Wanding Zhou
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/sesame |
| git_branch: master |
| git_last_commit: fbfbd8f |
| git_last_commit_date: 2022-03-16 22:31:33 -0400 (Wed, 16 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:41 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the sesame package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sesame.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1783/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sesame 1.13.36 (landing page) Wanding Zhou
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: sesame |
| Version: 1.13.36 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sesame.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings sesame_1.13.36.tar.gz |
| StartedAt: 2022-03-17 20:16:06 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:31:01 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 895.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sesame.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sesame.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings sesame_1.13.36.tar.gz
###
##############################################################################
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/sesame.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sesame/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sesame' version '1.13.36'
* 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 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 (user + system) or elapsed time > 5s
user system elapsed
sesameQC_plotHeatSNPs 22.33 4.46 27.14
sesameQC_calcStats 22.09 3.83 26.28
DMR 24.96 0.50 26.89
DML 23.83 0.97 25.75
KYCG_plotEnrichAll 18.84 1.04 22.72
inferSpecies 17.95 1.41 20.75
KYCG_plotMeta 16.40 1.04 18.30
sesameQC_plotBetaByDesign 13.84 3.33 17.17
dyeBiasCorrMostBalanced 16.00 0.78 18.39
matchDesign 15.05 0.76 16.17
getSexInfo 13.78 0.98 16.16
diffRefSet 10.89 0.78 12.81
sesameQC_plotBar 10.61 0.95 12.91
compareMouseTissueReference 10.76 0.50 11.95
compareMouseStrainReference 10.29 0.59 11.57
sdf_read_table 9.92 0.58 10.87
testEnrichmentGSEA 8.92 1.38 11.35
KYCG_annoProbes 9.55 0.65 11.53
testEnrichment 9.55 0.54 11.48
controls 8.42 0.72 10.56
inferSex 8.23 0.86 9.80
dyeBiasCorr 8.33 0.64 10.39
getRefSet 8.56 0.41 9.69
dyeBiasCorrTypeINorm 8.01 0.83 9.20
KYCG_buildGeneDBs 7.89 0.47 9.35
visualizeGene 7.70 0.29 9.09
openSesame 7.14 0.53 8.76
dbStats 6.99 0.67 8.58
prepSesame 6.95 0.70 8.89
detectionIB 6.12 1.29 7.78
probeSuccessRate 6.80 0.57 8.82
sdf_write_table 7.03 0.26 7.69
createUCSCtrack 6.68 0.45 7.83
inferStrain 6.01 1.08 7.81
bisConversionControl 6.46 0.47 7.86
listAvailableMasks 6.53 0.34 7.97
inferTissue 5.69 1.09 7.47
inferSexKaryotypes 6.04 0.62 7.00
formatVCF 5.66 0.50 10.89
estimateLeukocyte 5.28 0.43 6.54
neob 4.84 0.58 5.78
scrubSoft 3.97 1.25 5.22
sesameQC_rankStats 3.99 1.12 5.81
detectionPnegEcdf 4.61 0.25 5.56
deidentify 4.11 0.30 5.14
* 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:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL sesame
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'sesame' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'sesame'
finding HTML links ... done
BetaValueToMValue html
DML html
