• using R Under development (unstable) (2012-08-11 r60235)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘pacose/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘pacose’ version ‘1.2’
• 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 for executable files ... OK
• checking for hidden files and directories ... OK
• checking whether package ‘pacose’ 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 loading without being on the library search path ... 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 line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... OK
• checking examples ... ERROR
  Running examples in ‘pacose-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: ipacose
  > ### Title: The iPACOSE algorithm for graph estimation
  > ### Aliases: ipacose
  > ### Keywords: algebra multivariate
  >
  > ### ** Examples
  >
  > require(mvtnorm)
  > require(igraph0)
  >
  > omega <- matrix(c(1 , -0.477, 0.304, 0.478, -0.591, 0 ,
  + -0.477, 2 , 0.206, 0 , 0.382 , 0 ,
  + 0.304 , 0.206 , 1 , 0 , 0.181 , 0.242,
  + 0.478 , 0 , 0 , 3 , 0.141 , 0 ,
  + -0.591, 0.382 , 0.181, 0.141, 1 , 0 ,
  + 0 , 0 , 0.242, 0 , 0 , 2 ),
  + nrow = 6, ncol = 6)
  > gr <- graph.adjacency((omega!=0),mode="undirected",diag=FALSE)
  > x <- rmvnorm(n=100,sigma=solve(omega))
  >
  > # First estimation with ridge.net, the threshold is, for this toy example,
  > # arbitrarily set to 0.05
  > pcor0.0 <- ridge.net(x)$pcor
  > pcor0 <- (abs(pcor0.0) > 0.05)+0
  >
  > # Use iPACOSE to estimate iteratively the partial correlation matrix
  > pcor1 <- ipacose(x=x,pc=pcor0,method="pacose.ridge",
  + cutoff=0.05,gr=NULL,cv.method="HKB")
  Error in graph[[9]][[3]] : subscript out of bounds
  Calls: ipacose ... get.adjacency.dense -> %in% -> match -> list.vertex.attributes
  Execution halted