Check results for 'rrcov'

using R version 2.15.0 Patched (2012-03-31 r58888)
using platform: sparc-sun-solaris2.10 (32-bit)
using session charset: UTF-8
checking for file ‘rrcov/DESCRIPTION’ ... OK
this is package ‘rrcov’ version ‘1.3-01’
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 ‘rrcov’ 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 ... NOTE
File ‘rrcov/R/zzz.R’:
.onLoad calls:
require("methods")
cat(paste(title, " (version ", ver, ")\n", sep = ""))

Package startup functions should not change the search path.
Package startup functions should use ‘packageStartupMessage’ to
generate messages.
See section ‘Good practice’ in ?.onAttach.

..covSBic: warning in determinant(cov, log = FALSE): partial argument
match of 'log' to 'logarithm'
..covSRocke: warning in determinant(cov, log = FALSE): partial argument
match of 'log' to 'logarithm'
CovMest: warning in determinant(mest$s, log = FALSE): partial argument
match of 'log' to 'logarithm'
CovMve: warning in determinant(xcov$cov, log = TRUE): partial argument
match of 'log' to 'logarithm'
covMest: warning in determinant(mest$s, log = FALSE): partial argument
match of 'log' to 'logarithm'
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 ... NOTE
File ‘/home/ripley/R/Lib32/rrcov/libs/rrcov.so’:
Found ‘__f90_stop’, possibly from ‘stop’ (Fortran)
Object: ‘fsada.o’

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checking installed files from ‘inst/doc’ ... NOTE
The following files are already in R: ‘jss.bst’, ‘jss.cls’
Please remove them from your package.
checking examples ... [117s/117s] OK
checking for unstated dependencies in tests ... OK
checking tests ... [361s/362s] OK
Running ‘thubert.R’ [28s/28s]
Comparing ‘thubert.Rout’ to ‘thubert.Rout.save’ ...477,496c477,496
< 1 -0.0045773 0.0549267 0.02698656
< 2 0.0965384 0.0109426 0.02063108
< 3 0.0416353 0.0107242 0.02541740
< 4 -0.1234169 0.0056391 -0.03062310
< 5 0.0010063 -0.0179974 -0.02308289
< 6 -0.1235640 0.0274857 -0.02424650
< 7 -0.0388886 0.0428451 -0.12122500
< 8 -0.1548665 0.0178563 -0.01746690
< 9 0.0150163 0.0165039 -0.11600674
< 10 0.1733165 -0.0603964 -0.02890552
< 11 0.1029635 0.0728556 0.00056662
< 12 0.1377507 0.1076671 -0.00724301
< 13 0.1382985 -0.0258913 -0.06404825
< 14 0.0252256 -0.0062022 0.02752700
< 15 -0.0143890 -0.0300723 0.00142708
< 16 -0.0265579 -0.0672450 0.03909250
< 17 0.0402824 -0.0920752 0.03365219
< 18 -0.0931485 -0.0481563 -0.03960396
< 19 -0.1563735 0.0321830 -0.01398074
< 20 -0.0601237 0.0077557 0.07390044
---
> 1 -0.0045773 0.0549267 -0.02698656
> 2 0.0965384 0.0109426 -0.02063108
> 3 0.0416353 0.0107242 -0.02541740
> 4 -0.1234169 0.0056391 0.03062310
> 5 0.0010063 -0.0179974 0.02308289
> 6 -0.1235640 0.0274857 0.02424650
> 7 -0.0388886 0.0428451 0.12122500
> 8 -0.1548665 0.0178563 0.01746690
> 9 0.0150163 0.0165039 0.11600674
> 10 0.1733165 -0.0603964 0.02890552
> 11 0.1029635 0.0728556 -0.00056662
> 12 0.1377507 0.1076671 0.00724301
> 13 0.1382985 -0.0258913 0.06404825
> 14 0.0252256 -0.0062022 -0.02752700
> 15 -0.0143890 -0.0300723 -0.00142708