DMR html
KYCG_annoProbes html
KYCG_buildGeneDBs html
KYCG_getDBs html
KYCG_listDBGroups html
KYCG_plotBar html
KYCG_plotDot html
KYCG_plotEnrichAll html
KYCG_plotLollipop html
KYCG_plotMeta html
KYCG_plotMetaEnrichment html
KYCG_plotPointRange html
KYCG_plotVolcano html
KYCG_plotWaterfall html
MValueToBetaValue html
SDFcollapseToPfx html
SigDF html
addMask html
aggregateTestEnrichments html
assemble_plots html
binSignals html
bisConversionControl html
checkLevels html
chipAddressToSignal html
cnSegmentation html
compareDatbaseSetOverlap html
compareMouseStrainReference html
compareMouseTissueReference html
controls html
createDBNetwork html
createUCSCtrack html
dataFrame2sesameQC html
dbStats html
deidentify html
detectionIB html
detectionPnegEcdf html
detectionPoobEcdf html
detectionPoobEcdf2 html
diffRefSet html
dmContrasts html
dyeBiasCorr html
dyeBiasCorrMostBalanced html
dyeBiasCorrTypeINorm html
dyeBiasL html
estimateCellComposition html
estimateLeukocyte html
formatVCF html
getAFTypeIbySumAlleles html
getAFs html
getBetas html
getBinCoordinates html
getRefSet html
getSexInfo html
inferEthnicity html
inferInfiniumIChannel html
inferSex html
inferSexKaryotypes html
inferSpecies html
inferStrain html
inferTissue html
initFileSet html
listAvailableMasks html
mapFileSet html
mapToMammal40 html
matchDesign html
meanIntensity html
medianTotalIntensity html
negControls html
neob html
noMasked html
noob html
normControls html
openSesame html
openSesameToFile html
parseGEOsignalMU html
predictAgeHorvath353 html
predictAgeSkinBlood html
predictMouseAgeInMonth html
prefixMask html
prefixMaskButC html
prefixMaskButCG html
prepSesame html
prepSesameList html
print.DMLSummary html
print.fileSet html
probeID_designType html
probeSuccessRate html
qualityMask html
reIdentify html
readFileSet html
readIDATpair html
resetMask html
scrub html
scrubSoft html
sdfPlatform html
sdf_read_table html
sdf_write_table html
searchIDATprefixes html
segmentBins html
sesame-package html
sesameAnno_download html
sesameAnno_get html
sesameAnno_getManifestDF html
sesameData_getAnno html
sesameQC-class html
sesameQC_calcStats html
sesameQC_getStats html
sesameQC_plotBar html
sesameQC_plotBetaByDesign html
sesameQC_plotHeatSNPs html
sesameQC_plotIntensVsBetas html
sesameQC_plotRedGrnQQ html
sesameQC_rankStats html
setMask html
signalMU html
sliceFileSet html
summaryExtractTest html
testEnrichment html
testEnrichmentFisher html
testEnrichmentGSEA html
testEnrichmentSpearman html
totalIntensities html
twoCompsEst2 html
updateSigDF html
visualizeGene html
visualizeProbes html
visualizeRegion html
visualizeSegments html
** 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)
Making 'packages.html' ... done
sesame.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
Attaching package: 'BiocGenerics'
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.max, which.min
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading sesameData.
----------------------------------------------------------
| SEnsible Step-wise Analysis of DNA MEthylation (SeSAMe)
| --------------------------------------------------------
| Please cache auxiliary data by "sesameDataCache()".
| This needs to be done only once per SeSAMe installation.
