Package: DEGraph

Version: 1.9.3

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DEGraph_1.9.3.tar.gz

StartedAt: 2012-06-20 23:16:43 -0700 (Wed, 20 Jun 2012)

EndedAt: 2012-06-20 23:19:06 -0700 (Wed, 20 Jun 2012)

EllapsedTime: 143.3 seconds

RetCode: 1

Status:  ERROR

CheckDir: DEGraph.Rcheck

Warnings: NA

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/DEGraph.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'DEGraph/DESCRIPTION' ... OK
* this is package 'DEGraph' version '1.9.3'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 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 ... OK
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                                old_size new_size compress
  Loi2008_DEGraphVignette.RData    571Kb    426Kb       xz
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... ERROR
Running examples in 'DEGraph-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getConnectedComponentList
> ### Title: Given a graph, returns a list of its connected components (which
> ###   are also graph objects), ordered by decreasing number of nodes
> ### Aliases: getConnectedComponentList
> 
> ### ** Examples
> 
> data("Loi2008_DEGraphVignette")
> exprData <- exprLoi2008
> rn <- rownames(exprData)
> 
> ## Retrieve expression levels data for genes from one KEGG pathway
> graph <- grListKEGG[[1]]
> pname <- attr(graph, "label")
> cat(verbose, "Pathway name: ", pname)
Pathway name: 
> 
> sgraph <- getSignedGraph(graph, verbose=TRUE)
Interactions:
 Named chr [1:392] "indirect effect" "indirect effect" ...
 - attr(*, "names")= chr [1:392] "hsa:10725˜hsa:7124" "hsa:10725˜hsa:1437" "hsa:4772˜hsa:7124" "hsa:4772˜hsa:1437" ...
intNames
         activation binding/association            compound     indirect effect 
                294                  22                  44                  22 
         inhibition 
                 10 
Positive interactions:
List of 2
 $ activation: int [1:294] 11 12 13 14 15 16 17 18 19 20 ...
 $ expression: int(0) 
Negative interactions:
List of 2
 $ inhibition: int [1:10] 168 169 170 171 172 173 174 175 176 177
 $ repression: int(0) 
Removing unsigned edges from graph...
 Edges to remove:
  Named chr [1:88] "indirect effect" "indirect effect" ...
  - attr(*, "names")= chr [1:88] "hsa:10725˜hsa:7124" "hsa:10725˜hsa:1437" "hsa:4772˜hsa:7124" "hsa:4772˜hsa:1437" ...
 edgesToRemove
 binding/association            compound     indirect effect 
                  22                  44                  22 
 A graphNEL graph with directed edges
 Number of Nodes = 137 
 Number of Edges = 304 
Removing unsigned edges from graph...done
Creating sign matrix...
Creating sign matrix...done
> print(sgraph)
Error: The edgemode slot no longer exists.
Use 'updateGraph' to update this graph object.
Execution halted

* installing *source* package 'DEGraph' ...
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'DEGraph.Rnw' 
** testing if installed package can be loaded

* DONE (DEGraph)

name	user	system	elapsed
AN.test	6.587	0.283	7.641
BS.test	6.027	0.248	6.927
annLoi2008	0.245	0.004	0.270
classLoi2008	0.256	0.004	0.267
exprLoi2008	0.253	0.013	0.282