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CHECK report for ChAMP on veracruz1

This page was generated on 2018-02-20 15:03:13 -0500 (Tue, 20 Feb 2018).

Package 208/1473HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChAMP 2.9.10
Yuan Tian
Snapshot Date: 2018-02-19 17:00:21 -0500 (Mon, 19 Feb 2018)
URL: https://git.bioconductor.org/packages/ChAMP
Branch: RELEASE_3_6
Last Commit: 52901fe
Last Changed Date: 2018-01-08 06:35:24 -0500 (Mon, 08 Jan 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ChAMP
Version: 2.9.10
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChAMP_2.9.10.tar.gz
StartedAt: 2018-02-20 01:33:46 -0500 (Tue, 20 Feb 2018)
EndedAt: 2018-02-20 01:41:01 -0500 (Tue, 20 Feb 2018)
EllapsedTime: 435.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ChAMP.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChAMP_2.9.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ChAMP.Rcheck’
* using R version 3.4.3 (2017-11-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChAMP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChAMP’ version ‘2.9.10’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘minfi’ ‘ChAMPdata’ ‘FEM’ ‘DMRcate’ ‘Illumina450ProbeVariants.db’
  ‘IlluminaHumanMethylationEPICmanifest’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘ChAMP’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc       9.6Mb
    extdata   1.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘rmarkdown’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Problems with news in ‘inst/NEWS.Rd’:
  inst/NEWS.Rd:74: unexpected END_OF_INPUT '
  '
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'prettydoc'
  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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... 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, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/ChAMP.Rcheck/00check.log’
for details.



Installation output

ChAMP.Rcheck/00install.out

* installing *source* package ‘ChAMP’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘igraph::edges’ by ‘graph::edges’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::intersection’ by ‘graph::intersection’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::degree’ by ‘graph::degree’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::union’ by ‘graph::union’ when loading ‘FEM’
Warning: replacing previous import ‘limma::plotMA’ by ‘BiocGenerics::plotMA’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::colSums’ by ‘BiocGenerics::colSums’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::colMeans’ by ‘BiocGenerics::colMeans’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::rowMeans’ by ‘BiocGenerics::rowMeans’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::rowSums’ by ‘BiocGenerics::rowSums’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::which’ by ‘BiocGenerics::which’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::normalize’ by ‘BiocGenerics::normalize’ when loading ‘FEM’
Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP'
Warning: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP'
Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP'
Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘igraph::edges’ by ‘graph::edges’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::intersection’ by ‘graph::intersection’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::degree’ by ‘graph::degree’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::union’ by ‘graph::union’ when loading ‘FEM’
Warning: replacing previous import ‘limma::plotMA’ by ‘BiocGenerics::plotMA’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::colSums’ by ‘BiocGenerics::colSums’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::colMeans’ by ‘BiocGenerics::colMeans’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::rowMeans’ by ‘BiocGenerics::rowMeans’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::rowSums’ by ‘BiocGenerics::rowSums’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::which’ by ‘BiocGenerics::which’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::normalize’ by ‘BiocGenerics::normalize’ when loading ‘FEM’
Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP'
Warning: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP'
Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP'
Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP'
* DONE (ChAMP)

Tests output


Example timings

ChAMP.Rcheck/ChAMP-Ex.timings

nameusersystemelapsed
Block.GUI0.0010.0000.001
ChAMP-package000
CpG.GUI0.0010.0000.001
DMP.GUI0.0000.0000.001
DMR.GUI0.0010.0000.001
QC.GUI0.0010.0010.001
champ.Block0.0000.0000.001
champ.CNA000
champ.DMP0.0010.0000.001
champ.DMR0.0000.0000.001
champ.EpiMod0.0010.0000.001
champ.GSEA0.0010.0000.001
champ.QC0.0000.0000.001
champ.SVD0.0010.0000.001
champ.filter0.0000.0010.001
champ.import0.0010.0000.000
champ.impute0.0010.0000.001
champ.load0.0000.0010.001
champ.norm0.0010.0000.001
champ.process000
champ.refbase0.0010.0010.001
champ.runCombat0.0010.0000.001