Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 12:20:55 -0400 (Tue, 09 Apr 2019).
Package 965/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
MethylMix 2.13.0 Olivier Gevaert
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: MethylMix |
Version: 2.13.0 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethylMix.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MethylMix_2.13.0.tar.gz |
StartedAt: 2019-04-09 04:10:47 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 04:15:57 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 310.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MethylMix.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethylMix.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MethylMix_2.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MethylMix.Rcheck' * using R Under development (unstable) (2019-03-09 r76216) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'MethylMix/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'MethylMix' version '2.13.0' * 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 'MethylMix' 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 ... NOTE Namespace in Imports field not imported from: 'digest' All declared Imports should be used. * 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 MethylMix_Predict 32.69 0.04 32.74 MethylMix 32.07 0.05 32.11 MethylMix_PlotModel 31.89 0.03 31.92 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed MethylMix_Predict 32.84 0.02 32.88 MethylMix_PlotModel 32.19 0.02 32.20 MethylMix 27.48 0.04 27.53 * 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: 1 NOTE See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MethylMix.Rcheck/00check.log' for details.
MethylMix.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MethylMix_2.13.0.tar.gz && rm -rf MethylMix.buildbin-libdir && mkdir MethylMix.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MethylMix.buildbin-libdir MethylMix_2.13.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MethylMix_2.13.0.zip && rm MethylMix_2.13.0.tar.gz MethylMix_2.13.0.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 2583k 100 2583k 0 0 22.7M 0 --:--:-- --:--:-- --:--:-- 24.2M install for i386 * installing *source* package 'MethylMix' ... ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'MethylMix' finding HTML links ... done BatchData html ClusterProbes html ComBat_NoFiles html Download_DNAmethylation html Download_GeneExpression html GEcancer html GetData html METcancer html METnormal html MethylMix html MethylMix_MixtureModel html MethylMix_ModelGeneExpression html MethylMix_ModelSingleGene html MethylMix_PlotModel html MethylMix_Predict html MethylMix_RemoveFlipOver html Preprocess_CancerSite_Methylation27k html Preprocess_CancerSite_Methylation450k html Preprocess_DNAmethylation html Preprocess_GeneExpression html Preprocess_MAdata_Cancer html Preprocess_MAdata_Normal html ProbeAnnotation html SNPprobes html TCGA_BatchCorrection_MolecularData html TCGA_GENERIC_BatchCorrection html TCGA_GENERIC_CheckBatchEffect html TCGA_GENERIC_CleanUpSampleNames html TCGA_GENERIC_GetSampleGroups html TCGA_GENERIC_LoadIlluminaMethylationData html TCGA_GENERIC_MET_ClusterProbes_Helper_ClusterGenes_with_hclust html TCGA_GENERIC_MergeData html TCGA_Load_MolecularData html TCGA_Process_EstimateMissingValues html betaEst_2 html blc_2 html combineForEachOutput html get_firehoseData html predictOneGene 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 'MethylMix' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'MethylMix' as MethylMix_2.13.0.zip * DONE (MethylMix) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'MethylMix' successfully unpacked and MD5 sums checked
MethylMix.Rcheck/tests_i386/testthat.Rout R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences" Copyright (C) 2019 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(MethylMix) > > test_check("MethylMix") Found 251 samples with both methylation and expression data. Correlating methylation data with gene expression... Found 9 transcriptionally predictive genes. Starting Beta mixture modeling. Running Beta mixture model on 9 genes and on 251 samples. ERBB2 : 2 components are best. FAAH : 2 components are best. FOXD1 : 2 components are best. ME1 : 2 components are best. MGMT : 2 components are best. OAS1 : 2 components are best. SOX10 : 2 components are best. TRAF6 : 2 components are best. ZNF217 : 2 components are best. == testthat results =========================================================== OK: 3 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 32.51 0.09 32.59 |
MethylMix.Rcheck/tests_x64/testthat.Rout R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences" Copyright (C) 2019 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(MethylMix) > > test_check("MethylMix") Found 251 samples with both methylation and expression data. Correlating methylation data with gene expression... Found 9 transcriptionally predictive genes. Starting Beta mixture modeling. Running Beta mixture model on 9 genes and on 251 samples. ERBB2 : 2 components are best. FAAH : 2 components are best. FOXD1 : 2 components are best. ME1 : 2 components are best. MGMT : 2 components are best. OAS1 : 2 components are best. SOX10 : 2 components are best. TRAF6 : 2 components are best. ZNF217 : 2 components are best. == testthat results =========================================================== OK: 3 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 29.17 0.14 29.29 |
MethylMix.Rcheck/examples_i386/MethylMix-Ex.timings
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MethylMix.Rcheck/examples_x64/MethylMix-Ex.timings
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