Wanding Zhou
| Snapshot Date: 2019-04-07 17:01:41 -0400 (Sun, 07 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 2019-04-08 12:34:46 -0400 (Mon, 08 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 | OK | [ OK ] | OK |
| 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: 2019-04-08 03:48:37 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 04:08:34 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 1197.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sesame.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.1.15.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/sesame.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 69.943 3.621 74.979
RGChannelSetToSigSets 33.918 2.951 37.703
as.data.frame.sesameQC 24.579 0.841 26.798
SigSetToRatioSet 20.741 0.418 22.006
dyeBiasCorrMostBalanced 17.593 0.568 18.749
detectionPoobEcdf 17.362 0.466 17.922
diffRefSet 13.368 0.353 14.867
SigSetsToRGChannelSet 11.759 0.341 12.591
SNPcheck 11.429 0.289 12.952
print.sesameQC 10.538 0.652 11.323
openSesame 10.679 0.384 12.124
sesameQC 10.244 0.594 10.923
detectionPnegEcdf 9.076 0.179 9.329
noobsb 7.393 0.642 8.109
detectionPnegNorm 6.786 0.238 7.119
IG-methods 6.781 0.114 7.275
detectionPfixedNorm 6.731 0.151 6.938
detectionPnegNormTotal 6.641 0.149 6.836
detectionPnegNormGS 6.268 0.147 6.476
estimateLeukocyte 6.152 0.209 6.854
getSexInfo 5.715 0.234 6.026
visualizeGene 5.264 0.188 5.925
getProbesByGene 5.165 0.128 5.735
getBetas 5.156 0.091 5.283
makeExampleSeSAMeDataSet 4.782 0.207 5.024
SigSetList-methods 4.881 0.096 5.297
inferEthnicity 4.776 0.167 5.002
* 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’ ... ** 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)
sesame.Rcheck/tests/testthat.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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
106.332 13.268 130.593
sesame.Rcheck/sesame-Ex.timings
| name | user | system | elapsed | |
| BetaValueToMValue | 0.001 | 0.000 | 0.001 | |
| IG-methods | 6.781 | 0.114 | 7.275 | |
| IG-replace-methods | 0.001 | 0.000 | 0.001 | |
| II-methods | 0.001 | 0.000 | 0.002 | |
| II-replace-methods | 0.007 | 0.003 | 0.010 | |
| IR-methods | 0.001 | 0.000 | 0.001 | |
| IR-replace-methods | 0.002 | 0.001 | 0.002 | |
| MValueToBetaValue | 0.000 | 0.000 | 0.001 | |
| RGChannelSetToSigSets | 33.918 | 2.951 | 37.703 | |
| SNPcheck | 11.429 | 0.289 | 12.952 | |
| SigSet-class | 0.004 | 0.001 | 0.005 | |
| SigSetList-methods | 4.881 | 0.096 | 5.297 | |
| SigSetList | 0.327 | 0.029 | 0.357 | |
| SigSetListFromIDATs | 0.178 | 0.017 | 0.196 | |
| SigSetListFromPath | 0.320 | 0.032 | 0.358 | |
| SigSetToRatioSet | 20.741 | 0.418 | 22.006 | |
| SigSetsToRGChannelSet | 11.759 | 0.341 | 12.591 | |
| SignalSet | 0.004 | 0.000 | 0.005 | |
| as.data.frame.sesameQC | 24.579 | 0.841 | 26.798 | |
| bisConversionControl | 4.262 | 0.135 | 4.436 | |
| buildControlMatrix450k | 4.682 | 0.130 | 4.852 | |
| cnSegmentation | 69.943 | 3.621 | 74.979 | |
