Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2021-07-23 15:06:21 -0400 (Fri, 23 Jul 2021).

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 1745/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.10.4  (landing page)
Wanding Zhou
Snapshot Date: 2021-07-22 04:50:13 -0400 (Thu, 22 Jul 2021)
URL: https://git.bioconductor.org/packages/sesame
Branch: RELEASE_3_13
Last Commit: 323ca39
Last Changed Date: 2021-06-03 16:32:54 -0400 (Thu, 03 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.10.4
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sesame.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings sesame_1.10.4.tar.gz
StartedAt: 2021-07-23 05:54:09 -0400 (Fri, 23 Jul 2021)
EndedAt: 2021-07-23 06:24:21 -0400 (Fri, 23 Jul 2021)
EllapsedTime: 1812.3 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sesame.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings sesame_1.10.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/sesame.Rcheck'
* using R version 4.1.0 (2021-05-18)
* 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 '1.10.4'
* 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
DMR                         91.69   1.35  105.23
cnSegmentation              65.36   8.07   76.29
topSegments                 65.67   0.19   65.99
as.data.frame.sesameQC      21.47   2.47   24.07
sesameQC                    22.37   0.64   23.13
bSubMostVariable            18.71   1.85   21.47
compareMouseTissueReference 20.03   0.28   20.64
print.sesameQC              19.43   0.69   20.25
dyeBiasCorrMostBalanced     17.66   0.34   20.10
betaToAF                    14.37   1.57   16.86
SigSetsToRGChannelSet       14.14   0.21   14.72
qualityRank                 12.59   0.97   13.89
DML                         10.70   1.65   12.89
SigSetToRatioSet            10.95   0.66   11.79
getAutosomeProbes           11.30   0.20   12.33
diffRefSet                  10.61   0.20   11.00
bisConversionControl         8.38   0.79    9.41
summaryExtractCfList         8.84   0.08    9.03
SNPcheck                     8.47   0.26   10.42
sesamePlotIntensVsBetas      8.05   0.20    8.38
summaryExtractTest           8.17   0.03    8.31
compareMouseBloodReference   7.17   0.34    8.06
IGpass                       7.17   0.23    8.23
print.DMLSummary             7.27   0.06    7.43
inferStrain                  6.72   0.39    7.36
reIdentify                   6.76   0.05    6.81
IG-methods                   6.06   0.62    9.35
dyeBiasCorrTypeINorm         6.19   0.37    6.67
formatVCF                    6.15   0.09    6.61
SigSetList-methods           5.95   0.16    6.69
estimateLeukocyte            5.78   0.19    7.11
inferSex                     5.56   0.30    6.14
noobsb                       5.27   0.47    5.74
getBetas                     5.49   0.10    5.69
getSexInfo                   4.94   0.07    5.02
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
DMR                         75.77   0.52   76.61
topSegments                 66.38   0.21   66.69
cnSegmentation              58.05   1.39   59.91
sesameQC                    18.89   0.71   19.69
compareMouseTissueReference 19.02   0.25   19.48
as.data.frame.sesameQC      18.29   0.45   18.84
print.sesameQC              17.25   0.60   17.94
bSubMostVariable            16.42   0.16   16.69
betaToAF                    13.75   0.30   14.36
dyeBiasCorrMostBalanced     12.82   0.33   13.25
diffRefSet                  11.97   0.25   12.34
DML                         11.09   1.13   12.51
qualityRank                 11.05   0.25   11.51
SigSetToRatioSet            10.54   0.36   11.03
SigSetsToRGChannelSet       10.50   0.29   11.02
getAutosomeProbes            9.38   0.17    9.81
SNPcheck                     8.12   0.11    8.45
sesamePlotIntensVsBetas      7.89   0.19    8.18
summaryExtractCfList         7.56   0.09    7.77
summaryExtractTest           7.36   0.08    7.53
bisConversionControl         7.19   0.16    7.56
print.DMLSummary             7.25   0.09    7.51
compareMouseBloodReference   6.76   0.25    7.36
noobsb                       6.77   0.18    6.94
reIdentify                   6.73   0.02    6.75
