BioC 3.2: CHECK report for motifStack on oaxaca

Package: motifStack

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings motifStack_1.14.0.tar.gz

StartedAt: 2015-10-27 05:50:32 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:57:14 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 402.2 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 motifStack_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/motifStack.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.14.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘motifStack’ can be installed ... [24s/42s] OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
* 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 ... OK
* 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 ... [20s/27s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [13s/20s]
 [13s/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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-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	0.286	0.005	0.493
colorset	0.001	0.001	0.000
getRankedUniqueMotifs	0.004	0.000	0.010
highlightCol	0.001	0.000	0.002
mergeMotifs	0.534	0.012	0.898
motifCircos	0.010	0.000	0.013
motifCloud	0.006	0.000	0.015
motifPiles	0.012	0.001	0.019
motifSignature	0.005	0.000	0.011
motifStack	0.003	0.000	0.003
ouNode-class	0.004	0.000	0.004
pcm-class	0.697	0.120	1.731
pcm-methods	0.010	0.002	0.012
pfm-class	0.684	0.105	0.886
pfm-methods	0.010	0.001	0.011
pfm2pwm	1.254	0.028	2.006
plotMotifLogo	0.775	0.103	0.937
plotMotifLogoA	0.954	0.102	1.188
plotMotifLogoStack	0.745	0.108	0.937
plotMotifLogoStackWithTree	2.415	0.217	3.136
plotMotifOverMotif	0.929	0.103	1.192
plotMotifStackWithPhylog	0.006	0.000	0.012
plotMotifStackWithRadialPhylog	0.008	0.001	0.018
readPCM	0.018	0.001	0.034
reorderUPGMAtree	0.004	0.000	0.005