BioC 2.13: CHECK report for maDB on zin1

Package: maDB

Version: 1.34.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings maDB_1.34.0.tar.gz

StartedAt: 2014-04-05 02:12:24 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:13:25 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 61.0 seconds

RetCode: 0

Status:  OK

CheckDir: maDB.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/maDB.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maDB/DESCRIPTION’ ... OK
* this is package ‘maDB’ version ‘1.34.0’
* 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 ‘maDB’ can be installed ... [5s/5s] OK
* checking installed package size ... OK
* checking package 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
‘library’ or ‘require’ call to ‘pgUtils’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
drawVolcanoPlot: warning in rgb(r = abs(plog)/redvalue, g =
  abs(M)/bluevalue, b = 0): partial argument match of 'r' to 'red'
drawVolcanoPlot: warning in rgb(r = abs(plog)/redvalue, g =
  abs(M)/bluevalue, b = 0): partial argument match of 'g' to 'green'
drawVolcanoPlot: warning in rgb(r = abs(plog)/redvalue, g =
  abs(M)/bluevalue, b = 0): partial argument match of 'b' to 'blue'
* 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 ... NOTE
S3 methods shown with full name in documentation object 'format.latex':
  ‘format.latex’

S3 methods shown with full name in documentation object 'mean.center':
  ‘mean.center’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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’ ... NOTE
The following files should probably not be installed:
  ‘maDB.tex’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking examples ... [2s/2s] OK
* checking PDF version of manual ... OK

NOTE: There were 5 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/maDB.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
arrowProgress	0.004	0.000	0.004
calculateSimilarity	0.004	0.008	0.011
createJOINQuery	0.004	0.000	0.004
getPathFromFile	0.004	0.000	0.004
isDecimal	0.004	0.000	0.004
mapply	0.016	0.000	0.017
mean.center	0.004	0.000	0.003
meanWithoutNA	0.000	0.004	0.003
medianWithoutNA	0.004	0.000	0.004
multiGrep	0.004	0.000	0.004
progress	0.004	0.000	0.002
replaceAll	0.008	0.000	0.005
replaces	0.000	0.000	0.003