----------------------------------------------------------
>
> test_check("sesame")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
>
> proc.time()
user system elapsed
22.50 2.39 25.89
sesame.Rcheck/sesame-Ex.timings
| name | user | system | elapsed | |
| BetaValueToMValue | 0 | 0 | 0 | |
| DML | 23.83 | 0.97 | 25.75 | |
| DMR | 24.96 | 0.50 | 26.89 | |
| KYCG_annoProbes | 9.55 | 0.65 | 11.53 | |
| KYCG_buildGeneDBs | 7.89 | 0.47 | 9.35 | |
| KYCG_getDBs | 2.97 | 0.13 | 3.79 | |
| KYCG_listDBGroups | 0.02 | 0.01 | 0.03 | |
| KYCG_plotBar | 0.20 | 0.00 | 0.21 | |
| KYCG_plotDot | 0.17 | 0.00 | 0.17 | |
| KYCG_plotEnrichAll | 18.84 | 1.04 | 22.72 | |
| KYCG_plotLollipop | 0.10 | 0.00 | 0.09 | |
| KYCG_plotMeta | 16.40 | 1.04 | 18.30 | |
| KYCG_plotMetaEnrichment | 2.05 | 0.36 | 2.41 | |
| KYCG_plotPointRange | 1.55 | 0.13 | 1.67 | |
| KYCG_plotVolcano | 0.12 | 0.00 | 0.12 | |
| KYCG_plotWaterfall | 3.25 | 0.28 | 3.88 | |
| MValueToBetaValue | 0 | 0 | 0 | |
| SigDF | 0.30 | 0.04 | 0.89 | |
| addMask | 0.14 | 0.00 | 0.14 | |
| aggregateTestEnrichments | 1.81 | 0.19 | 2.00 | |
| bisConversionControl | 6.46 | 0.47 | 7.86 | |
| checkLevels | 3.09 | 0.29 | 3.74 | |
| cnSegmentation | 0.73 | 0.07 | 1.15 | |
| compareMouseStrainReference | 10.29 | 0.59 | 11.57 | |
| compareMouseTissueReference | 10.76 | 0.50 | 11.95 | |
| controls | 8.42 | 0.72 | 10.56 | |
| createUCSCtrack | 6.68 | 0.45 | 7.83 | |
| dataFrame2sesameQC | 0.71 | 0.13 | 1.19 | |
| dbStats | 6.99 | 0.67 | 8.58 | |
| deidentify | 4.11 | 0.30 | 5.14 | |
| detectionIB | 6.12 | 1.29 | 7.78 | |
| detectionPnegEcdf | 4.61 | 0.25 | 5.56 | |
| detectionPoobEcdf | 2.71 | 0.33 | 3.03 | |
| detectionPoobEcdf2 | 2.28 | 0.36 | 2.64 | |
| diffRefSet | 10.89 | 0.78 | 12.81 | |
| dmContrasts | 2.42 | 0.05 | 2.85 | |
| dyeBiasCorr | 8.33 | 0.64 | 10.39 | |
| dyeBiasCorrMostBalanced | 16.00 | 0.78 | 18.39 | |
| dyeBiasCorrTypeINorm | 8.01 | 0.83 | 9.20 | |
| dyeBiasL | 1.41 | 0.26 | 2.03 | |
| estimateLeukocyte | 5.28 | 0.43 | 6.54 | |
| formatVCF | 5.66 | 0.50 | 10.89 | |
| getAFTypeIbySumAlleles | 1.18 | 0.23 | 2.11 | |
| getAFs | 1.27 | 0.12 | 1.75 | |
| getBetas | 0.73 | 0.13 | 1.20 | |
| getRefSet | 8.56 | 0.41 | 9.69 | |
| getSexInfo | 13.78 | 0.98 | 16.16 | |
| inferEthnicity | 3.03 | 0.20 | 3.59 | |
| inferInfiniumIChannel | 0.27 | 0.21 | 0.47 | |
| inferSex | 8.23 | 0.86 | 9.80 | |
| inferSexKaryotypes | 6.04 | 0.62 | 7.00 | |
| inferSpecies | 17.95 | 1.41 | 20.75 | |
| inferStrain | 6.01 | 1.08 | 7.81 | |
| inferTissue | 5.69 | 1.09 | 7.47 | |
