Package: DEGraph

Version: 1.5.0

Command: mkdir DEGraph.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEGraph.buildbin-libdir DEGraph_1.5.0.tar.gz >DEGraph-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=DEGraph.buildbin-libdir --install="check:DEGraph-install.out" --force-multiarch --no-vignettes --timings DEGraph_1.5.0.tar.gz && mv DEGraph.buildbin-libdir/* DEGraph.Rcheck/ && rmdir DEGraph.buildbin-libdir

StartedAt: 2011-07-07 04:46:36 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 04:50:07 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 211.5 seconds

RetCode: 0

Status:  OK

CheckDir: DEGraph.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/DEGraph.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DEGraph/DESCRIPTION' ... OK
* this is package 'DEGraph' version '1.5.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'DEGraph' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
testOneGraph: no visible global function definition for
  'translateNCI2GeneID'
* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
                                old_size new_size compress
  Loi2008_DEGraphVignette.RData    571Kb    427Kb       xz
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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

install for i386

* installing *source* package 'DEGraph' ...
** R
** data
** demo
** inst
** preparing package for lazy loading
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.8.0 (2011-04-03) successfully loaded. See ?R.oo for help.
R.utils v1.7.5 (2011-04-12) successfully loaded. See ?R.utils for help.
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'DEGraph.Rnw' 
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)

add DLL for x64

* installing *source* package 'DEGraph' ...
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
Warning message:
In fun(...) : Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.
* MD5 sums
packaged installation of 'DEGraph' as DEGraph_1.5.0.zip

* DONE (DEGraph)

name	user	system	elapsed
AN.test	6.55	0.06	6.62
BS.test	5.13	0.02	5.21
annLoi2008	0.14	0.00	0.14
classLoi2008	0.12	0.01	0.14
exprLoi2008	0.16	0.00	0.16
getConnectedComponentList	2.37	0.00	2.37
getKEGGPathways	21.12	0.06	21.23
getSignedGraph	2.34	0.00	2.34
grListKEGG	1.04	0.00	1.04
graph.T2.test	2.78	0.00	2.78
hyper.test	5.28	0.02	5.30
laplacianFromA	0.35	0.00	0.34
plotValuedGraph	9.41	0.02	9.42
randomWAMGraph	0.46	0.01	0.48
testOneConnectedComponent	2.42	0.00	2.41
testOneGraph	7.53	0.02	7.55
twoSampleFromGraph	0.33	0.04	0.37
writeAdjacencyMatrix2KGML	0.34	0.02	0.36