Wanding Zhou
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/sesame |
| Branch: RELEASE_3_9 |
| Last Commit: 1b9bddf |
| Last Changed Date: 2019-05-02 11:54:12 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:02:47 -0400 (Wed, 16 Oct 2019).
| Package 1503/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| sesame 1.2.0 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 | |
| Package: sesame |
| Version: 1.2.0 |
| 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_1.2.0.tar.gz |
| StartedAt: 2019-10-16 06:48:37 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:06:43 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 1085.9 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_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/sesame.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.2.0’
* 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 89.368 9.573 98.990
RGChannelSetToSigSets 40.268 5.335 46.879
as.data.frame.sesameQC 27.989 1.717 29.749
detectionPoobEcdf 25.355 0.773 26.128
SigSetToRatioSet 22.937 0.670 24.189
dyeBiasCorrMostBalanced 18.693 0.956 19.654
print.sesameQC 17.571 1.410 18.980
sesameQC 16.706 1.063 17.770
diffRefSet 13.317 0.689 14.007
detectionPnegEcdf 12.688 0.317 13.004
SigSetsToRGChannelSet 12.354 0.534 12.892
noobsb 9.116 1.438 10.555
detectionPnegNorm 9.706 0.328 10.035
SNPcheck 9.537 0.415 11.116
detectionPfixedNorm 9.413 0.274 9.686
detectionPnegNormGS 8.942 0.285 9.228
detectionZero 8.779 0.382 9.162
detectionPnegNormTotal 8.884 0.265 9.149
getBetas 8.744 0.166 8.963
IG-methods 8.133 0.627 9.037
getSexInfo 7.329 0.477 7.805
totalIntensities 6.165 0.808 6.973
buildControlMatrix450k 6.101 0.276 6.376
openSesame 5.924 0.432 6.359
makeExampleSeSAMeDataSet 5.947 0.333 6.280
inferEthnicity 5.514 0.362 5.876
meanIntensity 5.510 0.294 5.802
bisConversionControl 5.194 0.275 5.469
estimateLeukocyte 4.618 0.397 5.049
* 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 3.6.1 (2019-07-05) -- "Action of the Toes"
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
141.835 17.208 145.558
sesame.Rcheck/sesame-Ex.timings
| name | user | system | elapsed | |
| BetaValueToMValue | 0.000 | 0.000 | 0.001 | |
| IG-methods | 8.133 | 0.627 | 9.037 | |
| IG-replace-methods | 0.003 | 0.001 | 0.004 | |
| II-methods | 0.001 | 0.000 | 0.002 | |
| II-replace-methods | 0.009 | 0.006 | 0.017 | |
| 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 | 40.268 | 5.335 | 46.879 | |
| SNPcheck | 9.537 | 0.415 | 11.116 | |
| SigSet-class | 0.005 | 0.002 | 0.006 | |
| SigSetList-methods | 3.253 | 0.189 | 3.554 | |
| SigSetList | 0.337 | 0.051 | 0.388 | |
| SigSetListFromIDATs | 0.177 | 0.031 | 0.208 | |
| SigSetListFromPath | 0.387 | 0.057 | 0.445 | |
| SigSetToRatioSet | 22.937 | 0.670 | 24.189 | |
| SigSetsToRGChannelSet | 12.354 | 0.534 | 12.892 | |
| SignalSet | 0.005 | 0.001 | 0.006 | |
| as.data.frame.sesameQC | 27.989 | 1.717 | 29.749 | |
| bisConversionControl | 5.194 | 0.275 | 5.469 | |
| buildControlMatrix450k | 6.101 | 0.276 | 6.376 | |
