- using R version 2.9.0 Under development (unstable) (2008-12-02 r47034)
- using session charset: UTF-8
- checking for file 'ape/DESCRIPTION' ... OK
- this is package 'ape' version '2.2-2'
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking whether package 'ape' can be installed ... 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 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
birth.step: no visible global function definition for ‘loglik’
chronopl.cv: no visible binding for global variable ‘tmp’
death.step: no visible global function definition for ‘loglik’
ht.move: no visible global function definition for ‘loglik’
loglik.pop: no visible binding for global variable ‘b.lin’
mcmc.popsize: no visible binding for '<<-' assignment to ‘loglik’
mcmc.popsize: no visible global function definition for ‘loglik’
plot.popsize: no visible binding for global variable ‘popsize’
pos.move: no visible global function definition for ‘loglik’
- checking Rd files ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking data for non-ASCII characters ... 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 ... OK
- creating ape-Ex.R ... OK
- checking examples ... ERROR
Running examples in 'ape-Ex.R' failed.
The error most likely occurred in:
> ### * ace
>
> flush(stderr()); flush(stdout())
>
> ### Name: ace
> ### Title: Ancestral Character Estimation
> ### Aliases: ace logLik.ace deviance.ace AIC.ace anova.ace
> ### Keywords: models
>
> ### ** Examples
>
> ### Just some random data...
> data(bird.orders)
> x <- rnorm(23)
> ### Compare the three methods for continuous characters:
> ace(x, bird.orders)
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(p[1]) : NaNs produced
Warning in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), hessian = TRUE) :
NA/Inf replaced by maximum positive value
$loglik
[1] 69.4859
$ace
24 25 26 27 28 29 30
0.14486501 0.13779047 0.03961056 0.19952298 0.21889447 0.14823409 0.17570662
31 32 33 34 35 36 37
0.21131933 0.24833314 0.28994152 0.25899255 0.35950657 0.19417155 0.19336125
38 39 40 41 42 43 44
0.25371586 0.29144287 0.30333683 0.28552899 0.37759191 0.33019148 0.37410228
45
0.40512709
$sigma2
[1] 0.015632150 0.002386939
$CI95
[,1] [,2]
[1,] -0.168499898 0.4582299
[2,] -0.191301280 0.4668822
[3,] -0.357054139 0.4362753
[4,] -0.161160368 0.5602063
[5,] -0.158791494 0.5965804
[6,] -0.143831935 0.4403001
[7,] -0.102451652 0.4538649
[8,] -0.036969826 0.4596085
[9,] -0.013563916 0.5102302
[10,] 0.006760152 0.5731229
[11,] -0.089210163 0.6071953
[12,] 0.038104678 0.6809085
[13,] -0.055013090 0.4433562
[14,] -0.055971621 0.4426941
[15,] 0.005561533 0.5018702
[16,] 0.044635594 0.5382501
[17,] 0.042220025 0.5644536
[18,] 0.002337522 0.5687205
[19,] 0.068108097 0.6870757
[20,] 0.062278007 0.5981050
[21,] 0.087535167 0.6606694
[22,] 0.098902594 0.7113516
$call
ace(x = x, phy = bird.orders)
attr(,"class")
[1] "ace"
> ace(x, bird.orders, method = "pic")
$ace
24 25 26 27 28 29
0.14486514 0.11650354 -0.22140524 0.36243033 0.37982609 0.15993555
30 31 32 33 34 35
0.30467262 0.27857807 0.59618157 0.55346095 0.13519648 0.95081220
36 37 38 39 40 41
0.07247573 0.18996664 0.58574236 0.49585533 0.41703151 -0.03056194
42 43 44 45
0.88252870 0.57893715 0.76310686 0.85055684
$CI95
[,1] [,2]
[1,] -6.892373 7.182104
[2,] -9.861399 10.094406
[3,] -13.163105 12.720295
[4,] -11.232873 11.957734
[5,] -12.502372 13.262024
[6,] -10.750220 11.070091
[7,] -10.440364 11.049709
[8,] -6.007715 6.564872
[9,] -10.444756 11.637119
[10,] -9.314719 10.421641
[11,] -12.506191 12.776584
[12,] -12.079632 13.981257
[13,] -10.418263 10.563215
[14,] -10.106972 10.486906
[15,] -9.589275 10.760760
[16,] -6.574378 7.566088
[17,] -8.972403 9.806466
[18,] -12.822987 12.761863
[19,] -11.636717 13.401775
[20,] -10.064076 11.221950
[21,] -10.245891 11.772104
[22,] -11.576295 13.277409
$call
ace(x = x, phy = bird.orders, method = "pic")
attr(,"class")
[1] "ace"
> ace(x, bird.orders, method = "GLS",
+ corStruct = corBrownian(1, bird.orders))
Warning in Initialize.corPhyl(corStruct, data.frame(x)) :
Row names in dataframe do not match tree tip names. data taken to be in the same order as in tree.
