Package: nem

Version: 2.12.0

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings nem_2.12.0.tar.gz

StartedAt: 2010-10-04 17:58:25 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 17:59:49 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 84.1 seconds

RetCode: 0

Status:  OK

CheckDir: nem.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/nem.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'nem/DESCRIPTION' ... OK
* this is package 'nem' version '2.12.0'
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* 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	0.000	0.000	0.001
BoutrosRNAi2002	0.142	0.007	0.159
SCCgraph	0.636	0.022	0.705
SahinRNAi2008	0.009	0.002	0.031
enumerate.models	0.005	0.001	0.006
generateNetwork	0.653	0.017	0.805
infer.edge.type	0.519	0.012	0.547
local.model.prior	0.001	0.000	0.001
nem	6.690	0.064	7.030
nem.bootstrap	0.001	0.000	0.001
nem.calcSignificance	0	0	0
nem.consensus	0	0	0
nem.cont.preprocess	0.452	0.013	0.478
nem.discretize	0.146	0.011	0.159
nem.jackknife	0	0	0
nemModelSelection	1.016	0.018	1.119
network.AIC	0.536	0.009	0.669
plotEffects	0.487	0.012	0.590
prune.graph	0.110	0.002	0.187
quicknem	0.000	0.001	0.001
selectEGenes	1.421	0.021	1.686
set.default.parameters	0	0	0
sim.intervention	0.460	0.011	0.548
subsets	0.001	0.001	0.000
transitive.closure	0.068	0.001	0.085
transitive.reduction	0.069	0.002	0.084