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This page was generated on 2021-07-23 15:06:51 -0400 (Fri, 23 Jul 2021).

CHECK results for sesame on machv2

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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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sesame.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sesame_1.10.4.tar.gz
StartedAt: 2021-07-22 23:36:17 -0400 (Thu, 22 Jul 2021)
EndedAt: 2021-07-22 23:56:35 -0400 (Thu, 22 Jul 2021)
EllapsedTime: 1217.7 seconds
RetCode: 0
Status:   OK  
CheckDir: sesame.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sesame.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sesame_1.10.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/sesame.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (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                         107.058  0.755 108.586
topSegments                 100.767  1.291 102.855
cnSegmentation               85.340  2.691  89.174
compareMouseTissueReference  29.505  0.376  30.384
bSubMostVariable             25.727  0.454  26.423
as.data.frame.sesameQC       25.243  0.748  26.361
sesameQC                     22.980  0.438  23.866
print.sesameQC               22.729  0.479  23.424
dyeBiasCorrMostBalanced      19.933  0.279  20.430
betaToAF                     15.248  0.341  16.328
DML                          14.496  0.856  16.064
diffRefSet                   14.680  0.162  15.066
qualityRank                  14.270  0.217  15.000
SigSetsToRGChannelSet        13.775  0.247  14.509
SigSetToRatioSet             13.546  0.379  14.237
getAutosomeProbes            13.638  0.122  13.997
summaryExtractCfList         11.058  0.096  11.502
print.DMLSummary             10.131  0.098  10.555
bisConversionControl          9.944  0.190  10.539
SNPcheck                      9.750  0.204  10.467
summaryExtractTest            9.686  0.063  10.042
sesamePlotIntensVsBetas       9.393  0.166   9.912
deidentify                    9.447  0.094   9.548
compareMouseBloodReference    8.494  0.197   9.533
SigSetList-methods            7.911  0.173   8.693
reIdentify                    7.840  0.052   7.898
IGpass                        7.206  0.152   7.851
inferStrain                   7.048  0.204   7.709
formatVCF                     7.126  0.064   8.038
getBetas                      6.958  0.050   7.237
inferSex                      6.643  0.148   7.200
estimateLeukocyte             6.588  0.123   6.918
getSexInfo                    6.021  0.077   6.105
IG-methods                    5.791  0.250   6.589
inferEthnicity                5.928  0.083   6.016
dyeBiasCorrTypeINorm          5.066  0.148   5.539
getAFTypeIbySumAlleles        4.891  0.123   5.419
DMLShrinkage                  4.711  0.116   5.160
* 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:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL sesame
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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-apple-darwin17.0 (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 
 95.059   9.127  94.729 

