False alarm. I cleared my workspace and re-started R and the problem has gone away. I'm curious to know how it occurred but I'm happy that it has been resolved. We now return you to your scheduled R programming...

Cheers,

Simon.


On 27/04/17 12:44, Simon Blomberg wrote:
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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