Wanding Zhou
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/sesame |
| Branch: RELEASE_3_10 |
| Last Commit: 55af6fe |
| Last Changed Date: 2019-10-29 13:11:14 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:47:39 -0400 (Wed, 15 Apr 2020).
| Package 1572/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| sesame 1.4.0 Wanding Zhou
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: sesame |
| Version: 1.4.0 |
| 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_1.4.0.tar.gz |
| StartedAt: 2020-04-15 05:38:08 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:52:55 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 886.3 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_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/sesame.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.4.0’
* 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 or elapsed time > 5s
user system elapsed
cnSegmentation 72.222 5.131 78.660
RGChannelSetToSigSets 33.673 2.695 37.232
detectionPoobEcdf 19.412 0.432 20.016
as.data.frame.sesameQC 18.474 0.747 19.721
dyeBiasCorrMostBalanced 15.171 0.524 15.838
DMR 13.050 0.300 13.520
diffRefSet 12.950 0.324 13.384
SigSetToRatioSet 11.289 0.253 11.731
sesameQC 10.197 0.573 10.876
SigSetsToRGChannelSet 10.322 0.323 10.842
print.sesameQC 9.836 0.581 10.528
detectionPnegEcdf 9.655 0.171 9.908
detectionPnegNormTotal 8.487 0.201 8.762
SNPcheck 8.348 0.280 8.802
detectionPnegNormGS 8.190 0.160 8.422
detectionPnegNorm 8.179 0.152 8.415
detectionPfixedNorm 7.820 0.141 8.027
openSesame 7.564 0.295 7.970
noobsb 7.039 0.626 7.715
DML 6.887 0.363 7.335
topLoci 6.113 0.710 6.960
getSexInfo 6.324 0.253 6.638
estimateLeukocyte 6.043 0.209 6.303
bisConversionControl 5.849 0.230 6.197
buildControlMatrix450k 5.734 0.152 6.077
getBetas 5.765 0.091 5.888
inferEthnicity 5.340 0.164 5.566
totalIntensities 5.225 0.196 5.477
topSegments 5.080 0.323 5.565
detectionZero 5.086 0.126 5.247
makeExampleSeSAMeDataSet 4.860 0.233 5.140
meanIntensity 4.946 0.138 5.119
* 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
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/3.6/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)
sesame.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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
96.173 6.918 100.753
sesame.Rcheck/sesame-Ex.timings
| name | user | system | elapsed | |
| BetaValueToMValue | 0.001 | 0.000 | 0.001 | |
| DML | 6.887 | 0.363 | 7.335 | |
| DMR | 13.05 | 0.30 | 13.52 | |
| IG-methods | 4.502 | 0.098 | 4.663 | |
| IG-replace-methods | 0.002 | 0.001 | 0.003 | |
| II-methods | 0.001 | 0.000 | 0.001 | |
| II-replace-methods | 0.008 | 0.004 | 0.012 | |
| IR-methods | 0.001 | 0.000 | 0.001 | |
| IR-replace-methods | 0.002 | 0.001 | 0.003 | |
| MValueToBetaValue | 0 | 0 | 0 | |
| RGChannelSetToSigSets | 33.673 | 2.695 | 37.232 | |
| SNPcheck | 8.348 | 0.280 | 8.802 | |
| SigSet-class | 0.002 | 0.000 | 0.003 | |
| SigSetList-methods | 2.369 | 0.070 | 2.465 | |
| SigSetList | 0.321 | 0.028 | 0.355 | |
| SigSetListFromIDATs | 0.177 | 0.017 | 0.214 | |
| SigSetListFromPath | 0.250 | 0.025 | 0.275 | |
| SigSetToRatioSet | 11.289 | 0.253 | 11.731 | |
| SigSetsToRGChannelSet | 10.322 | 0.323 | 10.842 | |
| SignalSet | 0.007 | 0.001 | 0.007 | |
