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fMarkovSwitching log file (check_x86_64_linux)

Tue Nov 11 14:47:18 2014: Checking package fMarkovSwitching (SVN revision 5975) ...
* using log directory ‘/mnt/building/build_2014-11-11-14-43/RF_PKG_CHECK/PKGS/fMarkovSwitching.Rcheck’
* using R version 3.1.2 Patched (2014-11-09 r66951)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘fMarkovSwitching/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fMarkovSwitching’ version ‘1.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Marcelo Perlin ’
New submission
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* 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 for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘fMarkovSwitching’ can be installed ... [1s/1s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard files/directories found at top level:
  ‘About_the_MS_Regression_Models_R.pdf’ ‘AdvScripts’
* checking for left-over 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Rdonlp2’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... WARNING
print:
  function(x, ...)
print.MS_Model:
  function(MS_Model_In)

print:
  function(x, ...)
print.MS_Simul:
  function(MS_Simul_In)

plot:
  function(x, ...)
plot.MS_Model:
  function(MS_Model_In)

plot:
  function(x, ...)
plot.MS_Simul:
  function(MS_Simul_In)

dim:
  function(x)
dim.MS_Model:
  function(MS_Model_In)

See section ‘Generic functions and methods’ of the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
MS_Regress_Fit: no visible global function definition for
  ‘donlp2Control’
MS_Regress_Fit: no visible global function definition for ‘donlp2’
MS_Regress_Simul: no visible binding for global variable ‘S’

Found the following assignments to the global environment:
File ‘fMarkovSwitching/R/MS_Regress_Fit.r’:
  assign("dep", dep, envir = .GlobalEnv)
  assign("indep_S", indep_S, envir = .GlobalEnv)
  assign("indep_nS", indep_nS, envir = .GlobalEnv)
  assign("k", k, envir = .GlobalEnv)
  assign("S", S, envir = .GlobalEnv)
  assign("distIn", distIn, envir = .GlobalEnv)
  assign("typeCall", typeCall, envir = .GlobalEnv)
  assign("typeCall", typeCall, envir = .GlobalEnv)
* checking Rd files ... WARNING
MS_Model-class.Rd: non-ASCII input and no declared encoding
MS_Regress_Fit.Rd: non-ASCII input and no declared encoding
MS_Regress_For.Rd: non-ASCII input and no declared encoding
MS_Regress_Lik.Rd: non-ASCII input and no declared encoding
MS_Regress_Simul.Rd: non-ASCII input and no declared encoding
plot.MS_Model.Rd: non-ASCII input and no declared encoding
problems found in ‘MS_Model-class.Rd’, ‘MS_Regress_Fit.Rd’, ‘MS_Regress_For.Rd’, ‘MS_Regress_Lik.Rd’, ‘MS_Regress_Simul.Rd’, ‘plot.MS_Model.Rd’
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'plot.MS_Model' but not in code:
  plot

Functions or methods with usage in documentation object 'plot.MS_Simul' but not in code:
  plot

Functions or methods with usage in documentation object 'print.MS_Model' but not in code:
  print

Codoc mismatches from documentation object 'MS_Regress_Lik':
MS_Regress_Lik
  Code: function(param, dep, indep_S, indep_nS, k, S, distIn, typeCall)
  Docs: function(param)
  Argument names in code not in docs:
    dep indep_S indep_nS k S distIn typeCall

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'plot.MS_Model':
  ‘plot’

Objects in \usage without \alias in documentation object 'plot.MS_Simul':
  ‘plot’

Objects in \usage without \alias in documentation object 'print.MS_Model':
  ‘print’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object 'dim.MS_Model':
  ‘dim.MS_Model’

S3 methods shown with full name in documentation object 'print.MS_Simul':
  ‘print.MS_Simul’

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 examples ... [56s/57s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
MS_Regress_Fit 28.981  0.044  29.556
MS_Regress_For 26.146  0.032  26.521
* checking PDF version of manual ... OK
* DONE

WARNING: There were 4 warnings.
NOTE: There were 5 notes.
See
  ‘/mnt/building/build_2014-11-11-14-43/RF_PKG_CHECK/PKGS/fMarkovSwitching.Rcheck/00check.log’
for details.

Run time: 136.21 seconds.