• using R Under development (unstable) (2012-05-19 r59366)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘rgenoud/DESCRIPTION’ ... OK
• this is package ‘rgenoud’ version ‘5.7-3’
• 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 ‘rgenoud’ 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 ... WARNING
  File ‘rgenoud/R/zzz.R’:
  .onAttach calls:
  cat(paste("## rgenoud (Version ", version, ", Build Date: ", BuildDate, ")\n", sep = ""))
  cat("## See http://sekhon.berkeley.edu/rgenoud for additional documentation.\n")
  
  Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
  See section ‘Good practice’ in ?.onAttach.
  
  .onAttach: warning in packageDescription("rgenoud", lib = rgenoudLib):
  partial argument match of 'lib' to 'lib.loc'
  genoud : gr: warning in assign("x", par, env = genoud.wrapper101.env):
  partial argument match of 'env' to 'envir'
  genoud : gr: warning in assign("helper", helper, env =
  genoud.wrapper101.env): partial argument match of 'env' to 'envir'
  genoud : gr: warning in assign("FiniteBadFitValue", FiniteBadFitValue,
  env = genoud.wrapper101.env): partial argument match of 'env' to
  'envir'
  genoud_transform : gr: warning in assign("x", par, env =
  genoud.wrapper101.env): partial argument match of 'env' to 'envir'
  genoud_transform : gr: warning in assign("helper", helper, env =
  genoud.wrapper101.env): partial argument match of 'env' to 'envir'
  genoud_transform : gr: warning in assign("FiniteBadFitValue",
  FiniteBadFitValue, env = genoud.wrapper101.env): partial argument
  match of 'env' to 'envir'
  genoud : fnLexicalSort: no visible binding for global variable ‘indx’
  genoud: multiple local function definitions for ‘fn1.bfgs’ with
  different formal arguments
  genoud: multiple local function definitions for ‘gr1’ with different
  formal arguments
  genoud: multiple local function definitions for ‘hess.fn’ with
  different formal arguments
  genoud_transform : fnLexicalSort: no visible binding for global
  variable ‘indx’
  genoud_transform: multiple local function definitions for ‘fn1.bfgs’
  with different formal arguments
  genoud_transform: multiple local function definitions for ‘gr1’ with
  different formal arguments
  Found .Internal calls in the following functions:
  ‘genoud’ ‘genoud_transform’
  with calls to .Internal functions
  ‘optimhess’
  
  Packages should not call .Internal(): it is not part of the API, for
  use only by R itself and subject to change without notice.
• 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 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 ‘/home/hornik/tmp/R.check/r-devel/Work/build/Packages/rgenoud/libs/rgenoud.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Object: ‘evaluate.o’
  Found ‘printf’, possibly from ‘printf’ (C)
  Object: ‘gradient.o’
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Object: ‘gradient.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Object: ‘gradient.o’
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Objects: ‘evaluate.o’, ‘genoud.o’, ‘math.o’, ‘operators.o’,
  ‘print_format.o’
  Found ‘stdout’, possibly from ‘stdout’ (C)
  Objects: ‘evaluate.o’, ‘genoud.o’, ‘gradient.o’, ‘math.o’,
  ‘operators.o’, ‘print_format.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 sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... NOTE
  The following directories should probably not be installed:
  ‘Figures’
  
  Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
  or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
• checking examples ... [14s/14s] OK
• checking for unstated dependencies in tests ... OK
• checking tests ... [14s/14s] OK
  Running ‘tests.R’ [14s/14s]
  Comparing ‘tests.Rout’ to ‘tests.Rout.save’ ...11c11
  < Mon May 21 17:41:52 2012
  ---
  > Wed May 4 00:50:43 2011
  169c169
  < Mon May 21 17:41:53 2012
  ---
  > Wed May 4 00:50:44 2011
  198c198
  < Mon May 21 17:41:53 2012
  ---
  > Wed May 4 00:50:44 2011
  356c356
  < Mon May 21 17:41:55 2012
  ---
  > Wed May 4 00:50:46 2011
  392c392
  < Mon May 21 17:41:55 2012
  ---
  > Wed May 4 00:50:46 2011
  550c550
  < Mon May 21 17:41:57 2012
  ---
  > Wed May 4 00:50:48 2011
  600c600
  < Mon May 21 17:41:57 2012
  ---
  > Wed May 4 00:50:48 2011
  822,823c822,823
  < Mon May 21 17:42:06 2012
  < Total run time : 0 hours 0 minutes and 9 seconds
  ---
  > Wed May 4 00:50:56 2011
  > Total run time : 0 hours 0 minutes and 8 seconds
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [2s/2s] OK
• checking re-building of vignette PDFs ... [5s/6s] OK
• checking PDF version of manual ... OK
  WARNING: There were 2 warnings.
  NOTE: There was 1 note.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/rgenoud.Rcheck/00check.log’
  for details.