BioC 2.13: CHECK report for GraphAT on perceval

Package: GraphAT

Version: 1.34.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GraphAT_1.34.0.tar.gz

StartedAt: 2014-04-05 01:51:26 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:52:29 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 63.2 seconds

RetCode: 0

Status:  OK

CheckDir: GraphAT.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/GraphAT.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 ‘GraphAT/DESCRIPTION’ ... OK
* this is package ‘GraphAT’ version ‘1.34.0’
* 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 ‘GraphAT’ can be installed ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘graph’ ‘methods’
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 ... NOTE
prepare_Rd: depthmat.Rd:28: Dropping empty section \references
* 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 examples ... [8s/8s] OK
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/GraphAT.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
Phenoclusters	1.203	0.356	1.574
causton	0.448	0.107	0.557
cellcycle	0.230	0.171	0.402
clust2Mat	0.012	0.053	0.065
depthmat	0.337	0.197	0.544
getpvalue	0.015	0.009	0.024
giaever	0.523	0.039	0.582
mRNAclusters	0.687	0.304	1.000
makeClustM	0.003	0.004	0.007
mat2UndirG	0.017	0.004	0.022
permPower	1.099	0.054	1.170
perms	0.003	0.005	0.008