Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1442/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
oligoClasses 1.68.0 (landing page) Benilton Carvalho
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the oligoClasses package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/oligoClasses.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: oligoClasses |
Version: 1.68.0 |
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_1.68.0.tar.gz |
StartedAt: 2024-11-20 00:44:59 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 00:52:40 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 461.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: oligoClasses.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### 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_1.68.0.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: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘oligoClasses/DESCRIPTION’ ... OK * this is package ‘oligoClasses’ version ‘1.68.0’ * 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.
oligoClasses.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL oligoClasses ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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)
oligoClasses.Rcheck/tests/doRUnit.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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/tmp/Rtmpio6Z4g/RLIBS_107fe50f03f5b/oligoClasses/unitTests" Welcome to oligoClasses version 1.68.0 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 1.70.0 ================================================================================ 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' The following object is masked from 'package:base': xor Attaching package ff - getOption("fftempdir")=="/tmp/Rtmp2CJPI5/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 -- Wed Nov 20 00:52:18 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 14.968 0.903 64.049
oligoClasses.Rcheck/oligoClasses-Ex.timings
name | user | system | elapsed | |
AlleleSet-class | 0.102 | 0.004 | 0.106 | |
AssayData-methods | 1.436 | 0.061 | 2.765 | |
AssayDataList | 0.003 | 0.000 | 0.003 | |
BeadStudioSet-class | 0.033 | 0.000 | 0.034 | |
CNSet-class | 0.024 | 0.001 | 0.025 | |
CopyNumberSet-class | 0.018 | 0.003 | 0.021 | |
CopyNumberSet-methods | 0.108 | 0.079 | 0.373 | |
FeatureSetExtensions-class | 0.083 | 0.009 | 0.092 | |
GRanges-methods | 0.256 | 0.028 | 0.297 | |
GenomeAnnotatedDataFrameFrom-methods | 0.439 | 0.021 | 0.846 | |
SnpSet-methods | 0.016 | 0.001 | 0.016 | |
SnpSet2-class | 0.021 | 0.002 | 0.022 | |
SnpSuperSet-class | 0.034 | 0.001 | 0.035 | |
affyPlatforms | 0.000 | 0.001 | 0.002 | |
batch | 0.027 | 0.001 | 0.027 | |
celfileDate | 0.019 | 0.005 | 0.273 | |
celfileName | 0 | 0 | 0 | |
checkExists | 0.003 | 0.002 | 0.037 | |
checkOrder | 0.121 | 0.002 | 0.125 | |
chromosome-methods | 0.000 | 0.001 | 0.001 | |
chromosome2integer | 0.001 | 0.001 | 0.000 | |
clusterOpts | 0.036 | 0.004 | 0.152 | |
data-efsExample | 0.001 | 0.001 | 0.001 | |
data-scqsExample | 0.001 | 0.001 | 0.002 | |
data-sfsExample | 0.001 | 0.001 | 0.002 | |
data-sqsExample | 0.001 | 0.001 | 0.004 | |
db | 0.000 | 0.001 | 0.000 | |
ff_matrix | 0.000 | 0.000 | 0.001 | |
ff_or_matrix-class | 0.000 | 0.000 | 0.001 | |
fileConnections | 0 | 0 | 0 | |
flags | 0.020 | 0.001 | 0.021 | |
gSet-class | 0.000 | 0.001 | 0.001 | |
gSetList-class | 0.000 | 0.001 | 0.001 | |
genomeBuild | 0.002 | 0.001 | 0.003 | |
geometry-methods | 0.594 | 0.041 | 0.913 | |
getBar | 0 | 0 | 0 | |
getSequenceLengths | 0.100 | 0.013 | 0.158 | |
i2p_p2i | 0 | 0 | 0 | |
integerMatrix | 0.001 | 0.000 | 0.001 | |
is.ffmatrix | 0.001 | 0.000 | 0.001 | |
isPackageLoaded | 0.001 | 0.000 | 0.001 | |
kind | 0.168 | 0.017 | 0.186 | |
largeObjects | 0.001 | 0.001 | 0.003 | |
ldOpts | 0.001 | 0.000 | 0.001 | |
library2 | 0.022 | 0.002 | 0.023 | |
list.celfiles | 0.013 | 0.002 | 0.119 | |
locusLevelData | 0.047 | 0.002 | 0.049 | |
makeFeatureGRanges | 0.847 | 0.029 | 0.885 | |
oligoSetExample | 0.143 | 0.021 | 0.171 | |
pdPkgFromBioC | 0 | 0 | 0 | |
requireAnnotation | 0.000 | 0.000 | 0.001 | |
splitVec | 0.001 | 0.002 | 0.003 | |