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This page was generated on 2022-01-24 13:07:00 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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

CHECK results for sesame on tokay2


To the developers/maintainers of the sesame package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sesame.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1775/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.12.7  (landing page)
Wanding Zhou
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/sesame
git_branch: RELEASE_3_14
git_last_commit: 1e3ec3a
git_last_commit_date: 2021-12-13 15:25:11 -0500 (Mon, 13 Dec 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: sesame
Version: 1.12.7
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sesame.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings sesame_1.12.7.tar.gz
StartedAt: 2022-01-24 02:20:04 -0500 (Mon, 24 Jan 2022)
EndedAt: 2022-01-24 02:51:38 -0500 (Mon, 24 Jan 2022)
EllapsedTime: 1894.7 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sesame.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings sesame_1.12.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/sesame.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sesame/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sesame' version '1.12.7'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 whether package 'sesame' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
cnSegmentation               55.42   3.67   65.64
visualizeSegments            57.69   0.64   58.95
DMR                          32.94   0.99   36.09
testEnrichment               24.68   0.45   25.92
bSubMostVariable             22.31   0.68   23.17
DML                          18.09   2.64   27.01
sdf_read_table               17.66   0.44   18.45
compareMouseTissueReference  17.23   0.21   22.64
diffRefSet                   16.15   0.52   17.22
testEnrichmentGene           15.64   0.19   16.61
getProbesByChromosome        14.80   0.19   17.16
compareMouseStrainReference  14.28   0.13   15.32
as.data.frame.sesameQC       13.14   1.06   14.39
print.sesameQC               13.34   0.73   14.25
attachManifest               13.22   0.72   20.06
getRefSet                    12.30   0.15   12.62
createUCSCtrack              11.72   0.22   12.25
visualizeGene                11.20   0.43   12.09
sesameQC                     11.09   0.50   11.75
sdf_write_table              11.28   0.18   11.62
dyeBiasCorrMostBalanced      11.09   0.22   18.13
bisConversionControl         10.93   0.34   12.26
bSubProbes                   10.42   0.82   11.58
getProbesByGene              10.76   0.29   11.87
inferStrain                  10.27   0.78   11.72
calcDatabaseSetStatisticsAll  9.64   1.36   13.18
inferTissue                   9.62   0.72   11.53
SNPcheck                      9.21   0.67   28.37
print.DMLSummary              9.69   0.16   10.14
getDatabaseSetOverlap         9.48   0.36   10.73
estimateLeukocyte             9.40   0.41   12.47
summaryExtractTest            8.80   0.24    9.33
deidentify                    8.65   0.25    9.56
dmContrasts                   8.64   0.14    8.95
reIdentify                    8.13   0.37    8.80
qualityMask                   6.22   0.19    7.20
qualityRank                   5.90   0.34    6.81
bSubComplete                  6.00   0.18    7.25
setMaskBySpecies              5.84   0.21    6.67
inferSex                      5.61   0.41    6.36
getNormCtls                   5.50   0.22    6.39
dyeBiasCorrTypeINorm          5.17   0.21    5.55
getAutosomeProbes             4.91   0.16    5.21
SigDF                         4.51   0.41    8.47
dyeBiasCorr                   4.63   0.27    5.22
probeSuccessRate              4.57   0.24    5.13
controls                      4.61   0.18    5.11
predictMouseAgeInMonth        3.78   0.13    5.14
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
visualizeSegments            56.15   0.66   57.42
cnSegmentation               53.84   1.08   55.44
DMR                          32.56   0.62   33.85
testEnrichment               23.98   0.61   25.41
bSubMostVariable             22.42   0.28   22.89
diffRefSet                   17.62   0.36   18.31
sdf_read_table               16.99   0.50   17.86
compareMouseTissueReference  15.78   0.25   16.39
testEnrichmentGene           14.75   0.24   15.48
compareMouseStrainReference  14.21   0.09   15.14
createUCSCtrack              13.54   0.19   14.08
getProbesByChromosome        13.30   0.19   13.67
as.data.frame.sesameQC       11.91   1.31   13.41
DML                          11.94   1.05   13.46
attachManifest               12.50   0.34   13.15
print.sesameQC               10.63   0.80   11.59
visualizeGene                10.80   0.38   11.62
getRefSet                    10.64   0.12   10.93
getProbesByGene              10.50   0.25   11.08
dmContrasts                  10.69   0.05   10.91
bSubProbes                   10.37   0.28   11.00
calcDatabaseSetStatisticsAll  9.88   0.43   11.75
deidentify                    9.87   0.26   10.55
print.DMLSummary              9.89   0.20   10.40
bisConversionControl          9.61   0.30   10.39
sdf_write_table               9.56   0.28   10.03
getDatabaseSetOverlap         9.46   0.28   10.23
inferTissue                   9.06   0.50   10.75
estimateLeukocyte             8.72   0.27    9.32
reIdentify                    8.81   0.16    9.30
inferStrain                   8.30   0.47    9.30
sesameQC                      8.33   0.36    8.85
summaryExtractTest            8.38   0.19    8.91
dyeBiasCorrMostBalanced       7.99   0.32    8.61
SNPcheck                      7.62   0.36    8.31
qualityRank                   5.47   0.34    6.28
inferSex                      5.17   0.34    5.80
setMaskBySpecies              5.32   0.17    5.79
getNormCtls                   5.35   0.11    5.79
qualityMask                   4.99   0.08    5.39
dyeBiasCorrTypeINorm          4.42   0.45    5.01
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

