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CHECK report for ChAMP on tokay2

This page was generated on 2018-10-17 08:37:56 -0400 (Wed, 17 Oct 2018).

Package 218/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChAMP 2.10.2
Yuan Tian
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ChAMP
Branch: RELEASE_3_7
Last Commit: 8f14386
Last Changed Date: 2018-09-13 02:42:10 -0400 (Thu, 13 Sep 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChAMP
Version: 2.10.2
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChAMP.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ChAMP_2.10.2.tar.gz
StartedAt: 2018-10-17 01:01:16 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 01:11:49 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 633.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ChAMP.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChAMP.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ChAMP_2.10.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ChAMP.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '2.10.2'
* 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::mutate' by 'plotly::mutate' when loading 'ChAMP'
  Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP'
  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 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP'
  Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP'
  Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP'
  Warning: replacing previous import 'GenomicRanges::sort' by 'globaltest::sort' when loading 'ChAMP'
  Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP'
  Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP'
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ChAMP.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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:75: unexpected END_OF_INPUT '
  '
Invalid citation information in 'inst/CITATION':
  Error in parse(file = cfile): C:/Users/biocbuild/bbs-3.7-bioc/meat/ChAMP.Rcheck/00_pkg_src/ChAMP/inst/CITATION:10:12: unexpected symbol
  9:            person("Stephan", "Beck")
  10:            person
                 ^
* 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
* 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 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 ... NOTE
champ.ebayGSEA : gseaWTfn: no visible global function definition for
  'wilcox.test'
Undefined global functions or variables:
  wilcox.test
Consider adding
  importFrom("stats", "wilcox.test")
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' ... 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, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/ChAMP.Rcheck/00check.log'
for details.

Installation output

ChAMP.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/ChAMP_2.10.2.tar.gz && rm -rf ChAMP.buildbin-libdir && mkdir ChAMP.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChAMP.buildbin-libdir ChAMP_2.10.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ChAMP_2.10.2.zip && rm ChAMP_2.10.2.tar.gz ChAMP_2.10.2.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 5890k  100 5890k    0     0  51.4M      0 --:--:-- --:--:-- --:--:-- 54.7M

install for i386

* installing *source* package 'ChAMP' ...
** R
** inst
** byte-compile and prepare 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 'igraph::path' by 'BiocGenerics::path' when loading 'FEM'
Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP'
Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP'
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 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP'
Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP'
Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP'
Warning: replacing previous import 'GenomicRanges::sort' by 'globaltest::sort' when loading 'ChAMP'
Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP'
Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP'
** help
*** installing help indices
  converting help for package 'ChAMP'
    finding HTML links ... done
    Block.GUI                               html  
    ChAMP-package                           html  
    CpG.GUI                                 html  
    DMP.GUI                                 html  
    DMR.GUI                                 html  
    QC.GUI                                  html  
    champ.Block                             html  
    champ.CNA                               html  
    champ.DMP                               html  
    champ.DMR                               html  
    champ.EpiMod                            html  
    champ.GSEA                              html  
    champ.QC                                html  
    champ.SVD                               html  
    champ.ebayGSEA                          html  
    champ.filter                            html  
    champ.import                            html  
    champ.impute                            html  
    champ.load                              html  
    champ.norm                              html  
    champ.process                           html  
    champ.refbase                           html  
    champ.runCombat                         html  
** 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 'igraph::path' by 'BiocGenerics::path' when loading 'FEM'
Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP'
Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP'
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 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP'
Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP'
Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP'
Warning: replacing previous import 'GenomicRanges::sort' by 'globaltest::sort' when loading 'ChAMP'
Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP'
Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP'
In R CMD INSTALL

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 'igraph::path' by 'BiocGenerics::path' 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'
Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP'
Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP'
Warning: replacing previous import 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP'
Warning: replacing previous import 'GenomicRanges::sort' by 'globaltest::sort' when loading 'ChAMP'
Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP'
Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP'
* MD5 sums
packaged installation of 'ChAMP' as ChAMP_2.10.2.zip
* DONE (ChAMP)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'ChAMP' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

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.ebayGSEA000
champ.filter000
champ.import000
champ.impute000
champ.load000
champ.norm000
champ.process000
champ.refbase000
champ.runCombat000

ChAMP.Rcheck/examples_x64/ChAMP-Ex.timings

nameusersystemelapsed
Block.GUI000
ChAMP-package0.000.010.02
CpG.GUI000
DMP.GUI0.020.000.02
DMR.GUI000
QC.GUI000
champ.Block000
champ.CNA000
champ.DMP000
champ.DMR000
champ.EpiMod000
champ.GSEA000
champ.QC000
champ.SVD0.010.000.01
champ.ebayGSEA000
champ.filter000
champ.import000
champ.impute000
champ.load000
champ.norm000
champ.process000
champ.refbase000
champ.runCombat000