BioC 2.13: CHECK report for paircompviz on perceval

Package: paircompviz

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch paircompviz_1.0.0.tar.gz

StartedAt: 2014-04-05 03:10:50 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:11:44 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 54.1 seconds

RetCode: 0

Status:  OK

CheckDir: paircompviz.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/paircompviz.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘paircompviz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘paircompviz’ version ‘1.0.0’
* 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 ‘paircompviz’ can be installed ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Rgraphviz’
A package should be listed in only one of these fields.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files are already in R: ‘jss.bst’, ‘jss.cls’
Please remove them from your package.
* checking examples ... [6s/6s] 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 were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/paircompviz.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
brokentrans	0.023	0.002	0.026
hasse	0.379	0.013	0.402
paircomp	3.100	0.083	3.274
paircompviz-package	0.106	0.002	0.115
transReduct	0.006	0.001	0.007