> 16 -0.0265579 -0.0672450 -0.03909250
> 17 0.0402824 -0.0920752 -0.03365219
> 18 -0.0931485 -0.0481563 0.03960396
> 19 -0.1563735 0.0321830 0.01398074
> 20 -0.0601237 0.0077557 -0.07390044
506,510c506,510
< [1,] 0.896892 0.247801 0.325364
< [2,] 0.181949 -0.025322 -0.021386
< [3,] 0.402643 -0.502152 -0.738699
< [4,] 0.010772 -0.575326 0.540043
< [5,] 0.015543 -0.595648 0.237399
---
> [1,] 0.896892 0.247801 -0.325364
> [2,] 0.181949 -0.025322 0.021386
> [3,] 0.402643 -0.502152 0.738699
> [4,] 0.010772 -0.575326 -0.540043
> [5,] 0.015543 -0.595648 -0.237399
1156,1175c1156,1175
< 1 -0.0045773 0.0549267 0.02698656
< 2 0.0965384 0.0109426 0.02063108
< 3 0.0416353 0.0107242 0.02541740
< 4 -0.1234169 0.0056391 -0.03062310
< 5 0.0010063 -0.0179974 -0.02308289
< 6 -0.1235640 0.0274857 -0.02424650
< 7 -0.0388886 0.0428451 -0.12122500
< 8 -0.1548665 0.0178563 -0.01746690
< 9 0.0150163 0.0165039 -0.11600674
< 10 0.1733165 -0.0603964 -0.02890552
< 11 0.1029635 0.0728556 0.00056662
< 12 0.1377507 0.1076671 -0.00724301
< 13 0.1382985 -0.0258913 -0.06404825
< 14 0.0252256 -0.0062022 0.02752700
< 15 -0.0143890 -0.0300723 0.00142708
< 16 -0.0265579 -0.0672450 0.03909250
< 17 0.0402824 -0.0920752 0.03365219
< 18 -0.0931485 -0.0481563 -0.03960396
< 19 -0.1563735 0.0321830 -0.01398074
< 20 -0.0601237 0.0077557 0.07390044
---
> 1 -0.0045773 0.0549267 -0.02698656
> 2 0.0965384 0.0109426 -0.02063108
> 3 0.0416353 0.0107242 -0.02541740
> 4 -0.1234169 0.0056391 0.03062310
> 5 0.0010063 -0.0179974 0.02308289
> 6 -0.1235640 0.0274857 0.02424650
> 7 -0.0388886 0.0428451 0.12122500
> 8 -0.1548665 0.0178563 0.01746690
> 9 0.0150163 0.0165039 0.11600674
> 10 0.1733165 -0.0603964 0.02890552
> 11 0.1029635 0.0728556 -0.00056662
> 12 0.1377507 0.1076671 0.00724301
> 13 0.1382985 -0.0258913 0.06404825
> 14 0.0252256 -0.0062022 -0.02752700
> 15 -0.0143890 -0.0300723 -0.00142708
> 16 -0.0265579 -0.0672450 -0.03909250
> 17 0.0402824 -0.0920752 -0.03365219
> 18 -0.0931485 -0.0481563 0.03960396
> 19 -0.1563735 0.0321830 0.01398074
> 20 -0.0601237 0.0077557 -0.07390044
1185,1189c1185,1189
< [1,] 0.896892 0.247801 0.325364
< [2,] 0.181949 -0.025322 -0.021386
< [3,] 0.402643 -0.502152 -0.738699
< [4,] 0.010772 -0.575326 0.540043
< [5,] 0.015543 -0.595648 0.237399
---
> [1,] 0.896892 0.247801 -0.325364
> [2,] 0.181949 -0.025322 0.021386
> [3,] 0.402643 -0.502152 0.738699
> [4,] 0.010772 -0.575326 -0.540043
> [5,] 0.015543 -0.595648 -0.237399
1282c1282
< Animals 28 2 1 31895.488713 NA
---
> Animals 28 2 1 177667.630089 NA
1285,1312c1285,1312
< Mountain beaver -146.604
< Cow 468.267
< Grey wolf -38.305
< Goat -47.284
< Guinea pig -148.810
< Dipliodocus 7308.503
< Asian elephant 5020.122
< Donkey 288.849
< Horse 683.118
< Potar monkey -58.490
< Cat -131.840
< Giraffe 707.517
< Gorilla 291.428
< Human 905.882
< African elephant 8483.165
< Triceratops 5864.626
< Rhesus monkey -11.053
< Kangaroo -88.230
< Golden hamster -152.872
< Mouse -153.397
< Rabbit -142.783
< Sheep 16.756
< Jaguar 31.078
< Chimpanzee 219.462
< Brachiosaurus 55166.658
