Multiple platform build/check report for BioC 3.8 - CHECK report for oligoClasses on merida1

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### Running command:
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###   /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_1.44.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/oligoClasses.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.44.0’
* 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-3.8-bioc/meat/oligoClasses.Rcheck/00check.log’
for details.

Installation output

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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/3.5/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)

Tests output


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, 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-3.8-bioc/meat/oligoClasses.Rcheck/tests"

$pathToUnitTests
[1] "/Library/Frameworks/R.framework/Versions/3.5/Resources/library/oligoClasses/unitTests"

Welcome to oligoClasses version 1.44.0


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 1.46.0
================================================================================
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/RtmppVoMhD"

- 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-3.8-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 16 01:42:04 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 
 20.315   1.144  21.588

Example timings

name	user	system	elapsed
AlleleSet-class	0.136	0.007	0.143
AssayData-methods	1.810	0.094	1.919
AssayDataList	0.004	0.000	0.004
BeadStudioSet-class	0.058	0.001	0.059
CNSet-class	0.049	0.001	0.051
CopyNumberSet-class	0.023	0.000	0.024
CopyNumberSet-methods	0.197	0.079	0.278
FeatureSetExtensions-class	0.156	0.003	0.159
GRanges-methods	0.420	0.039	0.464
GenomeAnnotatedDataFrame-class	1.292	0.159	1.769
GenomeAnnotatedDataFrameFrom-methods	1.456	0.022	1.488
SnpSet-methods	0.026	0.001	0.027
SnpSet2-class	0.028	0.000	0.028
SnpSuperSet-class	0.049	0.000	0.050
affyPlatforms	0.001	0.000	0.001
batch	0.049	0.000	0.049
celfileDate	0.021	0.008	0.031
celfileName	0.000	0.001	0.000
checkExists	0.007	0.001	0.009
checkOrder	0.218	0.013	0.239
chromosome-methods	0	0	0
chromosome2integer	0.001	0.000	0.001
clusterOpts	0.000	0.000	0.001
data-efsExample	0.001	0.001	0.002
data-scqsExample	0.002	0.001	0.003
data-sfsExample	0.001	0.001	0.002
data-sqsExample	0.001	0.001	0.003
db	0	0	0
ff_matrix	0.001	0.001	0.001
ff_or_matrix-class	0.001	0.000	0.001
fileConnections	0.001	0.000	0.000
flags	0.044	0.003	0.047
gSet-class	0.001	0.000	0.002
gSetList-class	0.001	0.000	0.002
genomeBuild	0.004	0.000	0.004
geometry-methods	0.160	0.008	0.168
getBar	0.000	0.000	0.001
getSequenceLengths	0.119	0.006	0.126
i2p_p2i	0.001	0.000	0.000
integerMatrix	0	0	0
is.ffmatrix	0.001	0.001	0.002
isPackageLoaded	0.002	0.000	0.002
kind	0.168	0.010	0.179
largeObjects	0.002	0.001	0.003
ldOpts	0.001	0.000	0.001
library2	0.038	0.002	0.039
list.celfiles	0.014	0.002	0.017
locusLevelData	0.080	0.009	0.089
makeFeatureGRanges	0.414	0.025	0.447
oligoSetExample	0.201	0.011	0.213
pdPkgFromBioC	0.001	0.000	0.001
requireAnnotation	0	0	0
splitVec	0.002	0.001	0.004

CHECK report for oligoClasses on merida1

Summary

Command output

Installation output

Tests output

Example timings