Zongli Xu
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/ENmix |
| Branch: RELEASE_3_9 |
| Last Commit: fa3ce89 |
| Last Changed Date: 2019-09-16 12:50:06 -0400 (Mon, 16 Sep 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:55:35 -0400 (Wed, 16 Oct 2019).
| Package 499/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ENmix 1.21.6 Zongli Xu
| 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 | |
| Package: ENmix |
| Version: 1.21.6 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ENmix.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ENmix_1.21.6.tar.gz |
| StartedAt: 2019-10-16 02:32:42 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:41:04 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 501.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ENmix.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ENmix.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ENmix_1.21.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ENmix.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (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 ‘1.21.6’ * 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 ... 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... 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: OK
ENmix.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ENmix ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
Loading required package: bumphunter
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Loading required package: digest
[read.metharray.sheet] Found the following CSV files:
[1] "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/minfiData/extdata/SampleSheet.csv"
RUNIT TEST PROTOCOL -- Wed Oct 16 02:40:55 2019
***********************************************
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
24.686 1.911 26.553
ENmix.Rcheck/ENmix-Ex.timings
| name | user | system | elapsed | |
| ComBat.mc | 0.001 | 0.001 | 0.002 | |
| QCfilter | 0 | 0 | 0 | |
| QCinfo | 0.001 | 0.000 | 0.001 | |
| bmiq.mc | 0.001 | 0.001 | 0.001 | |
| calc_detP | 0 | 0 | 0 | |
| ctrlsva | 0.000 | 0.000 | 0.001 | |
| dupicc | 0.002 | 0.001 | 0.001 | |
| estimateCellProp | 0 | 0 | 0 | |
| freqpoly | 0.001 | 0.000 | 0.001 | |
| getCGinfo | 0.000 | 0.001 | 0.001 | |
| getmeth | 0.001 | 0.000 | 0.001 | |
| methDataSet-class | 0.001 | 0.001 | 0.002 | |
| methyAge | 0.000 | 0.000 | 0.001 | |
| mpreprocess | 0.001 | 0.000 | 0.001 | |
| multifreqpoly | 0.001 | 0.000 | 0.000 | |
| nmode.mc | 0 | 0 | 0 | |
| norm.quantile | 0.001 | 0.001 | 0.000 | |
| normalize.quantile.450k | 0 | 0 | 0 | |
| oxBS.MLE | 0.003 | 0.001 | 0.005 | |
| pcrplot | 0.002 | 0.000 | 0.002 | |
| plotCtrl | 0.001 | 0.000 | 0.002 | |
| predSex | 0 | 0 | 0 | |
| preprocessENmix | 0.001 | 0.000 | 0.001 | |
| rcp | 0.001 | 0.000 | 0.001 | |
| readidat | 0 | 0 | 0 | |
| readmanifest | 0.000 | 0.000 | 0.001 | |
| relic | 0.005 | 0.001 | 0.005 | |
| rgDataSet-class | 0.001 | 0.001 | 0.002 | |
| rm.outlier | 0.002 | 0.001 | 0.002 | |