Package: nem

Version: 2.18.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch nem_2.18.0.tar.gz

StartedAt: 2012-03-24 02:47:12 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 02:49:01 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 109.1 seconds

RetCode: 0

Status:  OK

CheckDir: nem.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/nem.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'markowetz-thesis-2006.pdf' from 1155Kb to 844Kb
  consider running tools::compactPDF() on these files
* 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	0.001	0.000	0.000
BoutrosRNAi2002	0.144	0.007	0.155
SCCgraph	0.456	0.019	0.476
SahinRNAi2008	0.008	0.001	0.010
enumerate.models	0.004	0.001	0.004
generateNetwork	0.526	0.029	0.698
infer.edge.type	0.409	0.013	0.428
local.model.prior	0.000	0.000	0.001
nem	4.852	0.063	4.960
nem.bootstrap	0	0	0
nem.calcSignificance	0.000	0.001	0.000
nem.consensus	0.000	0.000	0.001
nem.cont.preprocess	0.423	0.012	0.436
nem.discretize	0.149	0.011	0.169
nem.jackknife	0.000	0.000	0.001
nemModelSelection	0.693	0.015	0.712
network.AIC	0.406	0.010	0.418
plotEffects	0.376	0.016	0.413
prune.graph	0.092	0.006	0.115
quicknem	0.000	0.000	0.001
selectEGenes	1.167	0.021	1.200
set.default.parameters	0.000	0.001	0.000
sim.intervention	0.304	0.009	0.325
subsets	0	0	0
transitive.closure	0.059	0.004	0.069
transitive.reduction	0.047	0.002	0.053