• using R version 2.14.1 Patched (2012-02-04 r58267)
• 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 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 ‘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 : 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 : 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_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
• 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 ... NOTE
  File ‘/home/hornik/tmp/R.check/r-patched/Work/build/Packages/rgenoud/libs/rgenoud.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘printf’, possibly from ‘printf’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
  
  Compiled code should not call functions which might terminate R nor
  write to stdout/stderr instead of to the console. The detected symbols
  are linked into the code but might come from libraries and not actually
  be called.
  
  See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking examples ... OK
• checking for unstated dependencies in tests ... OK
• checking tests ... OK
  Running ‘tests.R’
  Comparing ‘tests.Rout’ to ‘tests.Rout.save’ ...11c11
  < Mon Feb 6 04:40:12 2012
  ---
  > Wed May 4 00:50:43 2011
  169c169
  < Mon Feb 6 04:40:13 2012
  ---
  > Wed May 4 00:50:44 2011
  198c198
  < Mon Feb 6 04:40:13 2012
  ---
  > Wed May 4 00:50:44 2011
  356,357c356,357
  < Mon Feb 6 04:40:14 2012
  < Total run time : 0 hours 0 minutes and 1 seconds
  ---
  > Wed May 4 00:50:46 2011
  > Total run time : 0 hours 0 minutes and 2 seconds
  392c392
  < Mon Feb 6 04:40:14 2012
  ---
  > Wed May 4 00:50:46 2011
  550c550
  < Mon Feb 6 04:40:16 2012
  ---
  > Wed May 4 00:50:48 2011
  600c600
  < Mon Feb 6 04:40:16 2012
  ---
  > Wed May 4 00:50:48 2011
  822c822
  < Mon Feb 6 04:40:24 2012
  ---
  > Wed May 4 00:50:56 2011
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... OK
• checking re-building of vignette PDFs ... OK
• checking PDF version of manual ... OK