• using R Under development (unstable) (2012-05-22 r59404)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘accuracy/DESCRIPTION’ ... OK
• this is package ‘accuracy’ version ‘1.35’
• 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 ‘accuracy’ can be installed ... OK
• checking installed package size ... NOTE
  installed size is 6.2Mb
  sub-directories of 1Mb or more:
  data 5.5Mb
• 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 ... WARNING
  Error : .onLoad failed in loadNamespace() for ‘accuracy’, details:
  call: citation("accuracy")
  error: package ‘accuracy’ not found
  Error: package/namespace load failed for ‘accuracy’
  Execution halted
  
  It looks like this package has a loading problem when not on .libPaths:
  see the messages for details.
• 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
  Found the following possibly unsafe calls:
  File 'R/pzelig.R':
  found unlockBinding("sim", as.environment("package:Zelig"))
  found assignInNamespace("sim", sim.replacement, "Zelig")
  forceDispatch: warning in getMethod(f = f, sig = cl): partial argument
  match of 'sig' to 'signature'
  getPool: possible error in get(".EntropyPool", where = 1): unused
  argument(s) (where = 1)
  setPool: possible error in assign(".EntropyPool", pool, where = 1):
  unused argument(s) (where = 1)
  starr: possible error in dist(betas, metric = dmethod): unused
  argument(s) (metric = dmethod)
• 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 ... WARNING
  ‘library’ or ‘require’ calls not declared from:
  ‘MASS’ ‘nlme’ ‘nlme3’
  ‘data(package=)’ call not declared from: ‘MASS’
• 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 line endings in Makefiles ... OK
• checking for portable compilation flags in Makevars ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... NOTE
  The following files look like leftovers/mistakes:
  ‘accuracy_vignette.aux’, ‘accuracy_vignette.bbl’,
  ‘accuracy_vignette.blg’, ‘accuracy_vignette.log’
  Please remove them from your package.
  The following files should probably not be installed:
  ‘Makefile’, ‘accuracy_vignette.tex’
  
  Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
  or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
• checking examples ... [12s/20s] WARNING
  Found the following significant warnings:
  
  Warning: mean(<data.frame>) is deprecated.
  Warning: mean(<data.frame>) is deprecated.
  Warning: mean(<data.frame>) is deprecated.
  Warning: mean(<data.frame>) is deprecated.
  Warning: mean(<data.frame>) is deprecated.
  Warning: mean(<data.frame>) is deprecated.
  Warning: mean(<data.frame>) is deprecated.
  Warning: mean(<data.frame>) is deprecated.
  Warning: mean(<data.frame>) is deprecated.
  Deprecated functions may be defunct as soon as of the next release of
  R.
  See ?Deprecated.
• checking for unstated dependencies in vignettes ... NOTE
  ‘library’ or ‘require’ calls not declared from:
  ‘MASS’ ‘NISTnls’
  ‘data(package=)’ calls not declared from:
  ‘MASS’ ‘NISTnls’
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [51s/70s] OK
• checking re-building of vignette PDFs ... [56s/80s] OK
• checking PDF version of manual ... OK
  WARNING: There were 3 warnings.
  NOTE: There were 4 notes.
  See
  ‘/data/gannet/tmp/ripley/R/packages/tests-devel/accuracy.Rcheck/00check.log’
  for details.