• using R Under development (unstable) (2012-05-22 r59405)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘eco/DESCRIPTION’ ... OK
• this is package ‘eco’ version ‘3.1-5’
• 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 whether package ‘eco’ can be installed ... [7s/13s] 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 ... NOTE
  File ‘eco/R/onAttach.R’:
  .onAttach calls:
  cat(paste(pkg, ": ", title, "\nVersion: ", ver, "\n", sep = ""))
  
  Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
  See section ‘Good practice’ in ?.onAttach.
  
  .onAttach: warning in packageDescription(pkg, lib = mylib): partial
  argument match of 'lib' to 'lib.loc'
• 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 ‘/data/gannet/tmp/ripley/R/packages/tests-devel/eco.Rcheck/eco/libs/eco.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
  Objects: ‘gibbsEM.o’, ‘gibbsZBase.o’, ‘subroutines.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 ... [46s/67s] WARNING
  Found the following significant warnings:
  
  Warning: sd(<matrix>) is deprecated.
  Warning: sd(<matrix>) is deprecated.
  Warning: sd(<matrix>) is deprecated.
  Warning: sd(<matrix>) is deprecated.
  Warning: sd(<matrix>) is deprecated.
  Warning: sd(<matrix>) is deprecated.
  Warning: sd(<matrix>) is deprecated.
  Warning: sd(<matrix>) is deprecated.
  Warning: sd(<matrix>) is deprecated.
  Warning: sd(<matrix>) is deprecated.
  Warning: sd(<matrix>) is deprecated.
  Warning: sd(<matrix>) is deprecated.
  Deprecated functions may be defunct as soon as of the next release of
  R.
  See ?Deprecated.
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There were 2 notes.
  See
  ‘/data/gannet/tmp/ripley/R/packages/tests-devel/eco.Rcheck/00check.log’
  for details.