Wanding Zhou
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/sesame |
| git_branch: RELEASE_3_14 |
| git_last_commit: 88cfdf2 |
| git_last_commit_date: 2022-02-06 16:30:52 -0400 (Sun, 06 Feb 2022) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:21 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1775/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sesame 1.12.9 (landing page) Wanding Zhou
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: 1.12.9 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sesame.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings sesame_1.12.9.tar.gz |
| StartedAt: 2022-04-13 02:48:46 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 03:21:10 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 1943.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sesame.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sesame.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings sesame_1.12.9.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/sesame.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.12.9'
* 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
visualizeSegments 56.11 0.57 57.38
cnSegmentation 51.99 2.77 60.02
DMR 42.79 1.07 47.83
testEnrichment 24.73 0.47 26.10
bSubMostVariable 22.52 0.61 23.28
sdf_read_table 19.44 0.47 20.23
compareMouseTissueReference 17.34 0.33 18.81
diffRefSet 16.05 0.31 17.13
testEnrichmentGene 15.90 0.36 16.82
DML 12.86 2.07 16.11
print.sesameQC 14.25 0.51 14.92
attachManifest 13.48 0.89 18.55
getProbesByChromosome 14.11 0.22 16.16
compareMouseStrainReference 13.99 0.07 14.91
as.data.frame.sesameQC 11.91 0.89 12.95
getProbesByGene 12.07 0.24 16.04
visualizeGene 12.05 0.26 12.80
createUCSCtrack 12.02 0.20 12.58
bisConversionControl 11.30 0.37 13.62
getRefSet 11.47 0.16 11.76
dyeBiasCorrMostBalanced 11.43 0.18 18.42
sdf_write_table 11.25 0.28 11.82
calcDatabaseSetStatisticsAll 10.13 1.36 13.33
getDatabaseSetOverlap 11.03 0.25 11.87
estimateLeukocyte 10.94 0.29 13.92
SNPcheck 9.97 0.81 53.70
deidentify 10.23 0.18 11.06
bSubProbes 9.85 0.46 10.66
inferTissue 9.67 0.63 11.37
print.DMLSummary 9.86 0.16 10.34
summaryExtractTest 9.61 0.17 10.12
sesameQC 9.15 0.49 9.81
inferStrain 8.94 0.53 10.82
dmContrasts 9.33 0.10 9.59
reIdentify 8.79 0.33 9.44
inferSex 7.55 0.36 8.27
setMaskBySpecies 7.39 0.28 8.17
qualityRank 6.21 0.22 6.96
qualityMask 5.94 0.18 6.85
getNormCtls 5.73 0.19 6.41
dyeBiasCorrTypeINorm 5.72 0.10 5.97
bSubComplete 5.30 0.28 9.81
SigDF 5.15 0.30 9.67
dyeBiasCorr 5.21 0.19 5.69
getAutosomeProbes 5.12 0.10 5.37
getProbesByRegion 4.89 0.06 5.11
totalIntensities 4.64 0.17 5.12
probeSuccessRate 4.55 0.10 5.14
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
visualizeSegments 55.73 0.83 57.27
cnSegmentation 50.85 1.27 52.61
DMR 33.49 0.87 35.30
testEnrichment 25.89 1.03 27.78
bSubMostVariable 22.51 0.25 22.92
compareMouseTissueReference 17.80 0.22 18.39
diffRefSet 15.69 0.39 16.72
sdf_read_table 15.58 0.31 16.28
testEnrichmentGene 15.18 0.37 16.15
compareMouseStrainReference 14.53 0.14 15.47
visualizeGene 13.25 0.39 14.13
as.data.frame.sesameQC 12.28 1.07 13.53
DML 11.90 0.92 13.30
createUCSCtrack 11.98 0.28 12.58
getProbesByChromosome 11.50 0.19 11.86
calcDatabaseSetStatisticsAll 11.18 0.39 13.61
getDatabaseSetOverlap 11.04 0.39 11.97
print.sesameQC 10.28 0.98 11.44
bSubProbes 10.53 0.34 11.22
bisConversionControl 10.46 0.28 11.22
print.DMLSummary 10.41 0.22 10.91
inferTissue 10.04 0.44 11.62
attachManifest 10.13 0.33 10.81
getProbesByGene 10.05 0.26 10.65
deidentify 9.87 0.19 10.43
sdf_write_table 9.85 0.16 10.19
inferStrain 9.44 0.56 10.50
sesameQC 9.09 0.81 10.08
estimateLeukocyte 9.59 0.25 10.19
dmContrasts 9.65 0.17 10.01
getRefSet 9.59 0.14 9.94
reIdentify 9.42 0.24 9.99
summaryExtractTest 9.47 0.18 9.96
SNPcheck 8.09 0.22 8.64
dyeBiasCorrMostBalanced 8.03 0.17 8.84
getNormCtls 7.44 0.27 8.00
inferSex 6.58 0.50 7.39
