BioC 3.1: CHECK report for motifStack on zin2

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings motifStack_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/motifStack.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.12.0’
* 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 ... [14s/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 ... 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 ... [14s/15s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [9s/9s]
 [9s/9s] 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	0.248	0.004	0.251
colorset	0.001	0.000	0.000
getRankedUniqueMotifs	0.002	0.000	0.002
highlightCol	0.001	0.000	0.001
motifCircos	0.004	0.000	0.005
motifCloud	0.003	0.000	0.003
motifPiles	0.005	0.000	0.005
motifSignature	0.003	0.000	0.003
motifStack	0.001	0.000	0.002
ouNode-class	0.003	0.000	0.003
pcm-class	0.625	0.174	0.817
pcm-methods	0.008	0.000	0.009
pfm-class	0.644	0.111	0.774
pfm-methods	0.008	0.000	0.008
pfm2pwm	0.701	0.008	0.867
plotMotifLogo	0.644	0.166	0.827
plotMotifLogoA	0.893	0.180	1.095
plotMotifLogoStack	0.652	0.152	0.823
plotMotifLogoStackWithTree	2.108	0.292	2.479
plotMotifStackWithPhylog	0.003	0.000	0.003
plotMotifStackWithRadialPhylog	0.004	0.000	0.004
readPCM	0.018	0.000	0.017

BioC 3.1: CHECK report for motifStack on zin2

Summary

Command output