BioC 3.0: CHECK report for motifStack on oaxaca

Package: motifStack

Version: 1.10.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch motifStack_1.10.2.tar.gz

StartedAt: 2015-04-10 01:32:52 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:39:07 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 375.1 seconds

RetCode: 0

Status:  OK

CheckDir: motifStack.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 --no-multiarch motifStack_1.10.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/motifStack.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.10.2’
* 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 ... [28s/49s] 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’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/25s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [15s/17s]
 [15s/17s] 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/motifStack.Rcheck/00check.log’
for details.

* installing *source* package ‘motifStack’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graphics::plot’ when loading ‘seqLogo’
No methods found in "IRanges" for requests: sapply
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘graphics::plot’ when loading ‘seqLogo’
No methods found in "IRanges" for requests: sapply
* DONE (motifStack)

name	user	system	elapsed
DNAmotifAlignment	0.637	0.008	0.878
colorset	0.001	0.000	0.004
motifCloud	0.007	0.000	0.007
motifSignature	0.005	0.000	0.005
motifStack	0.003	0.000	0.004
ouNode-class	0.006	0.000	0.006
pcm-class	0.711	0.113	1.378
pcm-methods	0.011	0.002	0.013
pfm-class	0.924	0.102	1.055
pfm-methods	0.011	0.002	0.013
plotMotifLogo	0.788	0.110	0.976
plotMotifLogoA	0.990	0.108	1.143
plotMotifLogoStack	0.726	0.101	0.894
plotMotifLogoStackWithTree	2.696	0.249	3.228
plotMotifStackWithPhylog	0.007	0.000	0.010
plotMotifStackWithRadialPhylog	0.008	0.001	0.017
readPCM	0.020	0.001	0.036