Benilton Carvalho
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/oligoClasses |
| Branch: RELEASE_3_8 |
| Last Commit: d3e1134 |
| Last Changed Date: 2018-10-30 11:41:44 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:48:26 -0400 (Tue, 16 Apr 2019).
| Package 1076/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| oligoClasses 1.44.0 Benilton Carvalho
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: oligoClasses |
| Version: 1.44.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:oligoClasses.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings oligoClasses_1.44.0.tar.gz |
| StartedAt: 2019-04-16 01:49:50 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:53:06 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 196.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: oligoClasses.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:oligoClasses.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings oligoClasses_1.44.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/oligoClasses.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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:
‘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
Examples with CPU or elapsed time > 5s
user system elapsed
GenomeAnnotatedDataFrame-class 1.36 0.104 5.756
* 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
‘/home/biocbuild/bbs-3.8-bioc/meat/oligoClasses.Rcheck/00check.log’
for details.
oligoClasses.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL oligoClasses ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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)
oligoClasses.Rcheck/tests/doRUnit.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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] "/home/biocbuild/bbs-3.8-bioc/meat/oligoClasses.Rcheck/tests"
$pathToUnitTests
[1] "/home/biocbuild/bbs-3.8-bioc/R/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/Rtmpj7Elso"
- 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.....: /home/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 01:53:01 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
20.028 0.688 20.941
oligoClasses.Rcheck/oligoClasses-Ex.timings
| name | user | system | elapsed | |
| AlleleSet-class | 0.116 | 0.000 | 0.115 | |
| AssayData-methods | 2.036 | 0.052 | 2.111 | |
| AssayDataList | 0.004 | 0.000 | 0.008 | |
| BeadStudioSet-class | 0.064 | 0.000 | 0.067 | |
| CNSet-class | 0.052 | 0.000 | 0.055 | |
| CopyNumberSet-class | 0.036 | 0.000 | 0.036 | |
| CopyNumberSet-methods | 0.212 | 0.044 | 0.271 | |
| FeatureSetExtensions-class | 0.156 | 0.000 | 0.156 | |
| GRanges-methods | 0.420 | 0.024 | 0.445 | |
| GenomeAnnotatedDataFrame-class | 1.360 | 0.104 | 5.756 | |
| GenomeAnnotatedDataFrameFrom-methods | 1.484 | 0.004 | 1.559 | |
| SnpSet-methods | 0.036 | 0.000 | 0.034 | |
| SnpSet2-class | 0.032 | 0.008 | 0.041 | |
| SnpSuperSet-class | 0.044 | 0.000 | 0.044 | |
| affyPlatforms | 0.004 | 0.000 | 0.001 | |
| batch | 0.032 | 0.000 | 0.034 | |
| celfileDate | 0.024 | 0.004 | 0.322 | |
| celfileName | 0 | 0 | 0 | |
| checkExists | 0.008 | 0.000 | 0.007 | |
| checkOrder | 0.268 | 0.016 | 0.282 | |
| chromosome-methods | 0.000 | 0.000 | 0.001 | |
| chromosome2integer | 0.000 | 0.000 | 0.001 | |
| clusterOpts | 0.064 | 0.000 | 0.158 | |
| data-efsExample | 0.004 | 0.000 | 0.002 | |
| data-scqsExample | 0.000 | 0.000 | 0.001 | |
| data-sfsExample | 0.004 | 0.000 | 0.002 | |
| data-sqsExample | 0.000 | 0.000 | 0.002 | |
| db | 0 | 0 | 0 | |
| ff_matrix | 0 | 0 | 0 | |
| ff_or_matrix-class | 0 | 0 | 0 | |
| fileConnections | 0 | 0 | 0 | |
| flags | 0.040 | 0.000 | 0.043 | |
| gSet-class | 0.000 | 0.000 | 0.001 | |
| gSetList-class | 0.000 | 0.000 | 0.001 | |
| genomeBuild | 0.000 | 0.004 | 0.004 | |
| geometry-methods | 0.220 | 0.000 | 0.221 | |
| getBar | 0 | 0 | 0 | |
| getSequenceLengths | 0.156 | 0.000 | 0.190 | |
| i2p_p2i | 0.004 | 0.000 | 0.000 | |
| integerMatrix | 0 | 0 | 0 | |
| is.ffmatrix | 0.000 | 0.000 | 0.001 | |
| isPackageLoaded | 0.000 | 0.000 | 0.001 | |
| kind | 0.260 | 0.000 | 0.261 | |
| largeObjects | 0.000 | 0.000 | 0.003 | |
| ldOpts | 0.000 | 0.004 | 0.002 | |
| library2 | 0.060 | 0.000 | 0.057 | |
| list.celfiles | 0.02 | 0.00 | 0.05 | |
| locusLevelData | 0.104 | 0.000 | 0.106 | |
| makeFeatureGRanges | 0.396 | 0.032 | 0.430 | |
| oligoSetExample | 0.136 | 0.000 | 0.136 | |
| pdPkgFromBioC | 0 | 0 | 0 | |
| requireAnnotation | 0 | 0 | 0 | |
| splitVec | 0.004 | 0.000 | 0.002 | |