Package: nem

Version: 2.17.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch nem_2.17.0.tar.gz

StartedAt: 2011-05-09 15:56:05 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 15:58:01 -0700 (Mon, 09 May 2011)

EllapsedTime: 115.5 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 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘markowetz-thesis-2006.pdf’ from 1155Kb to 844Kb
     compacted ‘nem.pdf’ from 779Kb to 376Kb
  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
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	0.001	0.000	0.001
BoutrosRNAi2002	0.143	0.007	0.168
SCCgraph	0.584	0.023	0.736
SahinRNAi2008	0.009	0.001	0.010
enumerate.models	0.005	0.000	0.005
generateNetwork	0.564	0.017	0.958
infer.edge.type	0.462	0.011	0.593
local.model.prior	0.004	0.000	0.004
nem	6.030	0.071	6.416
nem.bootstrap	0	0	0
nem.calcSignificance	0.001	0.000	0.000
nem.consensus	0	0	0
nem.cont.preprocess	0.386	0.011	0.398
nem.discretize	0.165	0.013	0.182
nem.jackknife	0.001	0.000	0.001
nemModelSelection	0.926	0.017	0.984
network.AIC	0.468	0.009	0.506
plotEffects	0.463	0.013	0.579
prune.graph	0.083	0.002	0.130
quicknem	0	0	0
selectEGenes	1.278	0.019	1.422
set.default.parameters	0.001	0.000	0.001
sim.intervention	0.361	0.009	0.394
subsets	0	0	0
transitive.closure	0.053	0.002	0.067
transitive.reduction	0.056	0.001	0.061