Multiple platform build/check report for BioC 3.12 - 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_1.52.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/oligoClasses.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oligoClasses/DESCRIPTION’ ... OK
* this is package ‘oligoClasses’ version ‘1.52.0’
* checking package namespace information ... OK
* checking package dependencies ... 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 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’
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 ... 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-3.12-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/4.0/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)

Tests output


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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, 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] "/Users/biocbuild/bbs-3.12-bioc/meat/oligoClasses.Rcheck/tests"

$pathToUnitTests
[1] "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/oligoClasses/unitTests"

Welcome to oligoClasses version 1.52.0


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 1.54.1
================================================================================
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")=="/tmp/RtmpmsY0W5/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-3.12-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 -- Thu May  6 04:23:20 2021 
*********************************************** 
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 
 22.888   1.078  24.695

Example timings

name	user	system	elapsed
AlleleSet-class	0.177	0.035	0.300
AssayData-methods	2.054	0.061	2.123
AssayDataList	0.006	0.001	0.007
BeadStudioSet-class	0.063	0.001	0.064
CNSet-class	0.049	0.001	0.050
CopyNumberSet-class	0.032	0.002	0.033
CopyNumberSet-methods	0.208	0.175	0.386
FeatureSetExtensions-class	0.168	0.017	0.184
GRanges-methods	0.589	0.067	0.804
GenomeAnnotatedDataFrameFrom-methods	0.835	0.036	0.876
SnpSet-methods	0.028	0.000	0.029
SnpSet2-class	0.040	0.001	0.041
SnpSuperSet-class	0.068	0.001	0.070
affyPlatforms	0.001	0.000	0.001
batch	0.054	0.001	0.056
celfileDate	0.027	0.008	0.039
celfileName	0.000	0.000	0.001
checkExists	0.006	0.002	0.007
checkOrder	0.240	0.004	0.245
chromosome-methods	0.000	0.000	0.001
chromosome2integer	0.001	0.001	0.002
clusterOpts	0.048	0.005	0.055
data-efsExample	0.001	0.002	0.003
data-scqsExample	0.002	0.001	0.002
data-sfsExample	0.002	0.001	0.003
data-sqsExample	0.002	0.001	0.002
db	0	0	0
ff_matrix	0.001	0.000	0.001
ff_or_matrix-class	0.001	0.001	0.000
fileConnections	0.001	0.000	0.001
flags	0.039	0.000	0.039
gSet-class	0.001	0.000	0.002
gSetList-class	0.001	0.000	0.001
genomeBuild	0.004	0.000	0.003
geometry-methods	1.296	0.034	1.332
getBar	0.001	0.001	0.002
getSequenceLengths	0.114	0.011	0.125
i2p_p2i	0.000	0.001	0.000
integerMatrix	0.001	0.000	0.001
is.ffmatrix	0.001	0.000	0.001
isPackageLoaded	0.001	0.000	0.001
kind	0.278	0.015	0.293
largeObjects	0.002	0.003	0.005
ldOpts	0.002	0.001	0.003
library2	0.045	0.002	0.047
list.celfiles	0.013	0.003	0.018
locusLevelData	0.102	0.004	0.106
makeFeatureGRanges	0.493	0.025	0.567
oligoSetExample	0.190	0.005	0.196
pdPkgFromBioC	0	0	0
requireAnnotation	0.000	0.001	0.000
splitVec	0.002	0.003	0.006

CHECK report for oligoClasses on merida1

Summary

Command output

Installation output

Tests output

Example timings