getProbesByGene              6.45   0.14    6.69
IG-methods                   6.09   0.14    6.43
inferStrain                  5.62   0.31    6.19
SigSetList-methods           5.58   0.19    6.00
IGpass                       5.50   0.20    5.92
getBetas                     5.30   0.07    5.48
formatVCF                    5.29   0.07    5.72
inferSex                     4.71   0.19    5.10
* 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://155.52.207.165/BBS/3.13/bioc/src/contrib/sesame_1.10.4.tar.gz && rm -rf sesame.buildbin-libdir && mkdir sesame.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sesame.buildbin-libdir sesame_1.10.4.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL sesame_1.10.4.zip && rm sesame_1.10.4.tar.gz sesame_1.10.4.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  134k  100  134k    0     0  1069k      0 --:--:-- --:--:-- --:--:-- 1079k

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  
    DMLShrinkage                            html  
    DMR                                     html  
    IG-methods                              html  
    IG-replace-methods                      html  
REDIRECT:topic	 IG<- -> IG-replace-methods.html [ FAIL ]
REDIRECT:topic	 IG<-,SigSet-method -> IG-replace-methods.html [ FAIL ]
    IGpass                                  html  
    II-methods                              html  
    II-replace-methods                      html  
REDIRECT:topic	 II<- -> II-replace-methods.html [ FAIL ]
REDIRECT:topic	 II<-,SigSet-method -> II-replace-methods.html [ FAIL ]
    IIpass                                  html  
    IR-methods                              html  
    IR-replace-methods                      html  
REDIRECT:topic	 IR<- -> IR-replace-methods.html [ FAIL ]
REDIRECT:topic	 IR<-,SigSet-method -> IR-replace-methods.html [ FAIL ]
    IRpass                                  html  
    MValueToBetaValue                       html  
    RGChannelSetToSigSets                   html  
    SNPcheck                                html  
    SigSet-class                            html  
    SigSetList-class                        html  
    SigSetList-methods                      html  
    SigSetList                              html  
    SigSetListFromIDATs                     html  
    SigSetListFromPath                      html  
    SigSetToRatioSet                        html  
    SigSetsToRGChannelSet                   html  
    addMask                                 html  
    as.data.frame.sesameQC                  html  
    bSubComplete                            html  
    bSubMostVariable                        html  
    bSubProbes                              html  
    betaToAF                                html  
    binSignals                              html  
    bisConversionControl                    html  
    buildControlMatrix450k                  html  
    checkLevels                             html  
    chipAddressToSignal                     html  
    cnSegmentation                          html  
    compareMouseBloodReference              html  
    compareMouseTissueReference             html  
    createUCSCtrack                         html  
    ctl-methods                             html  
    ctl-replace-methods                     html  
REDIRECT:topic	 ctl<- -> ctl-replace-methods.html [ FAIL ]
REDIRECT:topic	 ctl<-,SigSet-method -> ctl-replace-methods.html [ FAIL ]
    deidentify                              html  
    detectionPfixedNorm                     html  
    detectionPnegEcdf                       html  
    detectionPnegNorm                       html  
    detectionPnegNormGS                     html  
    detectionPnegNormTotal                  html  
    detectionPoobEcdf                       html  
    detectionPoobEcdf2                      html  
    diffRefSet                              html  
    dyeBiasCorr                             html  
    dyeBiasCorrMostBalanced                 html  
    dyeBiasCorrTypeINorm                    html  
    estimateCellComposition                 html  
