Back to Multiple platform build/check report for BioC 3.15
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-11-30 13:54:47 -0500 (Tue, 30 Nov 2021).

CHECK results for ChAMP on riesling1

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: 2021-11-29 14:50:17 -0500 (Mon, 29 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: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChAMP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ChAMP_2.25.0.tar.gz
StartedAt: 2021-11-30 01:06:47 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 01:11:53 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 306.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChAMP.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChAMP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ChAMP_2.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ChAMP.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '2.25.0'
* 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 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 'D:/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
  'D:/biocbuild/bbs-3.15-bioc/meat/ChAMP.Rcheck/00check.log'
for details.



Installation output

ChAMP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.15/bioc/src/contrib/ChAMP_2.25.0.tar.gz && rm -rf ChAMP.buildbin-libdir && mkdir ChAMP.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChAMP.buildbin-libdir ChAMP_2.25.0.tar.gz && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ChAMP_2.25.0.zip && rm ChAMP_2.25.0.tar.gz ChAMP_2.25.0.zip
###
##############################################################################
##############################################################################


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

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  1 5940k    1 95635    0     0   496k      0  0:00:11 --:--:--  0:00:11  494k
100 5940k  100 5940k    0     0  9195k      0 --:--:-- --:--:-- --:--:-- 9181k
only one architecture so ignoring '--merge-multiarch'
* 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
  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.GSEA                              html  
    champ.QC                                html  
    champ.SVD                               html  
    champ.ebGSEA                            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 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
* MD5 sums
packaged installation of 'ChAMP' as ChAMP_2.25.0.zip
* DONE (ChAMP)
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
package 'ChAMP' successfully unpacked and MD5 sums checked

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.CNA000
champ.DMP000
champ.DMR000
champ.GSEA000
champ.QC000
champ.SVD000
champ.ebGSEA000
champ.filter000
champ.import000
champ.impute000
champ.load000
champ.norm000
champ.process000
champ.refbase000
champ.runCombat000