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BioC 3.4: CHECK report for MinimumDistance on morelia

This page was generated on 2016-09-21 03:51:38 -0700 (Wed, 21 Sep 2016).

Package 751/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MinimumDistance 1.17.0
Robert B Scharpf
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MinimumDistance
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  ERROR 
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  ERROR  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ ERROR ] OK 

Summary

Package: MinimumDistance
Version: 1.17.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MinimumDistance_1.17.0.tar.gz
StartedAt: 2016-09-20 09:21:09 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 09:24:49 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 219.4 seconds
RetCode: 1
Status:  ERROR 
CheckDir: MinimumDistance.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MinimumDistance_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/MinimumDistance.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MinimumDistance/DESCRIPTION’ ... OK
* this is package ‘MinimumDistance’ version ‘1.17.0’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘GenomicRanges’ ‘SummarizedExperiment’
  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
.compute_trio_posterior: no visible global function definition for
  ‘rowRanges’
.constructMDE: no visible global function definition for
  ‘SummarizedExperiment’
.dnacopy2granges: no visible global function definition for ‘GRanges’
.filter_mdexperiment: no visible global function definition for
  ‘rowRanges’
.pedigreeId: no visible global function definition for ‘colData’
MDRanges: no visible global function definition for ‘GRanges’
MinDistGRanges: no visible global function definition for ‘GRangesList’
MinDistGRanges: no visible global function definition for ‘GRanges’
MinDistPosterior: no visible global function definition for
  ‘GRangesList’
computeEmissionProbs: no visible global function definition for
  ‘SummarizedExperiment’
computeEmissionProbs: no visible global function definition for
  ‘rowRanges’
dataFrameFromRange2: no visible binding for global variable ‘data’
generatorTransitionProbs : toGRanges: no visible global function
  definition for ‘GRanges’
generatorTransitionProbs : toGRanges: no visible global function
  definition for ‘GRangesList’
generatorTransitionProbs: no visible global function definition for
  ‘GRanges’
logEmissionArray: no visible global function definition for ‘assays’
narrow2: no visible global function definition for ‘GRangesList’
narrowRangeForChromosome: no visible global function definition for
  ‘GRangesList’
narrowRanges: no visible global function definition for ‘GRangesList’
overlapsCentromere: no visible global function definition for ‘data’
pruneByFactor: no visible global function definition for ‘GRangesList’
segmentArray: no visible global function definition for ‘GRangesList’
segmentList: no visible global function definition for ‘GRangesList’
segmentMatrix: no visible global function definition for ‘GRanges’
segmentff_matrix: no visible global function definition for
  ‘GRangesList’
segmentff_matrix2: no visible global function definition for
  ‘GRangesList’
stackRangedDataList: no visible global function definition for
  ‘GRangesList’
trioSetListExample: no visible global function definition for ‘data’
MAP2,MinDistExperiment-GRanges: no visible global function definition
  for ‘GRangesList’
MAP2,MinDistExperiment-GRangesList: no visible global function
  definition for ‘GRangesList’
MAP2,MinDistExperiment-MinDistGRanges: no visible global function
  definition for ‘GRangesList’
MinDistExperiment,ArrayViews-ParentOffspring: no visible global
  function definition for ‘assays’
MinDistExperiment,ArrayViews-ParentOffspring: no visible global
  function definition for ‘rowRanges’
MinDistExperiment,ArrayViews-ParentOffspring: no visible global
  function definition for ‘colData’
calculateMindist,list: no visible binding for global variable ‘elt’
coerce,TrioSet-MinDistExperiment: no visible global function definition
  for ‘GRanges’
coerce,TrioSetList-RangedSummarizedExperiment: no visible global
  function definition for ‘GRanges’
coerce,TrioSetList-RangedSummarizedExperiment: no visible global
  function definition for ‘SummarizedExperiment’
father,RangedSummarizedExperiment: no visible global function
  definition for ‘assays’
mother,RangedSummarizedExperiment: no visible global function
  definition for ‘assays’
offspring,RangedSummarizedExperiment: no visible global function
  definition for ‘assays’
segment2,MinDistExperiment: no visible global function definition for
  ‘rowRanges’
segment2,MinDistExperiment: no visible global function definition for
  ‘GRangesList’
segs,MinDistPosterior: no visible global function definition for
  ‘granges’
show,MinDistPosterior: no visible global function definition for
  ‘granges’
subsetAndSort,MinDistExperiment: no visible global function definition
  for ‘rowRanges’
subsetAndSort,MinDistExperiment: no visible global function definition
  for ‘rowRanges<-’
Undefined global functions or variables:
  GRanges GRangesList SummarizedExperiment assays colData data elt
  granges rowRanges rowRanges<-
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
* 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
Codoc mismatches from documentation object 'MDRanges-class':
\S4method{reduce}{MDRanges}
  Code: function(x, drop.empty.ranges = FALSE, ...)
  Docs: function(x, ...)
  Argument names in code not in docs:
    drop.empty.ranges
  Mismatches in argument names:
    Position: 2 Code: drop.empty.ranges Docs: ...

* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 ERROR
Running the tests in ‘tests/doRUnit.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  MinimumDistance unit testing - 12 test functions, 3 errors, 0 failures
  ERROR in test_TrioSetList_construction: Error in .validate_assayDataElementReplace(obj, value) : 
    object and replacement value have different dimensions
  ERROR in test_MAP2: Error in (function (od, vd)  : 
    object and replacement value dimnames differ
  ERROR in test_posteriorCalls: Error in .Primitive("[")(structure(c(-4L, 9L, 2L, 26L, -33L, -28L, 5L,  : 
    subscript out of bounds
  Error: 
  
  unit testing failed (#test failures: 0, #R errors: 3)
  
  Execution halted
* 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 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/MinimumDistance.Rcheck/00check.log’
for details.

doRUnit.Rout.fail:


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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] "/Users/biocbuild/bbs-3.4-bioc/meat/MinimumDistance.Rcheck/tests"

$pathToUnitTests
[1] "/Users/biocbuild/bbs-3.4-bioc/meat/MinimumDistance.Rcheck/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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, 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, 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 objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

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")'.

Welcome to VanillaICE version 1.35.0
Welcome to MinimumDistance version  1.17.0

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 1.35.0
 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  ... Timing stopped at: 4.862 0.039 4.901 
Error in .validate_assayDataElementReplace(obj, value) : 
  object and replacement value have different dimensions
 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

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

Loading required package: rtracklayer
Timing stopped at: 2.201 0.093 2.295 
Error in (function (od, vd)  : 
  object and replacement value dimnames differ
 done successfully.



Executing test function test_pennParam  ...  done successfully.



Executing test function test_posteriorCalls  ... Warning in mapply(FUN = f, ..., SIMPLIFY = FALSE) :
  longer argument not a multiple of length of shorter
Timing stopped at: 0.041 0.001 0.137 
Error in .Primitive("[")(structure(c(-4L, 9L, 2L, 26L, -33L, -28L, 5L,  : 
  subscript out of bounds
 done successfully.



Executing test function test_cbsSplits  ...  done successfully.

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

RUNIT TEST PROTOCOL -- Tue Sep 20 09:24:47 2016 
*********************************************** 
Number of test functions: 12 
Number of errors: 3 
Number of failures: 0 

 
1 Test Suite : 
MinimumDistance unit testing - 12 test functions, 3 errors, 0 failures
ERROR in test_TrioSetList_construction: Error in .validate_assayDataElementReplace(obj, value) : 
  object and replacement value have different dimensions
ERROR in test_MAP2: Error in (function (od, vd)  : 
  object and replacement value dimnames differ
ERROR in test_posteriorCalls: Error in .Primitive("[")(structure(c(-4L, 9L, 2L, 26L, -33L, -28L, 5L,  : 
  subscript out of bounds
Error: 

unit testing failed (#test failures: 0, #R errors: 3)

Execution halted

MinimumDistance.Rcheck/00install.out:

* installing *source* package ‘MinimumDistance’ ...
** R
** data
** inst
** preparing 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)

MinimumDistance.Rcheck/MinimumDistance-Ex.timings:

nameusersystemelapsed
DNAcopyParam0.0200.0010.021
FilterParamMD2.0600.0852.157
MAP20.0360.0050.042
MDRanges-class0.0260.0010.027
MinDistGRanges-class0.0540.0030.057
MinDistGRanges0.0270.0000.027
ParentOffspring-class0.0010.0000.001
ParentOffspringList-class0.0020.0000.001
Pedigree0.0060.0000.006
TrioSet2.2810.0272.350
acf20.0020.0000.002
md_exp0.0010.0000.001
pedigreeGrid4.2190.1244.401
pedigreeViewports0.0030.0000.002