    estimateLeukocyte                       html  
    extra-methods                           html  
    extra-replace-methods                   html  
REDIRECT:topic	 extra<- -> extra-replace-methods.html [ FAIL ]
REDIRECT:topic	 extra<-,SigSet-method -> extra-replace-methods.html [ FAIL ]
    extractDesign                           html  
    formatVCF                               html  
    getAFTypeIbySumAlleles                  html  
    getAutosomeProbes                       html  
    getBetas                                html  
    getBinCoordinates                       html  
    getNormCtls                             html  
    getProbesByChromosome                   html  
    getProbesByGene                         html  
    getProbesByRegion                       html  
    getProbesByTSS                          html  
    getRefSet                               html  
    getSexInfo                              html  
    inferEthnicity                          html  
    inferSex                                html  
    inferSexKaryotypes                      html  
    inferStrain                             html  
    inferTypeIChannel                       html  
    initFileSet                             html  
    isUniqProbeID                           html  
    makeExampleSeSAMeDataSet                html  
    makeExampleTinyEPICDataSet              html  
    mapFileSet                              html  
    mask                                    html  
    meanIntensity                           html  
    noob                                    html  
    noobsb                                  html  
    oobG-methods                            html  
    oobG-replace-methods                    html  
REDIRECT:topic	 oobG<- -> oobG-replace-methods.html [ FAIL ]
REDIRECT:topic	 oobG<-,SigSet-method -> oobG-replace-methods.html [ FAIL ]
    oobGpass                                html  
    oobR-methods                            html  
    oobR-replace-methods                    html  
REDIRECT:topic	 oobR<- -> oobR-replace-methods.html [ FAIL ]
REDIRECT:topic	 oobR<-,SigSet-method -> oobR-replace-methods.html [ FAIL ]
    oobRpass                                html  
    openSesame                              html  
    openSesameToFile                        html  
    parseGEOSignalABFile                    html  
    predictAgeHorvath353                    html  
    predictAgePheno                         html  
    predictAgeSkinBlood                     html  
    predictMouseAgeInMonth                  html  
    print.DMLSummary                        html  
    print.fileSet                           html  
    print.sesameQC                          html  
    probeID_designType                      html  
    probeNames-methods                      html  
    pval-methods                            html  
    pval-replace-methods                    html  
REDIRECT:topic	 pval<- -> pval-replace-methods.html [ FAIL ]
REDIRECT:topic	 pval<-,SigSet-method -> pval-replace-methods.html [ FAIL ]
    qualityMask                             html  
    qualityRank                             html  
    reIdentify                              html  
    readFileSet                             html  
    readIDATpair                            html  
    reopenSesame                            html  
    resetMask                               html  
    restoreMask                             html  
    saveMask                                html  
    scrub                                   html  
    scrubSoft                               html  
    searchIDATprefixes                      html  
    segmentBins                             html  
    sesame-package                          html  
    sesamePlotIntensVsBetas                 html  
    sesamePlotRedGrnQQ                      html  
    sesameQC                                html  
    sesamize                                html  
    setMask                                 html  
    show-methods                            html  
