• using R version 2.14.0 (2011-10-31)
• using platform: i386-apple-darwin9.8.0 (32-bit)
• using session charset: ASCII
• checking for file 'ipred/DESCRIPTION' ... OK
• this is package 'ipred' version '0.8-11'
• 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 'ipred' 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
• loading checks for arch 'i386'
  ** 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
• loading checks for arch 'x86_64'
  ** 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 ... NOTE
  File 'ipred/R/zzz.R':
  .onLoad calls:
  require(rpart)
  require(MASS)
  require(mlbench)
  require(survival)
  require(class)
  require(nnet)
  
  Package startup functions should not change the search path.
  See section 'Good practice' in ?.onAttach.
  
• 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 line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... 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 examples ...
  ** running examples for arch 'i386' ... OK
  ** running examples for arch 'x86_64' ... OK
• checking for unstated dependencies in tests ... OK
• checking tests ...
  ** running tests for arch 'i386' OK
  Running 'ipred-bugs.R'
  Comparing 'ipred-bugs.Rout' to 'ipred-bugs.Rout.save' ...165c165
  < [1] 0.949367
  ---
  > [1] 0.9612632
  167c167
  < [1] 0.9148273
  ---
  > [1] 0.9073771
  Running 'ipred-segfault.R'
  Comparing 'ipred-segfault.Rout' to 'ipred-segfault.Rout.save' ...29c29
  < Out-of-bag estimate of misclassification error: 0.195
  ---
  > Out-of-bag estimate of misclassification error: 0.185
  32c32
  < [1] 1 1 1 2 2 2 1 1 1 1
  ---
  > [1] 1 1 1 1 2 2 1 1 1 1
  50c50
  < [1] 1 1 1 1 1 2 1 2 1 2
  ---
  > [1] 1 1 1 1 2 2 1 2 1 2
  56c56
  < [1] 1 1 1 1 2 2 1 2 1 2
  ---
  > [1] 1 1 1 1 1 2 1 2 1 2
  67c67
  < [8,] 0.1 0.9
  ---
  > [8,] 0.0 1.0
  79c79
  < [8,] 0.1 0.9
  ---
  > [8,] 0.0 1.0
  84,93c84,93
  < [1,] 1.000000000 0.000000000
  < [2,] 0.996441281 0.003558719
  < [3,] 1.000000000 0.000000000
  < [4,] 1.000000000 0.000000000
  < [5,] 0.484359233 0.515640767
  < [6,] 0.000000000 1.000000000
  < [7,] 1.000000000 0.000000000
  < [8,] 0.001138952 0.998861048
  < [9,] 1.000000000 0.000000000
  < [10,] 0.000000000 1.000000000
  ---
  > [1,] 1.0000000 0.000000000
  > [2,] 0.9976303 0.002369668
  > [3,] 1.0000000 0.000000000
  > [4,] 1.0000000 0.000000000
  > [5,] 0.5311111 0.468888889
  > [6,] 0.0000000 1.000000000
  > [7,] 1.0000000 0.000000000
  > [8,] 0.0000000 1.000000000
  > [9,] 1.0000000 0.000000000
  > [10,] 0.0000000 1.000000000
  106c106
  < Misclassification error: 0.035
  ---
  > Misclassification error: 0.04
  147c147
  < Misclassification error: 0.11
  ---
  > Misclassification error: 0.095
  158c158
  < Misclassification error: 0.07
  ---
  > Misclassification error: 0.085
  170,171c170,171
  < Misclassification error: 0.0388
  < Standard deviation: 0.0029
  ---
  > Misclassification error: 0.0391
  > Standard deviation: 0.0027
  183c183
  < Misclassification error: 0.0332
  ---
  > Misclassification error: 0.0333
  201c201
  < Out-of-bag estimate of root mean squared error: 3.5077
  ---
  > Out-of-bag estimate of root mean squared error: 3.5394
  204,205c204,205
  < [1] 11.89640 13.53735 10.67191 11.90026 13.67112 10.47250 15.93565 15.76868
