Wanding Zhou
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/sesame |
| Branch: RELEASE_3_10 |
| Last Commit: 55af6fe |
| Last Changed Date: 2019-10-29 13:11:14 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:30:43 -0400 (Wed, 15 Apr 2020).
| Package 1572/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| sesame 1.4.0 Wanding Zhou
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: sesame |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sesame.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings sesame_1.4.0.tar.gz |
| StartedAt: 2020-04-15 06:34:07 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:57:11 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 1384.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sesame.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sesame.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings sesame_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/sesame.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.4.0'
* 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 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 or elapsed time > 5s
user system elapsed
cnSegmentation 59.24 6.18 68.01
RGChannelSetToSigSets 25.64 2.44 28.22
detectionPoobEcdf 23.69 0.05 23.73
dyeBiasCorrMostBalanced 16.20 0.37 18.28
as.data.frame.sesameQC 14.55 0.78 15.55
noobsb 12.56 0.99 13.55
detectionPnegEcdf 12.69 0.00 12.69
print.sesameQC 12.06 0.19 12.25
diffRefSet 11.95 0.13 12.13
detectionPnegNormGS 11.92 0.00 11.93
SigSetToRatioSet 11.58 0.15 12.58
SigSetsToRGChannelSet 10.87 0.71 12.23
detectionPnegNorm 11.27 0.00 11.26
detectionPnegNormTotal 9.64 0.00 9.64
sesameQC 9.04 0.09 9.14
DMR 8.83 0.24 9.42
detectionPfixedNorm 9.01 0.00 9.02
openSesame 5.68 2.19 7.87
getSexInfo 7.32 0.09 7.42
SNPcheck 6.73 0.30 10.61
getBetas 6.83 0.10 6.92
meanIntensity 6.72 0.09 6.81
bisConversionControl 5.56 0.11 5.67
makeExampleSeSAMeDataSet 5.51 0.14 5.66
buildControlMatrix450k 5.11 0.14 5.25
DML 4.44 0.75 5.75
inferEthnicity 4.98 0.10 5.08
estimateLeukocyte 4.05 0.33 5.15
SigSetList-methods 2.22 0.12 5.72
visualizeGene 0.72 0.01 5.64
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
cnSegmentation 55.47 1.30 56.76
RGChannelSetToSigSets 28.05 1.54 29.62
detectionPoobEcdf 21.68 0.14 21.82
as.data.frame.sesameQC 19.38 0.78 20.16
dyeBiasCorrMostBalanced 17.80 0.47 18.27
diffRefSet 14.83 0.17 15.00
DMR 12.50 0.23 12.73
SigSetsToRGChannelSet 11.97 0.26 12.24
SigSetToRatioSet 11.53 0.17 11.71
detectionPnegNorm 10.08 0.04 10.20
detectionPnegNormGS 8.37 0.10 8.47
print.sesameQC 7.97 0.29 8.27
DML 7.31 0.92 8.36
SNPcheck 7.85 0.22 8.06
detectionPnegEcdf 7.78 0.05 7.83
detectionPnegNormTotal 7.32 0.03 7.35
detectionPfixedNorm 7.34 0.00 7.34
sesameQC 6.81 0.28 7.10
noobsb 6.22 0.36 6.58
detectionZero 6.08 0.14 6.22
getSexInfo 5.88 0.13 6.00
bisConversionControl 5.80 0.14 5.94
getBetas 5.53 0.05 5.58
IG-methods 5.03 0.11 5.14
* 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
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/sesame_1.4.0.tar.gz && rm -rf sesame.buildbin-libdir && mkdir sesame.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sesame.buildbin-libdir sesame_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL sesame_1.4.0.zip && rm sesame_1.4.0.tar.gz sesame_1.4.0.zip
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% 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 101k 100 101k 0 0 2837k 0 --:--:-- --:--:-- --:--:-- 3182k
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
DMR html
IG-methods html
IG-replace-methods html
II-methods html
II-replace-methods html
IR-methods html
IR-replace-methods 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
SignalSet html
finding level-2 HTML links ... done
as.data.frame.sesameQC html
binSignals html
bisConversionControl html
buildControlMatrix450k html
chipAddressToSignal html
cnSegmentation html
ctl-methods html
ctl-replace-methods html
detectionPfixedNorm html
detectionPnegEcdf html
detectionPnegNorm html
detectionPnegNormGS html
detectionPnegNormTotal html
detectionPoobEcdf html
detectionZero html
diffRefSet html
dyeBiasCorr html
dyeBiasCorrMostBalanced html
dyeBiasCorrTypeINorm html
estimateCellComposition html
estimateLeukocyte html
getAFTypeIbySumAlleles html
getBetas html
getBinCoordinates html
getNormCtls html
getProbesByGene html
getProbesByRegion html
getProbesByTSS html
getRefSet html
getSegment html
getSexInfo html
inferEthnicity html
inferSex html
inferSexKaryotypes html
inferTypeIChannel html
initFileSet html
makeExampleSeSAMeDataSet html
makeExampleTinyEPICDataSet html
mapFileSet html
meanIntensity html
noob html
noobsb html
oobG-methods html
oobG-replace-methods html
oobR-methods html
oobR-replace-methods html
openSesame html
openSesameToFile html
parseGEOSignalABFile html
predictAgeHorvath353 html
predictAgePheno html
predictAgeSkinBlood html
print.fileSet html
print.sesameQC html
probeNames-methods html
pval-methods html
pval-replace-methods html
readFileSet html
readIDATpair html
reopenSesame html
searchIDATprefixes html
segmentBins html
sesame-package html
sesameQC html
sesamize html
show-methods html
signalR6toS4 html
sliceFileSet html
subsetSignal html
topLoci html
topSegments html
totalIntensities html
totalIntensityZscore 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_1.4.0.zip
* DONE (sesame)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'sesame' successfully unpacked and MD5 sums checked
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sesame.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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: 1 | FAILED: 0 ]
>
> proc.time()
user system elapsed
73.96 5.82 81.15
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sesame.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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: 1 | FAILED: 0 ]
>
> proc.time()
user system elapsed
82.03 5.10 89.07
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sesame.Rcheck/examples_i386/sesame-Ex.timings
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sesame.Rcheck/examples_x64/sesame-Ex.timings
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