Wanding Zhou
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/sesame |
| Branch: master |
| Last Commit: 6138fb0 |
| Last Changed Date: 2019-04-01 16:29:04 -0400 (Mon, 01 Apr 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:20:42 -0400 (Tue, 09 Apr 2019).
| Package 1473/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| sesame 1.1.15 Wanding Zhou
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped |
| Package: sesame |
| Version: 1.1.15 |
| 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_1.1.15.tar.gz |
| StartedAt: 2019-04-09 05:26:47 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 05:45:25 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 1117.5 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_1.1.15.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/sesame.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.1.15’
* 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 98.291 10.691 108.993
RGChannelSetToSigSets 39.585 5.093 46.300
detectionPoobEcdf 30.829 0.898 31.771
as.data.frame.sesameQC 25.118 1.495 26.621
SigSetToRatioSet 22.605 0.752 23.364
dyeBiasCorrMostBalanced 18.654 0.921 19.585
print.sesameQC 16.678 1.314 17.993
sesameQC 15.954 1.042 16.996
diffRefSet 14.351 0.609 14.964
SigSetsToRGChannelSet 11.902 0.531 12.435
detectionPnegEcdf 11.769 0.303 12.072
noobsb 9.910 1.247 11.157
detectionPnegNorm 10.378 0.288 10.667
getBetas 9.819 0.206 10.026
detectionPnegNormTotal 9.776 0.242 10.019
detectionPfixedNorm 9.621 0.310 9.931
detectionPnegNormGS 9.598 0.286 9.883
SNPcheck 8.684 0.475 9.257
getSexInfo 8.104 0.453 8.555
openSesame 6.693 0.459 7.156
openSesameToFile 6.497 0.293 6.791
buildControlMatrix450k 6.343 0.234 6.577
makeExampleSeSAMeDataSet 6.001 0.333 6.334
bisConversionControl 6.004 0.276 6.280
meanIntensity 5.729 0.262 5.991
detectionZero 5.733 0.229 5.963
IG-methods 5.677 0.151 5.918
totalIntensities 5.347 0.463 5.810
inferEthnicity 5.218 0.291 5.509
estimateLeukocyte 4.751 0.385 5.177
* 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 Under development (unstable) (2019-03-18 r76245) -- "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, colMeans, colSums, 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, rowMeans, rowSums,
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 FAILED: 0
>
> proc.time()
user system elapsed
132.924 16.330 137.714
sesame.Rcheck/sesame-Ex.timings
| name | user | system | elapsed | |
| BetaValueToMValue | 0 | 0 | 0 | |
| IG-methods | 5.677 | 0.151 | 5.918 | |
| IG-replace-methods | 0.002 | 0.000 | 0.003 | |
| II-methods | 0.001 | 0.000 | 0.001 | |
| II-replace-methods | 0.009 | 0.006 | 0.016 | |
| IR-methods | 0.001 | 0.000 | 0.002 | |
| IR-replace-methods | 0.003 | 0.002 | 0.005 | |
| MValueToBetaValue | 0.000 | 0.000 | 0.001 | |
| RGChannelSetToSigSets | 39.585 | 5.093 | 46.300 | |
| SNPcheck | 8.684 | 0.475 | 9.257 | |
| SigSet-class | 0.002 | 0.000 | 0.003 | |
| SigSetList-methods | 3.073 | 0.145 | 3.265 | |
| SigSetList | 0.396 | 0.064 | 0.461 | |
| SigSetListFromIDATs | 0.143 | 0.024 | 0.167 | |
| SigSetListFromPath | 0.310 | 0.051 | 0.361 | |
| SigSetToRatioSet | 22.605 | 0.752 | 23.364 | |
| SigSetsToRGChannelSet | 11.902 | 0.531 | 12.435 | |
