Multiple platform build/check report for BioC 3.14 - CHECK results for oligoClasses on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: oligoClasses

Version: 1.56.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:oligoClasses.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings oligoClasses_1.56.0.tar.gz

StartedAt: 2022-04-12 23:53:02 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 23:59:22 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 379.8 seconds

RetCode: 0

Status: WARNINGS

CheckDir: oligoClasses.Rcheck

Warnings: 2

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:oligoClasses.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings oligoClasses_1.56.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/oligoClasses.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oligoClasses/DESCRIPTION' ... OK
* this is package 'oligoClasses' version '1.56.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'doMC', '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 whether package 'oligoClasses' can be installed ... OK
* checking installed package size ... OK
* checking package 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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: 'RSQLite'
  All declared Imports should be used.
Unexported object imported by a ':::' call: 'Biobase:::assayDataEnvLock'
  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 ... NOTE
getSequenceLengths: no visible binding for global variable 'seqlengths'
chromosome,gSetList: no visible global function definition for
  'chromosomeList'
coerce,CNSet-CopyNumberSet: no visible global function definition for
  'totalCopynumber'
geometry,FeatureSet: no visible global function definition for 'getPD'
Undefined global functions or variables:
  chromosomeList getPD seqlengths totalCopynumber
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'CNSet,ANY,ANY,ANY'
  generic '[' and siglist 'gSetList,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'scriptsForExampleData/CreateExampleData.R'
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                     user system elapsed
GenomeAnnotatedDataFrameFrom-methods 1.51   0.04    8.27
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'doRUnit.R'
 OK
** running tests for arch 'x64' ...
  Running 'doRUnit.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/oligoClasses.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/oligoClasses_1.56.0.tar.gz && rm -rf oligoClasses.buildbin-libdir && mkdir oligoClasses.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=oligoClasses.buildbin-libdir oligoClasses_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL oligoClasses_1.56.0.zip && rm oligoClasses_1.56.0.tar.gz oligoClasses_1.56.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  365k  100  365k    0     0   484k      0 --:--:-- --:--:-- --:--:--  484k
100  365k  100  365k    0     0   484k      0 --:--:-- --:--:-- --:--:--  484k

install for i386

* installing *source* package 'oligoClasses' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'oligoClasses'
    finding HTML links ... done
    AlleleSet-class                         html  
    finding level-2 HTML links ... done

    AlleleSet-methods                       html  
    AssayData-methods                       html  
    AssayDataList                           html  
    BeadStudioSet-class                     html  
    BeadStudioSetList-class                 html  
    CNSet-class                             html  
    ClassesNotExported                      html  
    CopyNumberSet-class                     html  
    CopyNumberSet-methods                   html  
    DBPDInfo-class                          html  
    FeatureSetExtensions-class              html  
    GRanges-methods                         html  
    GenomeAnnotatedDataFrame-class          html  
    GenomeAnnotatedDataFrameFrom-methods    html  
    SnpSet-methods                          html  
    SnpSet2-class                           html  
    SnpSuperSet-class                       html  
    SummarizedExperiment-methods            html  
    affyPlatforms                           html  
    annotationPackages                      html  
    assayDataList-methods                   html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/oligoClasses.buildbin-libdir/00LOCK-oligoClasses/00new/oligoClasses/help/assayDataList.html
    batch                                   html  
    batchStatistics                         html  
    celfileDate                             html  
    celfileName                             html  
    checkExists                             html  
    checkOrder                              html  
    chromosome-methods                      html  
    chromosome2integer                      html  
    clusterOpts                             html  
    clusterOptsDeprecated                   html  
    createFF                                html  
    data-efsExample                         html  
    data-scqsExample                        html  
    data-sfsExample                         html  
    data-sqsExample                         html  
    db                                      html  
    defunct                                 html  
    exprs-methods                           html  
    featureDataList-methods                 html  
    ff_matrix                               html  
    ff_or_matrix-class                      html  
    ffdf                                    html  
    fileConnections                         html  
    flags                                   html  
    gSet-class                              html  
    gSetList-class                          html  
    generics                                html  
    genomeBuild                             html  
    geometry-methods                        html  
    getBar                                  html  
    getSequenceLengths                      html  
    i2p_p2i                                 html  
    integerMatrix                           html  
    is.ffmatrix                             html  
    isPackageLoaded                         html  
    isSnp-methods                           html  
    kind                                    html  
    largeObjects                            html  
    ldOpts                                  html  
    length-methods                          html  
    library2                                html  
    list.celfiles                           html  
    locusLevelData                          html  
    makeFeatureGRanges                      html  
    manufacturer-methods                    html  
    ocLapply                                html  
    oligoSetExample                         html  
    oligoSnpSet-methods                     html  
    parStatus                               html  
    pdPkgFromBioC                           html  
    platform-methods                        html  
    pmFragmentLength-methods                html  
    position-methods                        html  
    requireAnnotation                       html  
    requireClusterPkgSetDeprecated          html  
    sampleNames-methods                     html  
    splitVec                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'oligoClasses' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'oligoClasses' as oligoClasses_1.56.0.zip
* DONE (oligoClasses)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'oligoClasses' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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

Attaching package: 'BiocGenerics'

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.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-3.14-bioc/meat/oligoClasses.Rcheck/tests_i386"

$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.14-bioc/R/library/oligoClasses/unitTests"

Welcome to oligoClasses version 1.56.0


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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: RSQLite
Loading required package: oligo
================================================================================
Welcome to oligo version 1.58.0
================================================================================
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'

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

    xor

Attaching package ff
- getOption("fftempdir")=="C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpEX2tiC/ff"

- 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.....: C:/Users/biocbuild/bbs-3.14-bioc/meat/oligoClasses.Rcheck/tests_i386
================================================================================