Warning in Initialize.corPhyl(corStruct, data.frame(x)) :
Row names in dataframe do not match tree tip names. data taken to be in the same order as in tree.
Warning in Initialize.corPhyl(X[[1L]], ...) :
Row names in dataframe do not match tree tip names. data taken to be in the same order as in tree.
$ace
24 25 26 27 28 29 30
0.14486514 0.13779023 0.03961013 0.19952231 0.21889379 0.14823414 0.17570696
31 32 33 34 35 36 37
0.21131958 0.24833352 0.28994180 0.25899274 0.35950711 0.19417180 0.19336105
38 39 40 41 42 43 44
0.25371656 0.29144313 0.30333729 0.28552933 0.37759260 0.33019173 0.37410259
45
0.40512751
$CI95
[,1] [,2]
[1,] 0.1448651 0.1448651
[2,] -2.3228405 2.5984210
[3,] -3.7868947 3.8661149
[4,] -3.1977779 3.5968225
[5,] -3.4759962 3.9137837
[6,] -1.5788146 1.8752829
[7,] -1.8843580 2.2357719
[8,] -2.0423904 2.4650295
[9,] -2.2481465 2.7448135
[10,] -2.5325002 3.1123839
[11,] -3.3588228 3.8768082
[12,] -2.9337557 3.6527699
[13,] -2.1692131 2.5575567
[14,] -2.2805229 2.6672450
[15,] -2.2627248 2.7701579
[16,] -2.2499528 2.8328390
[17,] -2.4132483 3.0199228
[18,] -2.6802074 3.2512661
[19,] -2.8831307 3.6383159
[20,] -2.4673684 3.1277518
[21,] -2.6393096 3.3875148
[22,] -2.8275930 3.6378480
$call
ace(x = x, phy = bird.orders, method = "GLS", corStruct = corBrownian(1,
bird.orders))
attr(,"class")
[1] "ace"
> ### For discrete characters:
> x <- factor(c(rep(0, 5), rep(1, 18)))
> ans <- ace(x, bird.orders, type = "d")
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(sum(liks[nb.tip + 1, ])) : NaNs produced
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(sum(liks[nb.tip + 1, ])) : NaNs produced
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(sum(liks[nb.tip + 1, ])) : NaNs produced
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(sum(liks[nb.tip + 1, ])) : NaNs produced
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(sum(liks[nb.tip + 1, ])) : NaNs produced
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(sum(liks[nb.tip + 1, ])) : NaNs produced
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(sum(liks[nb.tip + 1, ])) : NaNs produced
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(sum(liks[nb.tip + 1, ])) : NaNs produced
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(sum(liks[nb.tip + 1, ])) : NaNs produced
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(sum(liks[nb.tip + 1, ])) : NaNs produced
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(sum(liks[nb.tip + 1, ])) : NaNs produced
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
> #### Showing the likelihoods on each node:
> plot(bird.orders, type = "c", FALSE, label.offset = 1)
> co <- c("blue", "yellow")
> tiplabels(pch = 22, bg = co[as.numeric(x)], cex = 2, adj = 1)
> nodelabels(thermo = ans$lik.anc, piecol = co, cex = 0.75)
> ### An example of the use of the argument `ip':
> tr <- character(4)
> tr[1] <- "((((t10:5.03,t2:5.03):2.74,(t9:4.17,"
> tr[2] <- "t5:4.17):3.60):2.80,(t3:4.05,t7:"
> tr[3] <- "4.05):6.53):2.32,((t6:4.38,t1:4.38):"
> tr[4] <- "2.18,(t8:2.17,t4:2.17):4.39):6.33);"
> tr <- read.tree(text = paste(tr, collapse = ""))
> y <- c(rep(1, 6), rep(2, 4))
> ### The default `ip = 0.1' makes ace fails:
> ace(y, tr, type = "d")
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Warning in log(sum(liks[nb.tip + 1, ])) : NaNs produced
Warning in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
NA/Inf replaced by maximum positive value
Error in nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) :
non-finite value supplied by 'nlm'
Calls: ace -> nlm
Execution halted