html  
    pedigreeName                            html  
    pedigreeViewports                       html  
    plotDenovo                              html  
    range-ILimit-method                     html  
    segment2                                html  
    finding level-2 HTML links ... done

** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
** testing if installed package can be loaded from final location
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'MinimumDistance' ...
** testing if installed package can be loaded
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
* MD5 sums
packaged installation of 'MinimumDistance' as MinimumDistance_1.34.0.zip
* DONE (MinimumDistance)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'MinimumDistance' successfully unpacked and MD5 sums checked

Tests output

MinimumDistance.Rcheck/tests_i386/doRUnit.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> ## from xmapcore package
> if( require( "RUnit", quietly=TRUE ) ) {
+   pkg <- "MinimumDistance"
+ 
+   if( Sys.getenv( "RCMDCHECK" ) == "FALSE" ) {
+     path <- file.path( getwd(), "..", "inst", "unitTests" )
+   } else {
+     path <- system.file( package=pkg, "unitTests" )
+   }
+ 
+   cat( "\nRunning unit tests\n" )
+   print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) )
+   library( package=pkg, character.only=TRUE )
+ 
+   ##xmap.clear.cache()
+ 
+   ##Fail on warnings
+   options( warn=1 )
+ 
+   ## Get the pattern (if there is one?)
+   patt <- Sys.getenv( "RUNITFILEPATTERN" )
+   if( is.null( patt ) || nchar( patt ) == 0 ) {
+     testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+                                  dirs=path,
+                                  testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ))
+   } else {
+     ##testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=paste( "^runit\\.", patt, "\\.[rR]$", sep="" ), dirs=path )
+     testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+                                  testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ),
+                                  dirs=path )
+   }
+   tests <- runTestSuite( testSuite )
+ 
+   pathReport <- file.path( path, "report" )
+ 
+   cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" )
+   printTextProtocol( tests, showDetails=FALSE )
+   printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) )
+   printTextProtocol( tests, showDetails=TRUE,  fileName=paste( pathReport, ".txt", sep="" ) )
+ 
+   printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) )
+ 
+   tmp <- getErrors( tests )
+   if( tmp$nFail > 0 | tmp$nErr > 0 ){
+     stop( paste( "\n\nunit testing failed (#test failures: ",
+                 tmp$nFail, ", #R errors: ",
+                 tmp$nErr, ")\n\n", sep=""))
+   }
+ } else {
+   warning( "cannot run unit tests -- package RUnit is not available" )
+ }

Running unit tests
$pkg
[1] "MinimumDistance"

$getwd
[1] "C:/Users/biocbuild/bbs-3.12-bioc/meat/MinimumDistance.Rcheck/tests_i386"

$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.12-bioc/R/library/MinimumDistance/unitTests"

Loading required package: VanillaICE
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: GenomicRanges
Loading required package: stats4
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: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
Welcome to VanillaICE version 1.52.0
Welcome to MinimumDistance version  1.34.0

Attaching package: 'MinimumDistance'

The following object is masked from 'package:VanillaICE':

    acf2



Executing test function test_MDE  ...  done successfully.



Executing test function test_Pedigree_construction  ... Welcome to oligoClasses version 1.52.0
 done successfully.



Executing test function test_subsetPedigree  ... Error in validObject(.Object) : 
  invalid class "Pedigree" object: fatherNames can not be the same as the offspringNames
 done successfully.



Executing test function test_TrioSet  ...  done successfully.



Executing test function test_TrioSetList_construction  ...  done successfully.



Executing test function test_TrioSetListdataExamples  ...  done successfully.



Executing test function test_calculateMindist  ... Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load and register a 'foreach' adaptor
        Example - Using 'multicore' for 2 cores:
             library(doMC)
             registerDoMC(2)
================================================================================
 done successfully.



Executing test function test_callDenovoSegments  ... 
Attaching package: 'data.table'

The following object is masked from 'package:SummarizedExperiment':

    shift

The following object is masked from 'package:GenomicRanges':

    shift

The following object is masked from 'package:IRanges':

    shift

The following objects are masked from 'package:S4Vectors':

    first, second

Welcome to human610quadv1bCrlmm version 1.0.3
 done successfully.



Executing test function test_MAP2  ... Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:VanillaICE':

    deletion

The following object is masked from 'package:base':

    strsplit

Loading required package: rtracklayer
Analyzing: NA12891 
Analyzing: NA12892 
Analyzing: NA12878 
Analyzing: md_NA12878 
 done successfully.



Executing test function test_pennParam  ...  done successfully.



Executing test function test_posteriorCalls  ...  done successfully.



Executing test function test_cbsSplits  ...  done successfully.

------------------- UNIT TEST SUMMARY ---------------------

RUNIT TEST PROTOCOL -- Thu May 06 04:46:59 2021 
*********************************************** 
Number of test functions: 12 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MinimumDistance unit testing - 12 test functions, 0 errors, 0 failures
> 
> proc.time()
   user  system elapsed 
  43.98    1.96   47.07 

MinimumDistance.Rcheck/tests_x64/doRUnit.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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.

