Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:25:17 -0400 (Wed, 15 Apr 2020).
Package 1783/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
variancePartition 1.16.1 Gabriel E. Hoffman
| 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: variancePartition |
Version: 1.16.1 |
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:variancePartition.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings variancePartition_1.16.1.tar.gz |
StartedAt: 2020-04-15 07:19:35 -0400 (Wed, 15 Apr 2020) |
EndedAt: 2020-04-15 07:36:49 -0400 (Wed, 15 Apr 2020) |
EllapsedTime: 1034.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: variancePartition.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:variancePartition.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings variancePartition_1.16.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/variancePartition.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 'variancePartition/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'variancePartition' version '1.16.1' * 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 'variancePartition' 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed fitVarPartModel-method 23.44 3.83 69.53 extractVarPart 14.67 3.43 54.25 fitExtractVarPartModel-method 5.17 1.24 40.88 getVarianceComponents 5.05 1.25 26.29 residuals-VarParFitList-method 5.43 0.82 24.58 plotCompareP-method 3.36 0.60 24.53 varPartConfInf 3.92 0.01 23.69 plotPercentBars 2.72 0.52 24.48 sortCols-method 2.52 0.71 25.94 plotVarPart-method 2.63 0.47 21.95 voomWithDreamWeights 2.50 0.22 21.82 dream-method 2.50 0.14 30.17 plotCorrStructure 1.71 0.15 15.14 colinearityScore 0.75 0.07 10.28 as.data.frame-varPartResults-method 0.60 0.01 11.92 as.matrix-varPartResults-method 0.55 0.02 9.44 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed fitVarPartModel-method 22.42 2.70 66.53 extractVarPart 13.00 1.87 46.71 getVarianceComponents 5.55 0.94 26.20 fitExtractVarPartModel-method 4.92 1.24 39.11 residuals-VarParFitList-method 4.83 0.76 18.80 plotCompareP-method 3.74 0.39 24.33 varPartConfInf 4.05 0.00 19.53 dream-method 2.88 0.23 35.50 plotPercentBars 2.17 0.29 18.78 sortCols-method 2.06 0.39 21.42 plotVarPart-method 1.73 0.56 19.39 voomWithDreamWeights 1.69 0.14 17.95 plotCorrStructure 1.42 0.07 13.92 colinearityScore 0.94 0.08 10.82 as.data.frame-varPartResults-method 0.78 0.06 12.58 as.matrix-varPartResults-method 0.62 0.00 11.46 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... Running 'runTests.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
variancePartition.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/variancePartition_1.16.1.tar.gz && rm -rf variancePartition.buildbin-libdir && mkdir variancePartition.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=variancePartition.buildbin-libdir variancePartition_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL variancePartition_1.16.1.zip && rm variancePartition_1.16.1.tar.gz variancePartition_1.16.1.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 1381k 100 1381k 0 0 7722k 0 --:--:-- --:--:-- --:--:-- 7936k install for i386 * installing *source* package 'variancePartition' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for 'eBayes' from package 'limma' in package 'variancePartition' Creating a new generic function for 'classifyTestsF' in package 'variancePartition' Creating a generic function for 'topTable' from package 'limma' in package 'variancePartition' ** help *** installing help indices converting help for package 'variancePartition' finding HTML links ... done ESS-method html MArrayLM2-class html VarParCIList-class html VarParFitList-class html as.data.frame-varPartResults-method html as.matrix-varPartResults-method html calcVarPart-method html canCorPairs html classifyTestsF-MArrayLM2-method html classifyTestsF html colinearityScore html dot-getAllUniContrasts html dot-isMixedModelFormula html dot-standard_transform html dream-method html eBayes-method html extractVarPart html fitExtractVarPartModel-method html fitVarPartModel-method html getContrast-method html getVarianceComponents html ggColorHue html plotCompareP-method html plotContrasts html plotCorrMatrix html plotCorrStructure html plotPercentBars html plotStratify html plotStratifyBy html plotVarPart-method html residuals-VarParFitList-method html sortCols-method html subset.MArrayLM2-method html toptable-method html varParFrac-class html varPartConfInf html varPartDEdata html varPartData html varPartResults-class html voomWithDreamWeights 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 'variancePartition' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'variancePartition' as variancePartition_1.16.1.zip * DONE (variancePartition) * installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library' package 'variancePartition' successfully unpacked and MD5 sums checked
variancePartition.Rcheck/tests_i386/runTests.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. > BiocGenerics:::testPackage("variancePartition") 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 object is masked from 'package:limma': plotMA 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'variancePartition' The following object is masked from 'package:limma': classifyTestsF Dividing work into 10 chunks... Total:8 s Dividing work into 10 chunks... Total:9 s Dividing work into 10 chunks... Total:11 s > proc.time() user system elapsed 5.10 0.43 32.48 Warning messages: 1: In dream(geneExpr[1:10, ], form, info, L1) : Contrasts with only a single non-zero term are already evaluated by default. 2: In eBayes(fit1) : Empircal Bayes moderated test is no longer supported for dream analysis Returning original results for use downstream 3: In dream(geneExpr[1:10, ], form, info, L2) : Contrasts with only a single non-zero term are already evaluated by default. 4: In eBayes(fit2) : Empircal Bayes moderated test is no longer supported for dream analysis Returning original results for use downstream 5: In dream(geneExpr[1:10, ], form, info, L) : Contrasts with only a single non-zero term are already evaluated by default. 6: In eBayes(fit) : Empircal Bayes moderated test is no longer supported for dream analysis Returning original results for use downstream |
variancePartition.Rcheck/tests_x64/runTests.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. > BiocGenerics:::testPackage("variancePartition") 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 object is masked from 'package:limma': plotMA 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'variancePartition' The following object is masked from 'package:limma': classifyTestsF Dividing work into 10 chunks... Total:9 s Dividing work into 10 chunks... Total:12 s Dividing work into 10 chunks... Total:8 s > proc.time() user system elapsed 5.09 0.40 32.82 Warning messages: 1: In dream(geneExpr[1:10, ], form, info, L1) : Contrasts with only a single non-zero term are already evaluated by default. 2: In eBayes(fit1) : Empircal Bayes moderated test is no longer supported for dream analysis Returning original results for use downstream 3: In dream(geneExpr[1:10, ], form, info, L2) : Contrasts with only a single non-zero term are already evaluated by default. 4: In eBayes(fit2) : Empircal Bayes moderated test is no longer supported for dream analysis Returning original results for use downstream 5: In dream(geneExpr[1:10, ], form, info, L) : Contrasts with only a single non-zero term are already evaluated by default. 6: In eBayes(fit) : Empircal Bayes moderated test is no longer supported for dream analysis Returning original results for use downstream |
variancePartition.Rcheck/examples_i386/variancePartition-Ex.timings
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variancePartition.Rcheck/examples_x64/variancePartition-Ex.timings
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