sesame.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/sesame_1.12.7.tar.gz && rm -rf sesame.buildbin-libdir && mkdir sesame.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sesame.buildbin-libdir sesame_1.12.7.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL sesame_1.12.7.zip && rm sesame_1.12.7.tar.gz sesame_1.12.7.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  140k  100  140k    0     0   745k      0 --:--:-- --:--:-- --:--:--  748k

install for i386

* installing *source* package 'sesame' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'sesame'
    finding HTML links ... done
    BetaValueToMValue                       html  
    DML                                     html  
    DMR                                     html  
    MValueToBetaValue                       html  
    RGChannelSetToSigDFs                    html  
    SNPcheck                                html  
    SigDF                                   html  
    SigDFToRatioSet                         html  
    SigDFsToRGChannelSet                    html  
    addMask                                 html  
    as.data.frame.sesameQC                  html  
    attachManifest                          html  
    bSubComplete                            html  
    bSubMostVariable                        html  
    bSubProbes                              html  
    binSignals                              html  
    bisConversionControl                    html  
    calcDatabaseSetStatistics1              html  
    calcDatabaseSetStatisticsAll            html  
    checkLevels                             html  
    chipAddressToSignal                     html  
    cnSegmentation                          html  
    compareDatbaseSetOverlap                html  
    compareMouseStrainReference             html  
    compareMouseTissueReference             html  
    controls                                html  
    createDatabaseSetNetwork                html  
    createUCSCtrack                         html  
    deidentify                              html  
    detectionPnegEcdf                       html  
    detectionPoobEcdf                       html  
    detectionPoobEcdf2                      html  
    diffRefSet                              html  
    dmContrasts                             html  
    dyeBiasCorr                             html  
    dyeBiasCorrMostBalanced                 html  
    dyeBiasCorrTypeINorm                    html  
    dyeBiasDistortion                       html  
    estimateCellComposition                 html  
    estimateLeukocyte                       html  
    extractDesign                           html  
    formatVCF                               html  
    getAFTypeIbySumAlleles                  html  
    getAutosomeProbes                       html  
    getBetas                                html  
    getBinCoordinates                       html  
    getDatabaseSetOverlap                   html  
    getNormCtls                             html  
    getProbesByChromosome                   html  
    getProbesByGene                         html  
    getProbesByRegion                       html  
    getProbesByTSS                          html  
    getRefSet                               html  
    getSexInfo                              html  
    inferEthnicity                          html  
    inferInfiniumIChannel                   html  
    inferSex                                html  
    inferSexKaryotypes                      html  
    inferSpecies                            html  
    inferStrain                             html  
    inferTissue                             html  
    initFileSet                             html  
    isUniqProbeID                           html  
    mapFileSet                              html  
    meanIntensity                           html  
    medianTotalIntensity                    html  
    neob                                    html  
    noMasked                                html  
    noob                                    html  
    openSesame                              html  
    openSesameToFile                        html  
    plotLollipop                            html  
    plotVolcano                             html  
    predictAgeHorvath353                    html  
