• using R version 2.15.0 Patched (2012-05-04 r59314)
• using platform: sparc-sun-solaris2.10 (32-bit)
• using session charset: UTF-8
• checking for file ‘BradleyTerry2/DESCRIPTION’ ... OK
• this is package ‘BradleyTerry2’ version ‘1.0-0’
• 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 .dll and .exe 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 installed files from ‘inst/doc’ ... OK
• checking examples ... [83s/83s] OK
• checking for unstated dependencies in tests ... OK
• checking tests ... [150s/150s] OK
  Running ‘add1.R’ [33s/33s]
  Comparing ‘add1.Rout’ to ‘add1.Rout.save’ ... OK
  Running ‘baseball.R’ [25s/25s]
  Comparing ‘baseball.Rout’ to ‘baseball.Rout.save’ ... OK
  Running ‘countsToBinomial.R’
  Comparing ‘countsToBinomial.Rout’ to ‘countsToBinomial.Rout.save’ ... OK
  Running ‘flatlizards.R’ [32s/32s]
  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
  253,257c253,257
  < Iteration 3. Score = 0.2863055
  < Iteration 4. Score = 0.003826825
  < Iteration 5. Score = 0.0001770635
  < Iteration 6. Score = 9.288226e-06
  < Iteration 7. Score = 6.800941e-07
  ---
  > Iteration 3. Score = 0.2862628
  > Iteration 4. Score = 0.003823299
  > Iteration 5. Score = 0.0001768978
  > Iteration 6. Score = 9.279559e-06
  > Iteration 7. Score = 6.79458e-07
  268,273c268,273
  < ..lizard096 2.045e+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
  343c343
  < lizard096 20.44774520 3.874532e+07
  ---
  > lizard096 20.46394884 3.874532e+07
  425c425
  < ..lizard099 -8.404838e-08
  ---
  > ..lizard099 -8.396993e-08
  Running ‘nested.R’ [25s/25s]
  Comparing ‘nested.Rout’ to ‘nested.Rout.save’ ... OK
  Running ‘predict.R’ [29s/29s]
  Comparing ‘predict.Rout’ to ‘predict.Rout.save’ ...16,20c16,20
  < Iteration 3. Score = 0.2863055
  < Iteration 4. Score = 0.003826825
  < Iteration 5. Score = 0.0001770635
  < Iteration 6. Score = 9.288226e-06
  < Iteration 7. Score = 6.800941e-07
  ---
  > Iteration 3. Score = 0.2862628
  > Iteration 4. Score = 0.003823299
  > Iteration 5. Score = 0.0001768978
  > Iteration 6. Score = 9.279559e-06
  > Iteration 7. Score = 6.79458e-07
  33c33
  < [1] 19.61847 NA
  ---
  > [1] 19.63468 NA
  99c99
  < [1] 19.6184728 0.6275379
  ---
  > [1] 19.634676 0.627538
  106c106
  < [1] 19.6184728 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 ... [43s/43s] OK
• checking re-building of vignette PDFs ... [79s/80s] OK
• checking PDF version of manual ... OK