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This page was generated on 2021-11-25 14:05:26 -0500 (Thu, 25 Nov 2021).

CHECK results for ChAMP on merida1

To the developers/maintainers of the ChAMP package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChAMP.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 287/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChAMP 2.25.0  (landing page)
Yuan Tian
Snapshot Date: 2021-11-24 14:50:13 -0500 (Wed, 24 Nov 2021)
git_url: https://git.bioconductor.org/packages/ChAMP
git_branch: master
git_last_commit: f25a72d
git_last_commit_date: 2021-10-26 12:10:43 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  NO, package depends on 'DMRcate' which is not available

Summary

Package: ChAMP
Version: 2.25.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChAMP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChAMP_2.25.0.tar.gz
StartedAt: 2021-11-25 01:31:52 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 01:42:57 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 664.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChAMP.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChAMP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChAMP_2.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/ChAMP.Rcheck’
* using R Under development (unstable) (2021-11-01 r81125)
* 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 ‘2.25.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'minfi', 'ChAMPdata', 'DMRcate', 'Illumina450ProbeVariants.db',
  'IlluminaHumanMethylationEPICmanifest', 'DT', 'RPMM'
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) 
  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'
See ‘/Users/biocbuild/bbs-3.15-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.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'
champ.process: no visible global function definition for 'champ.EpiMod'
Undefined global functions or variables:
  champ.EpiMod 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-3.15-bioc/meat/ChAMP.Rcheck/00check.log’
for details.



Installation output

ChAMP.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChAMP
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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.GUI000
ChAMP-package000
CpG.GUI0.0000.0000.001
DMP.GUI000
DMR.GUI0.0000.0000.001
QC.GUI000
champ.Block0.0000.0010.000
champ.CNA0.0000.0000.001
champ.DMP000
champ.DMR000
champ.GSEA0.0000.0000.001
champ.QC000
champ.SVD000
champ.ebGSEA0.0000.0010.000
champ.filter000
champ.import0.0000.0000.001
champ.impute000
champ.load0.0010.0000.000
champ.norm0.0010.0000.000
champ.process0.0010.0000.000
champ.refbase0.0000.0010.000
champ.runCombat000