    predictAgeSkinBlood                     html  
    predictMouseAgeInMonth                  html  
    print.DMLSummary                        html  
    print.SigDF                             html  
    print.fileSet                           html  
    print.sesameQC                          html  
    probeID_designType                      html  
    probeSuccessRate                        html  
    qualityMask                             html  
    qualityRank                             html  
    reIdentify                              html  
    readFileSet                             html  
    readIDATpair                            html  
    reopenSesame                            html  
    resetMask                               html  
    scrub                                   html  
    scrubSoft                               html  
    sdfPlatform                             html  
    sdf_read_table                          html  
    sdf_write_table                         html  
    searchIDATprefixes                      html  
    segmentBins                             html  
    sesame-package                          html  
    sesamePlotIntensVsBetas                 html  
    sesamePlotRedGrnQQ                      html  
    sesameQC                                html  
    sesamize                                html  
    setMask                                 html  
    setMaskBySpecies                        html  
    signalMU                                html  
    sliceFileSet                            html  
    summaryExtractTest                      html  
    testEnrichment                          html  
    testEnrichment1                         html  
    testEnrichmentFGSEA                     html  
    testEnrichmentFisher                    html  
    testEnrichmentGene                      html  
    testEnrichmentSpearman                  html  
    totalIntensities                        html  
    twoCompsEst2                            html  
    visualizeGene                           html  
    visualizeProbes                         html  
    visualizeRegion                         html  
    visualizeSegments                       html  
** 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

install for x64

* installing *source* package 'sesame' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sesame' as sesame_1.12.7.zip
* DONE (sesame)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'sesame' successfully unpacked and MD5 sums checked

Tests output

sesame.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.

> library(testthat)
> library(sesame)
Loading required package: sesameData
Loading required package: ExperimentHub
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, 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

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: rmarkdown
Loading sesameData.

----------------------------------------------------------
| SEnsible Step-wise Analysis of DNA MEthylation (SeSAMe)
| --------------------------------------------------------
| Please cache the annotation data for your array platform
| (e.g. EPIC) by calling "sesameDataCache("EPIC")"
| or "sesameDataCacheAll()". This needs to be done only
| once per SeSAMe installation.
----------------------------------------------------------

> 
> test_check("sesame")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  15.70    2.20   18.26 

sesame.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> library(testthat)
> library(sesame)
Loading required package: sesameData
Loading required package: ExperimentHub
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, 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

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: rmarkdown
Loading sesameData.

----------------------------------------------------------
| SEnsible Step-wise Analysis of DNA MEthylation (SeSAMe)
| --------------------------------------------------------
| Please cache the annotation data for your array platform
| (e.g. EPIC) by calling "sesameDataCache("EPIC")"
| or "sesameDataCacheAll()". This needs to be done only
| once per SeSAMe installation.
----------------------------------------------------------

> 
> test_check("sesame")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  18.60    1.37   20.29 

