CRAN Package Check Results for Package ouch

Last updated on 2021-07-27 07:50:35 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.17 6.41 37.48 43.89 ERROR
r-devel-linux-x86_64-debian-gcc 2.17 4.59 33.21 37.80 OK
r-devel-linux-x86_64-fedora-clang 2.17 67.89 OK
r-devel-linux-x86_64-fedora-gcc 2.17 57.17 OK
r-devel-windows-x86_64 2.17 13.00 63.00 76.00 OK
r-devel-windows-x86_64-gcc10-UCRT 2.17 OK
r-patched-linux-x86_64 2.17 6.15 41.04 47.19 OK
r-patched-solaris-x86 2.17 83.70 OK
r-release-linux-x86_64 2.17 5.16 41.73 46.89 OK
r-release-macos-arm64 2.17 OK
r-release-macos-x86_64 2.17 OK
r-release-windows-ix86+x86_64 2.17 17.00 63.00 80.00 OK
r-oldrel-macos-x86_64 2.17 OK
r-oldrel-windows-ix86+x86_64 2.17 12.00 79.00 91.00 OK

Check Details

Version: 2.17
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'geiger'
Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.17
Check: examples
Result: ERROR
    Running examples in 'ouch-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: hansen
    > ### Title: Ornstein-Uhlenbeck models of trait evolution
    > ### Aliases: hansen hansentree-class
    > ### Keywords: models
    >
    > ### ** Examples
    >
    > ## Analysis of sexual size dimorphism data
    > tree <- with(anolis.ssd,ouchtree(node,ancestor,time/max(time),species))
    > plot(tree,node.names=TRUE)
    >
    > h1 <- brown(anolis.ssd['log.SSD'],tree)
    > h1
    
    call:
    brown(data = anolis.ssd["log.SSD"], tree = tree)
     nodes ancestors times labels log.SSD
    1 1 <NA> 0.0000 <NA> NA
    2 2 1 0.1614 <NA> NA
    3 3 2 0.1845 <NA> NA
    4 4 3 0.4778 <NA> NA
    5 5 3 0.3909 <NA> NA
    6 6 3 0.5026 <NA> NA
    7 7 3 0.2372 <NA> NA
    8 8 7 0.6986 <NA> NA
    9 9 7 0.4864 <NA> NA
    10 10 9 0.6838 <NA> NA
    11 11 3 0.2783 <NA> NA
    12 12 11 0.5529 <NA> NA
    13 13 11 0.4259 <NA> NA
    14 14 3 0.2826 <NA> NA
    15 15 14 0.3998 <NA> NA
    16 16 1 1.0000 oc -0.00512
    17 17 2 1.0000 eq 0.08454
    18 18 4 1.0000 co 0.24703
    19 19 4 1.0000 aln 0.24837
    20 20 5 1.0000 ol 0.09844
    21 21 5 1.0000 in 0.06137
    22 22 6 1.0000 cu 0.09501
    23 23 6 1.0000 ri 0.08947
    24 24 8 1.0000 sa 0.28893
    25 25 8 1.0000 op 0.15963
    26 26 9 1.0000 va 0.14766
    27 27 9 1.0000 li 0.38873
    28 28 10 1.0000 ga 0.28768
    29 29 10 1.0000 gr 0.39786
    30 30 12 1.0000 br 0.17106
    31 31 12 1.0000 di 0.13801
    32 32 13 1.0000 kr 0.23478
    33 33 13 1.0000 cr 0.39796
    34 34 13 1.0000 st 0.15737
    35 35 3 1.0000 cy 0.26024
    36 36 14 1.0000 alu 0.08216
    37 37 15 1.0000 lo 0.13108
    38 38 15 1.0000 an 0.13547
    
    sigma squared:
     [,1]
    [1,] 0.01396655
    
    theta:
    NULL
     loglik deviance aic aic.c sic dof
     19.17721 -38.35443 -34.35443 -33.75443 -32.08344 2.00000
    > plot(h1)
    >
    > h2 <- hansen(anolis.ssd['log.SSD'],tree,anolis.ssd['OU.1'],sqrt.alpha=1,sigma=1)
    > h2
    
