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Package 305/467HostnameOS / ArchBUILDCHECKBUILD BIN
nem 2.16.1
Holger Froehlich
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/nem
Last Changed Rev: 55118 / Revision: 59457
Last Changed Date: 2011-04-28 02:27:19 -0700 (Thu, 28 Apr 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: nem
Version: 2.16.1
Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings nem_2.16.1.tar.gz
StartedAt: 2011-10-20 13:41:49 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 13:43:07 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 77.9 seconds
RetCode: 0
Status:  OK 
CheckDir: nem.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/nem.Rcheck’
* using R version 2.13.2 (2011-09-30)
* 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 ‘2.16.1’
* checking package namespace 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 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

nem.Rcheck/00install.out:

* installing *source* package ‘nem’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (nem)

nem.Rcheck/nem-Ex.timings:

nameusersystemelapsed
BFSlevel000
BoutrosRNAi20020.0520.0040.059
SCCgraph0.4200.0080.429
SahinRNAi20080.0040.0000.005
enumerate.models0.0040.0000.007
generateNetwork0.4240.0400.564
infer.edge.type0.3960.0080.445
local.model.prior000
nem4.6240.1045.026
nem.bootstrap000
nem.calcSignificance000
nem.consensus000
nem.cont.preprocess0.3160.0080.322
nem.discretize0.0680.0000.067
nem.jackknife000
nemModelSelection0.6280.0200.692
network.AIC0.2920.0040.294
plotEffects0.3000.0280.400
prune.graph0.0920.0600.284
quicknem000
selectEGenes0.8720.0040.876
set.default.parameters000
sim.intervention0.3160.0000.317
subsets000
transitive.closure0.0640.0360.187
transitive.reduction0.0720.0240.185