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
|