VanillaICE 1.46.0
Robert Scharpf
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/VanillaICE |
| Branch: RELEASE_3_9 |
| Last Commit: 1566ddf |
| Last Changed Date: 2019-05-02 11:53:08 -0400 (Thu, 02 May 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 <- "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] "/Users/biocbuild/bbs-3.9-bioc/meat/VanillaICE.Rcheck/tests"
$pathToUnitTests
[1] "/Library/Frameworks/R.framework/Versions/3.6/Resources/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, 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, 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 1.46.0
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 1.46.0
Executing test function test_ArrayViews ... done successfully.
Executing test function test_columnSubset ... Writing parsed files to /tmp/RtmpbbLz3e
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/RtmpbbLz3e
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 1.42.0
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 -- Wed Oct 16 07:45:31 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
32.058 3.478 34.912