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...



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:

tr1 <- rtree(10)


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));")


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

 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=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!



Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat.
Senior Lecturer and Consultant Statistician
School of Biological Sciences
The University of Queensland
St. Lucia Queensland 4072
T: +61 7 3365 2506
email: S.Blomberg1_at_uq.edu.au

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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