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Package 315/479HostnameOS / ArchBUILDCHECKBUILD BIN
nem 2.17.0
Holger Froehlich
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/nem
Last Changed Rev: 54930 / Revision: 56603
Last Changed Date: 2011-04-19 05:43:21 -0700 (Tue, 19 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ OK ] OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: nem
Version: 2.17.0
Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch nem_2.17.0.tar.gz
StartedAt: 2011-07-07 05:24:19 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 05:25:38 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 79.4 seconds
RetCode: 0
Status:  OK  
CheckDir: nem.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/nem.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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

nem.Rcheck/00install.out:

* installing *source* package 'nem' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: class
Loading required package: grid
Warning in fun(...) :
  Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'nem.Rnw' using 'latin1' 
** testing if installed package can be loaded
Warning message:
In fun(...) : Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.

* DONE (nem)

nem.Rcheck/nem-Ex.timings:

nameusersystemelapsed
BFSlevel000
BoutrosRNAi20020.060.000.06
SCCgraph0.420.000.42
SahinRNAi2008000
enumerate.models0.020.000.02
generateNetwork0.430.020.45
infer.edge.type0.330.000.33
local.model.prior000
nem4.830.004.83
nem.bootstrap000
nem.calcSignificance000
nem.consensus000
nem.cont.preprocess0.280.000.29
nem.discretize0.080.000.07
nem.jackknife000
nemModelSelection0.620.010.66
network.AIC0.330.000.33
plotEffects0.260.020.28
prune.graph0.070.000.06
quicknem000
selectEGenes0.890.000.89
set.default.parameters000
sim.intervention0.270.000.26
subsets000
transitive.closure0.050.000.05
transitive.reduction0.040.000.05