- 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.