| SignalSet | 0.007 | 0.001 | 0.009 | |
| as.data.frame.sesameQC | 25.118 | 1.495 | 26.621 | |
| bisConversionControl | 6.004 | 0.276 | 6.280 | |
| buildControlMatrix450k | 6.343 | 0.234 | 6.577 | |
| cnSegmentation | 98.291 | 10.691 | 108.993 | |
| ctl-methods | 0.004 | 0.001 | 0.005 | |
| ctl-replace-methods | 0.001 | 0.000 | 0.001 | |
| detectionPfixedNorm | 9.621 | 0.310 | 9.931 | |
| detectionPnegEcdf | 11.769 | 0.303 | 12.072 | |
| detectionPnegNorm | 10.378 | 0.288 | 10.667 | |
| detectionPnegNormGS | 9.598 | 0.286 | 9.883 | |
| detectionPnegNormTotal | 9.776 | 0.242 | 10.019 | |
| detectionPoobEcdf | 30.829 | 0.898 | 31.771 | |
| detectionZero | 5.733 | 0.229 | 5.963 | |
| diffRefSet | 14.351 | 0.609 | 14.964 | |
| dyeBiasCorr | 0.469 | 0.114 | 0.584 | |
| dyeBiasCorrMostBalanced | 18.654 | 0.921 | 19.585 | |
| dyeBiasCorrTypeINorm | 2.994 | 0.555 | 3.549 | |
| estimateLeukocyte | 4.751 | 0.385 | 5.177 | |
| getAFTypeIbySumAlleles | 0.132 | 0.014 | 0.145 | |
| getBetas | 9.819 | 0.206 | 10.026 | |
| getNormCtls | 0.205 | 0.023 | 0.229 | |
| getProbesByGene | 4.006 | 0.227 | 4.236 | |
| getProbesByRegion | 0.056 | 0.011 | 0.067 | |
| getProbesByTSS | 0.291 | 0.027 | 0.318 | |
| getRefSet | 3.889 | 0.184 | 4.073 | |
| getSexInfo | 8.104 | 0.453 | 8.555 | |
| inferEthnicity | 5.218 | 0.291 | 5.509 | |
| inferSex | 3.368 | 0.297 | 3.664 | |
| inferSexKaryotypes | 4.250 | 0.397 | 4.647 | |
| inferTypeIChannel | 0.137 | 0.050 | 0.187 | |
| initFileSet | 0.044 | 0.002 | 0.046 | |
| makeExampleSeSAMeDataSet | 6.001 | 0.333 | 6.334 | |
| makeExampleTinyEPICDataSet | 0.011 | 0.000 | 0.011 | |
| mapFileSet | 0.084 | 0.006 | 0.090 | |
| meanIntensity | 5.729 | 0.262 | 5.991 | |
| noob | 0.015 | 0.000 | 0.015 | |
| noobsb | 9.910 | 1.247 | 11.157 | |
| oobG-methods | 0.000 | 0.000 | 0.001 | |
| oobG-replace-methods | 0.003 | 0.002 | 0.004 | |
| oobR-methods | 0.001 | 0.000 | 0.001 | |
| oobR-replace-methods | 0.002 | 0.001 | 0.002 | |
| openSesame | 6.693 | 0.459 | 7.156 | |
| openSesameToFile | 6.497 | 0.293 | 6.791 | |
| parseGEOSignalABFile | 0.705 | 0.376 | 1.562 | |
| predictAgeHorvath353 | 1.284 | 0.461 | 0.192 | |
| predictAgePheno | 0.126 | 0.042 | 0.168 | |
| predictAgeSkinBlood | 0.109 | 0.037 | 0.146 | |
| print.fileSet | 0.042 | 0.009 | 0.051 | |
| print.sesameQC | 16.678 | 1.314 | 17.993 | |
| probeNames-methods | 0.037 | 0.004 | 0.042 | |
| pval-methods | 0.001 | 0.001 | 0.001 | |
| pval-replace-methods | 0.005 | 0.006 | 0.010 | |
| readFileSet | 0.159 | 0.055 | 0.214 | |
| readIDATpair | 0.221 | 0.035 | 0.257 | |
| searchIDATprefixes | 0.011 | 0.006 | 0.020 | |
| sesame-package | 1.723 | 0.326 | 2.049 | |
| sesameQC | 15.954 | 1.042 | 16.996 | |
| sesamize | 0.000 | 0.001 | 0.001 | |
| show-methods | 0.002 | 0.001 | 0.003 | |
| signalR6toS4 | 0.004 | 0.001 | 0.005 | |
| sliceFileSet | 0.084 | 0.007 | 0.092 | |
| subsetSignal | 0.425 | 0.030 | 0.455 | |
| totalIntensities | 5.347 | 0.463 | 5.810 | |
| totalIntensityZscore | 2.565 | 0.107 | 2.672 | |
| visualizeGene | 4.045 | 0.324 | 4.452 | |
| visualizeProbes | 1.305 | 0.067 | 1.373 | |
| visualizeRegion | 0.697 | 0.071 | 0.767 | |
| visualizeSegments | 1.159 | 0.106 | 1.267 | |