BioC 3.4: CHECK report for MMDiff2 on malbec1

Package: MMDiff2

Version: 1.2.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MMDiff2_1.2.0.tar.gz

StartedAt: 2017-04-14 23:55:40 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:59:24 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 224.1 seconds

RetCode: 0

Status:  OK

CheckDir: MMDiff2.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MMDiff2_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/MMDiff2.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MMDiff2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MMDiff2’ version ‘1.2.0’
* 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 for sufficient/correct file permissions ... 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        31.928  1.936  33.899
DBAmmd-Accessors  9.396  0.156   9.559
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/MMDiff2.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
Cfp1-Peaks	0.000	0.000	0.001
DBAmmd-Accessors	9.396	0.156	9.559
DBAmmd-class	0.024	0.000	0.028
MMD	0.000	0.000	0.001
compDists	31.928	1.936	33.899
compHists	2.880	0.004	2.886
compPvals	1.816	0.364	2.187
estimateFragmentCenters	1.452	0.028	1.480
getPeakReads	0.244	0.000	0.349
mm9-Genes	0.000	0.000	0.001
plotDISTS4Peak	1.248	0.024	1.276
plotDists	1.068	0.044	1.111
plotPeak	3.796	0.384	4.185
reportResults	1.056	0.232	1.293
runShinyMMDiff2	0	0	0
server.MMDiff2	0	0	0
ui.MMDiff2	0.000	0.000	0.001