Package: MMDiff2

Version: 1.11.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --install=check:MMDiff2.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MMDiff2_1.11.0.tar.gz

StartedAt: 2019-04-09 04:21:08 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:26:04 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 295.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MMDiff2.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --install=check:MMDiff2.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MMDiff2_1.11.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MMDiff2.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.11.0'
* 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-3.9-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 or elapsed time > 5s
                  user system elapsed
compDists        29.31   8.22   38.17
plotPeak         12.00   0.39   12.39
DBAmmd-Accessors  9.10   0.54    9.62
compHists         5.08   0.88    5.99
* 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-3.9-bioc/meat/MMDiff2.Rcheck/00check.log'
for details.

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch i386 CMD INSTALL --no-multiarch MMDiff2
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* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
* installing *source* package 'MMDiff2' ...
** 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

name	user	system	elapsed
Cfp1-Peaks	0	0	0
DBAmmd-Accessors	9.10	0.54	9.62
DBAmmd-class	0.03	0.01	0.09
MMD	0	0	0
compDists	29.31	8.22	38.17
compHists	5.08	0.88	5.99
compPvals	2.46	0.60	3.06
estimateFragmentCenters	2.46	0.24	2.70
getPeakReads	0.29	0.01	3.30
mm9-Genes	0	0	0
plotDISTS4Peak	2.64	0.27	2.91
plotDists	2.26	0.16	2.42
plotPeak	12.00	0.39	12.39
reportResults	2.21	0.25	2.45
runShinyMMDiff2	0	0	0
server.MMDiff2	0	0	0
ui.MMDiff2	0	0	0