• using R version 2.15.0 Patched (2012-03-31 r58888)
• using platform: sparc-sun-solaris2.10 (32-bit)
• using session charset: UTF-8
• checking for file ‘NeMo/DESCRIPTION’ ... OK
• this is package ‘NeMo’ version ‘1.0.1’
• package encoding: UTF-8
• 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 .dll and .exe files ... OK
• checking whether package ‘NeMo’ 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 ... 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 ‘/home/ripley/R/Lib32/NeMo/libs/NeMo.so’:
  Found ‘__1cDstdEcerr_’, possibly from ‘std::cerr’ (C++)
  Objects: ‘graphical-models.o’, ‘motif-search.o’,
  ‘nr-permutation.o’, ‘util.o’
  Found ‘__1cDstdEcout_’, possibly from ‘std::cout’ (C++)
  Objects: ‘heap.o’, ‘motif-search.o’, ‘motif-tree.o’, ‘util.o’
  
  Compiled code should not call functions 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 ... ERROR
  Running examples in ‘NeMo-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: countMotif
  > ### Title: Count motifs or subgraphs in a network.
  > ### Aliases: countMotif
  > ### Keywords: models
  >
  > ### ** Examples
  >
  >
  > #
  > # Count all 3-vertices subgraph from an adjacency matrix
  > #
  >
  > # Define a "small" network.
  > network <- matrix( c( 0, 1, 1, 1, 0, 1, 1, 1, 0), 3, 3)
  >
  > # Count all 3-vertices subgraph
  > counts <- countMotif( network, 3 )
  >
  >
  > #
  > # From a file
  > #
  >
  > # Build absolute path of one network example file
  > file.name <- system.file("networks", "Hpylo.txt", package="NeMo")
  >
  > # Count all 4-vertices subgraph
  > counts <- countMotif( file.name, 4 )
  Can't open motif DB file : /tmp/RtmpIoTcwC/RLIBS_490a778db92/NeMo/networks/motif-u-4.db
  Error in res[[nb.motifs + m]] : subscript out of bounds
  Calls: countMotif -> count.motifs
  Execution halted