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BioC 3.5: CHECK report for ChAMP on tokay2

This page was generated on 2017-09-13 13:41:43 -0400 (Wed, 13 Sep 2017).

Package 198/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChAMP 2.8.9
Yuan Tian
Snapshot Date: 2017-09-12 17:18:08 -0400 (Tue, 12 Sep 2017)
URL: https://git.bioconductor.org/packages/ChAMP
Last Commit: 1ebb5f2
Last Changed Date: 2017-08-08 11:28:21 -0400 (Tue, 08 Aug 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: ChAMP
Version: 2.8.9
Command: rm -rf ChAMP.buildbin-libdir ChAMP.Rcheck && mkdir ChAMP.buildbin-libdir ChAMP.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChAMP.buildbin-libdir ChAMP_2.8.9.tar.gz >ChAMP.Rcheck\00install.out 2>&1 && cp ChAMP.Rcheck\00install.out ChAMP-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ChAMP.buildbin-libdir --install="check:ChAMP-install.out" --force-multiarch --no-vignettes --timings ChAMP_2.8.9.tar.gz
StartedAt: 2017-09-12 22:37:42 -0400 (Tue, 12 Sep 2017)
EndedAt: 2017-09-12 22:47:20 -0400 (Tue, 12 Sep 2017)
EllapsedTime: 578.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ChAMP.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ChAMP.buildbin-libdir ChAMP.Rcheck && mkdir ChAMP.buildbin-libdir ChAMP.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChAMP.buildbin-libdir ChAMP_2.8.9.tar.gz >ChAMP.Rcheck\00install.out 2>&1 && cp ChAMP.Rcheck\00install.out ChAMP-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ChAMP.buildbin-libdir --install="check:ChAMP-install.out" --force-multiarch --no-vignettes --timings ChAMP_2.8.9.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ChAMP.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChAMP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChAMP' version '2.8.9'
* 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 whether package 'ChAMP' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP'
  Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' 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'
See 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ChAMP.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc       9.4Mb
    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:67: unexpected END_OF_INPUT '
  '
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 2 WARNINGs, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/ChAMP.Rcheck/00check.log'
for details.


ChAMP.Rcheck/00install.out:


install for i386

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

install for x64

* installing *source* package 'ChAMP' ...
** 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'
* MD5 sums
packaged installation of 'ChAMP' as ChAMP_2.8.9.zip
* DONE (ChAMP)

ChAMP.Rcheck/examples_i386/ChAMP-Ex.timings:

nameusersystemelapsed
Block.GUI000
ChAMP-package000
CpG.GUI000
DMP.GUI000
DMR.GUI000
QC.GUI000
champ.Block000
champ.CNA000
champ.DMP000
champ.DMR000
champ.EpiMod000
champ.GSEA000
champ.QC000
champ.SVD000
champ.filter000
champ.import000
champ.impute000
champ.load000
champ.norm000
champ.process000
champ.refbase0.010.000.01
champ.runCombat000

ChAMP.Rcheck/examples_x64/ChAMP-Ex.timings:

nameusersystemelapsed
Block.GUI000
ChAMP-package000
CpG.GUI000
DMP.GUI000
DMR.GUI000
QC.GUI000
champ.Block000
champ.CNA000
champ.DMP000
champ.DMR000
champ.EpiMod000
champ.GSEA0.020.000.02
champ.QC000
champ.SVD000
champ.filter000
champ.import000
champ.impute000
champ.load000
champ.norm000
champ.process000
champ.refbase000
champ.runCombat0.000.010.02