Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:39:21 -0400 (Tue, 09 Apr 2019).
Package 1003/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
missMethyl 1.17.1 Belinda Phipson
| 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: missMethyl |
Version: 1.17.1 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings missMethyl_1.17.1.tar.gz |
StartedAt: 2019-04-09 02:05:09 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 02:13:32 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 503.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: missMethyl.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings missMethyl_1.17.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/missMethyl.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘missMethyl/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘missMethyl’ version ‘1.17.1’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘missMethyl’ 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 * 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 ... NOTE Found the following apparent S3 methods exported but not registered: SWAN.MethyLumiSet SWAN.RGChannelSet SWAN.default varFit.DGEList varFit.MethylSet varFit.default See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .aveQuantile: no visible global function definition for ‘approx’ .getFlatAnnotation: no visible binding for global variable ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’ .getFlatAnnotation: no visible binding for global variable ‘IlluminaHumanMethylationEPICanno.ilm10b4.hg19’ .plotBias: no visible global function definition for ‘par’ .plotBias: no visible global function definition for ‘plot’ .plotBias: no visible global function definition for ‘lines’ .plotBias: no visible global function definition for ‘lowess’ .subsetQuantileNorm: no visible global function definition for ‘approx’ SWAN.MethyLumiSet: no visible global function definition for ‘DataFrame’ SWAN.MethyLumiSet: no visible global function definition for ‘phenoData’ SWAN.MethyLumiSet: no visible global function definition for ‘packageVersion’ SWAN.default: no visible binding for global variable ‘IlluminaHumanMethylation450kmanifest’ SWAN.default: no visible binding for global variable ‘IlluminaHumanMethylationEPICmanifest’ SWAN.default: no visible global function definition for ‘colData’ SWAN.default: no visible global function definition for ‘packageVersion’ densityByProbeType: no visible binding for global variable ‘IlluminaHumanMethylation450kmanifest’ densityByProbeType: no visible binding for global variable ‘IlluminaHumanMethylationEPICmanifest’ densityByProbeType : <anonymous>: no visible global function definition for ‘density’ densityByProbeType: no visible global function definition for ‘plot’ densityByProbeType: no visible global function definition for ‘density’ densityByProbeType: no visible global function definition for ‘lines’ densityByProbeType: no visible global function definition for ‘legend’ gometh: no visible global function definition for ‘p.adjust’ gsameth: no visible global function definition for ‘phyper’ gsameth: no visible global function definition for ‘p.adjust’ topVar: no visible global function definition for ‘p.adjust’ Undefined global functions or variables: DataFrame IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno.ilm10b4.hg19 IlluminaHumanMethylationEPICmanifest approx colData density legend lines lowess p.adjust packageVersion par phenoData phyper plot Consider adding importFrom("graphics", "legend", "lines", "par", "plot") importFrom("stats", "approx", "density", "lowess", "p.adjust", "phyper") importFrom("utils", "packageVersion") to your NAMESPACE file. * 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 ... OK Examples with CPU or elapsed time > 5s user system elapsed topRUV 35.274 0.116 35.511 RUVadj 34.402 0.744 35.750 SWAN 31.462 0.156 32.145 topGSA 30.429 0.550 31.246 RUVfit 27.588 0.044 28.026 getAdj 27.408 0.195 27.930 densityByProbeType 15.366 0.048 15.503 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.9-bioc/meat/missMethyl.Rcheck/00check.log’ for details.
missMethyl.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL missMethyl ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘missMethyl’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (missMethyl)
missMethyl.Rcheck/missMethyl-Ex.timings
name | user | system | elapsed | |
RUVadj | 34.402 | 0.744 | 35.750 | |
RUVfit | 27.588 | 0.044 | 28.026 | |
SWAN | 31.462 | 0.156 | 32.145 | |
contrasts.varFit | 0.064 | 0.004 | 0.069 | |
densityByProbeType | 15.366 | 0.048 | 15.503 | |
getAdj | 27.408 | 0.195 | 27.930 | |
getINCs | 0.732 | 0.024 | 0.759 | |
getLeveneResiduals | 0.01 | 0.00 | 0.01 | |
getMappedEntrezIDs | 0.001 | 0.000 | 0.000 | |
gometh | 0.001 | 0.000 | 0.000 | |
gsameth | 0.001 | 0.000 | 0.000 | |
topGSA | 30.429 | 0.550 | 31.246 | |
topRUV | 35.274 | 0.116 | 35.511 | |
topVar | 0.014 | 0.000 | 0.013 | |
varFit | 0.013 | 0.000 | 0.014 | |