• 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 ‘PMA/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘PMA’ version ‘1.0.8’
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking whether package ‘PMA’ can be installed ... OK
• checking installed package size ... NOTE
  installed size is 8.1Mb
  sub-directories of 1Mb or more:
  data 6.3Mb
  libs 1.6Mb
• 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
  cor.xl.ImputeData: no visible global function definition for
  ‘impute.knn’
• 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 ... NOTE
  S3 methods shown with full name in documentation object 'PMA-internal':
  ‘plot.multiccaperm’ ‘print.multicca’ ‘print.multiccaperm’
  ‘plot.spccv’ ‘print.spccv’ ‘print.spc’ ‘plot.ccaperm’ ‘print.pmdl1l1’
  ‘print.pmdl1l1cv’ ‘plot.pmdl1l1cv’ ‘plot.pmdl1flcv’ ‘print.pmdl1fl’
  ‘print.pmdl1flcv’ ‘print.cca’ ‘print.ccaperm’
  
  The \usage entries for S3 methods should use the \method markup and not
  their full name.
  See the chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.
• 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 ... WARNING
  File ‘/data/blackswan/ripley/R/packages/tests-devel/PMA.Rcheck/PMA/libs/PMA.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Objects: ‘FLSAGeneral.o’, ‘MaxFlowGraph.o’
  Found ‘exit’, possibly from ‘exit’ (C)
  Object: ‘MaxFlowGraph.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 ... [32s/32s] OK
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There were 3 notes.
  See
  ‘/data/blackswan/ripley/R/packages/tests-devel/PMA.Rcheck/00check.log’
  for details.