qualityRank 6.84 0.19 7.51
getProbesByRegion 6.70 0.14 7.00
setMaskBySpecies 6.50 0.17 6.98
qualityMask 5.55 0.21 6.10
bSubComplete 5.42 0.10 5.67
getSexInfo 5.10 0.27 5.53
SigDF 5.11 0.22 5.66
totalIntensities 5.16 0.14 5.62
dyeBiasCorr 4.94 0.22 5.82
getAutosomeProbes 5.00 0.10 5.25
probeSuccessRate 4.67 0.24 5.25
* 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://155.52.207.166/BBS/3.14/bioc/src/contrib/sesame_1.12.9.tar.gz && rm -rf sesame.buildbin-libdir && mkdir sesame.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sesame.buildbin-libdir sesame_1.12.9.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL sesame_1.12.9.zip && rm sesame_1.12.9.tar.gz sesame_1.12.9.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 140k 100 140k 0 0 528k 0 --:--:-- --:--:-- --:--:-- 531k
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
MValueToBetaValue html
RGChannelSetToSigDFs html
SNPcheck html
SigDF html
SigDFToRatioSet html
SigDFsToRGChannelSet html
addMask html
as.data.frame.sesameQC html
attachManifest html
bSubComplete html
bSubMostVariable html
bSubProbes html
binSignals html
bisConversionControl html
calcDatabaseSetStatistics1 html
calcDatabaseSetStatisticsAll html
checkLevels html
chipAddressToSignal html
cnSegmentation html
compareDatbaseSetOverlap html
compareMouseStrainReference html
compareMouseTissueReference html
controls html
createDatabaseSetNetwork html
createUCSCtrack html
deidentify html
detectionPnegEcdf html
detectionPoobEcdf html
detectionPoobEcdf2 html
diffRefSet html
dmContrasts html
dyeBiasCorr html
dyeBiasCorrMostBalanced html
dyeBiasCorrTypeINorm html
dyeBiasDistortion html
estimateCellComposition html
estimateLeukocyte html
extractDesign html
formatVCF html
getAFTypeIbySumAlleles html
getAutosomeProbes html
getBetas html
getBinCoordinates html
getDatabaseSetOverlap html
getNormCtls html
getProbesByChromosome html
getProbesByGene html
getProbesByRegion html
getProbesByTSS html
getRefSet html
getSexInfo html
inferEthnicity html
inferInfiniumIChannel html
inferSex html
inferSexKaryotypes html
inferSpecies html
inferStrain html
inferTissue html
initFileSet html
isUniqProbeID html
mapFileSet html
meanIntensity html
medianTotalIntensity html
neob html
noMasked html
noob html
openSesame html
openSesameToFile html
plotLollipop html
plotVolcano html
predictAgeHorvath353 html
predictAgeSkinBlood html
predictMouseAgeInMonth html
print.DMLSummary html
print.SigDF html
print.fileSet html
print.sesameQC html
probeID_designType html
probeSuccessRate html
qualityMask html
qualityRank html
reIdentify html
readFileSet html
readIDATpair html
reopenSesame html
resetMask html
scrub html
scrubSoft html
sdfPlatform html
sdf_read_table html
sdf_write_table html
searchIDATprefixes html
segmentBins html
sesame-package html
sesamePlotIntensVsBetas html
sesamePlotRedGrnQQ html
sesameQC html
sesamize html
setMask html
setMaskBySpecies html
signalMU html
sliceFileSet html
summaryExtractTest html
testEnrichment html
testEnrichment1 html
testEnrichmentFGSEA html
testEnrichmentFisher html
testEnrichmentGene html
testEnrichmentSpearman html
totalIntensities 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_1.12.9.zip
* DONE (sesame)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'sesame' successfully unpacked and MD5 sums checked
|
sesame.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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
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 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 0 | SKIP 0 | PASS 1 ]
>
> proc.time()
user system elapsed
16.85 2.50 19.70
|
sesame.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 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 0 | SKIP 0 | PASS 1 ]
>
> proc.time()
user system elapsed
17.62 1.59 19.53
|
|
sesame.Rcheck/examples_i386/sesame-Ex.timings
|
sesame.Rcheck/examples_x64/sesame-Ex.timings
|