Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:10:02 -0400 (Wed, 15 Apr 2020).
Package 520/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ENmix 1.22.6 Zongli Xu
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: ENmix |
Version: 1.22.6 |
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ENmix.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ENmix_1.22.6.tar.gz |
StartedAt: 2020-04-15 03:00:10 -0400 (Wed, 15 Apr 2020) |
EndedAt: 2020-04-15 03:05:21 -0400 (Wed, 15 Apr 2020) |
EllapsedTime: 310.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ENmix.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ENmix.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ENmix_1.22.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/ENmix.Rcheck’ * using R version 3.6.3 (2020-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ENmix/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ENmix’ version ‘1.22.6’ * 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 ‘ENmix’ 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 ... WARNING Invalid citation information in ‘inst/CITATION’: Error in parse(file = cfile): /home/biocbuild/bbs-3.10-bioc/meat/ENmix.Rcheck/00_pkg_src/ENmix/inst/CITATION:64:12: unexpected symbol 63: person("Jack,A.", "Taylor") 64: person ^ * 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 ... 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 ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... 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: 1 WARNING See ‘/home/biocbuild/bbs-3.10-bioc/meat/ENmix.Rcheck/00check.log’ for details.
ENmix.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL ENmix ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘ENmix’ ... ** 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 (ENmix)
ENmix.Rcheck/tests/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-pc-linux-gnu (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("ENmix") 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, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from 'package:base': aperm, apply, rowsum Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) Loading required package: minfiData Loading required package: minfi Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: bumphunter Loading required package: locfit locfit 1.5-9.4 2020-03-24 Loading required package: IlluminaHumanMethylation450kmanifest Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19 Loading required package: digest [read.metharray.sheet] Found the following CSV files: [1] "/home/biocbuild/bbs-3.10-bioc/R/library/minfiData/extdata/SampleSheet.csv" RUNIT TEST PROTOCOL -- Wed Apr 15 03:05:17 2020 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : ENmix RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 15.388 0.424 15.875
ENmix.Rcheck/ENmix-Ex.timings
name | user | system | elapsed | |
QCfilter | 0 | 0 | 0 | |
QCinfo | 0.000 | 0.000 | 0.001 | |
calc_detP | 0 | 0 | 0 | |
ctrlsva | 0.000 | 0.000 | 0.001 | |
dupicc | 0.000 | 0.000 | 0.001 | |
estimateCellProp | 0 | 0 | 0 | |
freqpoly | 0 | 0 | 0 | |
getCGinfo | 0.000 | 0.000 | 0.001 | |
getmeth | 0.000 | 0.000 | 0.001 | |
methDataSet-class | 0.000 | 0.000 | 0.001 | |
methyAge | 0.000 | 0.000 | 0.001 | |
mpreprocess | 0 | 0 | 0 | |
multifreqpoly | 0 | 0 | 0 | |
nmode.mc | 0.000 | 0.000 | 0.001 | |
norm.quantile | 0 | 0 | 0 | |
normalize.quantile.450k | 0 | 0 | 0 | |
oxBS.MLE | 0.004 | 0.000 | 0.021 | |
pcrplot | 0.000 | 0.004 | 0.001 | |
plotCtrl | 0 | 0 | 0 | |
predSex | 0 | 0 | 0 | |
preprocessENmix | 0 | 0 | 0 | |
rcp | 0 | 0 | 0 | |
readidat | 0 | 0 | 0 | |
readmanifest | 0 | 0 | 0 | |
relic | 0.000 | 0.000 | 0.002 | |
rgDataSet-class | 0.000 | 0.000 | 0.001 | |
rm.outlier | 0.000 | 0.000 | 0.002 | |