    call:
    hansen(data = anolis.ssd["log.SSD"], tree = tree, regimes = anolis.ssd["OU.1"],
     sqrt.alpha = 1, sigma = 1)
     nodes ancestors times labels OU.1 log.SSD
    1 1 <NA> 0.0000 <NA> ns NA
    2 2 1 0.1614 <NA> ns NA
    3 3 2 0.1845 <NA> ns NA
    4 4 3 0.4778 <NA> ns NA
    5 5 3 0.3909 <NA> ns NA
    6 6 3 0.5026 <NA> ns NA
    7 7 3 0.2372 <NA> ns NA
    8 8 7 0.6986 <NA> ns NA
    9 9 7 0.4864 <NA> ns NA
    10 10 9 0.6838 <NA> ns NA
    11 11 3 0.2783 <NA> ns NA
    12 12 11 0.5529 <NA> ns NA
    13 13 11 0.4259 <NA> ns NA
    14 14 3 0.2826 <NA> ns NA
    15 15 14 0.3998 <NA> ns NA
    16 16 1 1.0000 oc ns -0.00512
    17 17 2 1.0000 eq ns 0.08454
    18 18 4 1.0000 co ns 0.24703
    19 19 4 1.0000 aln ns 0.24837
    20 20 5 1.0000 ol ns 0.09844
    21 21 5 1.0000 in ns 0.06137
    22 22 6 1.0000 cu ns 0.09501
    23 23 6 1.0000 ri ns 0.08947
    24 24 8 1.0000 sa ns 0.28893
    25 25 8 1.0000 op ns 0.15963
    26 26 9 1.0000 va ns 0.14766
    27 27 9 1.0000 li ns 0.38873
    28 28 10 1.0000 ga ns 0.28768
    29 29 10 1.0000 gr ns 0.39786
    30 30 12 1.0000 br ns 0.17106
    31 31 12 1.0000 di ns 0.13801
    32 32 13 1.0000 kr ns 0.23478
    33 33 13 1.0000 cr ns 0.39796
    34 34 13 1.0000 st ns 0.15737
    35 35 3 1.0000 cy ns 0.26024
    36 36 14 1.0000 alu ns 0.08216
    37 37 15 1.0000 lo ns 0.13108
    38 38 15 1.0000 an ns 0.13547
    
    alpha:
     [,1]
    [1,] 1.467433
    
    sigma squared:
     [,1]
    [1,] 0.036078
    
    theta:
    $log.SSD
     ns
    0.1701043
    
     loglik deviance aic aic.c sic dof
     18.72447 -37.44894 -31.44894 -30.18579 -28.04246 3.00000
    > plot(h2)
    >
    > h3 <- hansen(anolis.ssd['log.SSD'],tree,anolis.ssd['OU.7'],sqrt.alpha=1,sigma=1)
    > h3
    
    call:
    hansen(data = anolis.ssd["log.SSD"], tree = tree, regimes = anolis.ssd["OU.7"],
     sqrt.alpha = 1, sigma = 1)
     nodes ancestors times labels OU.7 log.SSD
    1 1 <NA> 0.0000 <NA> anc NA
    2 2 1 0.1614 <NA> anc NA
    3 3 2 0.1845 <NA> anc NA
    4 4 3 0.4778 <NA> anc NA
    5 5 3 0.3909 <NA> anc NA
    6 6 3 0.5026 <NA> anc NA
    7 7 3 0.2372 <NA> anc NA
    8 8 7 0.6986 <NA> anc NA
    9 9 7 0.4864 <NA> anc NA
    10 10 9 0.6838 <NA> anc NA
    11 11 3 0.2783 <NA> anc NA
    12 12 11 0.5529 <NA> anc NA
    13 13 11 0.4259 <NA> anc NA
    14 14 3 0.2826 <NA> anc NA
    15 15 14 0.3998 <NA> anc NA
    16 16 1 1.0000 oc tw -0.00512
    17 17 2 1.0000 eq cg 0.08454
    18 18 4 1.0000 co tc 0.24703
    19 19 4 1.0000 aln tc 0.24837
    20 20 5 1.0000 ol gb 0.09844
    21 21 5 1.0000 in tw 0.06137
    22 22 6 1.0000 cu cg 0.09501
    23 23 6 1.0000 ri cg 0.08947
    24 24 8 1.0000 sa tg 0.28893
    25 25 8 1.0000 op gb 0.15963
    26 26 9 1.0000 va tw 0.14766
    27 27 9 1.0000 li tg 0.38873
    28 28 10 1.0000 ga cg 0.28768
    29 29 10 1.0000 gr tc 0.39786
    30 30 12 1.0000 br tr 0.17106
    31 31 12 1.0000 di tr 0.13801
    32 32 13 1.0000 kr gb 0.23478
    33 33 13 1.0000 cr tg 0.39796
    34 34 13 1.0000 st tc 0.15737
    35 35 3 1.0000 cy tg 0.26024
    36 36 14 1.0000 alu gb 0.08216
    37 37 15 1.0000 lo tr 0.13108
    38 38 15 1.0000 an tw 0.13547
    
    alpha:
     [,1]
    [1,] 1.701222
    
    sigma squared:
     [,1]
    [1,] 0.008972998
    
    theta:
    $log.SSD
     anc cg gb tc tg tr
     0.42888400 -0.07846662 -0.03522045 0.10092536 0.27268559 -0.06731370
     tw
    -0.09102223
    
     loglik deviance aic aic.c sic dof
     36.13374 -72.26747 -54.26747 -40.42132 -44.04803 9.00000
    > plot(h3)
    > ### Darwin's finches
    > library(geiger)
    Error in library(geiger) : there is no package called 'geiger'
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang