Wanding Zhou
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/sesame |
| git_branch: RELEASE_3_13 |
| git_last_commit: 867cb46 |
| git_last_commit_date: 2021-10-07 23:00:13 -0400 (Thu, 07 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:22 -0400 (Fri, 15 Oct 2021).
|
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 1745/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sesame 1.10.5 (landing page) Wanding Zhou
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: sesame |
| Version: 1.10.5 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sesame.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings sesame_1.10.5.tar.gz |
| StartedAt: 2021-10-15 05:33:35 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 06:04:24 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 1849.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sesame.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sesame.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings sesame_1.10.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/sesame.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.10.5'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DMR 79.63 2.43 125.63
cnSegmentation 67.88 4.82 77.16
topSegments 55.63 0.21 56.05
as.data.frame.sesameQC 19.43 2.39 22.00
print.sesameQC 20.13 0.72 20.99
compareMouseTissueReference 19.72 0.34 20.48
dyeBiasCorrMostBalanced 18.16 0.34 22.33
bSubMostVariable 17.39 0.94 19.47
sesameQC 17.11 0.77 18.05
betaToAF 14.79 0.64 17.06
SigSetsToRGChannelSet 14.22 0.42 15.19
DML 11.99 1.87 14.76
diffRefSet 12.41 0.16 13.12
qualityRank 11.89 0.21 12.47
getAutosomeProbes 11.59 0.23 13.93
print.DMLSummary 11.43 0.10 11.70
SigSetToRatioSet 10.53 0.54 11.27
SNPcheck 9.45 0.26 16.19
IG-methods 7.34 1.71 14.78
IGpass 8.25 0.30 14.91
bisConversionControl 7.97 0.57 9.00
sesamePlotIntensVsBetas 7.82 0.20 8.19
compareMouseBloodReference 7.72 0.23 9.20
summaryExtractCfList 7.23 0.08 7.48
summaryExtractTest 7.19 0.11 7.47
SigSetList-methods 6.25 0.36 7.58
inferStrain 5.98 0.36 6.67
getBetas 5.82 0.03 6.01
estimateLeukocyte 5.54 0.31 7.62
formatVCF 5.65 0.03 6.19
dyeBiasCorrTypeINorm 4.95 0.32 5.62
inferSex 5.00 0.22 5.64
getAFTypeIbySumAlleles 4.58 0.17 5.09
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DMR 79.14 0.54 80.19
topSegments 64.54 0.23 64.93
cnSegmentation 60.81 1.25 62.76
compareMouseTissueReference 22.55 0.33 23.19
as.data.frame.sesameQC 18.77 0.53 19.44
sesameQC 18.16 0.70 19.03
print.sesameQC 16.61 0.76 17.55
bSubMostVariable 16.90 0.30 17.37
betaToAF 13.33 0.73 14.58
DML 12.27 1.29 14.05
diffRefSet 12.72 0.20 13.09
dyeBiasCorrMostBalanced 12.22 0.41 12.80
SigSetsToRGChannelSet 11.14 0.41 11.89
SigSetToRatioSet 10.89 0.39 11.49
qualityRank 10.17 0.28 10.81
getAutosomeProbes 8.31 0.26 8.77
compareMouseBloodReference 8.00 0.36 8.81
bisConversionControl 7.61 0.28 8.29
SNPcheck 7.61 0.19 8.15
sesamePlotIntensVsBetas 6.70 0.37 7.24
print.DMLSummary 6.86 0.08 7.10
formatVCF 6.38 0.18 7.06
summaryExtractTest 6.36 0.08 6.58
summaryExtractCfList 6.28 0.05 6.49
IG-methods 6.17 0.13 6.72
inferStrain 5.71 0.41 6.45
SigSetList-methods 5.68 0.32 6.62
getBetas 5.47 0.08 5.68
IGpass 5.28 0.18 5.78
estimateLeukocyte 5.19 0.16 5.52
reIdentify 5.19 0.08 5.45
inferSex 4.89 0.28 5.48
getRefSet 5.00 0.09 5.09
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/sesame_1.10.5.tar.gz && rm -rf sesame.buildbin-libdir && mkdir sesame.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sesame.buildbin-libdir sesame_1.10.5.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL sesame_1.10.5.zip && rm sesame_1.10.5.tar.gz sesame_1.10.5.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 135k 100 135k 0 0 697k 0 --:--:-- --:--:-- --:--:-- 699k
install for i386
* 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
DMLShrinkage html
DMR html
IG-methods html
IG-replace-methods html
IGpass html
II-methods html
II-replace-methods html
IIpass html
IR-methods html
IR-replace-methods html
IRpass html
MValueToBetaValue html
RGChannelSetToSigSets html
SNPcheck html
SigSet-class html
SigSetList-class html
SigSetList-methods html
SigSetList html
SigSetListFromIDATs html
SigSetListFromPath html
SigSetToRatioSet html
SigSetsToRGChannelSet html
