Multiple platform build/check report for BioC 3.11 - CHECK report for sesame on celaya2

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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_1.5.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/sesame.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.5.2’
* 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          97.705 10.118 110.666
RGChannelSetToSigSets   49.635  5.591  55.393
as.data.frame.sesameQC  23.650  1.443  25.788
dyeBiasCorrMostBalanced 22.153  0.972  23.132
DMR                     19.849  0.716  20.917
diffRefSet              18.949  0.636  19.589
print.sesameQC          15.960  1.131  17.093
SigSetToRatioSet        16.567  0.495  17.310
SigSetsToRGChannelSet   15.212  0.930  16.367
sesameQC                14.768  1.049  15.817
detectionPoobEcdf       14.473  1.066  15.745
getRefSet               10.261  0.305  10.567
DML                      9.819  0.704  10.647
topLoci                  8.898  1.543  10.442
SNPcheck                 9.725  0.333  10.071
getBetas                 9.743  0.183   9.927
topSegments              7.517  0.718   8.235
noobsb                   6.583  1.144   8.083
openSesame               6.431  0.551   6.987
estimateLeukocyte        6.485  0.402   6.891
detectionPnegEcdf        6.548  0.326   7.048
getSegment               6.406  0.358   6.766
getSexInfo               5.167  0.434   5.601
IG-methods               4.828  0.315   5.231
* 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

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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/4.0/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


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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, 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, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading sesameData.
> 
> test_check("sesame")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 19 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
140.276  20.137 143.955

Example timings

name	user	system	elapsed
BetaValueToMValue	0.000	0.001	0.001
DML	9.819	0.704	10.647
DMR	19.849	0.716	20.917
IG-methods	4.828	0.315	5.231
IG-replace-methods	0.002	0.001	0.003
II-methods	0.001	0.001	0.001
II-replace-methods	0.010	0.008	0.017
IR-methods	0.001	0.001	0.002
IR-replace-methods	0.003	0.002	0.005
MValueToBetaValue	0.001	0.000	0.001
RGChannelSetToSigSets	49.635	5.591	55.393
SNPcheck	9.725	0.333	10.071
SigSet-class	0.006	0.001	0.007
SigSetList-methods	3.245	0.146	3.400
SigSetList	0.486	0.065	0.550
SigSetListFromIDATs	0.236	0.033	0.269
SigSetListFromPath	0.468	0.068	0.537
SigSetToRatioSet	16.567	0.495	17.310
SigSetsToRGChannelSet	15.212	0.930	16.367
as.data.frame.sesameQC	23.650	1.443	25.788
bisConversionControl	3.588	0.422	4.010
buildControlMatrix450k	3.459	0.254	3.788
cnSegmentation	97.705	10.118	110.666
ctl-methods	0.005	0.001	0.006
ctl-replace-methods	0.001	0.001	0.002
detectionPfixedNorm	3.665	0.242	3.941
detectionPnegEcdf	6.548	0.326	7.048
detectionPnegNorm	3.957	0.279	4.252
detectionPnegNormGS	3.781	0.253	4.124
detectionPnegNormTotal	3.632	0.276	3.910
detectionPoobEcdf	14.473	1.066	15.745
detectionZero	3.215	0.239	3.454
diffRefSet	18.949	0.636	19.589
dyeBiasCorr	0.214	0.093	0.307
dyeBiasCorrMostBalanced	22.153	0.972	23.132
dyeBiasCorrTypeINorm	4.433	0.522	4.956
estimateLeukocyte	6.485	0.402	6.891
getAFTypeIbySumAlleles	0.092	0.009	0.101
getBetas	9.743	0.183	9.927
getNormCtls	0.269	0.025	0.295
getProbesByGene	3.227	0.118	3.348
getProbesByRegion	0.111	0.013	0.125
getProbesByTSS	1.501	0.257	1.759
getRefSet	10.261	0.305	10.567
getSegment	6.406	0.358	6.766
getSexInfo	5.167	0.434	5.601
inferEthnicity	3.340	0.305	3.644
inferSex	2.236	0.352	2.589
inferSexKaryotypes	2.143	0.340	2.484
inferTypeIChannel	0.088	0.042	0.130
initFileSet	0.066	0.005	0.071
makeExampleSeSAMeDataSet	3.401	0.473	3.875
makeExampleTinyEPICDataSet	0.014	0.000	0.015
mapFileSet	0.088	0.006	0.093
meanIntensity	3.232	0.264	3.498
noob	0.017	0.000	0.018
noobsb	6.583	1.144	8.083
oobG-methods	0.001	0.001	0.002
oobG-replace-methods	0.003	0.002	0.006
oobR-methods	0.001	0.000	0.002
oobR-replace-methods	0.002	0.001	0.004
openSesame	6.431	0.551	6.987
openSesameToFile	3.779	0.296	4.075
parseGEOSignalABFile	0.833	0.682	2.241
predictAgeHorvath353	1.861	1.028	0.642
predictAgePheno	0.375	0.039	0.414
predictAgeSkinBlood	0.304	0.037	0.342
print.fileSet	0.062	0.019	0.084
print.sesameQC	15.960	1.131	17.093
probeNames-methods	0.080	0.003	0.083
pval-methods	0.001	0.000	0.001
pval-replace-methods	0.005	0.007	0.012
readFileSet	0.113	0.011	0.124
readIDATpair	0.185	0.029	0.213
searchIDATprefixes	0.011	0.006	0.018
sesame-package	2.150	0.494	2.644
sesameQC	14.768	1.049	15.817
show-methods	0.003	0.002	0.004
sliceFileSet	0.089	0.006	0.095
subsetSignal	0.239	0.034	0.274
topLoci	8.898	1.543	10.442
topSegments	7.517	0.718	8.235
totalIntensities	3.607	0.415	4.021
totalIntensityZscore	3.733	0.097	3.829
visualizeGene	2.102	0.086	2.189
visualizeProbes	1.826	0.048	1.876
visualizeRegion	1.399	0.059	1.459
visualizeSegments	1.407	0.131	1.540

CHECK report for sesame on celaya2

Summary

Command output

Installation output

Tests output

Example timings