Package: sesame

Version: 1.0.0

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_1.0.0.tar.gz

StartedAt: 2019-04-16 02:44:58 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:52:29 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 451.7 seconds

RetCode: 0

Status:  OK

CheckDir: sesame.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/sesame.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.0.0’
* 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 or elapsed time > 5s
                             user system elapsed
cnSegmentation             81.434  4.500  87.617
dyeBiasCorrMostBalanced    18.390  0.646  19.518
diffRefSet                 14.748  0.412  15.565
detectionPoobEcdf           9.761  0.220  10.127
noobsb                      9.049  0.652   9.771
detectionPnegEcdf           9.201  0.189   9.621
bisConversionControl        8.337  0.244   8.647
detectionPnegNormGS         7.837  0.197   8.331
detectionPnegNorm           7.729  0.254   8.076
getBetasTypeIbySumChannels  7.472  0.211   7.830
detectionPnegNormTotal      7.118  0.159   7.397
predictAgeHorvath353        4.840  1.793   0.601
getSexInfo                  6.211  0.264   6.584
getBetas                    6.095  0.156   6.314
inferEthnicity              5.477  0.244   5.858
buildControlMatrix450k      5.113  0.154   5.319
totalIntensities            4.967  0.177   5.204
SNPcheck                    4.866  0.139   5.076
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL sesame
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘sesame’ ...
** 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
* DONE (sesame)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, 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 
 25.818   0.870  27.315 

name	user	system	elapsed
BetaValueToMValue	0.000	0.001	0.000
IG-methods	2.882	0.060	2.968
IG-replace-methods	0.001	0.000	0.001
II-methods	0	0	0
II-replace-methods	0.004	0.004	0.008
IR-methods	0.001	0.001	0.001
IR-replace-methods	0.002	0.001	0.003
MValueToBetaValue	0.000	0.001	0.001
SNPcheck	4.866	0.139	5.076
SigSet-class	0.008	0.001	0.008
SigSetList-methods	1.057	0.060	1.163
SigSetList	0.644	0.036	0.682
SigSetListFromIDATs	0.318	0.016	0.340
SigSetListFromPath	0.547	0.028	0.579
SignalSet	0.004	0.001	0.005
bisConversionControl	8.337	0.244	8.647
buildControlMatrix450k	5.113	0.154	5.319
cnSegmentation	81.434	4.500	87.617
ctl-methods	0.002	0.000	0.003
ctl-replace-methods	0.001	0.000	0.001
detectionPnegEcdf	9.201	0.189	9.621
detectionPnegNorm	7.729	0.254	8.076
detectionPnegNormGS	7.837	0.197	8.331
detectionPnegNormTotal	7.118	0.159	7.397
detectionPoobEcdf	9.761	0.220	10.127
diffRefSet	14.748	0.412	15.565
dyeBiasCorr	0.320	0.062	0.383
dyeBiasCorrMostBalanced	18.390	0.646	19.518
dyeBiasCorrTypeINorm	2.018	0.300	2.349
estimateLeukocyte	2.343	0.155	2.573
getAFTypeIbySumAlleles	0.498	0.037	0.545
getBetas	6.095	0.156	6.314
getBetasTypeIbySumChannels	7.472	0.211	7.830
getNormCtls	0.354	0.018	0.372
getProbesByGene	1.688	0.068	1.767
getProbesByRegion	0.069	0.007	0.077
getProbesByTSS	0.201	0.016	0.217
getRefSet	2.759	0.100	2.897
getSexInfo	6.211	0.264	6.584
inferEthnicity	5.477	0.244	5.858
inferSex	2.823	0.251	3.171
inferSexKaryotypes	2.581	0.200	2.869
makeExampleSeSAMeDataSet	4.694	0.183	4.926
makeExampleTinyEPICDataSet	2.524	0.058	2.612
meanIntensity	4.563	0.176	4.774
noob	0.028	0.001	0.029
noobsb	9.049	0.652	9.771
oobG-methods	0.001	0.000	0.001
oobG-replace-methods	0.002	0.001	0.003
oobR-methods	0.001	0.001	0.001
oobR-replace-methods	0.002	0.001	0.003
openSesame	0.047	0.067	3.048
predictAgeHorvath353	4.840	1.793	0.601
predictAgePheno	0.094	0.017	0.111
predictAgeSkinBlood	0.096	0.014	0.110
pval-methods	0.001	0.000	0.001
pval-replace-methods	0.003	0.002	0.006
readIDATpair	0.299	0.041	0.341
searchIDATprefixes	0.008	0.004	0.012
sesame-package	1.938	0.215	2.174
sesamize	0	0	0
show-methods	0.001	0.000	0.002
signalR6toS4	0.004	0.001	0.004
subsetSignal	0.208	0.017	0.227
totalIntensities	4.967	0.177	5.204
totalIntensityZscore	1.819	0.054	1.885
visualizeGene	1.350	0.089	1.448
visualizeProbes	0.990	0.035	1.039
visualizeRegion	0.700	0.030	0.746
visualizeSegments	1.324	0.073	1.406