• using R Under development (unstable) (2012-08-11 r60235)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘MSToolkit/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘MSToolkit’ version ‘2.0’
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Package suggested but not available for checking: ‘Rlsf’
• 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 ‘MSToolkit’ 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 ... NOTE
  Foreign function call(s) with ‘PACKAGE’ argument in different package:
  .Call("lsf_job_submit", ..., PACKAGE = "Rlsf")
  See the chapter ‘System and foreign language interfaces’ of the
  ‘Writing R Extensions’ manual.
• checking R code for possible problems ... WARNING
  File ‘MSToolkit/R/zzz.R’:
  .onAttach calls:
  cat(copyright, sep = "\n")
  cat("#########################################################\n")
  cat("# Unit tests #\n")
  cat("# > mstoolkitUnitTests( ) #\n")
  cat("##########################################################\n")
  cat("################################################################################\n")
  cat("# You are running the package from a grid node. To take advantage of it, use #\n")
  cat("# the grid argument in ?analyzeData #\n")
  cat("################################################################################\n")
  
  Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
  See section ‘Good practice’ in ?.onAttach.
  
  .checkReplicates: warning in dir("ReplicateData", pattern =
  "[0-9]{4}\\.csv$", full = TRUE): partial argument match of 'full' to
  'full.names'
  .onAttach: warning in .packages(all = TRUE): partial argument match of
  'all' to 'all.available'
  analyzeRep: warning in performAnalysis(analysisCode, seed = seed, data
  = idata, software = software, subset = intSubset, dataChanges =
  dataChanges, doses = doses, infile = infile): partial argument match
  of 'subset' to 'subset.'
  checkSymmetricPDMatrix: warning in eigen(mat, sym = TRUE, EISPACK =
  TRUE, only.values = TRUE): partial argument match of 'sym' to
  'symmetric'
  ectdDateFormat: warning in get("dateFormat", env = .ectdEnv): partial
  argument match of 'env' to 'envir'
  ectdDateFormat: warning in assign("dateFormat", format, env =
  .ectdEnv): partial argument match of 'env' to 'envir'
  ectdLogFile: warning in get("logfile", env = .ectdEnv): partial
  argument match of 'env' to 'envir'
  ectdLogFile: warning in assign("logfile", file, env = .ectdEnv):
  partial argument match of 'env' to 'envir'
  ectdVerbose: warning in get("verbose", env = .ectdEnv): partial
  argument match of 'env' to 'envir'
  ectdVerbose: warning in assign("verbose", verbose, env = .ectdEnv):
  partial argument match of 'env' to 'envir'
  .ectdSubmit: no visible global function definition for ‘Sys.putenv’
  analyzeData: no visible binding for global variable ‘lsf.job.status’
  createContinuousCovariates: no visible binding for global variable
  ‘nSubjects’
  createDiscreteCovariates: no visible binding for global variable
  ‘nSubjects’
  createExternalCovariates: no visible binding for global variable
  ‘nSubjects’
  createExternalParameters: no visible binding for global variable
  ‘nSubjects’
  createInterims: no visible binding for global variable ‘nSubjects’
  createNormalParameters: no visible binding for global variable
  ‘nSubjects’
  createResponse: no visible global function definition for ‘ectdstop’
  mstoolkitUnitTests: no visible binding for global variable
  ‘unitTestPath’
  mstoolkitUnitTests: no visible binding for global variable
  ‘systemTestPath’
  validNames : <anonymous>: no visible binding for global variable ‘..nm’
  Found .Internal calls in the following functions:
  ‘ectdStop’ ‘ectdWarning’
  with calls to .Internal functions
  ‘.dfltWarn’ ‘.signalCondition’ ‘stop’ ‘warning’
  
  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 examples ... [1s/1s] OK
• checking for unstated dependencies in tests ... OK
• checking tests ... [6s/6s] OK
  Running ‘doRUnit.R’ [6s/6s]
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There were 2 notes.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/MSToolkit.Rcheck/00check.log’
  for details.