Package: nem

Version: 2.17.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings nem_2.17.0.tar.gz

StartedAt: 2011-05-09 18:36:12 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 18:38:09 -0700 (Mon, 09 May 2011)

EllapsedTime: 116.6 seconds

RetCode: 0

Status:  OK

CheckDir: nem.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/nem.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* 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 '2.17.0'
* checking package name space information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: doMC
* 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 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 ... NOTE
nem.calcSignificance: no visible global function definition for
  'registerDoMC'
nem.calcSignificance: no visible global function definition for
  '%dopar%'
nem.calcSignificance: no visible global function definition for
  'foreach'
nem.featureselection: no visible global function definition for
  'registerDoMC'
nem.featureselection: no visible global function definition for
  '%dopar%'
nem.featureselection: no visible global function definition for
  'foreach'
nem.featureselection: no visible binding for global variable 'd'
nemModelSelection: no visible global function definition for
  'registerDoMC'
nemModelSelection: no visible global function definition for '%dopar%'
nemModelSelection: no visible global function definition for 'foreach'
nemModelSelection: no visible binding for global variable 'lam'
nemModelSelection: no visible binding for global variable 'r'
score: no visible global function definition for 'registerDoMC'
score: no visible global function definition for '%dopar%'
score: no visible global function definition for 'foreach'
score: no visible binding for global variable 'm'
* 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 for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... 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 ...
*** tangling vignette sources ...
   'nem.Rnw' using 'latin1' 
** testing if installed package can be loaded
Warning message:
In fun(...) : Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.

* DONE (nem)

name	user	system	elapsed
BFSlevel	0	0	0
BoutrosRNAi2002	0.06	0.00	0.06
SCCgraph	0.39	0.02	0.41
SahinRNAi2008	0	0	0
enumerate.models	0.01	0.00	0.01
generateNetwork	0.40	0.02	0.43
infer.edge.type	0.31	0.00	0.31
local.model.prior	0	0	0
nem	4.65	0.04	4.70
nem.bootstrap	0	0	0
nem.calcSignificance	0	0	0
nem.consensus	0	0	0
nem.cont.preprocess	0.23	0.00	0.23
nem.discretize	0.14	0.00	0.14
nem.jackknife	0	0	0
nemModelSelection	0.61	0.02	0.63
network.AIC	0.32	0.01	0.33
plotEffects	0.28	0.00	0.28
prune.graph	0.04	0.02	0.06
quicknem	0	0	0
selectEGenes	0.90	0.02	0.91
set.default.parameters	0	0	0
sim.intervention	0.23	0.00	0.23
subsets	0	0	0
transitive.closure	0.05	0.00	0.05
transitive.reduction	0.04	0.00	0.04