Package: VanillaICE

Version: 1.44.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:VanillaICE.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings VanillaICE_1.44.0.tar.gz

StartedAt: 2019-04-16 03:37:20 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:41:03 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 223.0 seconds

RetCode: 0

Status:  OK

CheckDir: VanillaICE.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:VanillaICE.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings VanillaICE_1.44.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/VanillaICE.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VanillaICE/DESCRIPTION’ ... OK
* this is package ‘VanillaICE’ version ‘1.44.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘doMPI’ ‘doRedis’
* 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 ‘VanillaICE’ 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 ... NOTE
Namespace in Imports field not imported from: ‘BSgenome.Hsapiens.UCSC.hg18’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘SummarizedExperiment:::.ShallowSimpleListAssays0’
  See the note in ?`:::` about the use of this operator.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/VanillaICE.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL VanillaICE
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘VanillaICE’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c rinit.c -o rinit.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c viterbi.c -o viterbi.o
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o VanillaICE.so rinit.o viterbi.o -lm -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/VanillaICE/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘distance’ in package ‘VanillaICE’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (VanillaICE)

R version 3.5.3 (2019-03-11) -- "Great Truth"
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 <- "VanillaICE"
+ 
+ 	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=2 )
+ 
+ 	## 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] "VanillaICE"

$getwd
[1] "/home/biocbuild/bbs-3.8-bioc/meat/VanillaICE.Rcheck/tests"

$pathToUnitTests
[1] "/home/biocbuild/bbs-3.8-bioc/R/library/VanillaICE/unitTests"

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: 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

Welcome to VanillaICE version 1.44.0
Loading required package: BSgenome.Hsapiens.UCSC.hg18
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
Loading required package: data.table

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

Loading required package: foreach
Loading required package: oligoClasses
Welcome to oligoClasses version 1.44.0


Executing test function test_ArrayViews  ...  done successfully.



Executing test function test_columnSubset  ... Writing parsed files to /tmp/RtmpeS3tDT
 done successfully.



Executing test function test_FilterParam  ...  done successfully.



Executing test function test_EmissionParam  ...  done successfully.



Executing test function test_SnpArrayExperiment  ... Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'SnpDataFrame' for signature '"numeric"'
Error in VanillaICE:::SnpDataFrame(DataFrame(x = 3)) : 
  isSnp must be specified
Error in .local(object, isSnp, ...) : isSnp must be specified
Error in validObject(.Object) : 
  invalid class "SummarizedExperiment" object: 
  nb of rows in 'assay' (5) must equal nb of rows in 'rowData' (0)
Error in SnpArrayExperiment(x, y, rowRanges = rowranges) : 
   isSnp must be the same length as rowRanges
 done successfully.



Executing test function test_SnpArrayExperiment2  ... Writing parsed files to /tmp/RtmpeS3tDT
 done successfully.



Executing test function test_SnpGRanges  ...  done successfully.



Executing test function test_acf2  ...  done successfully.



Executing test function test_hmm_cnset  ... Loading required package: crlmm
Loading required package: preprocessCore
Welcome to crlmm version 1.40.0

Attaching package: 'crlmm'

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

    genotypes

 done successfully.



Executing test function test_state4  ...  done successfully.



Executing test function test_rowMAD  ...  done successfully.



Executing test function test_scaleBy  ...  done successfully.



Executing test function test_duplicatedMapLocs  ...  done successfully.



Executing test function test_sweepMode.R  ...  done successfully.



Executing test function test_Viterbi  ...  done successfully.



Executing test function test_baf_emission  ...  done successfully.



Executing test function test_cn_NAs  ...  done successfully.



Executing test function test_emission_for_list  ...  done successfully.



Executing test function test_emission_update  ...  done successfully.



Executing test function test_multiple_chromosomes  ...  done successfully.



Executing test function test_null_assignment  ...  done successfully.



Executing test function test_oligoset_comparison  ...  done successfully.



Executing test function test_summarized_exp  ...  done successfully.



Executing test function test_updating  ...  done successfully.

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

RUNIT TEST PROTOCOL -- Tue Apr 16 03:40:58 2019 
*********************************************** 
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
VanillaICE unit testing - 24 test functions, 0 errors, 0 failures
> 
> proc.time()
   user  system elapsed 
 22.016   0.644  22.310 

name	user	system	elapsed
ArrayViews-class	3.560	0.036	3.646
CopyNumScanParams	0.004	0.000	0.004
EmissionParam-methods	0.008	0.000	0.010
FilterParam-class	0.000	0.000	0.003
HMM	1.228	0.008	1.238
HMMList-class	0.792	0.036	0.828
HmmParam	0.004	0.000	0.004
IO	0.004	0.000	0.007
IdiogramParams-class	0.204	0.024	0.245
SnpArrayExperiment-class	0.216	0.008	0.225
SnpExperiment	0.040	0.000	0.042
SnpGRanges	0.048	0.000	0.045
TransitionParam	0	0	0
cnvFilter	1.084	0.000	1.085
dropDuplicatedMapLocs	0.124	0.000	0.122
emissionParam	0.004	0.000	0.006
getExampleSnpExperiment	0	0	0
getHmmParams	0.008	0.004	0.014
hmm2	1.360	0.000	1.371
isHeterozygous	0.540	0.004	0.420
parseSourceFile	1.532	0.028	0.755
plotting	0.916	0.008	0.923
robust-statistics	0	0	0
snpArrayAssays	0.016	0.000	0.015
sourcePaths	0.008	0.000	0.006
sweepMode	0.312	0.000	0.314
threshold	0.000	0.000	0.001
viewports	0.000	0.000	0.002