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CHECK report for ChAMP on machv2

This page was generated on 2020-10-17 11:58:11 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ChAMP PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 269/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChAMP 2.18.3
Yuan Tian
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ChAMP
Branch: RELEASE_3_11
Last Commit: 8745a25
Last Changed Date: 2020-09-13 16:43:43 -0400 (Sun, 13 Sep 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ChAMP
Version: 2.18.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChAMP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChAMP_2.18.3.tar.gz
StartedAt: 2020-10-16 23:33:13 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:43:34 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 621.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ChAMP.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChAMP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChAMP_2.18.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ChAMP.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.18.3’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'minfi', 'ChAMPdata', 'DMRcate', 'Illumina450ProbeVariants.db',
  'IlluminaHumanMethylationEPICmanifest', 'DT'
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 ... WARNING
Found the following significant warnings:
  Note: possible error in 'dmrcate(myannotation, ': unused argument (mc.cores = cores) 
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/ChAMP.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 ... 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 ... NOTE
Namespace in Imports field not imported from: 'prettydoc'
  All declared Imports should be used.
Package in Depends field not imported from: 'DT'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
champ.DMR: possible error in dmrcate(myannotation, min.cpgs =
  minProbes, lambda = lambda, C = C, mc.cores = cores): unused argument
  (mc.cores = cores)
champ.EpiMod: no visible global function definition for 'GenStatM'
champ.EpiMod: no visible global function definition for 'DoIntEpi450k'
champ.EpiMod: no visible global function definition for 'DoEpiMod'
champ.EpiMod: no visible global function definition for 'FemModShow'
champ.ebGSEA : gseaWTfn: no visible global function definition for
  'wilcox.test'
champ.ebGSEA: no visible global function definition for 'stopCluster'
champ.norm: no visible global function definition for 'stopCluster'
Undefined global functions or variables:
  DoEpiMod DoIntEpi450k FemModShow GenStatM stopCluster 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 ... WARNING
Duplicated \argument entries in documentation object 'champ.SVD':
  ‘Rplot’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/ChAMP.Rcheck/00check.log’
for details.



Installation output

ChAMP.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChAMP
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘ChAMP’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate' 
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
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 'plotly::last_plot' by 'ggplot2::last_plot' 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'
Note: possible error in 'dmrcate(myannotation, ': unused argument (mc.cores = cores) 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate'
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
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 'plotly::last_plot' by 'ggplot2::last_plot' 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 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate'
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
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 'plotly::last_plot' by 'ggplot2::last_plot' 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.GUI0.0010.0000.001
ChAMP-package0.0010.0000.001
CpG.GUI0.0000.0000.001
DMP.GUI0.0010.0010.001
DMR.GUI0.0000.0010.001
QC.GUI0.0000.0010.000
champ.Block0.0010.0010.001
champ.CNA0.0000.0000.001
champ.DMP000
champ.DMR000
champ.EpiMod0.0000.0000.001
champ.GSEA0.0010.0010.000
champ.QC0.0000.0000.001
champ.SVD0.0000.0000.001
champ.ebGSEA0.0010.0000.000
champ.filter000
champ.import0.0000.0010.001
champ.impute0.0010.0000.000
champ.load000
champ.norm000
champ.process0.0000.0010.001
champ.refbase0.0000.0000.001
champ.runCombat0.0010.0000.000