| as.data.frame.sesameQC | 18.474 | 0.747 | 19.721 | |
| bisConversionControl | 5.849 | 0.230 | 6.197 | |
| buildControlMatrix450k | 5.734 | 0.152 | 6.077 | |
| cnSegmentation | 72.222 | 5.131 | 78.660 | |
| ctl-methods | 0.003 | 0.000 | 0.004 | |
| ctl-replace-methods | 0.001 | 0.001 | 0.001 | |
| detectionPfixedNorm | 7.820 | 0.141 | 8.027 | |
| detectionPnegEcdf | 9.655 | 0.171 | 9.908 | |
| detectionPnegNorm | 8.179 | 0.152 | 8.415 | |
| detectionPnegNormGS | 8.190 | 0.160 | 8.422 | |
| detectionPnegNormTotal | 8.487 | 0.201 | 8.762 | |
| detectionPoobEcdf | 19.412 | 0.432 | 20.016 | |
| detectionZero | 5.086 | 0.126 | 5.247 | |
| diffRefSet | 12.950 | 0.324 | 13.384 | |
| dyeBiasCorr | 0.179 | 0.060 | 0.239 | |
| dyeBiasCorrMostBalanced | 15.171 | 0.524 | 15.838 | |
| dyeBiasCorrTypeINorm | 2.087 | 0.262 | 2.365 | |
| estimateLeukocyte | 6.043 | 0.209 | 6.303 | |
| getAFTypeIbySumAlleles | 0.055 | 0.007 | 0.061 | |
| getBetas | 5.765 | 0.091 | 5.888 | |
| getNormCtls | 0.131 | 0.010 | 0.142 | |
| getProbesByGene | 3.095 | 0.118 | 3.240 | |
| getProbesByRegion | 0.056 | 0.006 | 0.061 | |
| getProbesByTSS | 0.231 | 0.014 | 0.245 | |
| getRefSet | 2.809 | 0.077 | 2.914 | |
| getSegment | 4.523 | 0.143 | 4.710 | |
| getSexInfo | 6.324 | 0.253 | 6.638 | |
| inferEthnicity | 5.340 | 0.164 | 5.566 | |
| inferSex | 1.402 | 0.164 | 1.591 | |
| inferSexKaryotypes | 1.706 | 0.188 | 1.909 | |
| inferTypeIChannel | 0.082 | 0.026 | 0.107 | |
| initFileSet | 0.059 | 0.002 | 0.061 | |
| makeExampleSeSAMeDataSet | 4.860 | 0.233 | 5.140 | |
| makeExampleTinyEPICDataSet | 0.013 | 0.000 | 0.013 | |
| mapFileSet | 0.066 | 0.003 | 0.070 | |
| meanIntensity | 4.946 | 0.138 | 5.119 | |
| noob | 0.018 | 0.000 | 0.019 | |
| noobsb | 7.039 | 0.626 | 7.715 | |
| oobG-methods | 0.001 | 0.000 | 0.001 | |
| oobG-replace-methods | 0.002 | 0.001 | 0.004 | |
| oobR-methods | 0.000 | 0.001 | 0.001 | |
| oobR-replace-methods | 0.001 | 0.001 | 0.003 | |
| openSesame | 7.564 | 0.295 | 7.970 | |
| openSesameToFile | 2.628 | 0.143 | 2.787 | |
| parseGEOSignalABFile | 0.413 | 0.186 | 1.018 | |
| predictAgeHorvath353 | 0.929 | 0.246 | 0.171 | |
| predictAgePheno | 0.128 | 0.023 | 0.154 | |
| predictAgeSkinBlood | 0.168 | 0.020 | 0.190 | |
| print.fileSet | 0.057 | 0.006 | 0.067 | |
| print.sesameQC | 9.836 | 0.581 | 10.528 | |
| probeNames-methods | 0.018 | 0.002 | 0.019 | |
| pval-methods | 0.001 | 0.000 | 0.001 | |
| pval-replace-methods | 0.002 | 0.002 | 0.004 | |
| readFileSet | 0.103 | 0.027 | 0.132 | |
| readIDATpair | 0.157 | 0.014 | 0.172 | |
| searchIDATprefixes | 0.007 | 0.002 | 0.010 | |
| sesame-package | 1.409 | 0.171 | 1.601 | |
| sesameQC | 10.197 | 0.573 | 10.876 | |
| sesamize | 0.000 | 0.000 | 0.001 | |
| show-methods | 0.001 | 0.000 | 0.002 | |
| signalR6toS4 | 0.004 | 0.000 | 0.004 | |
| sliceFileSet | 0.073 | 0.004 | 0.077 | |
| subsetSignal | 0.169 | 0.019 | 0.188 | |
| topLoci | 6.113 | 0.710 | 6.960 | |
| topSegments | 5.080 | 0.323 | 5.565 | |
| totalIntensities | 5.225 | 0.196 | 5.477 | |
| totalIntensityZscore | 2.494 | 0.062 | 2.580 | |
| visualizeGene | 1.129 | 0.027 | 1.167 | |
| visualizeProbes | 1.491 | 0.063 | 1.582 | |
| visualizeRegion | 0.616 | 0.017 | 0.639 | |
| visualizeSegments | 1.523 | 0.142 | 1.726 | |