|
oligoClasses.Rcheck/tests_i386/doRUnit.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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
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] "C:/Users/biocbuild/bbs-3.10-bioc/meat/oligoClasses.Rcheck/tests_i386"
$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.10-bioc/R/library/oligoClasses/unitTests"
Welcome to oligoClasses version 1.48.0
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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: RSQLite
Loading required package: oligo
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo'
================================================================================
Welcome to oligo version 1.50.0
================================================================================
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")=="C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpyg28xa"
- 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")==37570478.08 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==1878523904 -- consider a different value for tuning your system
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
- Probesets: 20,000
- Samples..: 100
- Path.....: C:/Users/biocbuild/bbs-3.10-bioc/meat/oligoClasses.Rcheck/tests_i386
================================================================================
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 -- Wed Apr 15 05:16:31 2020
***********************************************
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
18.95 2.18 22.67
|
oligoClasses.Rcheck/tests_x64/doRUnit.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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
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] "C:/Users/biocbuild/bbs-3.10-bioc/meat/oligoClasses.Rcheck/tests_x64"
$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.10-bioc/R/library/oligoClasses/unitTests"
Welcome to oligoClasses version 1.48.0
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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: RSQLite
Loading required package: oligo
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo'
================================================================================
Welcome to oligo version 1.50.0
================================================================================
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")=="C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpqmed5p"
- 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")==685831618.56 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==34291580928 -- consider a different value for tuning your system
================================================================================
Large dataset support for 'oligo/crlmm': Enabled
- Probesets: 20,000
- Samples..: 100
- Path.....: C:/Users/biocbuild/bbs-3.10-bioc/meat/oligoClasses.Rcheck/tests_x64
================================================================================
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 -- Wed Apr 15 05:16:53 2020
***********************************************
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
20.03 0.82 20.84
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