BioC 3.4: CHECK report for MMDiff2 on morelia

Package: MMDiff2

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MMDiff2_1.2.0.tar.gz

StartedAt: 2017-04-15 05:11:29 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 05:16:19 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 290.6 seconds

RetCode: 0

Status:  OK

CheckDir: MMDiff2.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MMDiff2_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/MMDiff2.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 sizes of PDF files under ‘inst/doc’ ... 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 45.999  8.842  54.887
plotPeak   8.646  0.839  10.650
* 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
  ‘/Users/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	0.001	0.000	0.001
DBAmmd-Accessors	3.821	0.435	4.258
DBAmmd-class	0.026	0.001	0.050
MMD	0.002	0.000	0.002
compDists	45.999	8.842	54.887
compHists	3.809	0.351	4.167
compPvals	1.880	0.272	2.153
estimateFragmentCenters	1.847	0.136	1.984
getPeakReads	0.263	0.114	0.579
mm9-Genes	0.001	0.000	0.001
plotDISTS4Peak	1.345	0.140	1.487
plotDists	1.265	0.127	1.392
plotPeak	8.646	0.839	10.650
reportResults	1.477	0.167	1.644
runShinyMMDiff2	0.001	0.000	0.000
server.MMDiff2	0.001	0.000	0.001
ui.MMDiff2	0.001	0.000	0.001