Wanding Zhou
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/sesame |
| Branch: RELEASE_3_8 |
| Last Commit: 8a9c43d |
| Last Changed Date: 2018-10-30 11:42:09 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 12:10:46 -0400 (Tue, 16 Apr 2019).
| Package 1429/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| sesame 1.0.0 Wanding Zhou
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: sesame |
| Version: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2019-04-16 02:44:58 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:52:29 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 451.7 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_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/sesame.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.0.0’
* 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 81.434 4.500 87.617
dyeBiasCorrMostBalanced 18.390 0.646 19.518
diffRefSet 14.748 0.412 15.565
detectionPoobEcdf 9.761 0.220 10.127
noobsb 9.049 0.652 9.771
detectionPnegEcdf 9.201 0.189 9.621
bisConversionControl 8.337 0.244 8.647
detectionPnegNormGS 7.837 0.197 8.331
detectionPnegNorm 7.729 0.254 8.076
getBetasTypeIbySumChannels 7.472 0.211 7.830
detectionPnegNormTotal 7.118 0.159 7.397
predictAgeHorvath353 4.840 1.793 0.601
getSexInfo 6.211 0.264 6.584
getBetas 6.095 0.156 6.314
inferEthnicity 5.477 0.244 5.858
buildControlMatrix450k 5.113 0.154 5.319
totalIntensities 4.967 0.177 5.204
SNPcheck 4.866 0.139 5.076
* 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/3.5/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 version 3.5.3 (2019-03-11) -- "Great Truth"
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, lengths, 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 sesameData.
>
> test_check("sesame")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 3 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
25.818 0.870 27.315
sesame.Rcheck/sesame-Ex.timings
| name | user | system | elapsed | |
| BetaValueToMValue | 0.000 | 0.001 | 0.000 | |
| IG-methods | 2.882 | 0.060 | 2.968 | |
| IG-replace-methods | 0.001 | 0.000 | 0.001 | |
| II-methods | 0 | 0 | 0 | |
| II-replace-methods | 0.004 | 0.004 | 0.008 | |
| IR-methods | 0.001 | 0.001 | 0.001 | |
| IR-replace-methods | 0.002 | 0.001 | 0.003 | |
| MValueToBetaValue | 0.000 | 0.001 | 0.001 | |
| SNPcheck | 4.866 | 0.139 | 5.076 | |
| SigSet-class | 0.008 | 0.001 | 0.008 | |
| SigSetList-methods | 1.057 | 0.060 | 1.163 | |
| SigSetList | 0.644 | 0.036 | 0.682 | |
| SigSetListFromIDATs | 0.318 | 0.016 | 0.340 | |
| SigSetListFromPath | 0.547 | 0.028 | 0.579 | |
| SignalSet | 0.004 | 0.001 | 0.005 | |
| bisConversionControl | 8.337 | 0.244 | 8.647 | |
| buildControlMatrix450k | 5.113 | 0.154 | 5.319 | |
| cnSegmentation | 81.434 | 4.500 | 87.617 | |
| ctl-methods | 0.002 | 0.000 | 0.003 | |
| ctl-replace-methods | 0.001 | 0.000 | 0.001 | |
| detectionPnegEcdf | 9.201 | 0.189 | 9.621 | |
| detectionPnegNorm | 7.729 | 0.254 | 8.076 | |
| detectionPnegNormGS | 7.837 | 0.197 | 8.331 | |
| detectionPnegNormTotal | 7.118 | 0.159 | 7.397 | |
| detectionPoobEcdf | 9.761 | 0.220 | 10.127 | |
| diffRefSet | 14.748 | 0.412 | 15.565 | |
| dyeBiasCorr | 0.320 | 0.062 | 0.383 | |
| dyeBiasCorrMostBalanced | 18.390 | 0.646 | 19.518 | |
| dyeBiasCorrTypeINorm | 2.018 | 0.300 | 2.349 | |
| estimateLeukocyte | 2.343 | 0.155 | 2.573 | |
| getAFTypeIbySumAlleles | 0.498 | 0.037 | 0.545 | |
| getBetas | 6.095 | 0.156 | 6.314 | |
| getBetasTypeIbySumChannels | 7.472 | 0.211 | 7.830 | |
| getNormCtls | 0.354 | 0.018 | 0.372 | |
| getProbesByGene | 1.688 | 0.068 | 1.767 | |
| getProbesByRegion | 0.069 | 0.007 | 0.077 | |
| getProbesByTSS | 0.201 | 0.016 | 0.217 | |
| getRefSet | 2.759 | 0.100 | 2.897 | |
| getSexInfo | 6.211 | 0.264 | 6.584 | |
| inferEthnicity | 5.477 | 0.244 | 5.858 | |
| inferSex | 2.823 | 0.251 | 3.171 | |
| inferSexKaryotypes | 2.581 | 0.200 | 2.869 | |
| makeExampleSeSAMeDataSet | 4.694 | 0.183 | 4.926 | |
| makeExampleTinyEPICDataSet | 2.524 | 0.058 | 2.612 | |
| meanIntensity | 4.563 | 0.176 | 4.774 | |
| noob | 0.028 | 0.001 | 0.029 | |
| noobsb | 9.049 | 0.652 | 9.771 | |
| oobG-methods | 0.001 | 0.000 | 0.001 | |
| oobG-replace-methods | 0.002 | 0.001 | 0.003 | |
| oobR-methods | 0.001 | 0.001 | 0.001 | |
| oobR-replace-methods | 0.002 | 0.001 | 0.003 | |
| openSesame | 0.047 | 0.067 | 3.048 | |
| predictAgeHorvath353 | 4.840 | 1.793 | 0.601 | |
| predictAgePheno | 0.094 | 0.017 | 0.111 | |
| predictAgeSkinBlood | 0.096 | 0.014 | 0.110 | |
| pval-methods | 0.001 | 0.000 | 0.001 | |
| pval-replace-methods | 0.003 | 0.002 | 0.006 | |
| readIDATpair | 0.299 | 0.041 | 0.341 | |
| searchIDATprefixes | 0.008 | 0.004 | 0.012 | |
| sesame-package | 1.938 | 0.215 | 2.174 | |
| sesamize | 0 | 0 | 0 | |
| show-methods | 0.001 | 0.000 | 0.002 | |
| signalR6toS4 | 0.004 | 0.001 | 0.004 | |
| subsetSignal | 0.208 | 0.017 | 0.227 | |
| totalIntensities | 4.967 | 0.177 | 5.204 | |
| totalIntensityZscore | 1.819 | 0.054 | 1.885 | |
| visualizeGene | 1.350 | 0.089 | 1.448 | |
| visualizeProbes | 0.990 | 0.035 | 1.039 | |
| visualizeRegion | 0.700 | 0.030 | 0.746 | |
| visualizeSegments | 1.324 | 0.073 | 1.406 | |