  < [9] 17.64140 17.54231
  ---
  > [1] 17.52261 10.07663 12.96417 13.86483 14.07599 16.60311 NA 21.18277
  > [9] 16.92367 NA
  208,209c208,209
  < [1] 21.13210 17.05773 14.36727 13.23833 11.40763 12.36486 19.00303 14.98115
  < [9] 19.09551 17.23454
  ---
  > [1] 17.988182 11.996216 19.349240 16.608268 11.051775 15.140120 10.996003
  > [8] 9.471202 14.869813 13.846185
  211,212c211,212
  < [1] 21.13210 17.05773 14.36727 13.23833 11.40763 12.36486 19.00303 14.98115
  < [9] 19.09551 17.23454
  ---
  > [1] 17.988182 11.996216 19.349240 16.608268 11.051775 15.140120 10.996003
  > [8] 9.471202 14.869813 13.846185
  214,215c214,215
  < [1] 21.27480 16.62497 14.46233 13.44548 11.68707 12.79660 19.37107 15.25045
  < [9] 19.05139 18.08567
  ---
  > [1] 18.163683 12.034196 19.291462 16.861436 11.071367 15.258870 11.600688
  > [8] 9.460784 14.971003 13.922154
  223c223
  < Root mean squared error: 2.5998
  ---
  > Root mean squared error: 2.6627
  234c234
  < Root mean squared error: 2.6421
  ---
  > Root mean squared error: 2.5703
  262c262
  < Root mean squared error: 2.6975
  ---
  > Root mean squared error: 2.6721
  284c284
  < 154.0000 154.0000 154.0000 154.0000 0.0858 0.0769 0.1111
  ---
  > 183.0000 183.0000 183.0000 183.0000 0.0421 0.0342 0.0475
  290c290
  < 146.0000 146.0000 146.0000 146.0000 0.0673 0.0544 0.1145
  ---
  > 130.000 130.000 130.000 130.000 0.501 0.489 0.532
  296c296
  < 122.000 122.000 122.000 122.000 0.306 0.274 0.377
  ---
  > 160.0000 160.0000 160.0000 160.0000 0.0421 0.0359 0.0568
  302c302
  < 119.0000 119.0000 119.0000 119.0000 0.0986 0.0807 0.1145
  ---
  > 152.0000 152.0000 152.0000 152.0000 0.0475 0.0378 0.0514
  308c308
  < 150.0000 150.0000 150.0000 150.0000 0.0242 0.0169 0.0411
  ---
  > 130.000 130.000 130.000 130.000 0.489 0.399 0.532
  314c314
  < 136.0000 136.0000 136.0000 136.0000 0.0412 0.0342 0.0522
  ---
  > 149.0000 149.0000 149.0000 149.0000 0.0302 0.0172 0.0342
  320c320
  < 122.000 122.000 122.000 122.000 0.306 0.274 0.377
  ---
  > 141.000 141.000 141.000 141.000 0.489 0.398 0.532
  326c326
  < 149.0000 149.0000 149.0000 149.0000 0.0552 0.0544 0.0691
  ---
  > 160.0000 160.0000 160.0000 160.0000 0.0315 0.0187 0.0359
  332c332
  < 123.000 123.000 123.000 123.000 0.366 0.317 0.399
  ---
  > 169.000 169.000 169.000 169.000 0.175 0.137 0.209
  338c338
  < 163.0000 163.0000 163.0000 163.0000 0.0522 0.0444 0.0552
  ---
  > 132.0000 132.0000 132.0000 132.0000 0.1050 0.0718 0.1191
  356c356
  < Brier's score: 0.076
  ---
  > Brier's score: 0.0955
  369c369
  < Brier's score: 0.0898
  ---
  > Brier's score: 0.069
  403,404c403,404
  < [1] 19.884659 7.979953 15.136274 17.090984 10.593808 15.343204 17.641397
  < [8] 12.360645 14.277689 10.893690
  ---
  > [1] 6.440993 14.435812 10.847327 14.837533 13.010493 6.156936 20.132612
  > [8] 6.879375 14.076470 16.636056
  Running 'ipred-smalltest.R'
  Comparing 'ipred-smalltest.Rout' to 'ipred-smalltest.Rout.save' ... OK
  Running 'ipred-tests.R'
  Comparing 'ipred-tests.Rout' to 'ipred-tests.Rout.save' ...739c739
  < Out-of-bag estimate of misclassification error: 0.0366
  ---
  > Out-of-bag estimate of misclassification error: 0.0381
  747c747
  < Out-of-bag estimate of root mean squared error: 3.9905
