BioC 3.1: CHECK report for motifStack on petty

Package: motifStack

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings motifStack_1.12.0.tar.gz

StartedAt: 2015-10-09 00:28:42 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:40:26 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 703.8 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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/motifStack.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.12.0’
* 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 ... [25s/26s] 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 ... 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/81s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
plotMotifLogoStackWithTree 2.649  0.223  11.042
pcm-class                  0.917  0.168  10.516
pfm2pwm                    0.921  0.049   6.542
* 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
* DONE

Status: OK

* installing *source* package ‘motifStack’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
No methods found in "IRanges" for requests: sapply
** 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’
No methods found in "IRanges" for requests: sapply
* DONE (motifStack)

name	user	system	elapsed
DNAmotifAlignment	0.336	0.030	0.571
colorset	0.001	0.000	0.000
getRankedUniqueMotifs	0.004	0.000	0.004
highlightCol	0.001	0.000	0.001
motifCircos	0.012	0.000	0.086
motifCloud	0.007	0.000	0.006
motifPiles	0.013	0.000	0.038
motifSignature	0.006	0.001	0.006
motifStack	0.003	0.000	0.004
ouNode-class	0.004	0.001	0.003
pcm-class	0.917	0.168	10.516
pcm-methods	0.009	0.002	0.011
pfm-class	0.906	0.125	3.226
pfm-methods	0.009	0.002	0.098
pfm2pwm	0.921	0.049	6.542
plotMotifLogo	0.855	0.104	3.780
plotMotifLogoA	1.117	0.113	3.038
plotMotifLogoStack	0.888	0.116	3.043
plotMotifLogoStackWithTree	2.649	0.223	11.042
plotMotifStackWithPhylog	0.008	0.000	0.008
plotMotifStackWithRadialPhylog	0.010	0.001	0.044
readPCM	0.015	0.001	0.016