| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:41:01 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 1438/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| oligoClasses 1.64.0 (landing page) Benilton Carvalho
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: oligoClasses |
| Version: 1.64.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:oligoClasses.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings oligoClasses_1.64.0.tar.gz |
| StartedAt: 2023-11-02 12:45:35 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 12:50:33 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 297.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: oligoClasses.Rcheck |
| Warnings: 3 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:oligoClasses.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings oligoClasses_1.64.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/oligoClasses.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oligoClasses/DESCRIPTION’ ... OK
* this is package ‘oligoClasses’ version ‘1.64.0’
* 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 loading without being on the library search path ... OK
* checking 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: (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 PDF version of manual ... OK
* DONE
Status: 3 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/oligoClasses.Rcheck/00check.log’
for details.
oligoClasses.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL oligoClasses ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
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, 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] "/home/biocbuild/bbs-3.18-bioc/meat/oligoClasses.Rcheck/tests"
$pathToUnitTests
[1] "/home/biocbuild/tmp/RtmpPsfagi/RLIBS_1ae7a5248c6af5/oligoClasses/unitTests"
Welcome to oligoClasses version 1.64.0
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 1.66.0
================================================================================
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")=="/home/biocbuild/tmp/RtmpP3qf8U/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.....: /home/biocbuild/bbs-3.18-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 Nov 2 12:50:28 2023
***********************************************
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
22.103 0.971 23.979
oligoClasses.Rcheck/oligoClasses-Ex.timings
| name | user | system | elapsed | |
| AlleleSet-class | 0.150 | 0.016 | 0.167 | |
| AssayData-methods | 1.400 | 0.068 | 1.496 | |
| AssayDataList | 0.004 | 0.002 | 0.006 | |
| BeadStudioSet-class | 0.057 | 0.000 | 0.057 | |
| CNSet-class | 0.043 | 0.000 | 0.043 | |
| CopyNumberSet-class | 0.032 | 0.000 | 0.032 | |
| CopyNumberSet-methods | 0.144 | 0.035 | 0.182 | |
| FeatureSetExtensions-class | 0.132 | 0.008 | 0.141 | |
| GRanges-methods | 1.174 | 0.004 | 1.180 | |
| GenomeAnnotatedDataFrameFrom-methods | 0.541 | 0.019 | 0.570 | |
| SnpSet-methods | 0.026 | 0.000 | 0.027 | |
| SnpSet2-class | 0.036 | 0.000 | 0.037 | |
| SnpSuperSet-class | 0.057 | 0.000 | 0.058 | |
| affyPlatforms | 0.001 | 0.000 | 0.001 | |
| batch | 0.047 | 0.000 | 0.047 | |
| celfileDate | 0.017 | 0.004 | 0.028 | |
| celfileName | 0 | 0 | 0 | |
| checkExists | 0.005 | 0.000 | 0.005 | |
| checkOrder | 0.158 | 0.012 | 0.170 | |
| chromosome-methods | 0.000 | 0.000 | 0.001 | |
| chromosome2integer | 0.000 | 0.000 | 0.001 | |
| clusterOpts | 0.001 | 0.000 | 0.001 | |
| data-efsExample | 0.001 | 0.000 | 0.002 | |
| data-scqsExample | 0.001 | 0.000 | 0.001 | |
| data-sfsExample | 0.001 | 0.000 | 0.001 | |
| data-sqsExample | 0.001 | 0.000 | 0.001 | |
| db | 0 | 0 | 0 | |
| ff_matrix | 0.000 | 0.000 | 0.001 | |
| ff_or_matrix-class | 0 | 0 | 0 | |
| fileConnections | 0.000 | 0.000 | 0.001 | |
| flags | 0.038 | 0.000 | 0.038 | |
| gSet-class | 0.001 | 0.000 | 0.001 | |
| gSetList-class | 0.001 | 0.000 | 0.000 | |
| genomeBuild | 0.004 | 0.000 | 0.004 | |
| geometry-methods | 0.804 | 0.020 | 0.841 | |
| getBar | 0 | 0 | 0 | |
| getSequenceLengths | 0.114 | 0.008 | 0.124 | |
| i2p_p2i | 0 | 0 | 0 | |
| integerMatrix | 0.001 | 0.000 | 0.000 | |
| is.ffmatrix | 0.001 | 0.000 | 0.001 | |
| isPackageLoaded | 0.001 | 0.000 | 0.001 | |
| kind | 0.302 | 0.008 | 0.310 | |
| largeObjects | 0.002 | 0.000 | 0.003 | |
| ldOpts | 0.001 | 0.000 | 0.002 | |
| library2 | 0.031 | 0.000 | 0.031 | |
| list.celfiles | 0.016 | 0.000 | 0.019 | |
| locusLevelData | 0.064 | 0.000 | 0.064 | |
| makeFeatureGRanges | 0.340 | 0.008 | 0.349 | |
| oligoSetExample | 0.154 | 0.004 | 0.158 | |
| pdPkgFromBioC | 0 | 0 | 0 | |
| requireAnnotation | 0 | 0 | 0 | |
| splitVec | 0.001 | 0.003 | 0.003 | |