< Rat -152.075
< Mole -151.325
< Pig 107.229
---
> Mountain beaver -209.815
> Cow 405.056
> Grey wolf -101.516
> Goat -110.495
> Guinea pig -212.021
> Dipliodocus 7245.292
> Asian elephant 4956.911
> Donkey 225.639
> Horse 619.907
> Potar monkey -121.700
> Cat -195.051
> Giraffe 644.306
> Gorilla 228.217
> Human 842.672
> African elephant 8419.954
> Triceratops 5801.415
> Rhesus monkey -74.263
> Kangaroo -151.441
> Golden hamster -216.083
> Mouse -216.608
> Rabbit -205.993
> Sheep -46.455
> Jaguar -32.133
> Chimpanzee 156.252
> Brachiosaurus 55103.448
> Rat -215.286
> Mole -214.536
> Pig 44.018
1318c1318
< [1] 178.59
---
> [1] 421.51
1432c1432
< bushfire 38 5 1 37423.626544 NA
---
> bushfire 38 5 1 38435.075910 NA
1478c1478
< [1] 193.45
---
> [1] 196.05
1543,1546c1543,1546
< [1,] -0.4326888 0.086058
< [2,] -0.6275437 0.227680
< [3,] 0.6472465 0.269032
< [4,] 0.0064233 0.931868
---
> [1,] -0.4326888 -0.086058
> [2,] -0.6275437 -0.227680
> [3,] 0.6472465 -0.269032
> [4,] 0.0064233 -0.931868
1553c1553
< [1] 2.1725 1.1006
---
> [1] 2.2578 1.0667
1557,1560c1557,1560
< [1,] 0.64756 0.086967
< [2,] 0.56924 0.337528
< [3,] -0.34363 0.919561
< [4,] 0.37222 0.181438
---
> [1,] 0.44401 -0.0093574
> [2,] 0.61072 0.4064696
> [3,] -0.62867 0.1201164
> [4,] -0.18613 0.9056859
1561a1562,1576
> Warning messages:
> 1: In center(x) : This function (pcaPP::l1median)is outdated.
>
>
> For better performance try any of pcaPP::l1median_* instead. Preferably pcaPP::l1median_HoCrJo.
>
>
> Otherwise use (trace = -1) for suppressing this warning.
> 2: In center(x) : This function (pcaPP::l1median)is outdated.
>
>
> For better performance try any of pcaPP::l1median_* instead. Preferably pcaPP::l1median_HoCrJo.
>
>
> Otherwise use (trace = -1) for suppressing this warning.
Running ‘tlda.R’ [33s/33s]
Comparing ‘tlda.Rout’ to ‘tlda.Rout.save’ ...122c122
< a_i from the vector a <- c(0, 0, 0, 1)
---
> a_i from the vector a <- c(0, 0, 0, -1)
269c269
< a_i from the vector a <- c(0, 0, 0, 1)
---
> a_i from the vector a <- c(0, 0, 0, -1)
421c421
< a_i from the vector a <- c(0, 0, 0, 1)
---
> a_i from the vector a <- c(0, 0, 0, -1)
568c568
< a_i from the vector a <- c(0, 0, 0, 1)
---
> a_i from the vector a <- c(0, 0, 0, -1)
720c720
< a_i from the vector a <- c(0, 0, 0, 1)
---
> a_i from the vector a <- c(0, 0, 0, -1)
867c867
< a_i from the vector a <- c(0, 0, 0, 1)
---
> a_i from the vector a <- c(0, 0, 0, -1)
Running ‘tldapp.R’ [163s/163s]
Comparing ‘tldapp.Rout’ to ‘tldapp.Rout.save’ ... OK
Running ‘tmcd4.R’
Comparing ‘tmcd4.Rout’ to ‘tmcd4.Rout.save’ ...499,500c499,500
< the line with equation 0 (x_i1-m_1) + 1 (x_i2-m_2) = 0 with (m_1,m_2)
< the mean of these observations.
---
> the line with equation 5.2182e-16 (x_i1-m_1) + -1 (x_i2-m_2) = 0 with
> (m_1,m_2) the mean of these observations.
508,509c508,509
< the line with equation 0 (x_i1-m_1) + 1 (x_i2-m_2) = 0 with (m_1,m_2)
< the mean of these observations.
---
> the line with equation 5.2182e-16 (x_i1-m_1) + -1 (x_i2-m_2) = 0 with
> (m_1,m_2) the mean of these observations.