Example timings

sesame.Rcheck/examples_i386/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML18.09 2.6427.01
DMR32.94 0.9936.09
MValueToBetaValue000
RGChannelSetToSigDFs000
SNPcheck 9.21 0.6728.37
SigDF4.510.418.47
SigDFToRatioSet000
SigDFsToRGChannelSet000
addMask0.110.010.13
as.data.frame.sesameQC13.14 1.0614.39
attachManifest13.22 0.7220.06
bSubComplete6.000.187.25
bSubMostVariable22.31 0.6823.17
bSubProbes10.42 0.8211.58
bisConversionControl10.93 0.3412.26
calcDatabaseSetStatisticsAll 9.64 1.3613.18
checkLevels1.320.062.25
cnSegmentation55.42 3.6765.64
compareDatbaseSetOverlap3.170.083.42
compareMouseStrainReference14.28 0.1315.32
compareMouseTissueReference17.23 0.2122.64
controls4.610.185.11
createDatabaseSetNetwork2.910.073.15
createUCSCtrack11.72 0.2212.25
deidentify8.650.259.56
detectionPnegEcdf0.180.020.20
detectionPoobEcdf1.690.011.71
detectionPoobEcdf21.130.001.12
diffRefSet16.15 0.5217.22
dmContrasts8.640.148.95
dyeBiasCorr4.630.275.22
dyeBiasCorrMostBalanced11.09 0.2218.13
dyeBiasCorrTypeINorm5.170.215.55
dyeBiasDistortion1.170.051.21
estimateLeukocyte 9.40 0.4112.47
formatVCF2.510.223.49
getAFTypeIbySumAlleles3.560.074.08
getAutosomeProbes4.910.165.21
getBetas3.080.113.35
getDatabaseSetOverlap 9.48 0.3610.73
getNormCtls5.500.226.39
getProbesByChromosome14.80 0.1917.16
getProbesByGene10.76 0.2911.87
getProbesByRegion4.550.104.80
getProbesByTSS0.20.00.2
getRefSet12.30 0.1512.62
getSexInfo3.110.363.63
inferEthnicity1.040.131.17
inferInfiniumIChannel0.440.060.50
inferSex5.610.416.36
inferSexKaryotypes2.780.283.28
inferSpecies000
inferStrain10.27 0.7811.72
inferTissue 9.62 0.7211.53
initFileSet0.030.010.05
mapFileSet0.050.020.06
meanIntensity1.880.292.31
medianTotalIntensity1.540.251.94
neob3.140.403.53
noMasked1.660.141.97
noob2.720.503.22
openSesame1.541.613.94
openSesameToFile1.710.542.25
plotLollipop0.920.050.97
plotVolcano0.110.000.11
predictAgeHorvath3532.910.123.32
predictAgeSkinBlood0.150.000.16
predictMouseAgeInMonth3.780.135.14
print.DMLSummary 9.69 0.1610.14
print.SigDF0.950.091.20
print.fileSet0.050.000.05
print.sesameQC13.34 0.7314.25
probeID_designType000
probeSuccessRate4.570.245.13
qualityMask6.220.197.20
qualityRank5.900.346.81
reIdentify8.130.378.80
readFileSet0.040.000.05
readIDATpair0.130.000.12
resetMask1.030.071.25
scrub2.170.292.47
scrubSoft3.740.444.17
sdfPlatform0.870.051.10
sdf_read_table17.66 0.4418.45
sdf_write_table11.28 0.1811.62
searchIDATprefixes0.010.000.11
sesame-package0.770.000.77
sesamePlotIntensVsBetas2.840.193.17
sesamePlotRedGrnQQ2.680.112.94
sesameQC11.09 0.5011.75
sesamize000
setMask3.110.093.39
setMaskBySpecies5.840.216.67
signalMU1.330.071.56
sliceFileSet2.610.112.88
summaryExtractTest8.800.249.33
testEnrichment24.68 0.4525.92
testEnrichmentGene15.64 0.1916.61
totalIntensities4.180.194.70
visualizeGene11.20 0.4312.09
visualizeProbes1.070.001.08
visualizeRegion0.440.000.44
visualizeSegments57.69 0.6458.95

