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BioC 3.5: CHECK report for MMDiff2 on tokay2

This page was generated on 2017-08-16 13:25:47 -0400 (Wed, 16 Aug 2017).

Package 838/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MMDiff2 1.4.0
Gabriele Schweikert
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/MMDiff2
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MMDiff2
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings MMDiff2_1.4.0.tar.gz
StartedAt: 2017-08-16 01:21:33 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:26:12 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 279.6 seconds
RetCode: 0
Status:  OK  
CheckDir: MMDiff2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings MMDiff2_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MMDiff2.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.4.0'
* 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 ... OK
* 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'
Undefined global functions or variables:
  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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
compDists        43.24   5.96   49.19
plotPeak          8.37   0.44   14.00
DBAmmd-Accessors  7.64   0.34    7.98
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/MMDiff2.Rcheck/00check.log'
for details.


MMDiff2.Rcheck/00install.out:

* installing *source* package 'MMDiff2' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MMDiff2)

MMDiff2.Rcheck/MMDiff2-Ex.timings:

nameusersystemelapsed
Cfp1-Peaks000
DBAmmd-Accessors7.640.347.98
DBAmmd-class0.100.000.15
MMD000
compDists43.24 5.9649.19
compHists3.830.724.54
compPvals2.230.122.36
estimateFragmentCenters2.840.303.14
getPeakReads0.970.003.28
mm9-Genes000
plotDISTS4Peak1.710.061.82
plotDists1.750.192.01
plotPeak 8.37 0.4414.00
reportResults1.860.031.89
runShinyMMDiff2000
server.MMDiff2000
ui.MMDiff2000