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CHECK report for sesame on malbec1

This page was generated on 2021-05-06 12:29:05 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the sesame package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1689/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sesame 1.8.12  (landing page)
Wanding Zhou
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/sesame
Branch: RELEASE_3_12
Last Commit: 37a1f75
Last Changed Date: 2021-04-29 15:57:06 -0400 (Thu, 29 Apr 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: sesame
Version: 1.8.12
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings sesame_1.8.12.tar.gz
StartedAt: 2021-05-06 05:58:48 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:15:20 -0400 (Thu, 06 May 2021)
EllapsedTime: 992.7 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings sesame_1.8.12.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/sesame.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.8.12’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
cnSegmentation              66.740  0.416  68.124
as.data.frame.sesameQC      48.268  0.220  49.861
DMR                         46.616  0.332  47.998
RGChannelSetToSigSets       32.832  1.388  38.328
topSegments                 28.252  0.164  32.594
print.sesameQC              25.584  0.456  26.343
sesameQC                    25.136  0.028  25.455
compareMouseTissueReference 24.336  0.124  25.178
bSubMostVariable            24.288  0.076  24.652
diffRefSet                  17.096  0.032  17.392
dyeBiasCorrMostBalanced     16.600  0.196  17.048
getAutosomeProbes           14.128  0.084  14.793
SigSetsToRGChannelSet       13.460  0.168  14.276
SNPcheck                    11.352  0.076  11.937
DML                          9.848  0.328  10.656
betaToAF                     9.072  0.184  10.162
detectionPoobEcdf2           8.044  0.016   8.101
estimateLeukocyte            7.932  0.060   8.242
openSesameToFile             7.476  0.000   7.543
formatVCF                    7.380  0.016   8.097
deidentify                   7.244  0.004   7.255
IGpass                       6.660  0.072   7.355
getBetas                     6.684  0.020   6.928
inferEthnicity               6.528  0.024   6.559
SigSetToRatioSet             6.324  0.020   6.615
reIdentify                   5.896  0.016   5.915
getProbesByGene              5.612  0.048   5.920
noobsb                       5.464  0.160   5.633
extra-methods                4.896  0.048   5.202
qualityRank                  4.732  0.052   5.252
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘sesame’ ...
** using staged installation
** R
** 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 (sesame)

Tests output

sesame.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> 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 0 | SKIP 0 | PASS 19 ]
> 
> proc.time()
   user  system elapsed 
 73.760   4.368  70.908 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML 9.848 0.32810.656
DMLShrinkage4.2600.0284.513
DMR46.616 0.33247.998
IG-methods3.0360.0523.752
IG-replace-methods1.1000.0281.356
IGpass6.6600.0727.355
II-methods1.2640.0081.498
II-replace-methods1.3200.0241.565
IIpass1.4280.0161.676
IR-methods1.0000.0161.244
IR-replace-methods1.4600.0081.680
IRpass1.2880.0241.534
MValueToBetaValue000
RGChannelSetToSigSets32.832 1.38838.328
SNPcheck11.352 0.07611.937
SigSet-class0.0040.0000.003
SigSetList-methods0.8280.0041.393
SigSetList0.6960.0360.731
SigSetListFromIDATs0.7840.0240.809
SigSetListFromPath0.660.000.66
SigSetToRatioSet6.3240.0206.615
SigSetsToRGChannelSet13.460 0.16814.276
as.data.frame.sesameQC48.268 0.22049.861
bSubComplete0.0280.0000.028
bSubMostVariable24.288 0.07624.652
bSubProbes0.5640.0000.565
betaToAF 9.072 0.18410.162
bisConversionControl3.8000.0404.065
buildControlMatrix450k1.9240.0001.928
checkLevels1.1200.0402.818
cnSegmentation66.740 0.41668.124
compareMouseBloodReference2.6520.0444.029
compareMouseTissueReference24.336 0.12425.178
createUCSCtrack1.4560.1081.593
ctl-methods1.1920.0081.425
ctl-replace-methods1.4080.0281.654
deidentify7.2440.0047.255
detectionMask1.6200.0241.860
detectionPfixedNorm2.3400.0442.388
detectionPnegEcdf3.2280.0203.253
detectionPnegNorm2.4280.0002.428
detectionPnegNormGS2.1880.0202.211
detectionPnegNormTotal2.8160.0042.823
detectionPoobEcdf4.7200.0404.771
detectionPoobEcdf28.0440.0168.101
detectionZero2.9320.0002.941
diffRefSet17.096 0.03217.392
dyeBiasCorr1.3840.0161.680
dyeBiasCorrMostBalanced16.600 0.19617.048
dyeBiasCorrTypeINorm3.5240.1123.858
estimateLeukocyte7.9320.0608.242
extra-methods4.8960.0485.202
extra-replace-methods1.2920.0081.513
formatVCF7.3800.0168.097
getAFTypeIbySumAlleles1.4160.0081.642
getAutosomeProbes14.128 0.08414.793
getBetas6.6840.0206.928
getNormCtls0.2640.0120.276
getProbesByChromosome0.0240.0120.035
getProbesByGene5.6120.0485.920
getProbesByRegion0.0960.0000.098
getProbesByTSS0.3360.0000.339
getRefSet3.5120.0123.524
getSexInfo3.5520.0403.596
inferEthnicity6.5280.0246.559
inferSex2.5840.0882.896
inferSexKaryotypes2.7400.0963.062
inferStrain3.8200.1124.381
inferTypeIChannel0.0640.0000.064
initFileSet0.0560.0040.060
makeExampleSeSAMeDataSet2.6360.0842.722
makeExampleTinyEPICDataSet0.0120.0000.009
mapFileSet0.0640.0000.064
meanIntensity2.720.002.72
noob0.0160.0000.015
noobsb5.4640.1605.633
oobG-methods1.2720.0201.520
oobG-replace-methods1.2080.0281.456
oobGpass1.8400.0482.116
oobR-methods1.2080.0241.448
oobR-replace-methods1.8480.0242.095
oobRpass1.1280.0121.358
openSesame3.7120.0043.729
openSesameToFile7.4760.0007.543
parseGEOSignalABFile0.3200.5801.076
predictAgeHorvath3530.8960.3840.192
predictAgePheno0.1600.0080.170
predictAgeSkinBlood0.1720.0080.180
predictMouseAgeInMonth0.0480.0120.279
print.fileSet0.0520.0000.055
print.sesameQC25.584 0.45626.343
probeID_designType0.0000.0000.001
probeNames-methods0.9560.0241.204
pval-methods1.1520.0441.430
pval-replace-methods1.6040.0561.880
qualityMask1.1960.0241.445
qualityRank4.7320.0525.252
reIdentify5.8960.0165.915
readFileSet0.0760.0080.084
readIDATpair0.2240.0040.225
resetMask1.6240.0241.873
restoreMask1.2720.0081.499
saveMask1.1800.0081.403
scrub0.0160.0000.014
scrubSoft0.0200.0000.019
searchIDATprefixes0.0040.0000.022
sesame-package1.5520.0081.569
sesameQC25.136 0.02825.455
sesamize000
show-methods1.0760.0081.307
signalMU2.5720.2763.070
sliceFileSet0.0600.0040.067
subsetSignal1.6680.0122.040
summaryExtractCfList3.8400.0244.114
summaryExtractSlope3.3920.0323.673
topSegments28.252 0.16432.594
totalIntensities2.7000.0322.846
totalIntensityZscore2.3800.0002.426
visualizeGene2.2840.0362.324
visualizeProbes2.0320.0002.037
visualizeRegion0.7360.0000.739
visualizeSegments2.2480.0362.509