| ctl-methods | 0.003 | 0.000 | 0.002 | |
| ctl-replace-methods | 0.001 | 0.000 | 0.001 | |
| detectionPfixedNorm | 6.731 | 0.151 | 6.938 | |
| detectionPnegEcdf | 9.076 | 0.179 | 9.329 | |
| detectionPnegNorm | 6.786 | 0.238 | 7.119 | |
| detectionPnegNormGS | 6.268 | 0.147 | 6.476 | |
| detectionPnegNormTotal | 6.641 | 0.149 | 6.836 | |
| detectionPoobEcdf | 17.362 | 0.466 | 17.922 | |
| detectionZero | 3.915 | 0.115 | 4.049 | |
| diffRefSet | 13.368 | 0.353 | 14.867 | |
| dyeBiasCorr | 0.237 | 0.051 | 0.291 | |
| dyeBiasCorrMostBalanced | 17.593 | 0.568 | 18.749 | |
| dyeBiasCorrTypeINorm | 2.438 | 0.342 | 2.811 | |
| estimateLeukocyte | 6.152 | 0.209 | 6.854 | |
| getAFTypeIbySumAlleles | 0.047 | 0.004 | 0.051 | |
| getBetas | 5.156 | 0.091 | 5.283 | |
| getNormCtls | 0.135 | 0.010 | 0.145 | |
| getProbesByGene | 5.165 | 0.128 | 5.735 | |
| getProbesByRegion | 0.064 | 0.008 | 0.072 | |
| getProbesByTSS | 0.186 | 0.013 | 0.205 | |
| getRefSet | 2.820 | 0.077 | 2.935 | |
| getSexInfo | 5.715 | 0.234 | 6.026 | |
| inferEthnicity | 4.776 | 0.167 | 5.002 | |
| inferSex | 1.959 | 0.168 | 2.144 | |
| inferSexKaryotypes | 2.130 | 0.197 | 2.347 | |
| inferTypeIChannel | 0.093 | 0.026 | 0.122 | |
| initFileSet | 0.053 | 0.002 | 0.054 | |
| makeExampleSeSAMeDataSet | 4.782 | 0.207 | 5.024 | |
| makeExampleTinyEPICDataSet | 0.011 | 0.000 | 0.012 | |
| mapFileSet | 0.049 | 0.002 | 0.051 | |
| meanIntensity | 4.530 | 0.141 | 4.726 | |
| noob | 0.015 | 0.000 | 0.015 | |
| noobsb | 7.393 | 0.642 | 8.109 | |
| oobG-methods | 0.001 | 0.001 | 0.001 | |
| oobG-replace-methods | 0.003 | 0.001 | 0.004 | |
| oobR-methods | 0.001 | 0.000 | 0.002 | |
| oobR-replace-methods | 0.002 | 0.000 | 0.002 | |
| openSesame | 10.679 | 0.384 | 12.124 | |
| openSesameToFile | 3.300 | 0.158 | 3.489 | |
| parseGEOSignalABFile | 0.443 | 0.186 | 1.015 | |
| predictAgeHorvath353 | 0.900 | 0.226 | 0.137 | |
| predictAgePheno | 0.104 | 0.026 | 0.130 | |
| predictAgeSkinBlood | 0.112 | 0.019 | 0.131 | |
| print.fileSet | 0.062 | 0.006 | 0.068 | |
| print.sesameQC | 10.538 | 0.652 | 11.323 | |
| probeNames-methods | 0.030 | 0.003 | 0.033 | |
| pval-methods | 0.000 | 0.000 | 0.001 | |
| pval-replace-methods | 0.002 | 0.004 | 0.006 | |
| readFileSet | 0.118 | 0.024 | 0.143 | |
| readIDATpair | 0.197 | 0.018 | 0.217 | |
| searchIDATprefixes | 0.008 | 0.003 | 0.010 | |
| sesame-package | 1.680 | 0.199 | 1.893 | |
| sesameQC | 10.244 | 0.594 | 10.923 | |
| sesamize | 0.000 | 0.000 | 0.001 | |
| show-methods | 0.002 | 0.001 | 0.002 | |
| signalR6toS4 | 0.003 | 0.000 | 0.004 | |
| sliceFileSet | 0.059 | 0.004 | 0.063 | |
| subsetSignal | 0.232 | 0.018 | 0.253 | |
| totalIntensities | 4.368 | 0.251 | 4.658 | |
| totalIntensityZscore | 1.731 | 0.055 | 1.816 | |
| visualizeGene | 5.264 | 0.188 | 5.925 | |
| visualizeProbes | 1.052 | 0.035 | 1.099 | |
| visualizeRegion | 0.640 | 0.037 | 0.681 | |
| visualizeSegments | 1.196 | 0.072 | 1.291 | |