addMask html
as.data.frame.sesameQC html
bSubComplete html
bSubMostVariable html
bSubProbes html
betaToAF html
binSignals html
bisConversionControl html
buildControlMatrix450k html
checkLevels html
chipAddressToSignal html
cnSegmentation html
compareMouseBloodReference html
compareMouseTissueReference html
createUCSCtrack html
ctl-methods html
ctl-replace-methods html
deidentify html
detectionPfixedNorm html
detectionPnegEcdf html
detectionPnegNorm html
detectionPnegNormGS html
detectionPnegNormTotal html
detectionPoobEcdf html
detectionPoobEcdf2 html
diffRefSet html
dyeBiasCorr html
dyeBiasCorrMostBalanced html
dyeBiasCorrTypeINorm html
estimateCellComposition html
estimateLeukocyte html
extra-methods html
extra-replace-methods html
extractDesign html
formatVCF html
getAFTypeIbySumAlleles html
getAutosomeProbes html
getBetas html
getBinCoordinates html
getNormCtls html
getProbesByChromosome html
getProbesByGene html
getProbesByRegion html
getProbesByTSS html
getRefSet html
getSexInfo html
inferEthnicity html
inferSex html
inferSexKaryotypes html
inferStrain html
inferTypeIChannel html
initFileSet html
isUniqProbeID html
makeExampleSeSAMeDataSet html
makeExampleTinyEPICDataSet html
mapFileSet html
mask html
meanIntensity html
noob html
noobsb html
oobG-methods html
oobG-replace-methods html
oobGpass html
oobR-methods html
oobR-replace-methods html
oobRpass html
openSesame html
openSesameToFile html
parseGEOSignalABFile html
predictAgeHorvath353 html
predictAgePheno html
predictAgeSkinBlood html
predictMouseAgeInMonth html
print.DMLSummary html
print.fileSet html
print.sesameQC html
probeID_designType html
probeNames-methods html
pval-methods html
pval-replace-methods html
qualityMask html
qualityRank html
reIdentify html
readFileSet html
readIDATpair html
reopenSesame html
resetMask html
restoreMask html
saveMask html
scrub html
scrubSoft html
searchIDATprefixes html
segmentBins html
sesame-package html
sesamePlotIntensVsBetas html
sesamePlotRedGrnQQ html
sesameQC html
sesamize html
setMask html
show-methods html
signalMU html
sliceFileSet html
subsetSignal html
summaryExtractCfList html
summaryExtractTest html
topSegments html
totalIntensities html
totalIntensityZscore html
twoCompsEst2 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
install for x64
* installing *source* package 'sesame' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sesame' as sesame_1.10.5.zip
* DONE (sesame)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'sesame' successfully unpacked and MD5 sums checked
|
sesame.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.max, which.min
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: rmarkdown
Loading sesameData.
----------------------------------------------------------
| SEnsible Step-wise Analysis of DNA MEthylation (SeSAMe)
| --------------------------------------------------------
| Please cache the annotation data for your array platform
| (e.g. EPIC) by calling "sesameDataCache("EPIC")"
| or "sesameDataCacheAll()". This needs to be done only
| once per SeSAMe installation.
----------------------------------------------------------
>
> test_check("sesame")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 19 ]
>
> proc.time()
user system elapsed
66.10 6.67 73.64
|
sesame.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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
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.max, which.min
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: rmarkdown
Loading sesameData.
----------------------------------------------------------
| SEnsible Step-wise Analysis of DNA MEthylation (SeSAMe)
| --------------------------------------------------------
| Please cache the annotation data for your array platform
| (e.g. EPIC) by calling "sesameDataCache("EPIC")"
| or "sesameDataCacheAll()". This needs to be done only
| once per SeSAMe installation.
----------------------------------------------------------
>
> test_check("sesame")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 19 ]
>
> proc.time()
user system elapsed
64.79 4.64 70.07
|
|
sesame.Rcheck/examples_i386/sesame-Ex.timings
|
sesame.Rcheck/examples_x64/sesame-Ex.timings
|