• 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 ‘BradleyTerry2/DESCRIPTION’ ... OK
• this is package ‘BradleyTerry2’ version ‘0.9-6’
• 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 ‘BradleyTerry2’ 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 ... OK
• 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 contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... NOTE
  The following files should probably not be installed:
  ‘mymacros.tex’
  
  Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
  or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
• checking examples ... [11s/11s] OK
• checking for unstated dependencies in tests ... OK
• checking tests ... [18s/19s] OK
  Running ‘add1.R’ [4s/4s]
  Comparing ‘add1.Rout’ to ‘add1.Rout.save’ ... OK
  Running ‘baseball.R’ [3s/3s]
  Comparing ‘baseball.Rout’ to ‘baseball.Rout.save’ ... OK
  Running ‘countsToBinomial.R’ [0s/0s]
  Comparing ‘countsToBinomial.Rout’ to ‘countsToBinomial.Rout.save’ ... OK
  Running ‘flatlizards.R’ [4s/4s]
  Comparing ‘flatlizards.Rout’ to ‘flatlizards.Rout.save’ ...102c102
  < Penalized deviance: 147.538
  ---
  > Penalized deviance: 147.5380
  129c129
  < 0.00013 0.44548 0.79609 1.17652 1.95884
  ---
  > 0.0001311 0.4454835 0.7960895 1.1765166 1.9588354
  166c166
  < 0.00001 0.44548 0.79609 1.17652 1.95884
  ---
  > 6.528e-06 4.455e-01 7.961e-01 1.177e+00 1.959e+00
  202c202
  < Iteration 4. Score = 0.007671321
  ---
  > Iteration 4. Score = 0.00767132
  217c217
  < ..lizard096 3.668e+01 3.875e+07 0.000 1.0000
  ---
  > ..lizard096 3.668e+01 3.875e+07 9.47e-07 1.0000
  268,273c268,273
  < ..lizard096 2.046e+01 3.875e+07 0.000 1.00000
  < ..lizard099 5.977e-01 7.378e-01 0.810 0.41784
  < throat.PC1[..] -5.362e-02 2.321e-02 -2.310 0.02089 *
  < throat.PC3[..] 2.276e-01 8.621e-02 2.640 0.00829 **
  < head.length[..] -8.434e-01 4.206e-01 -2.005 0.04494 *
  < SVL[..] 1.054e-01 7.764e-02 1.358 0.17457
  ---
  > ..lizard096 2.046e+01 3.875e+07 5.28e-07 1.0000
  > ..lizard099 5.977e-01 7.378e-01 0.810 0.4178
  > throat.PC1[..] -5.362e-02 2.321e-02 -2.310 0.0209 *
  > throat.PC3[..] 2.276e-01 8.621e-02 2.640 0.0083 **
  > head.length[..] -8.434e-01 4.206e-01 -2.005 0.0449 *
  > SVL[..] 1.054e-01 7.764e-02 1.358 0.1746
  Running ‘nested.R’ [3s/3s]
  Comparing ‘nested.Rout’ to ‘nested.Rout.save’ ... OK
  Running ‘predict.R’ [3s/4s]
  Comparing ‘predict.Rout’ to ‘predict.Rout.save’ ...99c99
  < [1] 19.6346765 0.6275379
  ---
  > [1] 19.634676 0.627538
  106c106
  < [1] 19.6346765 0.6275379
  ---
  > [1] 19.634676 0.627538
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [5s/5s] OK
• checking re-building of vignette PDFs ... [6s/7s] OK
• checking PDF version of manual ... OK
  NOTE: There was 1 note.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/BradleyTerry2.Rcheck/00check.log’
  for details.