Attaching package: 'ff'

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 -- Tue Apr 12 23:58:48 2022 
*********************************************** 
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
Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
3: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
4: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
5: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
6: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
7: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
8: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
> 
> proc.time()
   user  system elapsed 
  21.51    2.43   88.96


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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

Attaching package: 'BiocGenerics'

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.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-3.14-bioc/meat/oligoClasses.Rcheck/tests_x64"

$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.14-bioc/R/library/oligoClasses/unitTests"

Welcome to oligoClasses version 1.56.0


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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: RSQLite
Loading required package: oligo
================================================================================
Welcome to oligo version 1.58.0
================================================================================
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'

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

    xor

Attaching package ff
- getOption("fftempdir")=="C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpsBgWOD/ff"

- 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.....: C:/Users/biocbuild/bbs-3.14-bioc/meat/oligoClasses.Rcheck/tests_x64
================================================================================

Attaching package: 'ff'

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 -- Tue Apr 12 23:59:10 2022 
*********************************************** 
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
Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
3: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
4: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
5: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
6: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
7: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
8: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
> 
> proc.time()
   user  system elapsed 
  20.15    1.04   21.18

name	user	system	elapsed
AlleleSet-class	0.11	0.00	0.11
AssayData-methods	1.23	0.10	1.33
AssayDataList	0	0	0
BeadStudioSet-class	0.07	0.00	0.08
CNSet-class	0.05	0.00	0.05
CopyNumberSet-class	0.05	0.00	0.04
CopyNumberSet-methods	0.33	0.05	0.44
FeatureSetExtensions-class	0.15	0.00	0.16
GRanges-methods	0.49	0.03	0.51
GenomeAnnotatedDataFrameFrom-methods	1.51	0.04	8.27
SnpSet-methods	0.03	0.00	0.03
SnpSet2-class	0.03	0.00	0.03
SnpSuperSet-class	0.05	0.00	0.05
affyPlatforms	0	0	0
batch	0.03	0.00	0.03
celfileDate	0.03	0.00	0.03
celfileName	0	0	0
checkExists	0	0	0
checkOrder	0.21	0.00	0.20
chromosome-methods	0	0	0
chromosome2integer	0.00	0.02	0.02
clusterOpts	0	0	0
data-efsExample	0	0	0
data-scqsExample	0	0	0
data-sfsExample	0	0	0
data-sqsExample	0.00	0.01	0.02
db	0	0	0
ff_matrix	0	0	0
ff_or_matrix-class	0	0	0
fileConnections	0	0	0
flags	0.01	0.02	0.03
gSet-class	0	0	0
gSetList-class	0	0	0
genomeBuild	0	0	0
geometry-methods	0.55	0.19	0.73
getBar	0	0	0
getSequenceLengths	0.09	0.00	0.10
i2p_p2i	0	0	0
integerMatrix	0	0	0
is.ffmatrix	0	0	0
isPackageLoaded	0	0	0
kind	0.19	0.00	0.18
largeObjects	0	0	0
ldOpts	0	0	0
library2	0.03	0.00	0.03
list.celfiles	0.02	0.00	1.61
locusLevelData	0.15	0.00	0.16
makeFeatureGRanges	0.46	0.01	0.47
oligoSetExample	0.22	0.00	0.22
pdPkgFromBioC	0	0	0
requireAnnotation	0	0	0
splitVec	0	0	0

name	user	system	elapsed
AlleleSet-class	0.16	0.02	0.17
AssayData-methods	2.25	0.11	2.36
AssayDataList	0	0	0
BeadStudioSet-class	0.04	0.00	0.05
CNSet-class	0.05	0.00	0.04
CopyNumberSet-class	0.03	0.00	0.03
CopyNumberSet-methods	0.16	0.05	0.21
FeatureSetExtensions-class	0.12	0.00	0.12
GRanges-methods	0.55	0.09	0.64
GenomeAnnotatedDataFrameFrom-methods	0.87	0.03	0.90
SnpSet-methods	0.03	0.00	0.03
SnpSet2-class	0.05	0.00	0.05
SnpSuperSet-class	0.08	0.00	0.08
affyPlatforms	0	0	0
batch	0.04	0.00	0.04
celfileDate	0.03	0.00	0.03
celfileName	0	0	0
checkExists	0.02	0.00	0.02
checkOrder	0.31	0.00	0.31
chromosome-methods	0	0	0
chromosome2integer	0	0	0
clusterOpts	0	0	0
data-efsExample	0.02	0.00	0.01
data-scqsExample	0	0	0
data-sfsExample	0	0	0
data-sqsExample	0.00	0.01	0.02
db	0	0	0
ff_matrix	0	0	0
ff_or_matrix-class	0	0	0
fileConnections	0	0	0
flags	0.65	0.00	0.66
gSet-class	0	0	0
gSetList-class	0	0	0
genomeBuild	0.02	0.00	0.01
geometry-methods	0.56	0.02	0.58
getBar	0	0	0
getSequenceLengths	0.13	0.00	0.12
i2p_p2i	0	0	0
integerMatrix	0	0	0
is.ffmatrix	0	0	0
isPackageLoaded	0	0	0
kind	0.25	0.03	0.29
largeObjects	0	0	0
ldOpts	0	0	0
library2	0.05	0.00	0.05
list.celfiles	0.01	0.00	0.01
locusLevelData	0.08	0.00	0.08
makeFeatureGRanges	0.28	0.02	0.30
oligoSetExample	0.14	0.00	0.14
pdPkgFromBioC	0.00	0.01	0.01
requireAnnotation	0	0	0
splitVec	0	0	0

CHECK results for oligoClasses on tokay2

Summary

Command output

Installation output

Tests output

Example timings