Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

CHECK report for sesame on tokay1

This page was generated on 2019-04-13 11:29:27 -0400 (Sat, 13 Apr 2019).

Package 1429/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.0.0
Wanding Zhou
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/sesame
Branch: RELEASE_3_8
Last Commit: 8a9c43d
Last Changed Date: 2018-10-30 11:42:09 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sesame
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sesame.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings sesame_1.0.0.tar.gz
StartedAt: 2019-04-13 05:27:53 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:40:03 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 729.4 seconds
RetCode: 0
Status:  OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sesame.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings sesame_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/sesame.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.0.0'
* 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'
 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 or elapsed time > 5s
                            user system elapsed
cnSegmentation             63.46   1.78   65.23
dyeBiasCorrMostBalanced    14.40   0.31   23.83
noobsb                      8.34   0.39    8.73
diffRefSet                  8.28   0.11    8.50
bisConversionControl        7.00   0.11    7.14
detectionPnegNormGS         6.78   0.13    6.91
getBetasTypeIbySumChannels  6.75   0.11    6.86
getBetas                    6.65   0.08    6.73
detectionPoobEcdf           6.05   0.12    6.17
detectionPnegEcdf           6.09   0.03    6.12
detectionPnegNorm           5.85   0.05    5.89
getSexInfo                  5.06   0.09    5.15
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
cnSegmentation             66.30   1.11   67.40
dyeBiasCorrMostBalanced    12.08   0.27   12.34
noobsb                     10.41   0.36   10.77
bisConversionControl        8.98   0.11    9.09
diffRefSet                  8.33   0.19    8.52
detectionPnegNorm           8.38   0.07    8.43
detectionPnegEcdf           8.32   0.01    8.35
detectionPnegNormGS         7.22   0.06    7.29
detectionPoobEcdf           7.01   0.11    7.12
getBetasTypeIbySumChannels  5.90   0.08    5.98
SNPcheck                    5.28   0.11    5.39
detectionPnegNormTotal      5.22   0.01    5.23
* 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 https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/sesame_1.0.0.tar.gz && rm -rf sesame.buildbin-libdir && mkdir sesame.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sesame.buildbin-libdir sesame_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL sesame_1.0.0.zip && rm sesame_1.0.0.tar.gz sesame_1.0.0.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 50954  100 50954    0     0  1390k      0 --:--:-- --:--:-- --:--:-- 1554k

install for i386

* installing *source* package 'sesame' ...
** 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  
    IG-methods                              html  
    IG-replace-methods                      html  
    II-methods                              html  
    II-replace-methods                      html  
    IR-methods                              html  
    IR-replace-methods                      html  
    MValueToBetaValue                       html  
    SNPcheck                                html  
    SigSet-class                            html  
    SigSetList-class                        html  
    SigSetList-methods                      html  
    SigSetList                              html  
    SigSetListFromIDATs                     html  
    SigSetListFromPath                      html  
    SignalSet                               html  
    finding level-2 HTML links ... done

    binSignals                              html  
    bisConversionControl                    html  
    buildControlMatrix450k                  html  
    chipAddressToSignal                     html  
    cnSegmentation                          html  
    ctl-methods                             html  
    ctl-replace-methods                     html  
    detectionPnegEcdf                       html  
    detectionPnegNorm                       html  
    detectionPnegNormGS                     html  
    detectionPnegNormTotal                  html  
    detectionPoobEcdf                       html  
    diffRefSet                              html  
    dyeBiasCorr                             html  
    dyeBiasCorrMostBalanced                 html  
    dyeBiasCorrTypeINorm                    html  
    estimateCellComposition                 html  
    estimateLeukocyte                       html  
    getAFTypeIbySumAlleles                  html  
    getBetas                                html  
    getBetasTypeIbySumChannels              html  
    getBinCoordinates                       html  
    getNormCtls                             html  
    getProbesByGene                         html  
    getProbesByRegion                       html  
    getProbesByTSS                          html  
    getRefSet                               html  
    getSexInfo                              html  
    inferEthnicity                          html  
    inferSex                                html  
    inferSexKaryotypes                      html  
    makeExampleSeSAMeDataSet                html  
    makeExampleTinyEPICDataSet              html  
    meanIntensity                           html  
    noob                                    html  
    noobsb                                  html  
    oobG-methods                            html  
    oobG-replace-methods                    html  
    oobR-methods                            html  
    oobR-replace-methods                    html  
    openSesame                              html  
    predictAgeHorvath353                    html  
    predictAgePheno                         html  
    predictAgeSkinBlood                     html  
    pval-methods                            html  
    pval-replace-methods                    html  
    readIDATpair                            html  
    reopenSesame                            html  
    searchIDATprefixes                      html  
    segmentBins                             html  
    sesame-package                          html  
    sesamize                                html  
    show-methods                            html  
    signalR6toS4                            html  
    subsetSignal                            html  
    totalIntensities                        html  
    totalIntensityZscore                    html  
    visualizeGene                           html  
    visualizeProbes                         html  
    visualizeRegion                         html  
    visualizeSegments                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'sesame' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sesame' as sesame_1.0.0.zip
* DONE (sesame)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'sesame' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

sesame.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: AnnotationHub
Loading sesameData.
> 
> test_check("sesame")
== testthat results  ===========================================================
OK: 3 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  22.64    1.60   24.53 

sesame.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: AnnotationHub
Loading sesameData.
> 
> test_check("sesame")
== testthat results  ===========================================================
OK: 3 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  32.90    1.70   34.86 

