BioC 3.1: CHECK report for M3D on zin2

Package: M3D

Version: 1.3.4

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings M3D_1.3.4.tar.gz

StartedAt: 2015-10-09 03:03:48 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:07:50 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 241.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: M3D.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings M3D_1.3.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/M3D.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘M3D/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘M3D’ version ‘1.3.4’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘M3D’ can be installed ... [14s/22s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘parallel’
  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
M3D_Para: no visible global function definition for ‘detectCores’
M3D_Para: no visible global function definition for ‘mcmapply’
readENCODEdata: no visible global function definition for ‘SimpleList’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'readENCODEdata':
readENCODEdata
  Code: function(files, colData, eData = NaN)
  Docs: function(files, colData)
  Argument names in code not in docs:
    eData

* 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 ... [7s/10s] WARNING
Found the following significant warnings:

  Warning: 'rowData' is deprecated.
  Warning: 'rowData' is deprecated.
  Warning: 'rowData' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [14s/19s]
 [14s/20s] OK
* 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: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/M3D.Rcheck/00check.log’
for details.

* installing *source* package ‘M3D’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (M3D)

name	user	system	elapsed
M3D_Para	0	0	0
M3D_Wrapper	0.000	0.000	0.001
plotMethProfile	0.259	0.008	0.298
pvals	0	0	0
readENCODEdata	0	0	0