| cnSegmentation | 89.368 | 9.573 | 98.990 | |
| ctl-methods | 0.002 | 0.000 | 0.003 | |
| ctl-replace-methods | 0.001 | 0.000 | 0.001 | |
| detectionPfixedNorm | 9.413 | 0.274 | 9.686 | |
| detectionPnegEcdf | 12.688 | 0.317 | 13.004 | |
| detectionPnegNorm | 9.706 | 0.328 | 10.035 | |
| detectionPnegNormGS | 8.942 | 0.285 | 9.228 | |
| detectionPnegNormTotal | 8.884 | 0.265 | 9.149 | |
| detectionPoobEcdf | 25.355 | 0.773 | 26.128 | |
| detectionZero | 8.779 | 0.382 | 9.162 | |
| diffRefSet | 13.317 | 0.689 | 14.007 | |
| dyeBiasCorr | 0.528 | 0.129 | 0.656 | |
| dyeBiasCorrMostBalanced | 18.693 | 0.956 | 19.654 | |
| dyeBiasCorrTypeINorm | 2.816 | 0.563 | 3.378 | |
| estimateLeukocyte | 4.618 | 0.397 | 5.049 | |
| getAFTypeIbySumAlleles | 0.057 | 0.006 | 0.063 | |
| getBetas | 8.744 | 0.166 | 8.963 | |
| getNormCtls | 0.133 | 0.016 | 0.149 | |
| getProbesByGene | 3.194 | 0.115 | 3.312 | |
| getProbesByRegion | 0.102 | 0.019 | 0.119 | |
| getProbesByTSS | 0.576 | 0.085 | 0.660 | |
| getRefSet | 3.597 | 0.218 | 3.815 | |
| getSexInfo | 7.329 | 0.477 | 7.805 | |
| inferEthnicity | 5.514 | 0.362 | 5.876 | |
| inferSex | 3.126 | 0.328 | 3.455 | |
| inferSexKaryotypes | 3.772 | 0.433 | 4.206 | |
| inferTypeIChannel | 0.132 | 0.045 | 0.177 | |
| initFileSet | 0.063 | 0.004 | 0.066 | |
| makeExampleSeSAMeDataSet | 5.947 | 0.333 | 6.280 | |
| makeExampleTinyEPICDataSet | 0.014 | 0.000 | 0.015 | |
| mapFileSet | 0.075 | 0.007 | 0.082 | |
| meanIntensity | 5.510 | 0.294 | 5.802 | |
| noob | 0.022 | 0.001 | 0.023 | |
| noobsb | 9.116 | 1.438 | 10.555 | |
| oobG-methods | 0.001 | 0.000 | 0.001 | |
| oobG-replace-methods | 0.003 | 0.002 | 0.005 | |
| oobR-methods | 0.001 | 0.000 | 0.002 | |
| oobR-replace-methods | 0.002 | 0.001 | 0.003 | |
| openSesame | 5.924 | 0.432 | 6.359 | |
| openSesameToFile | 3.056 | 0.290 | 3.344 | |
| parseGEOSignalABFile | 0.710 | 0.371 | 1.503 | |
| predictAgeHorvath353 | 1.214 | 0.474 | 0.195 | |
| predictAgePheno | 0.138 | 0.054 | 0.192 | |
| predictAgeSkinBlood | 0.148 | 0.035 | 0.184 | |
| print.fileSet | 0.057 | 0.015 | 0.072 | |
| print.sesameQC | 17.571 | 1.410 | 18.980 | |
| probeNames-methods | 0.062 | 0.005 | 0.067 | |
| pval-methods | 0.001 | 0.000 | 0.001 | |
| pval-replace-methods | 0.004 | 0.006 | 0.010 | |
| readFileSet | 0.174 | 0.049 | 0.223 | |
| readIDATpair | 0.247 | 0.035 | 0.282 | |
| searchIDATprefixes | 0.011 | 0.007 | 0.018 | |
| sesame-package | 2.017 | 0.362 | 2.378 | |
| sesameQC | 16.706 | 1.063 | 17.770 | |
| sesamize | 0.000 | 0.000 | 0.001 | |
| show-methods | 0.001 | 0.001 | 0.002 | |
| signalR6toS4 | 0.003 | 0.001 | 0.004 | |
| sliceFileSet | 0.058 | 0.006 | 0.064 | |
| subsetSignal | 0.277 | 0.022 | 0.299 | |
| totalIntensities | 6.165 | 0.808 | 6.973 | |
| totalIntensityZscore | 2.473 | 0.122 | 2.595 | |
| visualizeGene | 4.017 | 0.292 | 4.313 | |
| visualizeProbes | 1.358 | 0.112 | 1.472 | |
| visualizeRegion | 1.043 | 0.105 | 1.149 | |
| visualizeSegments | 1.410 | 0.139 | 1.550 | |