    signalMU                                html  
    sliceFileSet                            html  
    subsetSignal                            html  
    summaryExtractCfList                    html  
    summaryExtractTest                      html  
    topSegments                             html  
    totalIntensities                        html  
    totalIntensityZscore                    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_1.10.4.zip
* DONE (sesame)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'sesame' successfully unpacked and MD5 sums checked

Tests output

sesame.Rcheck/tests_i386/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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
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, 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 1 | SKIP 0 | PASS 19 ]
> 
> proc.time()
   user  system elapsed 
  59.92    6.26   66.62 

sesame.Rcheck/tests_x64/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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
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, 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 1 | SKIP 0 | PASS 19 ]
> 
> proc.time()
   user  system elapsed 
  65.01    5.45   71.81 

Example timings

sesame.Rcheck/examples_i386/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML10.70 1.6512.89
DMLShrinkage3.390.103.61
DMR 91.69 1.35105.23
IG-methods6.060.629.35
IG-replace-methods1.110.051.25
IGpass7.170.238.23
II-methods1.220.071.38
II-replace-methods1.110.011.22
IIpass1.000.051.17
IR-methods1.230.031.37
IR-replace-methods0.990.091.19
IRpass1.030.041.19
MValueToBetaValue000
RGChannelSetToSigSets000
SNPcheck 8.47 0.2610.42
SigSet-class000
SigSetList-methods5.950.166.69
SigSetList0.580.090.67
SigSetListFromIDATs0.150.000.16
SigSetListFromPath0.460.080.53
SigSetToRatioSet10.95 0.6611.79
SigSetsToRGChannelSet14.14 0.2114.72
addMask0.170.000.17
as.data.frame.sesameQC21.47 2.4724.07
bSubComplete0.030.000.03
bSubMostVariable18.71 1.8521.47
bSubProbes0.280.010.29
betaToAF14.37 1.5716.86
bisConversionControl8.380.799.41
buildControlMatrix450k2.250.112.36
checkLevels1.250.061.76
cnSegmentation65.36 8.0776.29
compareMouseBloodReference7.170.348.06
compareMouseTissueReference20.03 0.2820.64
createUCSCtrack1.170.101.26
ctl-methods1.060.011.18
ctl-replace-methods1.020.051.14
deidentify3.890.033.92
detectionPfixedNorm0.30.00.3
detectionPnegEcdf1.170.001.17
detectionPnegNorm0.220.000.22
detectionPnegNormGS0.170.000.17
detectionPnegNormTotal0.170.000.17
detectionPoobEcdf2.350.052.39
detectionPoobEcdf22.920.002.92
diffRefSet10.61 0.2011.00
dyeBiasCorr1.510.161.78
dyeBiasCorrMostBalanced17.66 0.3420.10
dyeBiasCorrTypeINorm6.190.376.67
estimateLeukocyte5.780.197.11
extra-methods0.980.051.14
extra-replace-methods0.940.031.07
formatVCF6.150.096.61
getAFTypeIbySumAlleles3.700.164.12
getAutosomeProbes11.30 0.2012.33
getBetas5.490.105.69
getNormCtls0.150.000.15
getProbesByChromosome0.030.000.03
getProbesByGene4.100.144.50
getProbesByRegion0.060.000.07
getProbesByTSS0.170.010.18
getRefSet2.410.072.47
getSexInfo4.940.075.02
inferEthnicity4.200.084.31
inferSex5.560.306.14
inferSexKaryotypes2.390.122.63
inferStrain6.720.397.36
inferTypeIChannel0.060.000.06
initFileSet0.050.020.06
makeExampleSeSAMeDataSet1.980.082.06
makeExampleTinyEPICDataSet000
mapFileSet0.050.000.05
mask1.020.041.17
meanIntensity2.260.132.39
noob000
noobsb5.270.475.74
oobG-methods1.010.021.11
oobG-replace-methods0.800.060.97
oobGpass0.910.081.10
oobR-methods1.400.131.62
oobR-replace-methods0.990.061.14
oobRpass1.080.031.20
openSesame3.120.033.16
openSesameToFile2.530.022.55
parseGEOSignalABFile0.580.040.62
predictAgeHorvath3532.840.113.08
predictAgePheno0.140.020.16
predictAgeSkinBlood0.180.010.18
predictMouseAgeInMonth3.180.193.50
print.DMLSummary7.270.067.43
print.fileSet0.050.000.04
print.sesameQC19.43 0.6920.25
probeID_designType000
probeNames-methods1.100.001.21
pval-methods1.000.031.14
pval-replace-methods0.930.051.11
qualityMask1.600.141.84
qualityRank12.59 0.9713.89
reIdentify6.760.056.81
readFileSet0.070.000.06
