Package: nem

Version: 2.17.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings nem_2.17.0.tar.gz

StartedAt: 2011-07-07 01:35:10 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 01:36:30 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 79.9 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 2.14.0 Under development (unstable) (2011-06-15 r56138)
* 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 ‘2.17.0’
* 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 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 ... 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
** 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	0.064	0.000	0.060
SCCgraph	0.412	0.008	0.421
SahinRNAi2008	0.000	0.004	0.005
enumerate.models	0.004	0.000	0.008
generateNetwork	0.668	0.020	0.736
infer.edge.type	0.540	0.016	0.577
local.model.prior	0	0	0
nem	5.536	0.084	5.799
nem.bootstrap	0	0	0
nem.calcSignificance	0	0	0
nem.consensus	0	0	0
nem.cont.preprocess	0.232	0.000	0.235
nem.discretize	0.080	0.004	0.083
nem.jackknife	0	0	0
nemModelSelection	0.884	0.016	0.931
network.AIC	0.304	0.008	0.328
plotEffects	0.452	0.016	0.510
prune.graph	0.576	0.024	0.688
quicknem	0	0	0
selectEGenes	0.916	0.004	0.921
set.default.parameters	0	0	0
sim.intervention	0.216	0.004	0.218
subsets	0.000	0.000	0.001
transitive.closure	0.376	0.012	0.434
transitive.reduction	0.372	0.012	0.440