BioC 2.13: CHECK report for motifStack on zin1

Package: motifStack

Version: 1.6.5

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings motifStack_1.6.5.tar.gz

StartedAt: 2014-04-05 02:35:48 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:38:45 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 176.6 seconds

RetCode: 0

Status:  OK

CheckDir: motifStack.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/motifStack.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 ‘motifStack/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifStack’ version ‘1.6.5’
* 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 ‘motifStack’ can be installed ... [13s/21s] 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘coloredSymbols’ ‘getIC’ ‘getIE’ ‘hex2psrgb’ ‘highlightCol’
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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/14s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [12s/13s]
 [12s/13s] 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/motifStack.Rcheck/00check.log’
for details.

* installing *source* package ‘motifStack’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (motifStack)

name	user	system	elapsed
DNAmotifAlignment	0.416	0.008	0.425
colorset	0.000	0.004	0.002
motifCloud	0.004	0.000	0.007
motifSignature	0.008	0.000	0.007
motifStack	0.008	0.000	0.007
ouNode-class	0.008	0.000	0.005
pcm-class	0.544	0.132	0.841
pcm-methods	0.016	0.000	0.016
pfm-class	0.504	0.124	0.703
pfm-methods	0.020	0.000	0.031
plotMotifLogo	0.584	0.128	0.883
plotMotifLogoA	0.948	0.132	1.111
plotMotifLogoStack	0.588	0.112	0.809
plotMotifLogoStackWithTree	1.952	0.244	2.883
plotMotifStackWithPhylog	0.004	0.004	0.007
plotMotifStackWithRadialPhylog	0.008	0.000	0.009
readPCM	0.012	0.004	0.015