517,518c517,518
< X1 2.86e+00 -1.14e-16
< X2 -1.14e-16 0.00e+00
---
> X1 2.86e+00 3.91e-16
> X2 3.91e-16 0.00e+00
Running ‘tmest.R’ [11s/11s]
Comparing ‘tmest.Rout’ to ‘tmest.Rout.save’ ... OK
Running ‘tmest4.R’ [12s/12s]
Comparing ‘tmest4.Rout’ to ‘tmest4.Rout.save’ ... OK
Running ‘tmve4.R’
Comparing ‘tmve4.Rout’ to ‘tmve4.Rout.save’ ... OK
Running ‘togk4.R’
Comparing ‘togk4.Rout’ to ‘togk4.Rout.save’ ... OK
Running ‘tqda.R’ [13s/13s]
Comparing ‘tqda.Rout’ to ‘tqda.Rout.save’ ...239,240c239,240
< sexM 2.5253e-01 8.4108e-17 0.39697 -0.10606 0.98788 1.0571 0.38737
< index 8.4108e-17 2.1035e+02 41.49394 31.56162 93.85657 107.4510 41.95707
---
> sexM 2.5253e-01 -4.7913e-20 0.39697 -0.10606 0.98788 1.0571 0.38737
> index -4.7913e-20 2.1035e+02 41.49394 31.56162 93.85657 107.4510 41.95707
249,250c249,250
< sexM 2.5253e-01 8.4108e-17 -0.24444 -0.6500 -0.23485 -0.46667 -0.077778
< index 8.4108e-17 2.1035e+02 46.21313 31.3015 94.83081 105.04242 44.137374
---
> sexM 2.5253e-01 -4.7913e-20 -0.24444 -0.6500 -0.23485 -0.46667 -0.077778
> index -4.7913e-20 2.1035e+02 46.21313 31.3015 94.83081 105.04242 44.137374
466,467c466,467
< sexM 2.5253e-01 8.4108e-17 0.39697 -0.10606 0.98788 1.0571 0.38737
< index 8.4108e-17 2.1035e+02 41.49394 31.56162 93.85657 107.4510 41.95707
---
> sexM 2.5253e-01 -4.7913e-20 0.39697 -0.10606 0.98788 1.0571 0.38737
> index -4.7913e-20 2.1035e+02 41.49394 31.56162 93.85657 107.4510 41.95707
476,477c476,477
< sexM 2.5253e-01 8.4108e-17 -0.24444 -0.6500 -0.23485 -0.46667 -0.077778
< index 8.4108e-17 2.1035e+02 46.21313 31.3015 94.83081 105.04242 44.137374
---
> sexM 2.5253e-01 -4.7913e-20 -0.24444 -0.6500 -0.23485 -0.46667 -0.077778
> index -4.7913e-20 2.1035e+02 46.21313 31.3015 94.83081 105.04242 44.137374
693,694c693,694
< sexM 2.5253e-01 8.4108e-17 0.39697 -0.10606 0.98788 1.0571 0.38737
< index 8.4108e-17 2.1035e+02 41.49394 31.56162 93.85657 107.4510 41.95707
---
> sexM 2.5253e-01 -4.7913e-20 0.39697 -0.10606 0.98788 1.0571 0.38737
> index -4.7913e-20 2.1035e+02 41.49394 31.56162 93.85657 107.4510 41.95707
703,704c703,704
< sexM 2.5253e-01 8.4108e-17 -0.24444 -0.6500 -0.23485 -0.46667 -0.077778
< index 8.4108e-17 2.1035e+02 46.21313 31.3015 94.83081 105.04242 44.137374
---
> sexM 2.5253e-01 -4.7913e-20 -0.24444 -0.6500 -0.23485 -0.46667 -0.077778
> index -4.7913e-20 2.1035e+02 46.21313 31.3015 94.83081 105.04242 44.137374
920,921c920,921
< sexM 2.5253e-01 8.4108e-17 0.39697 -0.10606 0.98788 1.0571 0.38737
< index 8.4108e-17 2.1035e+02 41.49394 31.56162 93.85657 107.4510 41.95707
---
> sexM 2.5253e-01 -4.7913e-20 0.39697 -0.10606 0.98788 1.0571 0.38737
> index -4.7913e-20 2.1035e+02 41.49394 31.56162 93.85657 107.4510 41.95707
930,931c930,931
< sexM 2.5253e-01 8.4108e-17 -0.24444 -0.6500 -0.23485 -0.46667 -0.077778
< index 8.4108e-17 2.1035e+02 46.21313 31.3015 94.83081 105.04242 44.137374
---
> sexM 2.5253e-01 -4.7913e-20 -0.24444 -0.6500 -0.23485 -0.46667 -0.077778
> index -4.7913e-20 2.1035e+02 46.21313 31.3015 94.83081 105.04242 44.137374
Running ‘tsde.R’
Comparing ‘tsde.Rout’ to ‘tsde.Rout.save’ ... OK
Running ‘tsest.R’ [67s/68s]
Comparing ‘tsest.Rout’ to ‘tsest.Rout.save’ ... OK
checking for unstated dependencies in vignettes ... OK
checking package vignettes in ‘inst/doc’ ... OK
checking running R code from vignettes ... [38s/38s] OK
checking re-building of vignette PDFs ... [71s/70s] OK
checking PDF version of manual ... OK
NOTE: There were 3 notes.
See
‘/home/ripley/R/packages/tests32/rrcov.Rcheck/00check.log’
for details.