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CHECK report for MMDiff2 on tokay2

This page was generated on 2020-10-17 11:57:10 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE MMDiff2 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1110/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MMDiff2 1.16.0
Gabriele Schweikert
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/MMDiff2
Branch: RELEASE_3_11
Last Commit: fb17b2a
Last Changed Date: 2020-04-27 14:57:31 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK 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  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MMDiff2
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --install=check:MMDiff2.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MMDiff2_1.16.0.tar.gz
StartedAt: 2020-10-17 06:10:09 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:16:07 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 357.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: MMDiff2.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --install=check:MMDiff2.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MMDiff2_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/MMDiff2.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MMDiff2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MMDiff2' version '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'MMDiff2' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'MMDiff2'
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/MMDiff2.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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: 'methods'
  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
DBAmmd: no visible global function definition for 'new'
getReads: no visible global function definition for 'IRangesList'
Undefined global functions or variables:
  IRangesList new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
compDists        31.17   6.53   37.70
plotPeak         14.36   0.45   26.22
DBAmmd-Accessors 10.26   0.55   10.81
compHists         5.27   1.47    6.74
* 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/MMDiff2.Rcheck/00check.log'
for details.



Installation output

MMDiff2.Rcheck/00install.out

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch i386 CMD INSTALL --no-multiarch MMDiff2
###
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* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
* installing *source* package 'MMDiff2' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'MMDiff2'
** help
*** installing help indices
  converting help for package 'MMDiff2'
    finding HTML links ... done
    Cfp1-Peaks                              html  
    DBAmmd-Accessors                        html  
    DBAmmd-class                            html  
    MMD                                     html  
    compDists                               html  
    compHists                               html  
    compPvals                               html  
    estimateFragmentCenters                 html  
    getPeakReads                            html  
    mm9-Genes                               html  
    myGeneric                               html  
    plotDISTS4Peak                          html  
    plotDists                               html  
    plotPeak                                html  
    reportResults                           html  
    runShinyMMDiff2                         html  
    server.MMDiff2                          html  
    ui.MMDiff2                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'MMDiff2'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'MMDiff2'
** testing if installed package keeps a record of temporary installation path
* DONE (MMDiff2)
Making 'packages.html' ... done

Tests output


Example timings

MMDiff2.Rcheck/MMDiff2-Ex.timings

nameusersystemelapsed
Cfp1-Peaks000
DBAmmd-Accessors10.26 0.5510.81
DBAmmd-class0.030.010.05
MMD000
compDists31.17 6.5337.70
compHists5.271.476.74
compPvals2.030.162.20
estimateFragmentCenters2.670.282.95
getPeakReads0.520.532.32
mm9-Genes000
plotDISTS4Peak2.360.252.63
plotDists2.370.092.46
plotPeak14.36 0.4526.22
reportResults1.800.141.94
runShinyMMDiff2000
server.MMDiff2000
ui.MMDiff2000