  ---
  > Out-of-bag estimate of root mean squared error: 3.9809
  754c754
  < Out-of-bag estimate of root mean squared error: 2.8515
  ---
  > Out-of-bag estimate of root mean squared error: 2.8832
  763c763
  < Out-of-bag estimate of Brier's score: 0.1967
  ---
  > Out-of-bag estimate of Brier's score: 0.1925
  771c771
  < Out-of-bag estimate of misclassification error: 0.3551
  ---
  > Out-of-bag estimate of misclassification error: 0.3271
  ** running tests for arch 'x86_64' OK
  Running 'ipred-bugs.R'
  Comparing 'ipred-bugs.Rout' to 'ipred-bugs.Rout.save' ...165c165
  < [1] 0.949367
  ---
  > [1] 0.9612632
  167c167
  < [1] 0.9148273
  ---
  > [1] 0.9073771
  Running 'ipred-segfault.R'
  Comparing 'ipred-segfault.Rout' to 'ipred-segfault.Rout.save' ...29c29
  < Out-of-bag estimate of misclassification error: 0.195
  ---
  > Out-of-bag estimate of misclassification error: 0.185
  32c32
  < [1] 1 1 1 2 2 2 1 1 1 1
  ---
  > [1] 1 1 1 1 2 2 1 1 1 1
  50c50
  < [1] 1 1 1 1 1 2 1 2 1 2
  ---
  > [1] 1 1 1 1 2 2 1 2 1 2
  56c56
  < [1] 1 1 1 1 2 2 1 2 1 2
  ---
  > [1] 1 1 1 1 1 2 1 2 1 2
  67c67
  < [8,] 0.1 0.9
  ---
  > [8,] 0.0 1.0
  79c79
  < [8,] 0.1 0.9
  ---
  > [8,] 0.0 1.0
  84,93c84,93
  < [1,] 1.000000000 0.000000000
  < [2,] 0.996441281 0.003558719
  < [3,] 1.000000000 0.000000000
  < [4,] 1.000000000 0.000000000
  < [5,] 0.484359233 0.515640767
  < [6,] 0.000000000 1.000000000
  < [7,] 1.000000000 0.000000000
  < [8,] 0.001138952 0.998861048
  < [9,] 1.000000000 0.000000000
  < [10,] 0.000000000 1.000000000
  ---
  > [1,] 1.0000000 0.000000000
  > [2,] 0.9976303 0.002369668
  > [3,] 1.0000000 0.000000000
  > [4,] 1.0000000 0.000000000
  > [5,] 0.5311111 0.468888889
  > [6,] 0.0000000 1.000000000
  > [7,] 1.0000000 0.000000000
  > [8,] 0.0000000 1.000000000
  > [9,] 1.0000000 0.000000000
  > [10,] 0.0000000 1.000000000
  106c106
  < Misclassification error: 0.035
  ---
  > Misclassification error: 0.04
  147c147
  < Misclassification error: 0.11
  ---
  > Misclassification error: 0.095
  158c158
  < Misclassification error: 0.07
  ---
  > Misclassification error: 0.085
  170,171c170,171
  < Misclassification error: 0.0388
  < Standard deviation: 0.0029
  ---
  > Misclassification error: 0.0391
  > Standard deviation: 0.0027
  183c183
  < Misclassification error: 0.0332
  ---
  > Misclassification error: 0.0333
  201c201
  < Out-of-bag estimate of root mean squared error: 3.5077
  ---
  > Out-of-bag estimate of root mean squared error: 3.5394
  204,205c204,205
  < [1] 11.89640 13.53735 10.67191 11.90026 13.67112 10.47250 15.93565 15.76868
  < [9] 17.64140 17.54231
  ---
  > [1] 17.52261 10.07663 12.96417 13.86483 14.07599 16.60311 NA 21.18277
  > [9] 16.92367 NA
  208,209c208,209
  < [1] 21.13210 17.05773 14.36727 13.23833 11.40763 12.36486 19.00303 14.98115
  < [9] 19.09551 17.23454
  ---
  > [1] 17.988182 11.996216 19.349240 16.608268 11.051775 15.140120 10.996003
  > [8] 9.471202 14.869813 13.846185
  211,212c211,212
  < [1] 21.13210 17.05773 14.36727 13.23833 11.40763 12.36486 19.00303 14.98115
  < [9] 19.09551 17.23454
  ---
  > [1] 17.988182 11.996216 19.349240 16.608268 11.051775 15.140120 10.996003
  > [8] 9.471202 14.869813 13.846185
  214,215c214,215
