• using R Under development (unstable) (2012-02-06 r58287)
• using platform: i686-pc-linux-gnu (32-bit)
• using session charset: UTF-8
• checking for file ‘mboost/DESCRIPTION’ ... OK
• this is package ‘mboost’ version ‘2.1-1’
• 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 ‘mboost’ 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 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 should probably not be installed:
  ‘jmlr2e.sty’
  
  Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
  or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
• checking examples ... [50s/50s] OK
• checking differences from ‘mboost-Ex.Rout’ to ‘mboost-Ex.Rout.save’ ...
  254c254
  < 1.82015201 -0.02260988
  ---
  > 1.82015195 -0.02260988
  260c260
  < [1] 2.052033e-08
  ---
  > [1] 7.571584e-08
  263c263
  < [1] 3.927625e-12
  ---
  > [1] 2.815168e-13
  411c411
  < -0.1298897804 0.0003555854
  ---
  > -0.1298897900 0.0003555856
  429c429
  < -0.1298897992
  ---
  > -0.1298898010
  591c591
  < [1] 3.865352e-12
  ---
  > [1] 2.006573e-11
  951c951
  < Degrees of freedom (for mstop = 24): 4.481722
  ---
  > Degrees of freedom (for mstop = 24): 4.481737
  1349,1350c1349,1350
  < [ 1] ...................................... -- risk: 10338.67
  < [ 41] ...................................... -- risk: 10159.83
  ---
  > [ 1] ...................................... -- risk: 10338.66
  > [ 41] ...................................... -- risk: 10159.82
  1352c1352
  < Final risk: 10094.04
  ---
  > Final risk: 10094.03
  1374c1374
  < [101] ...................................... -- risk: 9976.167
  ---
  > [101] ...................................... -- risk: 9976.16
  1376c1376
  < Final risk: 9948.546
  ---
  > Final risk: 9948.539
  1382,1415c1382,1415
  < [ 151] ...................................... -- risk: 9843.546
  < [ 191] ...................................... -- risk: 9745.991
  < [ 231] ...................................... -- risk: 9654.791
  < [ 271] ...................................... -- risk: 9569.223
  < [ 311] ...................................... -- risk: 9488.74
  < [ 351] ...................................... -- risk: 9412.895
  < [ 391] ...................................... -- risk: 9341.311
  < [ 431] ...................................... -- risk: 9273.659
  < [ 471] ...................................... -- risk: 9209.649
  < [ 511] ...................................... -- risk: 9149.021
  < [ 551] ...................................... -- risk: 9091.541
  < [ 591] ...................................... -- risk: 9036.997
  < [ 631] ...................................... -- risk: 8985.196
  < [ 671] ...................................... -- risk: 8935.959
  < [ 711] ...................................... -- risk: 8889.126
  < [ 751] ...................................... -- risk: 8844.545
  < [ 791] ...................................... -- risk: 8802.079
  < [ 831] ...................................... -- risk: 8761.6
  < [ 871] ...................................... -- risk: 8722.99
  < [ 911] ...................................... -- risk: 8686.14
  < [ 951] ...................................... -- risk: 8650.946
  < [ 991] ...................................... -- risk: 8617.314
  < [1'031] ...................................... -- risk: 8585.156
  < [1'071] ...................................... -- risk: 8554.389
  < [1'111] ...................................... -- risk: 8524.936
  < [1'151] ...................................... -- risk: 8496.724
  < [1'191] ...................................... -- risk: 8469.686
  < [1'231] ...................................... -- risk: 8443.759
  < [1'271] ...................................... -- risk: 8418.884
  < [1'311] ...................................... -- risk: 8395.004
  < [1'351] ...................................... -- risk: 8372.068
  < [1'391] ...................................... -- risk: 8350.027
  < [1'431] ...................................... -- risk: 8328.833
  < [1'471] ...................................... -- risk: 8308.444
