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 12:15:08 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings sesame_1.2.0.tar.gz |
| StartedAt: 2019-10-16 04:58:13 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:10:28 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 734.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sesame.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings sesame_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/sesame.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 55.047 0.348 56.095
RGChannelSetToSigSets 31.844 1.717 36.213
dyeBiasCorrMostBalanced 18.056 0.224 18.805
as.data.frame.sesameQC 17.784 0.192 18.607
SigSetToRatioSet 16.069 0.095 16.268
detectionPoobEcdf 12.519 0.028 12.560
SigSetsToRGChannelSet 11.924 0.135 12.231
diffRefSet 11.029 0.065 11.136
print.sesameQC 8.390 0.120 8.510
sesameQC 7.691 0.012 7.702
SNPcheck 7.491 0.096 8.174
IG-methods 6.637 0.200 6.892
detectionPfixedNorm 6.595 0.000 6.595
detectionPnegNormTotal 6.279 0.000 6.282
detectionPnegEcdf 5.663 0.028 5.692
detectionPnegNorm 5.353 0.004 5.358
noobsb 5.224 0.052 5.279
* 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: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL sesame ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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-pc-linux-gnu (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
90.791 4.138 89.001
sesame.Rcheck/sesame-Ex.timings
| name | user | system | elapsed | |
| BetaValueToMValue | 0.001 | 0.000 | 0.000 | |
| IG-methods | 6.637 | 0.200 | 6.892 | |
| IG-replace-methods | 0.001 | 0.000 | 0.001 | |
| II-methods | 0.001 | 0.000 | 0.001 | |
| II-replace-methods | 0.008 | 0.000 | 0.008 | |
| IR-methods | 0.001 | 0.000 | 0.001 | |
| IR-replace-methods | 0.002 | 0.000 | 0.003 | |
| MValueToBetaValue | 0 | 0 | 0 | |
| RGChannelSetToSigSets | 31.844 | 1.717 | 36.213 | |
| SNPcheck | 7.491 | 0.096 | 8.174 | |
| SigSet-class | 0.003 | 0.000 | 0.003 | |
| SigSetList-methods | 2.341 | 0.016 | 2.409 | |
| SigSetList | 0.313 | 0.008 | 0.321 | |
| SigSetListFromIDATs | 0.146 | 0.000 | 0.146 | |
| SigSetListFromPath | 0.289 | 0.012 | 0.319 | |
| SigSetToRatioSet | 16.069 | 0.095 | 16.268 | |
| SigSetsToRGChannelSet | 11.924 | 0.135 | 12.231 | |
| SignalSet | 0.007 | 0.000 | 0.006 | |
| as.data.frame.sesameQC | 17.784 | 0.192 | 18.607 | |
| bisConversionControl | 3.819 | 0.068 | 3.888 | |
| buildControlMatrix450k | 3.419 | 0.000 | 3.420 | |
| cnSegmentation | 55.047 | 0.348 | 56.095 | |
| ctl-methods | 0.002 | 0.000 | 0.003 | |
| ctl-replace-methods | 0.001 | 0.000 | 0.001 | |
| detectionPfixedNorm | 6.595 | 0.000 | 6.595 | |
| detectionPnegEcdf | 5.663 | 0.028 | 5.692 | |
| detectionPnegNorm | 5.353 | 0.004 | 5.358 | |
| detectionPnegNormGS | 4.685 | 0.000 | 4.686 | |
| detectionPnegNormTotal | 6.279 | 0.000 | 6.282 | |
| detectionPoobEcdf | 12.519 | 0.028 | 12.560 | |
| detectionZero | 3.504 | 0.000 | 3.504 | |
| diffRefSet | 11.029 | 0.065 | 11.136 | |
| dyeBiasCorr | 0.329 | 0.000 | 0.328 | |
| dyeBiasCorrMostBalanced | 18.056 | 0.224 | 18.805 | |
| dyeBiasCorrTypeINorm | 2.055 | 0.012 | 2.068 | |
| estimateLeukocyte | 2.964 | 0.044 | 3.093 | |
| getAFTypeIbySumAlleles | 0.037 | 0.000 | 0.038 | |
| getBetas | 4.299 | 0.000 | 4.300 | |
| getNormCtls | 0.184 | 0.000 | 0.185 | |
| getProbesByGene | 2.178 | 0.016 | 2.287 | |
| getProbesByRegion | 0.039 | 0.000 | 0.039 | |
| getProbesByTSS | 0.128 | 0.000 | 0.128 | |
| getRefSet | 1.349 | 0.008 | 1.356 | |
| getSexInfo | 4.278 | 0.000 | 4.277 | |
| inferEthnicity | 3.153 | 0.000 | 3.152 | |
| inferSex | 1.666 | 0.008 | 1.675 | |
| inferSexKaryotypes | 2.093 | 0.100 | 2.193 | |
| inferTypeIChannel | 0.099 | 0.004 | 0.103 | |
| initFileSet | 0.057 | 0.000 | 0.056 | |
| makeExampleSeSAMeDataSet | 3.448 | 0.052 | 3.500 | |
| makeExampleTinyEPICDataSet | 0.009 | 0.000 | 0.010 | |
| mapFileSet | 0.067 | 0.000 | 0.067 | |
| meanIntensity | 4.481 | 0.000 | 4.480 | |
| noob | 0.012 | 0.000 | 0.013 | |
| noobsb | 5.224 | 0.052 | 5.279 | |
| oobG-methods | 0.001 | 0.000 | 0.001 | |
| oobG-replace-methods | 0.002 | 0.000 | 0.001 | |
| oobR-methods | 0.001 | 0.000 | 0.000 | |
| oobR-replace-methods | 0.001 | 0.000 | 0.001 | |
| openSesame | 4.290 | 0.051 | 4.498 | |
| openSesameToFile | 2.426 | 0.008 | 2.434 | |
| parseGEOSignalABFile | 0.366 | 0.422 | 0.950 | |
| predictAgeHorvath353 | 0.813 | 0.204 | 0.115 | |
| predictAgePheno | 0.099 | 0.004 | 0.103 | |
| predictAgeSkinBlood | 0.104 | 0.012 | 0.116 | |
| print.fileSet | 0.053 | 0.004 | 0.058 | |
| print.sesameQC | 8.39 | 0.12 | 8.51 | |
| probeNames-methods | 0.017 | 0.000 | 0.016 | |
| pval-methods | 0.001 | 0.000 | 0.001 | |
| pval-replace-methods | 0.003 | 0.000 | 0.003 | |
| readFileSet | 0.066 | 0.011 | 0.077 | |
| readIDATpair | 0.105 | 0.008 | 0.113 | |
| searchIDATprefixes | 0.007 | 0.000 | 0.022 | |
| sesame-package | 0.963 | 0.036 | 0.999 | |
| sesameQC | 7.691 | 0.012 | 7.702 | |
| sesamize | 0 | 0 | 0 | |
| show-methods | 0.001 | 0.000 | 0.002 | |
| signalR6toS4 | 0.001 | 0.002 | 0.003 | |
| sliceFileSet | 0.064 | 0.001 | 0.066 | |
| subsetSignal | 0.209 | 0.000 | 0.208 | |
| totalIntensities | 4.411 | 0.060 | 4.472 | |
| totalIntensityZscore | 1.417 | 0.000 | 1.418 | |
| visualizeGene | 3.619 | 0.152 | 3.809 | |
| visualizeProbes | 1.260 | 0.012 | 1.272 | |
| visualizeRegion | 0.56 | 0.00 | 0.56 | |
| visualizeSegments | 1.531 | 0.040 | 1.571 | |