> ## from xmapcore package
> if( require( "RUnit", quietly=TRUE ) ) {
+   pkg <- "MinimumDistance"
+ 
+   if( Sys.getenv( "RCMDCHECK" ) == "FALSE" ) {
+     path <- file.path( getwd(), "..", "inst", "unitTests" )
+   } else {
+     path <- system.file( package=pkg, "unitTests" )
+   }
+ 
+   cat( "\nRunning unit tests\n" )
+   print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) )
+   library( package=pkg, character.only=TRUE )
+ 
+   ##xmap.clear.cache()
+ 
+   ##Fail on warnings
+   options( warn=1 )
+ 
+   ## Get the pattern (if there is one?)
+   patt <- Sys.getenv( "RUNITFILEPATTERN" )
+   if( is.null( patt ) || nchar( patt ) == 0 ) {
+     testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+                                  dirs=path,
+                                  testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ))
+   } else {
+     ##testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=paste( "^runit\\.", patt, "\\.[rR]$", sep="" ), dirs=path )
+     testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+                                  testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ),
+                                  dirs=path )
+   }
+   tests <- runTestSuite( testSuite )
+ 
+   pathReport <- file.path( path, "report" )
+ 
+   cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" )
+   printTextProtocol( tests, showDetails=FALSE )
+   printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) )
+   printTextProtocol( tests, showDetails=TRUE,  fileName=paste( pathReport, ".txt", sep="" ) )
+ 
+   printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) )
+ 
+   tmp <- getErrors( tests )
+   if( tmp$nFail > 0 | tmp$nErr > 0 ){
+     stop( paste( "\n\nunit testing failed (#test failures: ",
+                 tmp$nFail, ", #R errors: ",
+                 tmp$nErr, ")\n\n", sep=""))
+   }
+ } else {
+   warning( "cannot run unit tests -- package RUnit is not available" )
+ }

Running unit tests
$pkg
[1] "MinimumDistance"

$getwd
[1] "C:/Users/biocbuild/bbs-3.12-bioc/meat/MinimumDistance.Rcheck/tests_x64"

$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.12-bioc/R/library/MinimumDistance/unitTests"

Loading required package: VanillaICE
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: GenomicRanges
Loading required package: stats4
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: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
Welcome to VanillaICE version 1.52.0
Welcome to MinimumDistance version  1.34.0

Attaching package: 'MinimumDistance'

The following object is masked from 'package:VanillaICE':

    acf2



Executing test function test_MDE  ...  done successfully.



Executing test function test_Pedigree_construction  ... Welcome to oligoClasses version 1.52.0
 done successfully.



Executing test function test_subsetPedigree  ... Error in validObject(.Object) : 
  invalid class "Pedigree" object: fatherNames can not be the same as the offspringNames
 done successfully.



Executing test function test_TrioSet  ...  done successfully.



Executing test function test_TrioSetList_construction  ...  done successfully.



Executing test function test_TrioSetListdataExamples  ...  done successfully.



Executing test function test_calculateMindist  ... Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load and register a 'foreach' adaptor
        Example - Using 'multicore' for 2 cores:
             library(doMC)
             registerDoMC(2)
================================================================================
 done successfully.



Executing test function test_callDenovoSegments  ... 
Attaching package: 'data.table'

The following object is masked from 'package:SummarizedExperiment':

    shift

The following object is masked from 'package:GenomicRanges':

    shift

The following object is masked from 'package:IRanges':

    shift

The following objects are masked from 'package:S4Vectors':

    first, second

Welcome to human610quadv1bCrlmm version 1.0.3
 done successfully.



Executing test function test_MAP2  ... Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:VanillaICE':

    deletion

The following object is masked from 'package:base':

    strsplit

Loading required package: rtracklayer
Analyzing: NA12891 
Analyzing: NA12892 
Analyzing: NA12878 
Analyzing: md_NA12878 
 done successfully.



Executing test function test_pennParam  ...  done successfully.



Executing test function test_posteriorCalls  ...  done successfully.



Executing test function test_cbsSplits  ...  done successfully.

------------------- UNIT TEST SUMMARY ---------------------

RUNIT TEST PROTOCOL -- Thu May 06 04:47:44 2021 
*********************************************** 
Number of test functions: 12 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MinimumDistance unit testing - 12 test functions, 0 errors, 0 failures
> 
> proc.time()
   user  system elapsed 
  42.28    1.51   43.85 

Example timings

MinimumDistance.Rcheck/examples_i386/MinimumDistance-Ex.timings

nameusersystemelapsed
DNAcopyParam0.020.000.02
FilterParamMD1.260.141.41
MAP20.070.030.09
MDRanges-class0.040.000.04
MinDistGRanges-class0.130.040.17
MinDistGRanges0.050.000.05
ParentOffspring-class000
ParentOffspringList-class000
Pedigree0.010.000.02
acf20.000.020.01
md_exp000
pedigreeGrid4.890.125.03
pedigreeViewports000

MinimumDistance.Rcheck/examples_x64/MinimumDistance-Ex.timings

nameusersystemelapsed
DNAcopyParam0.010.000.02
FilterParamMD1.940.041.98
MAP20.040.000.05
MDRanges-class0.020.020.03
MinDistGRanges-class0.060.020.08
MinDistGRanges0.030.000.03
ParentOffspring-class000
ParentOffspringList-class000
Pedigree000
acf2000
md_exp000
pedigreeGrid3.640.053.69
pedigreeViewports000