  ---
  > [ 151] ...................................... -- risk: 9843.537
  > [ 191] ...................................... -- risk: 9745.981
  > [ 231] ...................................... -- risk: 9654.78
  > [ 271] ...................................... -- risk: 9569.212
  > [ 311] ...................................... -- risk: 9488.728
  > [ 351] ...................................... -- risk: 9412.882
  > [ 391] ...................................... -- risk: 9341.297
  > [ 431] ...................................... -- risk: 9273.645
  > [ 471] ...................................... -- risk: 9209.634
  > [ 511] ...................................... -- risk: 9149.006
  > [ 551] ...................................... -- risk: 9091.526
  > [ 591] ...................................... -- risk: 9036.982
  > [ 631] ...................................... -- risk: 8985.181
  > [ 671] ...................................... -- risk: 8935.944
  > [ 711] ...................................... -- risk: 8889.11
  > [ 751] ...................................... -- risk: 8844.529
  > [ 791] ...................................... -- risk: 8802.064
  > [ 831] ...................................... -- risk: 8761.585
  > [ 871] ...................................... -- risk: 8722.975
  > [ 911] ...................................... -- risk: 8686.124
  > [ 951] ...................................... -- risk: 8650.931
  > [ 991] ...................................... -- risk: 8617.299
  > [1'031] ...................................... -- risk: 8585.141
  > [1'071] ...................................... -- risk: 8554.374
  > [1'111] ...................................... -- risk: 8524.921
  > [1'151] ...................................... -- risk: 8496.709
  > [1'191] ...................................... -- risk: 8469.672
  > [1'231] ...................................... -- risk: 8443.745
  > [1'271] ...................................... -- risk: 8418.87
  > [1'311] ...................................... -- risk: 8394.99
  > [1'351] ...................................... -- risk: 8372.054
  > [1'391] ...................................... -- risk: 8350.013
  > [1'431] ...................................... -- risk: 8328.82
  > [1'471] ...................................... -- risk: 8308.431
  1417c1417
  < Final risk: 8289.301
  ---
  > Final risk: 8289.288
  1420c1420
  < -36.995015 -35.596203 -34.085118 -32.349488 -30.277041 -27.732666 -24.322705
  ---
  > -36.995014 -35.596207 -34.085126 -32.349499 -30.277051 -27.732673 -24.322691
  1422c1422
  < -20.863451 -21.899778 -19.121766 -6.090494 2.438372 -4.941567 -7.667420
  ---
  > -20.863408 -21.899798 -19.121835 -6.090471 2.438464 -4.941604 -7.667532
  1424c1424
  < 2.660112 16.107870 12.731680 6.129816 7.150954 15.682249 30.314972
  ---
  > 2.660072 16.107960 12.731713 6.129780 7.150886 15.682172 30.314925
  1426c1426
  < 47.848824 52.733346 46.576854
  ---
  > 47.848885 52.733403 46.576792
  1459,1462c1459,1462
  < [1] -0.02478711 -0.01925254 0.07735510 0.24268927 0.39127892 0.49333021
  < [7] 0.58205157 0.65523850 0.67973447 0.64955713 0.60211202 0.54410925
  < [13] 0.44971270 0.34981919 0.33270628 0.36324091 0.37184588 0.37876602
  < [19] 0.39836919 0.42301404 0.36842328 0.22804990
  ---
  > [1] -0.02478725 -0.01925279 0.07735492 0.24268927 0.39127901 0.49333025
  > [7] 0.58205156 0.65523852 0.67973446 0.64955704 0.60211196 0.54410924
  > [13] 0.44971260 0.34981894 0.33270613 0.36324101 0.37184615 0.37876648
  > [19] 0.39836988 0.42301499 0.36842422 0.22805053
  1466c1466
  < 3.775258
  ---
  > 3.775259
  1481,1484c1481,1484
  < [1] -0.02478711 -0.01925254 0.07735510 0.24268927 0.39127892 0.49333021
  < [7] 0.58205157 0.65523850 0.67973447 0.64955713 0.60211202 0.54410925
  < [13] 0.44971270 0.34981919 0.33270628 0.36324091 0.37184588 0.37876602
  < [19] 0.39836919 0.42301404 0.36842328 0.22804990
  ---
  > [1] -0.02478725 -0.01925279 0.07735492 0.24268927 0.39127901 0.49333025
