Package: nem

Version: 2.15.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch nem_2.15.0.tar.gz

StartedAt: 2011-03-17 16:58:16 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 16:59:35 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 79.0 seconds

RetCode: 0

Status:  OK

CheckDir: nem.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/nem.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'nem/DESCRIPTION' ... OK
* this is package 'nem' version '2.15.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'nem' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated 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 examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'nem' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: class
Loading required package: grid
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (nem)

name	user	system	elapsed
BFSlevel	0	0	0
BoutrosRNAi2002	0.089	0.003	0.092
SCCgraph	0.413	0.010	0.423
SahinRNAi2008	0.006	0.001	0.007
enumerate.models	0.005	0.001	0.006
generateNetwork	0.429	0.008	0.472
infer.edge.type	0.332	0.006	0.341
local.model.prior	0	0	0
nem	4.537	0.026	4.571
nem.bootstrap	0.001	0.000	0.001
nem.calcSignificance	0	0	0
nem.consensus	0	0	0
nem.cont.preprocess	0.283	0.004	0.287
nem.discretize	0.134	0.003	0.137
nem.jackknife	0	0	0
nemModelSelection	0.640	0.007	0.649
network.AIC	0.336	0.003	0.339
plotEffects	0.325	0.004	0.332
prune.graph	0.067	0.001	0.078
quicknem	0.000	0.000	0.001
selectEGenes	1.021	0.005	1.025
set.default.parameters	0.000	0.000	0.001
sim.intervention	0.255	0.004	0.258
subsets	0.001	0.000	0.000
transitive.closure	0.044	0.002	0.050
transitive.reduction	0.047	0.001	0.051