• using R Under development (unstable) (2012-02-23 r58468)
• using platform: i686-pc-linux-gnu (32-bit)
• using session charset: UTF-8
• checking for file ‘tmle/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘tmle’ version ‘1.1.1’
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Package suggested but not available for checking: ‘DSA’
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking whether package ‘tmle’ 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 ‘tmle/R/zzz.R’:
  .onAttach calls:
  cat("Welcome to the tmle package, version 1.1\n")
  cat("This package is provided for academic use only.\n")
  cat("\nData-adaptive prediction algorithms are required to obtain reliable results.\nSuperLearner and DSA packages are strongly recommended.\n")
  cat("\nSuperLearner is available at http://www.stat.berkeley.edu/users/ecpolley/SL/\n")
  cat("DSA: http://www.stat.berkeley.edu/users/laan/Software/\n")
  cat("These packages depend on\n \tmodelUtils: http://www.stat.berkeley.edu/users/laan/Software/\n \tnnls: http://cran.r-project.org/web/packages/nnls/index.html\n \tquadprog: http://cran.r-project.org/web/packages/quadprog/index.html\n")
  cat("\nNew in version 1.1:\n")
  cat("\t Population mean parameter calculated when there is missing data, no variability in treatment assignment\n")
  cat("\t Poisson regression available for count data with user-supplied regression formula\n")
  cat("\t Binary mediating variable allowed\n")
  cat("\t Bug in missingness mechanism fixed\n")
  cat("\t Some arguments and return values have been modified. See help files for details\n")
  
  Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
  See section ‘Good practice’ in ?.onAttach.
  
  .estQcvSL: possible error in SuperLearner(Y = Y[train.observed], X =
  X[train.observed, ], newX = newX[fold_rows, ], V = V_SL,
  save.fit.library = FALSE, family = family, SL.library = SL.library,
  id = id[train.observed]): unused argument(s) (V = V_SL,
  save.fit.library = FALSE)
  estimateG: possible error in SuperLearner(Y = d[, 1], X = d[, -1], newX
  = newdata[, -1], family = "binomial", SL.library = SL.library, V = 5,
  id = id): unused argument(s) (V = 5)
  estimateQ: possible error in SuperLearner(Y[Delta == 1], X[Delta == 1,
  ], newX = newX, SL.library = SL.library, V = 5, family = family,
  save.fit.library = FALSE, id = id[Delta == 1]): unused argument(s) (V
  = 5, save.fit.library = FALSE)
• 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 'summary.tmle':
  ‘summary.tmle’ ‘summary.tmle.list’ ‘print.tmle’ ‘print.tmle.list’
  ‘print.summary.tmle’ ‘print.summary.tmle.list’
  
  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 examples ... [1s/1s] OK
• checking PDF version of manual ... OK
  NOTE: There were 3 notes.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/tmle.Rcheck/00check.log’
  for details.