Package: MinimumDistance

Version: 1.27.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MinimumDistance.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MinimumDistance_1.27.0.tar.gz

StartedAt: 2019-03-18 02:43:28 -0400 (Mon, 18 Mar 2019)

EndedAt: 2019-03-18 02:49:42 -0400 (Mon, 18 Mar 2019)

EllapsedTime: 374.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MinimumDistance.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MinimumDistance.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MinimumDistance_1.27.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MinimumDistance.Rcheck’
* using R Under development (unstable) (2019-01-21 r75999)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MinimumDistance/DESCRIPTION’ ... OK
* this is package ‘MinimumDistance’ version ‘1.27.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... NOTE
callDenovoSegments: no visible global function definition for
  ‘read.bsfiles’
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:
  RangedDataList elt read.bsfiles
* checking Rd files ... OK
* 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 ... 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 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 ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
pedigreeGrid 3.859  0.041   5.043
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/MinimumDistance.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL MinimumDistance
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘MinimumDistance’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘allNames’ in package ‘MinimumDistance’
Creating a generic function for ‘colMads’ from package ‘matrixStats’ in package ‘MinimumDistance’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MinimumDistance)

R Under development (unstable) (2019-01-21 r75999) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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] "/home/biocbuild/bbs-3.9-bioc/meat/MinimumDistance.Rcheck/tests"

$pathToUnitTests
[1] "/home/biocbuild/bbs-3.9-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, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, 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
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

Welcome to VanillaICE version 1.45.0
Welcome to MinimumDistance version  1.27.0

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 1.45.0
 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:DelayedArray':

    type

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 -- Mon Mar 18 02:49:30 2019 
*********************************************** 
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 
 51.242   0.718  60.735 

name	user	system	elapsed
DNAcopyParam	0.016	0.000	0.095
FilterParamMD	2.050	0.048	3.021
MAP2	0.063	0.000	0.108
MDRanges-class	0.033	0.000	0.041
MinDistGRanges-class	0.090	0.000	0.134
MinDistGRanges	0.067	0.000	0.112
ParentOffspring-class	0.001	0.000	0.001
ParentOffspringList-class	0.002	0.000	0.003
Pedigree	0.008	0.000	0.013
acf2	0.003	0.000	0.005
md_exp	0.000	0.000	0.002
pedigreeGrid	3.859	0.041	5.043
pedigreeViewports	0.003	0.001	0.003