Package: nem

Version: 2.15.0

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings nem_2.15.0.tar.gz

StartedAt: 2011-02-24 20:58:42 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 20:59:48 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 66.8 seconds

RetCode: 0

Status:  OK

CheckDir: nem.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/nem.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
Warning in fun(...) :
  Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.
** 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	0.06	0.00	0.06
SCCgraph	0.41	0.00	0.47
SahinRNAi2008	0.00	0.02	0.02
enumerate.models	0	0	0
generateNetwork	0.43	0.00	0.43
infer.edge.type	0.35	0.00	0.35
local.model.prior	0	0	0
nem	4.67	0.01	4.68
nem.bootstrap	0	0	0
nem.calcSignificance	0	0	0
nem.consensus	0	0	0
nem.cont.preprocess	0.31	0.00	0.32
nem.discretize	0.05	0.03	0.08
nem.jackknife	0	0	0
nemModelSelection	0.64	0.02	0.65
network.AIC	0.41	0.00	0.41
plotEffects	0.26	0.02	0.42
prune.graph	0.06	0.00	0.08
quicknem	0	0	0
selectEGenes	0.91	0.01	0.92
set.default.parameters	0	0	0
sim.intervention	0.25	0.00	0.25
subsets	0	0	0
transitive.closure	0.11	0.00	0.11
transitive.reduction	0.03	0.00	0.03