Package: MMDiff2

Version: 1.10.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --install=check:MMDiff2.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MMDiff2_1.10.0.tar.gz

StartedAt: 2019-04-13 03:56:03 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 04:01:01 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 297.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MMDiff2.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --install=check:MMDiff2.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MMDiff2_1.10.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MMDiff2.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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-3.8-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        21.85   5.98   27.83
plotPeak          9.12   0.19    9.33
DBAmmd-Accessors  7.25   0.26    7.62
* 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-3.8-bioc/meat/MMDiff2.Rcheck/00check.log'
for details.

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe --arch i386 CMD INSTALL --no-multiarch MMDiff2
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* installing to library 'C:/Users/biocbuild/bbs-3.8-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
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'MMDiff2'
* DONE (MMDiff2)
Making 'packages.html' ... done
In R CMD INSTALL

name	user	system	elapsed
Cfp1-Peaks	0	0	0
DBAmmd-Accessors	7.25	0.26	7.62
DBAmmd-class	0.02	0.02	0.03
MMD	0	0	0
compDists	21.85	5.98	27.83
compHists	3.26	0.63	3.89
compPvals	1.50	0.15	1.66
estimateFragmentCenters	1.77	0.08	1.84
getPeakReads	0.23	0.00	0.24
mm9-Genes	0	0	0
plotDISTS4Peak	1.52	0.11	1.62
plotDists	2.03	0.23	2.27
plotPeak	9.12	0.19	9.33
reportResults	1.54	0.11	1.64
runShinyMMDiff2	0	0	0
server.MMDiff2	0	0	0
ui.MMDiff2	0	0	0