Back to Multiple platform build/check report for BioC 3.8 |
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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 | |