  > [7] 0.58205156 0.65523852 0.67973446 0.64955704 0.60211196 0.54410924
  > [13] 0.44971260 0.34981894 0.33270613 0.36324101 0.37184615 0.37876648
  > [19] 0.39836988 0.42301499 0.36842422 0.22805053
  1488c1488
  < 3.775258
  ---
  > 3.775259
  1506,1509c1506,1509
  < [1] -0.02478711 -0.01925254 0.07735510 0.24268927 0.39127892 0.49333021
  < [7] 0.58205157 0.65523850 0.67973447 0.64955713 0.60211202 0.54410925
  < [13] 0.44971270 0.34981919 0.33270628 0.36324091 0.37184588 0.37876602
  < [19] 0.39836919 0.42301404 0.36842328 0.22804990
  ---
  > [1] -0.02478725 -0.01925279 0.07735492 0.24268927 0.39127901 0.49333025
  > [7] 0.58205156 0.65523852 0.67973446 0.64955704 0.60211196 0.54410924
  > [13] 0.44971260 0.34981894 0.33270613 0.36324101 0.37184615 0.37876648
  > [19] 0.39836988 0.42301499 0.36842422 0.22805053
  1513c1513
  < 3.775258
  ---
  > 3.775259
  2120c2120
  < 1093.549
  ---
  > 1093.545
  2600c2600
  < 140.4451
  ---
  > 140.4455
  OK
• checking for unstated dependencies in tests ... WARNING
  ‘data(package=)’ call not declared from: ‘mlbench’
• checking tests ... [181s/182s] OK
  Running ‘birds_Biometrics.R’ [14s/14s]
  Comparing ‘birds_Biometrics.Rout’ to ‘birds_Biometrics.Rout.save’ ...148c148
  < 0.501901965 -0.001984263
  ---
  > 0.501901966 -0.001984263
  198c198
  < 0.778022818 -0.002811598
  ---
  > 0.778022823 -0.002811598
  202c202
  < 0.59371219 -0.01241289
  ---
  > 0.59371220 -0.01241289
  210c210
  < -1.71264914 0.01108683
  ---
  > -1.71264915 0.01108683
  234,236c234,236
  < [ 241] ...................................... -- risk: 456.1802
  < [ 281] ...................................... -- risk: 455.1545
  < [ 321] ...................................... -- risk: 454.2507
  ---
  > [ 241] ...................................... -- risk: 456.1801
  > [ 281] ...................................... -- risk: 455.1544
  > [ 321] ...................................... -- risk: 454.2506
  254,265c254,265
  < [ 1] ...................................... -- risk: 502.0303
  < [ 41] ...................................... -- risk: 494.1493
  < [ 81] ...................................... -- risk: 490.0277
  < [ 121] ...................................... -- risk: 487.4495
  < [ 161] ...................................... -- risk: 485.6646
  < [ 201] ...................................... -- risk: 484.3156
  < [ 241] ...................................... -- risk: 483.2211
  < [ 281] ...................................... -- risk: 482.3221
  < [ 321] ...................................... -- risk: 481.5231
  < [ 361] ...................................... -- risk: 480.7767
  < [ 401] ...................................... -- risk: 480.0901
  < [ 441] ...................................... -- risk: 479.5036
  ---
  > [ 1] ...................................... -- risk: 502.0305
  > [ 41] ...................................... -- risk: 494.1495
  > [ 81] ...................................... -- risk: 490.0279
  > [ 121] ...................................... -- risk: 487.4498
  > [ 161] ...................................... -- risk: 485.6648
  > [ 201] ...................................... -- risk: 484.3158
  > [ 241] ...................................... -- risk: 483.2213
  > [ 281] ...................................... -- risk: 482.3224
  > [ 321] ...................................... -- risk: 481.5234
  > [ 361] ...................................... -- risk: 480.7769
  > [ 401] ...................................... -- risk: 480.0903
  > [ 441] ...................................... -- risk: 479.5039
  267c267
  < Final risk: 479.2248
  ---
  > Final risk: 479.225
  Running ‘bugfixes.R’ [42s/42s]
  Comparing ‘bugfixes.Rout’ to ‘bugfixes.Rout.save’ ... OK
  Running ‘mboost_illustrations.R’ [16s/16s]
  Comparing ‘mboost_illustrations.Rout’ to ‘mboost_illustrations.Rout.save’ ... OK
  Running ‘regtest-baselearner.R’ [39s/39s]
  Comparing ‘regtest-baselearner.Rout’ to ‘regtest-baselearner.Rout.save’ ...308,309c308,309
  < [6] -0.220643444 0.154919019 -0.300950310 -0.873054989 -0.519028732
