oligoClasses 1.40.0
Benilton Carvalho and Robert Scharpf
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/oligoClasses |
| Branch: RELEASE_3_6 |
| Last Commit: 32f4061 |
| Last Changed Date: 2017-10-30 12:39:21 -0400 (Mon, 30 Oct 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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 ) ) {
+ ## loading Biobase below b/c we're simply Import:ing it, rather than Depend:ing on it
+ ## then functions from there are not visible downstream
+ library(Biobase)
+ pkg <- "oligoClasses"
+
+ 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 )
+ options(warn=0)
+
+ ## 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" )
+ }
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, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Running unit tests
$pkg
[1] "oligoClasses"
$getwd
[1] "/Users/biocbuild/bbs-3.6-bioc/meat/oligoClasses.Rcheck/tests"
$pathToUnitTests
[1] "/Users/biocbuild/bbs-3.6-bioc/meat/oligoClasses.Rcheck/oligoClasses/unitTests"
Welcome to oligoClasses version 1.40.0
Executing test function test_annotation ... Annotation for genomewidesnp6Crlmm version 1.0.7 supports UCSC builds hg18 and hg19.
Build requested, but only build hg18 is available.
done successfully.
Executing test function test_BafLrrSetList ... done successfully.
Executing test function test_BeadStudioSet ... done successfully.
Executing test function test_CNSet_construction ... done successfully.
Executing test function test_CopyNumberSet_construction ... Loading required package: pd.mapping50k.hind240
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: RSQLite
Loading required package: oligo
================================================================================
Welcome to oligo version 1.42.0
================================================================================
Loading required package: DBI
Loading required package: pd.mapping50k.xba240
done successfully.
Executing test function test_GenomeAnnotatedDataFrameWithFF ... Loading required package: ff
Loading required package: bit
Attaching package bit
package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit
Attaching package: 'bit'
The following object is masked from 'package:base':
xor
Attaching package ff
- getOption("fftempdir")=="/tmp/RtmpKZrc4P"
- getOption("ffextension")=="ff"
- getOption("ffdrop")==TRUE
- getOption("fffinonexit")==TRUE
- getOption("ffpagesize")==65536
- getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
- Probesets: 20,000
- Samples..: 100
- Path.....: /Users/biocbuild/bbs-3.6-bioc/meat/oligoClasses.Rcheck/tests
================================================================================
Attaching package: 'ff'
The following objects are masked from 'package:bit':
clone, clone.default, clone.list
The following objects are masked from 'package:Biostrings':
mismatch, pattern
The following objects are masked from 'package:utils':
write.csv, write.csv2
The following objects are masked from 'package:base':
is.factor, is.ordered
done successfully.
Executing test function test_GenomeAnnotatedDataFrame_construction ... done successfully.
Executing test function test_dataExamples ... done successfully.
Executing test function test_oligoSnpSet_construction ... done successfully.
Executing test function test_conversions ... done successfully.
Executing test function test_makeFeatureRanges ... done successfully.
Executing test function test_oligoSnpSet ... done successfully.
------------------- UNIT TEST SUMMARY ---------------------
RUNIT TEST PROTOCOL -- Thu Apr 12 07:15:18 2018
***********************************************
Number of test functions: 12
Number of errors: 0
Number of failures: 0
1 Test Suite :
oligoClasses unit testing - 12 test functions, 0 errors, 0 failures
>
> proc.time()
user system elapsed
25.682 0.814 27.333