Package: nem

Version: 2.18.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings nem_2.18.0.tar.gz

StartedAt: 2012-03-24 01:41:11 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:42:27 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 75.9 seconds

RetCode: 0

Status:  OK

CheckDir: nem.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/nem.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... OK
* 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 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 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
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘nem.Rnw’ using ‘latin1’ 
** testing if installed package can be loaded

* DONE (nem)

name	user	system	elapsed
BFSlevel	0	0	0
BoutrosRNAi2002	0.056	0.004	0.061
SCCgraph	0.380	0.008	0.386
SahinRNAi2008	0.008	0.000	0.005
enumerate.models	0.000	0.000	0.003
generateNetwork	0.664	0.016	1.194
infer.edge.type	0.420	0.000	0.444
local.model.prior	0	0	0
nem	4.812	0.124	5.621
nem.bootstrap	0	0	0
nem.calcSignificance	0	0	0
nem.consensus	0	0	0
nem.cont.preprocess	0.188	0.004	0.264
nem.discretize	0.156	0.004	0.160
nem.jackknife	0	0	0
nemModelSelection	0.584	0.012	0.638
network.AIC	0.228	0.000	0.234
plotEffects	0.416	0.008	0.465
prune.graph	0.556	0.012	0.641
quicknem	0	0	0
selectEGenes	0.740	0.004	0.747
set.default.parameters	0	0	0
sim.intervention	0.160	0.008	0.168
subsets	0.000	0.000	0.001
transitive.closure	0.380	0.004	0.433
transitive.reduction	0.364	0.004	0.409