  < [11] 0.320637177 -0.303918057 -0.610811536 -0.686367706 0.342235454
  ---
  > [6] -0.220643444 0.154919020 -0.300950310 -0.873054989 -0.519028732
  > [11] 0.320637178 -0.303918057 -0.610811536 -0.686367706 0.342235455
  316c316
  < [46] 0.093509262 0.113732497 0.280359392 -0.037694530 -0.148325380
  ---
  > [46] 0.093509262 0.113732497 0.280359393 -0.037694530 -0.148325380
  319c319
  < [61] -0.371533883 0.042400169 0.125771267 -0.689991469 -0.022849336
  ---
  > [61] -0.371533883 0.042400169 0.125771267 -0.689991470 -0.022849336
  321c321
  < [71] 0.347018048 0.154893844 -0.104385886 0.829366070 0.433741503
  ---
  > [71] 0.347018048 0.154893844 -0.104385886 0.829366071 0.433741503
  323c323
  < [81] -0.332167838 -0.332316111 0.664484860 -0.063076836 -0.368592579
  ---
  > [81] -0.332167838 -0.332316111 0.664484860 -0.063076836 -0.368592580
  402c402
  < [1] -0.9167361
  ---
  > [1] -0.9167353
  Running ‘regtest-blackboost.R’ [15s/15s]
  Comparing ‘regtest-blackboost.Rout’ to ‘regtest-blackboost.Rout.save’ ... OK
  Running ‘regtest-family.R’ [12s/12s]
  Comparing ‘regtest-family.Rout’ to ‘regtest-family.Rout.save’ ... OK
  Running ‘regtest-gamboost.R’ [16s/16s]
  Comparing ‘regtest-gamboost.Rout’ to ‘regtest-gamboost.Rout.save’ ...36c36
  < [1] 6.625437
  ---
  > [1] 6.625438
  38c38
  < Degrees of freedom (for mstop = 34): 5.056182
  ---
  > Degrees of freedom (for mstop = 34): 5.056199
  208c208
  < [12,] 0.3426994
  ---
  > [12,] 0.3426993
  224,235c224,235
  < [1,] 5.059375e-01 9.071417e-01 0.9992658
  < [2,] 5.963551e-02 6.681175e-01 0.9969654
  < [3,] 4.438008e-03 4.607472e-01 0.9941774
  < [4,] 7.105703e-05 2.550525e-01 0.9897566
  < [5,] 3.469722e-16 6.147551e-03 0.9623562
  < [6,] 1.012072e-27 1.376472e-04 0.9351947
  < [7,] 2.348574e-40 2.145802e-06 0.9063236
  < [8,] 7.383737e-58 6.731226e-09 0.8677950
  < [9,] 1.953648e-78 7.669664e-12 0.8245871
  < [10,] 6.155754e-102 3.335810e-15 0.7778646
  < [11,] 1.619543e-141 7.275178e-21 0.7050833
  < [12,] 4.904272e-189 1.161265e-27 0.6266419
  ---
  > [1,] 5.059374e-01 9.071417e-01 0.9992658
  > [2,] 5.963542e-02 6.681175e-01 0.9969654
  > [3,] 4.437993e-03 4.607471e-01 0.9941774
  > [4,] 7.105658e-05 2.550524e-01 0.9897566
  > [5,] 3.469611e-16 6.147540e-03 0.9623562
  > [6,] 1.012013e-27 1.376467e-04 0.9351947
  > [7,] 2.348370e-40 2.145790e-06 0.9063236
  > [8,] 7.382807e-58 6.731171e-09 0.8677950
  > [9,] 1.953311e-78 7.669578e-12 0.8245871
  > [10,] 6.154361e-102 3.335760e-15 0.7778646
  > [11,] 1.619033e-141 7.275027e-21 0.7050833
  > [12,] 4.902193e-189 1.161233e-27 0.6266419
  319c319,326
  < > newData <- as.data.frame(rbind(colMeans(bodyfat)[-2], colMeans(bodyfat)[-2]+1*sapply(bodyfat, sd)[-2]))
  ---
  > > newData <- as.data.frame(rbind(mean(bodyfat)[-2], mean(bodyfat)[-2]+1*sd(bodyfat)[-2]))
  > Warning messages:
  > 1: mean(<data.frame>) is deprecated.
  > Use colMeans() or sapply(*, mean) instead.
  > 2: mean(<data.frame>) is deprecated.
  > Use colMeans() or sapply(*, mean) instead.
  > 3: sd(<data.frame>) is deprecated.
  > Use sapply(*, sd) instead.
  Running ‘regtest-glmboost.R’ [25s/25s]
  Comparing ‘regtest-glmboost.Rout’ to ‘regtest-glmboost.Rout.save’ ...300c300,307
  < > newData <- as.data.frame(rbind(colMeans(DF)[-1], colMeans(DF)[-2]+1*sapply(DF, sd)[-1]))
  ---
  > > newData <- as.data.frame(rbind(mean(DF)[-1], mean(DF)[-2]+1*sd(DF)[-1]))
  > Warning messages:
  > 1: mean(<data.frame>) is deprecated.
  > Use colMeans() or sapply(*, mean) instead.
  > 2: mean(<data.frame>) is deprecated.
  > Use colMeans() or sapply(*, mean) instead.
  > 3: sd(<data.frame>) is deprecated.
  > Use sapply(*, sd) instead.
  Running ‘regtest-hatmatrix.R’ [3s/3s]
  Comparing ‘regtest-hatmatrix.Rout’ to ‘regtest-hatmatrix.Rout.save’ ... OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [93s/130s] OK
• checking re-building of vignette PDFs ... [88s/137s] OK
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There was 1 note.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/mboost.Rcheck/00check.log’
  for details.