- using R Under development (unstable) (2013-05-20 r62767)
- using platform: x86_64-w64-mingw32 (64-bit)
- using session charset: ISO8859-1
- checking for file 'NetworkAnalysis/DESCRIPTION' ... OK
- this is package 'NetworkAnalysis' version '0.3-1'
- 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 hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'NetworkAnalysis' can be installed ... OK
- checking installed package size ... OK
- checking package directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over 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 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
- 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 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 contents of 'data' directory ... OK
- checking data for non-ASCII characters ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking for portable compilation flags in Makevars ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking compiled code ... NOTE
File 'd:/Rcompile/CRANpkg/lib/3.1/NetworkAnalysis/libs/i386/NetworkAnalysis.dll':
Found '_ZSt4cout', possibly from 'std::cout' (C++)
Object: 'class.o'
File 'd:/Rcompile/CRANpkg/lib/3.1/NetworkAnalysis/libs/x64/NetworkAnalysis.dll':
Found '_ZSt4cout', possibly from 'std::cout' (C++)
Object: 'class.o'
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
- checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... ERROR
Running examples in 'NetworkAnalysis-Ex.R' failed
The error most likely occurred in:
> ### Name: cost.int.metric
> ### Title: Integration of topological metrics for weighted networks.
> ### Aliases: cost.int.metric
> ### Keywords: Cost-integration metric.standardization
>
> ### ** Examples
>
>
> ## Generate a simple weighted graph (subtended by a covariance matrix)
> R <- cov(cbind(rnorm(100),rnorm(100),rnorm(100),rnorm(100),rnorm(100),rnorm(100)))
> print(R); naHeatmap(R)
[,1] [,2] [,3] [,4] [,5]
[1,] 0.8067620897 -0.0008554794 0.01707662 -0.04492540 0.15448389
[2,] -0.0008554794 0.9175323120 -0.04907559 -0.05549579 0.15145986
[3,] 0.0170766216 -0.0490755899 1.06970513 0.11362245 0.03592587
[4,] -0.0449253990 -0.0554957862 0.11362245 0.98341958 0.02770932
[5,] 0.1544838914 0.1514598619 0.03592587 0.02770932 1.36799276
[6,] -0.0954145791 -0.0186560504 -0.04183299 -0.09293719 -0.10252953
[,6]
[1,] -0.09541458
[2,] -0.01865605
[3,] -0.04183299
[4,] -0.09293719
[5,] -0.10252953
[6,] 0.93350463
>
> ## IMPORTANT: One should standardize the metric before proceeding to integration!
> R <- metric.standardization(R)
> naHeatmap(R)
>
> ## Compute the cost-integrated global (ge) and local efficiencies (le) of R.
> print(cost.int.metric(R,metric="ge"))
[1] 0.60933333 0.03344674
> print(cost.int.metric(R,metric="le"))
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Warning in subgraph(G, neighbors(G, v)) :
At structural_properties.c:1847 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead
Error in print(cost.int.metric(R, metric = "le")) :
error in evaluating the argument 'x' in selecting a method for function 'print': Error in neighbors(G, v) :
At type_indexededgelist.c:748 : cannot get neighbors, Invalid vertex id
Calls: cost.int.metric ... le.ind -> subgraph -> as.igraph.vs -> neighbors -> .Call
Execution halted