  < [1] 21.27480 16.62497 14.46233 13.44548 11.68707 12.79660 19.37107 15.25045
  < [9] 19.05139 18.08567
  ---
  > [1] 18.163683 12.034196 19.291462 16.861436 11.071367 15.258870 11.600688
  > [8] 9.460784 14.971003 13.922154
  223c223
  < Root mean squared error: 2.5998
  ---
  > Root mean squared error: 2.6627
  234c234
  < Root mean squared error: 2.6421
  ---
  > Root mean squared error: 2.5703
  262c262
  < Root mean squared error: 2.6975
  ---
  > Root mean squared error: 2.6721
  284c284
  < 154.0000 154.0000 154.0000 154.0000 0.0858 0.0769 0.1111
  ---
  > 183.0000 183.0000 183.0000 183.0000 0.0421 0.0342 0.0475
  290c290
  < 146.0000 146.0000 146.0000 146.0000 0.0673 0.0544 0.1145
  ---
  > 130.000 130.000 130.000 130.000 0.501 0.489 0.532
  296c296
  < 122.000 122.000 122.000 122.000 0.306 0.274 0.377
  ---
  > 160.0000 160.0000 160.0000 160.0000 0.0421 0.0359 0.0568
  302c302
  < 119.0000 119.0000 119.0000 119.0000 0.0986 0.0807 0.1145
  ---
  > 152.0000 152.0000 152.0000 152.0000 0.0475 0.0378 0.0514
  308c308
  < 150.0000 150.0000 150.0000 150.0000 0.0242 0.0169 0.0411
  ---
  > 130.000 130.000 130.000 130.000 0.489 0.399 0.532
  314c314
  < 136.0000 136.0000 136.0000 136.0000 0.0412 0.0342 0.0522
  ---
  > 149.0000 149.0000 149.0000 149.0000 0.0302 0.0172 0.0342
  320c320
  < 122.000 122.000 122.000 122.000 0.306 0.274 0.377
  ---
  > 141.000 141.000 141.000 141.000 0.489 0.398 0.532
  326c326
  < 149.0000 149.0000 149.0000 149.0000 0.0552 0.0544 0.0691
  ---
  > 160.0000 160.0000 160.0000 160.0000 0.0315 0.0187 0.0359
  332c332
  < 123.000 123.000 123.000 123.000 0.366 0.317 0.399
  ---
  > 169.000 169.000 169.000 169.000 0.175 0.137 0.209
  338c338
  < 163.0000 163.0000 163.0000 163.0000 0.0522 0.0444 0.0552
  ---
  > 132.0000 132.0000 132.0000 132.0000 0.1050 0.0718 0.1191
  356c356
  < Brier's score: 0.076
  ---
  > Brier's score: 0.0955
  369c369
  < Brier's score: 0.0898
  ---
  > Brier's score: 0.069
  403,404c403,404
  < [1] 19.884659 7.979953 15.136274 17.090984 10.593808 15.343204 17.641397
  < [8] 12.360645 14.277689 10.893690
  ---
  > [1] 6.440993 14.435812 10.847327 14.837533 13.010493 6.156936 20.132612
  > [8] 6.879375 14.076470 16.636056
  Running 'ipred-smalltest.R'
  Comparing 'ipred-smalltest.Rout' to 'ipred-smalltest.Rout.save' ... OK
  Running 'ipred-tests.R'
  Comparing 'ipred-tests.Rout' to 'ipred-tests.Rout.save' ...739c739
  < Out-of-bag estimate of misclassification error: 0.0366
  ---
  > Out-of-bag estimate of misclassification error: 0.0381
  747c747
  < Out-of-bag estimate of root mean squared error: 3.9905
  ---
  > Out-of-bag estimate of root mean squared error: 3.9809
  754c754
  < Out-of-bag estimate of root mean squared error: 2.8515
  ---
  > Out-of-bag estimate of root mean squared error: 2.8832
  763c763
  < Out-of-bag estimate of Brier's score: 0.1967
  ---
  > Out-of-bag estimate of Brier's score: 0.1925
  771c771
  < Out-of-bag estimate of misclassification error: 0.3551
  ---
  > Out-of-bag estimate of misclassification error: 0.3271
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking running R code from vignettes ... OK
• checking re-building of vignette PDFs ... OK
• checking PDF version of manual ... OK
• elapsed time (check, wall clock): 2:32