sesame.Rcheck/examples_x64/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML11.94 1.0513.46
DMR32.56 0.6233.85
MValueToBetaValue000
RGChannelSetToSigDFs000
SNPcheck7.620.368.31
SigDF4.220.214.72
SigDFToRatioSet000
SigDFsToRGChannelSet000
addMask0.090.000.09
as.data.frame.sesameQC11.91 1.3113.41
attachManifest12.50 0.3413.15
bSubComplete4.250.134.52
bSubMostVariable22.42 0.2822.89
bSubProbes10.37 0.2811.00
bisConversionControl 9.61 0.3010.39
calcDatabaseSetStatisticsAll 9.88 0.4311.75
checkLevels1.000.021.92
cnSegmentation53.84 1.0855.44
compareDatbaseSetOverlap3.010.033.23
compareMouseStrainReference14.21 0.0915.14
compareMouseTissueReference15.78 0.2516.39
controls4.120.134.56
createDatabaseSetNetwork2.810.093.08
createUCSCtrack13.54 0.1914.08
deidentify 9.87 0.2610.55
detectionPnegEcdf0.170.020.19
detectionPoobEcdf0.980.031.02
detectionPoobEcdf20.960.081.03
diffRefSet17.62 0.3618.31
dmContrasts10.69 0.0510.91
dyeBiasCorr4.150.324.84
dyeBiasCorrMostBalanced7.990.328.61
dyeBiasCorrTypeINorm4.420.455.01
dyeBiasDistortion2.160.092.25
estimateLeukocyte8.720.279.32
formatVCF2.560.123.51
getAFTypeIbySumAlleles3.750.134.14
getAutosomeProbes4.670.174.99
getBetas3.520.143.83
getDatabaseSetOverlap 9.46 0.2810.23
getNormCtls5.350.115.79
getProbesByChromosome13.30 0.1913.67
getProbesByGene10.50 0.2511.08
getProbesByRegion4.600.064.83
getProbesByTSS0.240.000.23
getRefSet10.64 0.1210.93
getSexInfo4.120.284.57
inferEthnicity1.020.081.10
inferInfiniumIChannel1.770.131.89
inferSex5.170.345.80
inferSexKaryotypes2.480.473.12
inferSpecies000
inferStrain8.300.479.30
inferTissue 9.06 0.5010.75
initFileSet0.030.000.03
mapFileSet0.030.000.04
meanIntensity1.800.152.11
medianTotalIntensity1.590.151.90
neob2.030.322.36
noMasked1.660.141.97
noob2.030.222.25
openSesame0.920.050.97
openSesameToFile1.890.061.95
plotLollipop0.920.050.97
plotVolcano0.110.000.11
predictAgeHorvath3532.890.053.08
predictAgeSkinBlood0.100.000.09
predictMouseAgeInMonth3.400.114.52
print.DMLSummary 9.89 0.2010.40
print.SigDF1.330.061.53
print.fileSet0.060.000.07
print.sesameQC10.63 0.8011.59
probeID_designType000
probeSuccessRate4.450.174.95
qualityMask4.990.085.39
qualityRank5.470.346.28
reIdentify8.810.169.30
readFileSet0.080.000.08
readIDATpair0.220.000.22
resetMask1.050.041.23
scrub2.110.242.35
scrubSoft3.600.313.91
sdfPlatform0.870.131.14
sdf_read_table16.99 0.5017.86
sdf_write_table 9.56 0.2810.03
searchIDATprefixes0.010.000.02
sesame-package1.080.001.08
sesamePlotIntensVsBetas2.390.122.71
sesamePlotRedGrnQQ2.440.022.61
sesameQC8.330.368.85
sesamize000
setMask2.800.143.08
setMaskBySpecies5.320.175.79
signalMU1.320.051.52
sliceFileSet2.650.042.87
summaryExtractTest8.380.198.91
testEnrichment23.98 0.6125.41
testEnrichmentGene14.75 0.2415.48
totalIntensities4.310.104.77
visualizeGene10.80 0.3811.62
visualizeProbes0.910.000.91
visualizeRegion0.430.030.47
visualizeSegments56.15 0.6657.42