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This page was generated on 2021-07-23 15:05:51 -0400 (Fri, 23 Jul 2021).

CHECK results for sesame on nebbiolo1

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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: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings sesame_1.10.4.tar.gz
StartedAt: 2021-07-22 11:33:32 -0400 (Thu, 22 Jul 2021)
EndedAt: 2021-07-22 11:47:45 -0400 (Thu, 22 Jul 2021)
EllapsedTime: 852.9 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings sesame_1.10.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/sesame.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘1.10.4’
* 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 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
DMR                         72.435  1.203  74.427
topSegments                 57.895  0.999  59.148
cnSegmentation              55.783  1.244  58.093
as.data.frame.sesameQC      19.892  0.676  20.823
print.sesameQC              17.858  0.524  18.654
compareMouseTissueReference 17.938  0.432  18.886
sesameQC                    17.358  0.444  18.055
bSubMostVariable            15.433  0.428  16.114
dyeBiasCorrMostBalanced     15.239  0.472  15.985
SigSetsToRGChannelSet       13.770  0.328  14.606
betaToAF                    13.593  0.472  14.669
SigSetToRatioSet             9.834  0.404  10.509
DML                          9.434  0.756  10.837
diffRefSet                   9.909  0.263  10.449
qualityRank                  9.277  0.219   9.913
getAutosomeProbes            8.332  0.296   8.892
bisConversionControl         7.863  0.248   8.538
SNPcheck                     7.631  0.276   8.453
summaryExtractCfList         6.795  0.168   7.215
sesamePlotIntensVsBetas      6.685  0.276   7.215
IG-methods                   6.604  0.328   7.477
summaryExtractTest           6.347  0.156   6.761
compareMouseBloodReference   5.832  0.177   6.776
print.DMLSummary             5.741  0.140   6.136
getBetas                     5.704  0.176   6.133
inferStrain                  5.708  0.143   6.277
formatVCF                    5.511  0.128   6.437
SigSetList-methods           5.139  0.168   5.822
reIdentify                   5.028  0.104   5.132
IGpass                       4.844  0.180   5.456
inferSex                     4.431  0.152   5.104
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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 
 65.723   7.945  66.337 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue000
DML 9.434 0.75610.837
DMLShrinkage2.3660.0612.676
DMR72.435 1.20374.427
IG-methods6.6040.3287.477
IG-replace-methods0.6800.0160.966
IGpass4.8440.1805.456
II-methods1.0570.0441.355
II-replace-methods0.8020.0241.079
IIpass0.7890.0201.060
IR-methods0.9580.0311.241
IR-replace-methods0.7920.0281.073
IRpass0.7510.0121.014
MValueToBetaValue000
RGChannelSetToSigSets0.0010.0000.000
SNPcheck7.6310.2768.453
SigSet-class0.0040.0000.005
SigSetList-methods5.1390.1685.822
SigSetList1.8320.0761.908
SigSetListFromIDATs0.1320.0000.132
SigSetListFromPath0.2650.0080.273
SigSetToRatioSet 9.834 0.40410.509
SigSetsToRGChannelSet13.770 0.32814.606
addMask0.2290.0040.233
as.data.frame.sesameQC19.892 0.67620.823
bSubComplete0.0270.0000.027
bSubMostVariable15.433 0.42816.114
bSubProbes0.4080.0440.452
betaToAF13.593 0.47214.669
bisConversionControl7.8630.2488.538
buildControlMatrix450k1.8770.0521.928
checkLevels2.1030.1284.371
cnSegmentation55.783 1.24458.093
compareMouseBloodReference5.8320.1776.776
compareMouseTissueReference17.938 0.43218.886
createUCSCtrack1.0470.1441.192
ctl-methods0.8110.0481.111
ctl-replace-methods1.5390.0721.774
deidentify3.9370.1034.040
detectionPfixedNorm0.5490.0000.749
detectionPnegEcdf2.2500.0682.668
detectionPnegNorm0.2580.0310.290
detectionPnegNormGS0.2090.0290.238
detectionPnegNormTotal0.2480.0680.316
detectionPoobEcdf2.4210.0592.479
detectionPoobEcdf22.6900.0242.715
diffRefSet 9.909 0.26310.449
dyeBiasCorr2.3170.0562.538
dyeBiasCorrMostBalanced15.239 0.47215.985
dyeBiasCorrTypeINorm3.1440.1643.560
estimateLeukocyte3.9930.1374.413
extra-methods0.7150.0120.997
extra-replace-methods1.1030.0481.403
formatVCF5.5110.1286.437
getAFTypeIbySumAlleles3.1390.0803.744
getAutosomeProbes8.3320.2968.892
getBetas5.7040.1766.133
getNormCtls0.1760.0000.176
getProbesByChromosome0.0260.0000.026
getProbesByGene2.8360.0963.206
getProbesByRegion0.0550.0000.054
getProbesByTSS0.1680.0040.172
getRefSet1.9530.0401.993
getSexInfo2.1990.0722.271
inferEthnicity4.0130.1084.121
inferSex4.4310.1525.104
inferSexKaryotypes2.0120.0602.245
inferStrain5.7080.1436.277
inferTypeIChannel0.050.000.05
initFileSet0.0370.0000.037
makeExampleSeSAMeDataSet1.2610.0361.296
makeExampleTinyEPICDataSet0.0040.0000.004
mapFileSet0.0350.0040.039
mask0.7370.0201.009
meanIntensity1.8870.0561.943
noob0.0040.0020.006
noobsb3.4880.1293.618
oobG-methods0.8410.0041.100
oobG-replace-methods0.8200.0080.994
oobGpass0.7470.0081.023
oobR-methods0.7600.0200.953
oobR-replace-methods1.6000.1121.879
oobRpass0.7470.0321.032
openSesame2.2720.0362.309
openSesameToFile2.4170.0722.488
parseGEOSignalABFile0.2330.4950.745
predictAgeHorvath3532.5760.6722.580
predictAgePheno0.0990.0040.103
predictAgeSkinBlood0.1140.0080.121
predictMouseAgeInMonth2.6770.1163.046
print.DMLSummary5.7410.1406.136
print.fileSet0.0340.0000.034
print.sesameQC17.858 0.52418.654
probeID_designType0.0000.0000.001
probeNames-methods0.7550.0191.026
pval-methods0.7850.0110.960
pval-replace-methods1.4990.0881.840
qualityMask1.1380.0411.342
qualityRank9.2770.2199.913
reIdentify5.0280.1045.132
readFileSet0.0530.0080.062
readIDATpair0.1530.0040.157
resetMask1.1010.0191.289
restoreMask0.7690.0131.033
saveMask1.1150.0231.394
scrub0.0070.0000.007
scrubSoft0.0090.0000.009
searchIDATprefixes0.0000.0030.005
sesame-package0.7920.0120.804
sesamePlotIntensVsBetas6.6850.2767.215
sesamePlotRedGrnQQ2.1100.0722.434
sesameQC17.358 0.44418.055
sesamize0.0010.0010.001
setMask0.2890.0280.317
show-methods0.7470.0161.029
signalMU1.3230.9442.534
sliceFileSet0.0350.0040.039
subsetSignal0.9250.0161.209
summaryExtractCfList6.7950.1687.215
summaryExtractTest6.3470.1566.761
topSegments57.895 0.99959.148
totalIntensities1.5380.0451.583
totalIntensityZscore1.5630.0001.563
visualizeGene1.4900.0071.498
visualizeProbes0.6960.0000.696
visualizeRegion0.3970.0070.405
visualizeSegments1.9730.0762.301