readIDATpair0.180.000.19
resetMask1.500.071.70
restoreMask1.140.031.27
saveMask0.930.051.08
scrub0.010.000.01
scrubSoft000
searchIDATprefixes0.000.000.03
sesame-package0.930.020.95
sesamePlotIntensVsBetas8.050.208.38
sesamePlotRedGrnQQ2.740.203.04
sesameQC22.37 0.6423.13
sesamize000
setMask0.340.040.37
show-methods0.990.061.17
signalMU2.120.292.54
sliceFileSet0.070.000.06
subsetSignal1.360.081.55
summaryExtractCfList8.840.089.03
summaryExtractTest8.170.038.31
topSegments65.67 0.1965.99
totalIntensities2.240.112.34
totalIntensityZscore1.730.061.80
visualizeGene1.250.021.27
visualizeProbes0.810.010.82
visualizeRegion0.900.030.93
visualizeSegments2.010.142.25

sesame.Rcheck/examples_x64/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML11.09 1.1312.51
DMLShrinkage3.150.063.33
DMR75.77 0.5276.61
IG-methods6.090.146.43
IG-replace-methods0.880.061.05
IGpass5.500.205.92
II-methods0.860.030.99
II-replace-methods0.890.041.04
IIpass1.220.011.35
IR-methods0.970.081.15
IR-replace-methods0.930.011.07
IRpass1.020.081.20
MValueToBetaValue000
RGChannelSetToSigSets000
SNPcheck8.120.118.45
SigSet-class000
SigSetList-methods5.580.196.00
SigSetList1.560.031.60
SigSetListFromIDATs0.150.000.14
SigSetListFromPath0.250.020.26
SigSetToRatioSet10.54 0.3611.03
SigSetsToRGChannelSet10.50 0.2911.02
addMask0.170.020.19
as.data.frame.sesameQC18.29 0.4518.84
bSubComplete0.030.000.03
bSubMostVariable16.42 0.1616.69
bSubProbes0.280.030.32
betaToAF13.75 0.3014.36
bisConversionControl7.190.167.56
buildControlMatrix450k1.360.111.47
checkLevels1.090.061.79
cnSegmentation58.05 1.3959.91
compareMouseBloodReference6.760.257.36
compareMouseTissueReference19.02 0.2519.48
createUCSCtrack0.940.020.96
ctl-methods1.250.061.42
ctl-replace-methods0.950.011.08
deidentify4.110.004.11
detectionPfixedNorm0.290.020.30
detectionPnegEcdf0.900.050.95
detectionPnegNorm0.220.030.25
detectionPnegNormGS0.190.010.21
detectionPnegNormTotal0.170.020.18
detectionPoobEcdf2.480.092.58
detectionPoobEcdf22.520.102.61
diffRefSet11.97 0.2512.34
dyeBiasCorr1.120.091.33
dyeBiasCorrMostBalanced12.82 0.3313.25
dyeBiasCorrTypeINorm4.170.264.55
estimateLeukocyte4.340.184.62
extra-methods0.890.071.07
extra-replace-methods0.920.041.06
formatVCF5.290.075.72
getAFTypeIbySumAlleles3.710.104.03
getAutosomeProbes9.380.179.81
getBetas5.300.075.48
getNormCtls0.140.000.14
getProbesByChromosome0.010.000.02
getProbesByGene6.450.146.69
getProbesByRegion0.050.000.05
getProbesByTSS0.170.000.17
getRefSet1.770.031.80
getSexInfo2.380.142.52
inferEthnicity3.390.113.50
inferSex4.710.195.10
inferSexKaryotypes1.920.092.12
inferStrain5.620.316.19
inferTypeIChannel0.030.000.03
initFileSet0.050.000.05
makeExampleSeSAMeDataSet1.450.051.50
makeExampleTinyEPICDataSet000
mapFileSet0.050.000.05
mask1.000.021.12
meanIntensity1.780.071.86
noob000
noobsb6.770.186.94
oobG-methods0.970.011.08
oobG-replace-methods0.900.061.06
oobGpass0.860.131.08
oobR-methods1.250.111.46
oobR-replace-methods0.890.061.07
oobRpass0.890.051.14
openSesame2.550.012.65
openSesameToFile2.30.02.3
parseGEOSignalABFile0.480.080.56
predictAgeHorvath3532.420.092.63
predictAgePheno0.100.000.09
predictAgeSkinBlood0.110.020.13
predictMouseAgeInMonth2.500.142.75
print.DMLSummary7.250.097.51
print.fileSet0.030.000.03
print.sesameQC17.25 0.6017.94
probeID_designType000
probeNames-methods1.090.061.30
pval-methods1.050.021.17
pval-replace-methods1.560.141.81
qualityMask1.230.011.36
qualityRank11.05 0.2511.51
reIdentify6.730.026.75
readFileSet0.080.000.08
readIDATpair0.160.000.16
resetMask1.290.061.47
restoreMask0.960.061.12
saveMask1.480.031.63
scrub000
scrubSoft0.020.000.01
searchIDATprefixes000
sesame-package1.450.001.46
sesamePlotIntensVsBetas7.890.198.18
sesamePlotRedGrnQQ3.190.143.42
sesameQC18.89 0.7119.69
sesamize000
setMask0.290.030.33
show-methods1.050.011.17
signalMU1.390.281.78
sliceFileSet0.050.000.05
subsetSignal1.030.051.17
summaryExtractCfList7.560.097.77
summaryExtractTest7.360.087.53
topSegments66.38 0.2166.69
totalIntensities1.860.121.98
totalIntensityZscore1.610.031.64
visualizeGene1.740.101.83
visualizeProbes0.930.010.95
visualizeRegion1.000.031.03
visualizeSegments2.000.072.17