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This page was generated on 2021-10-15 15:06:12 -0400 (Fri, 15 Oct 2021).

CHECK results for MMDiff2 on tokay2

To the developers/maintainers of the MMDiff2 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MMDiff2.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 1166/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MMDiff2 1.20.0  (landing page)
Gabriele Schweikert
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/MMDiff2
git_branch: RELEASE_3_13
git_last_commit: d1abce8
git_last_commit_date: 2021-05-19 12:20:25 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MMDiff2
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --install=check:MMDiff2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MMDiff2_1.20.0.tar.gz
StartedAt: 2021-10-15 02:07:29 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 02:12:28 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 299.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MMDiff2.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --install=check:MMDiff2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MMDiff2_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MMDiff2.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.20.0'
* 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-3.13-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        23.39   6.12   29.52
plotPeak         10.26   0.32   10.58
DBAmmd-Accessors  7.82   0.47    8.30
compHists         4.94   1.27    6.20
* 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-3.13-bioc/meat/MMDiff2.Rcheck/00check.log'
for details.



Installation output

MMDiff2.Rcheck/00install.out

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch i386 CMD INSTALL --no-multiarch MMDiff2
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.13-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-Accessors7.820.478.30
DBAmmd-class0.050.000.05
MMD000
compDists23.39 6.1229.52
compHists4.941.276.20
compPvals1.650.111.77
estimateFragmentCenters1.920.262.18
getPeakReads0.300.070.36
mm9-Genes000
plotDISTS4Peak1.540.201.75
plotDists1.520.121.64
plotPeak10.26 0.3210.58
reportResults1.880.162.03
runShinyMMDiff2000
server.MMDiff2000
ui.MMDiff2000