• using R Under development (unstable) (2012-08-14 r60253)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘SpectralGEM/DESCRIPTION’ ... OK
• this is package ‘SpectralGEM’ version ‘1.0’
• 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:
  .Rbuildindex.30091
  These were most likely included in error. See section ‘Package
  structure’ in the ‘Writing R Extensions’ manual.
• checking whether package ‘SpectralGEM’ 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 ... NOTE
  File ‘SpectralGEM/R/firstlib.R’:
  .First.lib calls:
  cat("SpectralGEM 0.1-1 loaded\n")
  
  Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
  See section ‘Good practice’ in ?.onAttach.
  
  full_matching: warning in read.table(paste("distance_", ext, ".matrix",
  sep = ""), nrows = 1, colClass = "character", header = F): partial
  argument match of 'colClass' to 'colClasses'
  MMfile: no visible binding for global variable ‘id.info’
  MMfile: no visible global function definition for ‘retur’
• checking Rd files ... NOTE
  prepare_Rd: H.Rd:16-18: Dropping empty section \details
  prepare_Rd: InFile.Rd:49-50: Dropping empty section \examples
  prepare_Rd: MMfile.Rd:45-47: Dropping empty section \examples
  prepare_Rd: SpectralGEM.Rd:21-23: Dropping empty section \details
  prepare_Rd: getExcludeFile.Rd:15-17: Dropping empty section \details
  prepare_Rd: getExcludeFile.Rd:18-24: Dropping empty section \value
  prepare_Rd: getRecord.Rd:15-17: Dropping empty section \details
  prepare_Rd: id.info.Rd:18-20: Dropping empty section \details
  prepare_Rd: id.info.Rd:21-24: Dropping empty section \source
  prepare_Rd: plotLam.Rd:19-20: Dropping empty section \value
  prepare_Rd: plotLam.Rd:26: Dropping empty section \seealso
  prepare_Rd: plotLam.Rd:27-28: Dropping empty section \examples
  prepare_Rd: updateExcludeFileDstr.Rd:17-19: Dropping empty section \details
  prepare_Rd: updateInputFile.Rd:17-19: Dropping empty section \details
  prepare_Rd: updateInputFile.Rd:20-26: Dropping empty section \value
• 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... NOTE
  File ‘/data/blackswan/ripley/R/packages/tests-devel/SpectralGEM.Rcheck/SpectralGEM/libs/SpectralGEM.so’:
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
  (Fortran)
  Objects: ‘GEM_sub.o’, ‘SpectralGEM_v2.2.o’
  Found ‘_gfortran_stop_string’, possibly from ‘stop’ (Fortran)
  Object: ‘GEM_sub.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 ... OK
• checking PDF version of manual ... OK
  NOTE: There were 4 notes.
  See
  ‘/data/blackswan/ripley/R/packages/tests-devel/SpectralGEM.Rcheck/00check.log’
  for details.