R Development Page

qfaBayes log file (check_x86_64_linux)

Wed Jan  6 17:25:51 2016: Checking package qfaBayes (SVN revision 675) ...
* using log directory ‘/mnt/building/build_2016-01-06-17-24/RF_PKG_CHECK/PKGS/qfaBayes.Rcheck’
* using R version 3.2.3 Patched (2016-01-05 r69875)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘qfaBayes/DESCRIPTION’ ... OK
* this is package ‘qfaBayes’ version ‘0.0-1’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Conor Lawless ’
New submission

The Title field should be in title case, current version then in title case:
‘Tools for modelling the growth dynamics of arrays of large numbers of colonies and performing quantitative fitness analysis (QFA).’
‘Tools for Modelling the Growth Dynamics of Arrays of Large Numbers of Colonies and Performing Quantitative Fitness Analysis (QFA).’

The Date field is over a month old.
* 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 ‘qfaBayes’ can be installed ... [4s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* 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 use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SHM_makeQFAfits: no visible binding for global variable ‘Group.1’
SHM_makeQFAfits: no visible binding for global variable
  ‘numericalfitness’
SHM_makeQFAfits: no visible global function definition for
  ‘makeFitness’
SHM_makeQFAfits: no visible binding for global variable ‘x’
SHM_makeQFAfits: no visible global function definition for ‘dtl’
plot_SHM_simple: no visible global function definition for ‘dtl’
visual_convergence_simple_check: no visible global function definition
  for ‘heidel.diag’
visual_convergence_simple_check: no visible global function definition
  for ‘effectiveSize’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘SHM_makeQFAfits’ ‘SHM_preprocess’ ‘visual_convergence_simple_check’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'SHM_postpro' but not in code:
  SHM_postpro

Codoc mismatches from documentation object 'plot_SHM_simple':
plot_SHM_simple
  Code: function(SHM_output, SHM, outfile = NULL)
  Docs: function(SHM_output, SHM)
  Argument names in code not in docs:
    outfile

* checking Rd \usage sections ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking PDF version of manual ... OK
* checking for code which exercises the package ... WARNING
No examples, no tests, no vignettes
* DONE

Status: 3 WARNINGs, 5 NOTEs
See
  ‘/mnt/building/build_2016-01-06-17-24/RF_PKG_CHECK/PKGS/qfaBayes.Rcheck/00check.log’
for details.


Run time: 30.6 seconds.