Example timings

sesame.Rcheck/sesame-Ex.timings

nameusersystemelapsed
BetaValueToMValue0.0000.0000.001
DML14.496 0.85616.064
DMLShrinkage4.7110.1165.160
DMR107.058 0.755108.586
IG-methods5.7910.2506.589
IG-replace-methods0.9340.0401.290
IGpass7.2060.1527.851
II-methods1.3690.0401.750
II-replace-methods1.0550.0411.376
IIpass1.0440.0381.276
IR-methods1.2770.0371.590
IR-replace-methods1.0130.0341.259
IRpass1.0740.0361.391
MValueToBetaValue0.0000.0010.000
RGChannelSetToSigSets0.0010.0010.001
SNPcheck 9.750 0.20410.467
SigSet-class0.0070.0010.008
SigSetList-methods7.9110.1738.693
SigSetList0.3980.0160.414
SigSetListFromIDATs0.2150.0090.224
SigSetListFromPath0.3360.0190.356
SigSetToRatioSet13.546 0.37914.237
SigSetsToRGChannelSet13.775 0.24714.509
addMask0.2460.0120.259
as.data.frame.sesameQC25.243 0.74826.361
bSubComplete0.0380.0040.042
bSubMostVariable25.727 0.45426.423
bSubProbes0.4740.0060.479
betaToAF15.248 0.34116.328
bisConversionControl 9.944 0.19010.539
buildControlMatrix450k3.4020.0753.479
checkLevels0.9340.1071.753
cnSegmentation85.340 2.69189.174
compareMouseBloodReference8.4940.1979.533
compareMouseTissueReference29.505 0.37630.384
createUCSCtrack2.1300.0302.161
ctl-methods0.9860.0361.284
ctl-replace-methods0.9970.0391.326
deidentify9.4470.0949.548
detectionPfixedNorm0.3180.0010.320
detectionPnegEcdf2.0580.0472.109
detectionPnegNorm0.3150.0030.318
detectionPnegNormGS0.3010.0010.303
detectionPnegNormTotal0.2110.0020.213
detectionPoobEcdf3.8090.0613.879
detectionPoobEcdf24.3840.0384.424
diffRefSet14.680 0.16215.066
dyeBiasCorr1.7800.0372.013
dyeBiasCorrMostBalanced19.933 0.27920.430
dyeBiasCorrTypeINorm5.0660.1485.539
estimateLeukocyte6.5880.1236.918
extra-methods0.9140.0271.156
extra-replace-methods1.0040.0341.234
formatVCF7.1260.0648.038
getAFTypeIbySumAlleles4.8910.1235.419
getAutosomeProbes13.638 0.12213.997
getBetas6.9580.0507.237
getNormCtls0.2430.0020.245
getProbesByChromosome0.8160.0100.827
getProbesByGene4.1700.0834.459
getProbesByRegion0.0730.0010.075
getProbesByTSS0.2860.0020.288
getRefSet3.5820.0753.659
getSexInfo6.0210.0776.105
inferEthnicity5.9280.0836.016
inferSex6.6430.1487.200
inferSexKaryotypes2.7310.0482.981
inferStrain7.0480.2047.709
inferTypeIChannel0.0640.0020.066
initFileSet0.0380.0040.041
makeExampleSeSAMeDataSet2.0460.0112.058
makeExampleTinyEPICDataSet0.5190.0120.531
mapFileSet0.0580.0030.062
mask1.0440.0321.279
meanIntensity3.0910.0603.153
noob0.0080.0010.009
noobsb4.1110.1544.268
oobG-methods1.0930.0391.405
oobG-replace-methods1.1010.0361.470
oobGpass0.9760.0341.353
oobR-methods1.5810.0971.882
oobR-replace-methods1.0650.0381.469
oobRpass1.0610.0381.416
openSesame4.0330.0264.062
openSesameToFile3.3690.0273.398
parseGEOSignalABFile0.3170.3320.933
predictAgeHorvath3533.3550.3973.982
predictAgePheno0.1420.0060.148
predictAgeSkinBlood0.1660.0070.175
predictMouseAgeInMonth3.6630.1434.130
print.DMLSummary10.131 0.09810.555
print.fileSet0.0440.0020.046
print.sesameQC22.729 0.47923.424
probeID_designType0.0010.0000.001
probeNames-methods1.1410.0391.377
pval-methods0.9850.0291.278
pval-replace-methods1.0730.0391.347
qualityMask2.1480.0682.541
qualityRank14.270 0.21715.000
reIdentify7.8400.0527.898
readFileSet0.0780.0050.084
readIDATpair0.2340.0060.241
resetMask1.4390.0581.700
restoreMask1.6900.0491.947
saveMask0.9830.0401.216
scrub0.0100.0010.010
scrubSoft0.0130.0010.014
searchIDATprefixes0.0040.0020.006
sesame-package1.1610.0051.167
sesamePlotIntensVsBetas9.3930.1669.912
sesamePlotRedGrnQQ2.1350.1772.587
sesameQC22.980 0.43823.866
sesamize0.0010.0000.001
setMask0.4780.0040.481
show-methods0.8840.0331.255
signalMU2.4961.0543.883
sliceFileSet0.0590.0040.064
subsetSignal1.2250.0451.687
summaryExtractCfList11.058 0.09611.502
summaryExtractTest 9.686 0.06310.042
topSegments100.767 1.291102.855
totalIntensities2.7960.0692.872
totalIntensityZscore2.3690.0122.383
visualizeGene1.7150.0341.750
visualizeProbes1.7130.0261.740
visualizeRegion0.5520.0070.559
visualizeSegments1.8540.1152.320