##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:oligoClasses.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings oligoClasses_1.67.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/oligoClasses.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oligoClasses/DESCRIPTION’ ... OK
* this is package ‘oligoClasses’ version ‘1.67.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 NOTE
Packages which this enhances but not available for checking:
  '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 code 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 whether startup messages can be suppressed ... 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 ... WARNING
checkRd: (-1) AlleleSet-methods.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AlleleSet-methods.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AlleleSet-methods.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AlleleSet-methods.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AlleleSet-methods.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AlleleSet-methods.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (5) BeadStudioSet-class.Rd:52: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSet-class.Rd:53-54: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSet-class.Rd:55-57: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSet-class.Rd:58: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSet-class.Rd:59-60: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSet-class.Rd:63: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSet-class.Rd:64-65: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSet-class.Rd:66-67: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSet-class.Rd:68: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSetList-class.Rd:44-58: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSetList-class.Rd:64-69: \item in \describe must have non-empty label
checkRd: (5) BeadStudioSetList-class.Rd:71-78: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:85-86: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:88-89: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:91-93: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:96-98: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:100-101: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:103-105: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:107: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:109: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:113: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:115-116: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:118: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:120-121: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:124-126: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:131-132: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:135-136: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:138: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:140-142: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:144-145: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:147-148: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:150-151: \item in \describe must have non-empty label
checkRd: (5) CNSet-class.Rd:153: \item in \describe must have non-empty label
checkRd: (5) GRanges-methods.Rd:28-38: \item in \describe must have non-empty label
checkRd: (5) GRanges-methods.Rd:49-60: \item in \describe must have non-empty label
checkRd: (5) GRanges-methods.Rd:62-67: \item in \describe must have non-empty label
checkRd: (5) GRanges-methods.Rd:69-75: \item in \describe must have non-empty label
checkRd: (5) GRanges-methods.Rd:77-85: \item in \describe must have non-empty label
checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:35-42: \item in \describe must have non-empty label
checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:44-54: \item in \describe must have non-empty label
checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:56-61: \item in \describe must have non-empty label
checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:68-73: \item in \describe must have non-empty label
checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:75-81: \item in \describe must have non-empty label
checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:84-89: \item in \describe must have non-empty label
checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:91-100: \item in \describe must have non-empty label
checkRd: (5) SnpSet2-class.Rd:55-60: \item in \describe must have non-empty label
checkRd: (5) SnpSet2-class.Rd:62-67: \item in \describe must have non-empty label
checkRd: (5) SnpSet2-class.Rd:69-73: \item in \describe must have non-empty label
checkRd: (5) chromosome-methods.Rd:44-45: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:43-44: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:45-46: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:47-49: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:50-52: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:53-59: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:61-66: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:69-70: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:72-77: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:79-80: \item in \describe must have non-empty label
checkRd: (5) gSet-class.Rd:81-86: \item in \describe must have non-empty label
checkRd: (5) gSetList-class.Rd:51-56: \item in \describe must have non-empty label
checkRd: (5) gSetList-class.Rd:58-64: \item in \describe must have non-empty label
checkRd: (5) gSetList-class.Rd:66-71: \item in \describe must have non-empty label
checkRd: (5) gSetList-class.Rd:74-79: \item in \describe must have non-empty label
checkRd: (5) gSetList-class.Rd:89-99: \item in \describe must have non-empty label
checkRd: (5) oligoSnpSet-methods.Rd:28-39: \item in \describe must have non-empty label
checkRd: (5) oligoSnpSet-methods.Rd:41-46: \item in \describe must have non-empty label
checkRd: (5) oligoSnpSet-methods.Rd:48-54: \item in \describe must have non-empty label
* 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 package vignettes ... NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/oligoClasses.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL oligoClasses
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘oligoClasses’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (oligoClasses)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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, aperm, 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, saveRDS, setdiff, 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] "/Users/biocbuild/bbs-3.20-bioc/meat/oligoClasses.Rcheck/tests"

$pathToUnitTests
[1] "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpwXLdqb/RLIBS_19ba43487337/oligoClasses/unitTests"

Welcome to oligoClasses version 1.67.0


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:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
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 1.69.2
================================================================================
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")=="/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpqyKLRl/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.....: /Users/biocbuild/bbs-3.20-bioc/meat/oligoClasses.Rcheck/tests
================================================================================

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 -- Sun Oct 27 21:43:49 2024 
*********************************************** 
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 
  6.921   0.271   7.402