• using R Under development (unstable) (2013-04-22 r62639)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘RSofia/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘RSofia’ version ‘1.1’
• 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 executable files ... OK
• checking for hidden files and directories ... NOTE
  Found the following hidden files and directories:
  .gitignore
  These were most likely included in error. See section ‘Package
  structure’ in the ‘Writing R Extensions’ manual.
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘RSofia’ can be installed ... [20s/15s] OK
• checking installed package size ... NOTE
  installed size is 5.1Mb
  sub-directories of 1Mb or more:
  libs 2.2Mb
  sofia-ml-read-only 2.7Mb
• 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
• 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 ‘RSofia/R/zzz.R’:
  .onLoad has wrong argument list ‘pkgname, libname’
  .onLoad calls:
  require("methods", character = TRUE, quietly = TRUE)
  
  Package startup functions should have two arguments with names starting
  with ‘lib’ and ‘pkg’, respectively.
  Package startup functions should not change the search path.
  See section ‘Good practice’ in '?.onAttach'.
  
  .onLoad: warning in require("methods", character = TRUE, quietly =
  TRUE): partial argument match of 'character' to 'character.only'
• checking Rd files ... NOTE
  prepare_Rd: parse_formula.Rd:23-26: Dropping empty section \seealso
  prepare_Rd: sofia.Rd:80: Dropping empty section \details
• 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 ... OK
• checking examples ... OK
• checking PDF version of manual ... OK
  NOTE: There were 4 notes.
  See
  ‘/data/blackswan/ripley/R/packages/tests-devel/RSofia.Rcheck/00check.log’
  for details.