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: 2011-02-24 16:21:07 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 16:22:10 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 63.4 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) (2011-01-10 r53950)
* 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 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 data for non-ASCII characters ... 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	0.085	0.003	0.088
SCCgraph	0.395	0.011	0.407
SahinRNAi2008	0.007	0.001	0.008
enumerate.models	0.003	0.001	0.004
generateNetwork	0.391	0.009	0.431
infer.edge.type	0.362	0.004	0.368
local.model.prior	0.001	0.000	0.000
nem	4.297	0.029	4.335
nem.bootstrap	0.001	0.000	0.000
nem.calcSignificance	0	0	0
nem.consensus	0	0	0
nem.cont.preprocess	0.258	0.003	0.262
nem.discretize	0.097	0.005	0.102
nem.jackknife	0	0	0
nemModelSelection	0.679	0.013	0.694
network.AIC	0.310	0.002	0.313
plotEffects	0.264	0.004	0.294
prune.graph	0.065	0.001	0.074
quicknem	0	0	0
selectEGenes	0.933	0.014	0.947
set.default.parameters	0.000	0.000	0.001
sim.intervention	0.247	0.003	0.250
subsets	0	0	0
transitive.closure	0.048	0.001	0.054
transitive.reduction	0.043	0.001	0.048