Package: nem

Version: 2.18.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch nem_2.18.0.tar.gz

StartedAt: 2012-01-09 04:29:51 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 04:31:04 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 72.9 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 2.14.1 (2011-12-22)
* 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 '2.18.0'
* checking package namespace 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 if there is a namespace ... 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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
Warning in library.dynam("Rgraphviz", package = "Rgraphviz") :
  use of library.dynam() without specifying both 'package' and 'lib.loc' is deprecated
Warning in fun(libname, pkgname) :
  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 in library.dynam("Rgraphviz", package = "Rgraphviz") :
  use of library.dynam() without specifying both 'package' and 'lib.loc' is deprecated
Warning message:
In fun(libname, pkgname) : 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	0.08	0.00	0.08
SCCgraph	0.39	0.00	0.42
SahinRNAi2008	0	0	0
enumerate.models	0.01	0.00	0.02
generateNetwork	0.30	0.01	0.33
infer.edge.type	0.37	0.00	0.37
local.model.prior	0	0	0
nem	3.74	0.04	3.77
nem.bootstrap	0	0	0
nem.calcSignificance	0	0	0
nem.consensus	0	0	0
nem.cont.preprocess	0.28	0.01	0.29
nem.discretize	0.06	0.02	0.08
nem.jackknife	0	0	0
nemModelSelection	0.51	0.00	0.51
network.AIC	0.29	0.00	0.28
plotEffects	0.32	0.00	0.40
prune.graph	0.05	0.01	0.07
quicknem	0	0	0
selectEGenes	0.75	0.00	0.75
set.default.parameters	0	0	0
sim.intervention	0.3	0.0	0.3
subsets	0	0	0
transitive.closure	0.03	0.00	0.03
transitive.reduction	0.03	0.02	0.05