Example timings

sesame.Rcheck/examples_i386/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
IG-methods2.400.042.45
IG-replace-methods000
II-methods000
II-replace-methods000
IR-methods000
IR-replace-methods000
MValueToBetaValue000
SNPcheck4.550.074.61
SigSet-class000
SigSetList-methods1.530.011.55
SigSetList0.780.020.79
SigSetListFromIDATs0.270.000.27
SigSetListFromPath0.420.010.44
SignalSet000
bisConversionControl7.000.117.14
buildControlMatrix450k4.620.114.74
cnSegmentation63.46 1.7865.23
ctl-methods0.010.000.02
ctl-replace-methods000
detectionPnegEcdf6.090.036.12
detectionPnegNorm5.850.055.89
detectionPnegNormGS6.780.136.91
detectionPnegNormTotal4.860.064.92
detectionPoobEcdf6.050.126.17
diffRefSet8.280.118.50
dyeBiasCorr0.170.050.22
dyeBiasCorrMostBalanced14.40 0.3123.83
dyeBiasCorrTypeINorm1.750.141.89
estimateLeukocyte2.930.113.06
getAFTypeIbySumAlleles0.570.020.58
getBetas6.650.086.73
getBetasTypeIbySumChannels6.750.116.86
getNormCtls0.270.030.30
getProbesByGene1.290.031.33
getProbesByRegion0.050.000.04
getProbesByTSS0.090.010.11
getRefSet1.910.051.96
getSexInfo5.060.095.15
inferEthnicity3.380.103.47
inferSex1.560.081.67
inferSexKaryotypes1.220.091.32
makeExampleSeSAMeDataSet4.660.054.70
makeExampleTinyEPICDataSet2.920.013.37
meanIntensity3.730.103.83
noob0.020.000.02
noobsb8.340.398.73
oobG-methods000
oobG-replace-methods000
oobR-methods000
oobR-replace-methods0.020.000.02
openSesame2.680.042.73
predictAgeHorvath3530.380.000.38
predictAgePheno0.080.000.07
predictAgeSkinBlood0.080.020.10
pval-methods000
pval-replace-methods000
readIDATpair0.20.00.2
searchIDATprefixes0.010.000.28
sesame-package2.300.052.35
sesamize000
show-methods000
signalR6toS4000
subsetSignal0.110.000.11
totalIntensities3.340.043.39
totalIntensityZscore1.440.021.45
visualizeGene1.380.081.86
visualizeProbes1.160.061.22
visualizeRegion0.470.060.53
visualizeSegments2.420.082.50

sesame.Rcheck/examples_x64/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
IG-methods2.870.052.92
IG-replace-methods000
II-methods000
II-replace-methods000
IR-methods000
IR-replace-methods000
MValueToBetaValue000
SNPcheck5.280.115.39
SigSet-class0.010.000.02
SigSetList-methods1.000.061.06
SigSetList0.990.000.99
SigSetListFromIDATs0.280.000.28
SigSetListFromPath0.440.000.44
SignalSet000
bisConversionControl8.980.119.09
buildControlMatrix450k4.410.144.55
cnSegmentation66.30 1.1167.40
ctl-methods000
ctl-replace-methods000
detectionPnegEcdf8.320.018.35
detectionPnegNorm8.380.078.43
detectionPnegNormGS7.220.067.29
detectionPnegNormTotal5.220.015.23
detectionPoobEcdf7.010.117.12
diffRefSet8.330.198.52
dyeBiasCorr0.220.030.25
dyeBiasCorrMostBalanced12.08 0.2712.34
dyeBiasCorrTypeINorm1.750.151.91
estimateLeukocyte1.790.081.88
getAFTypeIbySumAlleles0.330.020.34
getBetas4.390.064.46
getBetasTypeIbySumChannels5.900.085.98
getNormCtls0.190.000.19
getProbesByGene1.100.031.12
getProbesByRegion0.040.000.05
getProbesByTSS0.130.000.13
getRefSet2.930.052.98
getSexInfo3.770.143.91
inferEthnicity3.670.143.81
inferSex1.880.051.92
inferSexKaryotypes1.390.181.58
makeExampleSeSAMeDataSet3.390.103.48
makeExampleTinyEPICDataSet2.140.012.16
meanIntensity3.460.103.54
noob0.030.000.03
noobsb10.41 0.3610.77
oobG-methods000
oobG-replace-methods0.010.000.02
oobR-methods000
oobR-replace-methods000
openSesame2.830.012.84
predictAgeHorvath3530.330.010.35
predictAgePheno0.090.000.09
predictAgeSkinBlood0.080.000.08
pval-methods000
pval-replace-methods000
readIDATpair0.220.000.21
searchIDATprefixes000
sesame-package1.350.021.36
sesamize000
show-methods000
signalR6toS4000
subsetSignal0.140.000.14
totalIntensities3.780.083.86
totalIntensityZscore1.410.031.44
visualizeGene1.120.041.17
visualizeProbes1.080.051.13
visualizeRegion0.380.020.39
visualizeSegments1.340.071.43