Hi Emmanuel and other list members.
I am having some problems creating and working with trees (phylo
objects) in ape. Has anyone else seen this error? The following code
reproduces the errors:
library(ape)
tr1 <- rtree(10)
plot(tr1)
Error in .reorder_ape(x, order, index.only, length(x$tip.label), io) :
object 'neworder_phylo' not found
tr2 <- rcoal(10)
Error in .reorder_ape(x, order, index.only, length(x$tip.label), io) :
object 'neworder_phylo' not found
tr3 <- read.tree(text="((a, b), (c, d));")
compute.brlen(tr3)
Error in .reorder_ape(x, order, index.only, length(x$tip.label), io) :
object 'neworder_phylo' not found
########## All have the same traceback:
> traceback()
4: .reorder_ape(x, order, index.only, length(x$tip.label), io)
3: reorder.phylo(phy, "postorder")
2: reorder(phy, "postorder")
1: compute.brlen(tr3)
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 17.04
Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.19.so
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ape_4.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.10 magrittr_1.5 splines_3.4.0 MASS_7.3-47
[5] munsell_0.4.3 colorspace_1.3-2 lattice_0.20-35 minqa_1.2.4
[9] stringr_1.2.0 glmmADMB_0.8.3.3 plyr_1.8.4 tcltk_3.4.0
[13] tools_3.4.0 parallel_3.4.0 nnet_7.3-12 grid_3.4.0
[17] nlme_3.1-131 gtable_0.2.0 coda_0.19-1 fortunes_1.5-4
[21] lme4_1.1-13 lazyeval_0.2.0 tibble_1.3.0 Matrix_1.2-8
[25] R2admb_0.7.15 nloptr_1.0.4 ggplot2_2.2.1 effects_3.1-2
[29] stringi_1.1.5 compiler_3.4.0 scales_0.4.1
I am not getting the error on two other machines with the same OS and
(as far as I can tell) the same setup. Any help would be greatly
appreciated!
Cheers,
Simon.
--
Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat.
Senior Lecturer and Consultant Statistician
School of Biological Sciences
The University of Queensland
St. Lucia Queensland 4072
Australia
T: +61 7 3365 2506
email: S.Blomberg1_at_uq.edu.au
http://www.evolutionarystatistics.org
Policies:
1. I will NOT analyse your data for you.
2. Your deadline is your problem.
Basically, I'm not interested in doing research and
I never have been. I'm interested in understanding,
which is quite a different thing. And often to
understand something you have to work it out for
yourself because no one else has done it.
- David Blackwell
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