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CHECK report for ChAMP on malbec2

This page was generated on 2019-10-16 12:03:36 -0400 (Wed, 16 Oct 2019).

Package 246/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChAMP 2.14.0
Yuan Tian
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ChAMP
Branch: RELEASE_3_9
Last Commit: d180295
Last Changed Date: 2019-05-02 11:53:46 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChAMP
Version: 2.14.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ChAMP.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ChAMP_2.14.0.tar.gz
StartedAt: 2019-10-16 00:25:06 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:32:11 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 425.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ChAMP.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ChAMP.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ChAMP_2.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ChAMP.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘2.14.0’
* 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 ... 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:81: unexpected END_OF_INPUT '
  '
Invalid citation information in ‘inst/CITATION’:
  Error in parse(file = cfile): /home/biocbuild/bbs-3.9-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
* 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.ebGSEA : 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’ ... OK
* 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, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/ChAMP.Rcheck/00check.log’
for details.



Installation output

ChAMP.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ChAMP
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘ChAMP’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: replacing previous import ‘igraph::edges’ by ‘graph::edges’ when loading ‘FEM’ 
2: replacing previous import ‘igraph::intersection’ by ‘graph::intersection’ when loading ‘FEM’ 
3: replacing previous import ‘igraph::degree’ by ‘graph::degree’ when loading ‘FEM’ 
4: replacing previous import ‘igraph::union’ by ‘graph::union’ when loading ‘FEM’ 
5: replacing previous import ‘limma::plotMA’ by ‘BiocGenerics::plotMA’ when loading ‘FEM’ 
6: replacing previous import ‘igraph::path’ by ‘BiocGenerics::path’ when loading ‘FEM’ 
7: replacing previous import ‘Matrix::which’ by ‘BiocGenerics::which’ when loading ‘FEM’ 
8: 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'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
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::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'
** testing if installed package can be loaded from final location
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::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'
** testing if installed package keeps a record of temporary installation path
* DONE (ChAMP)

Tests output


Example timings

ChAMP.Rcheck/ChAMP-Ex.timings

nameusersystemelapsed
Block.GUI000
ChAMP-package000
CpG.GUI000
DMP.GUI000
DMR.GUI000
QC.GUI000
champ.Block000
champ.CNA0.0010.0000.001
champ.DMP0.0010.0000.001
champ.DMR0.0010.0000.001
champ.EpiMod000
champ.GSEA000
champ.QC000
champ.SVD000
champ.ebGSEA000
champ.filter000
champ.import000
champ.impute000
champ.load0.0010.0000.001
champ.norm0.0000.0000.001
champ.process0.0000.0000.001
champ.refbase0.0000.0000.001
champ.runCombat0.0000.0000.001