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Package 308/472HostnameOS / ArchBUILDCHECKBUILD BIN
nem 2.17.0
Holger Froehlich
Snapshot Date: 2011-06-21 19:21:48 -0700 (Tue, 21 Jun 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/nem
Last Changed Rev: 54930 / Revision: 56351
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 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

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: 2011-06-22 04:19:43 -0700 (Wed, 22 Jun 2011)
EndedAt: 2011-06-22 04:21:40 -0700 (Wed, 22 Jun 2011)
EllapsedTime: 117.4 seconds
RetCode: 0
Status:  OK 
CheckDir: nem.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/nem.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* 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 ... 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 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

nem.Rcheck/00install.out:

* 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)

nem.Rcheck/nem-Ex.timings:

nameusersystemelapsed
BFSlevel0.0010.0000.000
BoutrosRNAi20020.1410.0070.149
SCCgraph0.5750.0210.610
SahinRNAi20080.0090.0010.011
enumerate.models0.0050.0000.005
generateNetwork0.5600.0150.645
infer.edge.type0.4600.0100.484
local.model.prior0.0010.0000.001
nem5.9990.0596.161
nem.bootstrap0.0010.0000.001
nem.calcSignificance0.0000.0000.001
nem.consensus0.0010.0010.000
nem.cont.preprocess0.380.010.39
nem.discretize0.2020.0110.218
nem.jackknife000
nemModelSelection0.8820.0170.904
network.AIC0.4700.0090.480
plotEffects0.3890.0090.433
prune.graph0.0930.0030.131
quicknem000
selectEGenes1.3130.0191.344
set.default.parameters000
sim.intervention0.3580.0090.369
subsets000
transitive.closure0.0540.0020.067
transitive.reduction0.0550.0020.061