| initFileSet | 0.94 | 0.08 | 1.37 | |
| listAvailableMasks | 6.53 | 0.34 | 7.97 | |
| mapFileSet | 0.02 | 0.00 | 0.19 | |
| mapToMammal40 | 1.93 | 0.13 | 2.81 | |
| matchDesign | 15.05 | 0.76 | 16.17 | |
| meanIntensity | 0.69 | 0.13 | 1.18 | |
| medianTotalIntensity | 0.58 | 0.15 | 1.23 | |
| neob | 4.84 | 0.58 | 5.78 | |
| noMasked | 1.98 | 0.39 | 2.72 | |
| noob | 1.74 | 0.60 | 2.33 | |
| openSesame | 7.14 | 0.53 | 8.76 | |
| openSesameToFile | 3.73 | 0.42 | 4.16 | |
| parseGEOsignalMU | 0.75 | 0.58 | 1.33 | |
| predictAgeHorvath353 | 2.63 | 0.15 | 3.12 | |
| predictAgeSkinBlood | 3.78 | 0.19 | 4.66 | |
| predictMouseAgeInMonth | 3.11 | 0.34 | 4.16 | |
| prefixMask | 1.23 | 0.16 | 1.73 | |
| prefixMaskButC | 0.21 | 0.02 | 0.22 | |
| prefixMaskButCG | 0.09 | 0.00 | 0.09 | |
| prepSesame | 6.95 | 0.70 | 8.89 | |
| prepSesameList | 0.02 | 0.00 | 0.02 | |
| print.DMLSummary | 3.50 | 0.23 | 4.44 | |
| print.fileSet | 0.73 | 0.11 | 1.11 | |
| probeID_designType | 0 | 0 | 0 | |
| probeSuccessRate | 6.80 | 0.57 | 8.82 | |
| qualityMask | 3.66 | 0.34 | 4.91 | |
| reIdentify | 4.36 | 0.14 | 4.84 | |
| readFileSet | 0.04 | 0.00 | 0.05 | |
| readIDATpair | 0.11 | 0.00 | 0.11 | |
| resetMask | 0.38 | 0.03 | 0.78 | |
| scrub | 2.36 | 0.81 | 3.17 | |
| scrubSoft | 3.97 | 1.25 | 5.22 | |
| sdfPlatform | 1.28 | 0.16 | 1.80 | |
| sdf_read_table | 9.92 | 0.58 | 10.87 | |
| sdf_write_table | 7.03 | 0.26 | 7.69 | |
| searchIDATprefixes | 0 | 0 | 0 | |
| sesame-package | 2.30 | 0.13 | 2.77 | |
| sesameAnno_download | 0 | 0 | 0 | |
| sesameAnno_get | 0 | 0 | 0 | |
| sesameAnno_getManifestDF | 0 | 0 | 0 | |
| sesameData_getAnno | 0 | 0 | 0 | |
| sesameQC_calcStats | 22.09 | 3.83 | 26.28 | |
| sesameQC_getStats | 1.44 | 0.23 | 1.67 | |
| sesameQC_plotBar | 10.61 | 0.95 | 12.91 | |
| sesameQC_plotBetaByDesign | 13.84 | 3.33 | 17.17 | |
| sesameQC_plotHeatSNPs | 22.33 | 4.46 | 27.14 | |
| sesameQC_plotIntensVsBetas | 2.02 | 0.56 | 2.92 | |
| sesameQC_plotRedGrnQQ | 1.85 | 0.33 | 2.53 | |
| sesameQC_rankStats | 3.99 | 1.12 | 5.81 | |
| setMask | 0.08 | 0.02 | 0.10 | |
| signalMU | 1.00 | 0.18 | 1.53 | |
| sliceFileSet | 0.03 | 0.00 | 0.05 | |
| summaryExtractTest | 3.64 | 0.21 | 4.53 | |
| testEnrichment | 9.55 | 0.54 | 11.48 | |
| testEnrichmentGSEA | 8.92 | 1.38 | 11.35 | |
| totalIntensities | 2.40 | 0.33 | 3.59 | |
| updateSigDF | 2.71 | 0.22 | 3.66 | |
| visualizeGene | 7.70 | 0.29 | 9.09 | |
| visualizeProbes | 4.03 | 0.22 | 4.59 | |
| visualizeRegion | 0.69 | 0.05 | 0.74 | |
| visualizeSegments | 1.51 | 0.06 | 1.92 | |