Package: oligoClasses

Version: 1.45.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:oligoClasses.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings oligoClasses_1.45.0.tar.gz

StartedAt: 2019-04-09 02:35:07 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:38:45 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 218.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: oligoClasses.Rcheck

Warnings: 2

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:oligoClasses.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings oligoClasses_1.45.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/oligoClasses.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oligoClasses/DESCRIPTION’ ... OK
* this is package ‘oligoClasses’ version ‘1.45.0’
* 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 for sufficient/correct file permissions ... 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
* 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’
pdPkgFromBioC: no visible binding for global variable ‘contrib.url’
pdPkgFromBioC: no visible global function definition for
  ‘available.packages’
pdPkgFromBioC: no visible global function definition for
  ‘install.packages’
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:
  available.packages chromosomeList contrib.url getPD install.packages
  seqlengths totalCopynumber
Consider adding
  importFrom("utils", "available.packages", "contrib.url",
             "install.packages")
to your NAMESPACE file.
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/oligoClasses.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL oligoClasses
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘oligoClasses’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (oligoClasses)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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, basename, cbind, colMeans, colSums, 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, 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-3.9-bioc/meat/oligoClasses.Rcheck/tests"

$pathToUnitTests
[1] "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/oligoClasses/unitTests"

Welcome to oligoClasses version 1.45.0


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 1.47.0
================================================================================
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/Rtmp9C71uY"

- 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-3.9-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 -- Tue Apr  9 02:38:38 2019 
*********************************************** 
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 
 22.503   1.180  23.866 

name	user	system	elapsed
AlleleSet-class	0.148	0.008	0.155
AssayData-methods	1.364	0.131	1.506
AssayDataList	0.005	0.001	0.006
BeadStudioSet-class	0.060	0.000	0.062
CNSet-class	0.045	0.000	0.046
CopyNumberSet-class	0.022	0.000	0.022
CopyNumberSet-methods	0.173	0.080	0.323
FeatureSetExtensions-class	0.136	0.001	0.139
GRanges-methods	0.483	0.011	0.503
GenomeAnnotatedDataFrame-class	1.171	0.148	1.618
GenomeAnnotatedDataFrameFrom-methods	1.561	0.026	1.603
SnpSet-methods	0.031	0.001	0.031
SnpSet2-class	0.050	0.001	0.050
SnpSuperSet-class	0.075	0.001	0.075
affyPlatforms	0.001	0.000	0.001
batch	0.060	0.000	0.062
celfileDate	0.032	0.010	0.043
celfileName	0.001	0.001	0.000
checkExists	0.007	0.001	0.009
checkOrder	0.241	0.012	0.254
chromosome-methods	0.000	0.000	0.001
chromosome2integer	0.001	0.001	0.001
clusterOpts	0.001	0.000	0.002
data-efsExample	0.002	0.001	0.003
data-scqsExample	0.002	0.001	0.003
data-sfsExample	0.002	0.001	0.003
data-sqsExample	0.002	0.001	0.003
db	0.000	0.000	0.001
ff_matrix	0.001	0.000	0.001
ff_or_matrix-class	0.001	0.001	0.000
fileConnections	0	0	0
flags	0.036	0.002	0.038
gSet-class	0.002	0.001	0.002
gSetList-class	0.001	0.000	0.002
genomeBuild	0.005	0.000	0.005
geometry-methods	0.212	0.010	0.226
getBar	0.001	0.000	0.001
getSequenceLengths	0.160	0.008	0.172
i2p_p2i	0.000	0.001	0.000
integerMatrix	0.001	0.000	0.001
is.ffmatrix	0.001	0.000	0.002
isPackageLoaded	0.001	0.000	0.001
kind	0.213	0.013	0.232
largeObjects	0.002	0.001	0.003
ldOpts	0.002	0.000	0.002
library2	0.043	0.003	0.045
list.celfiles	0.018	0.003	0.024
locusLevelData	0.093	0.008	0.103
makeFeatureGRanges	0.438	0.021	0.463
oligoSetExample	0.185	0.005	0.191
pdPkgFromBioC	0	0	0
requireAnnotation	0	0	0
splitVec	0.002	0.001	0.003