Hi Simon and others,

  I ran into the same problems a few days ago and I suspect it's
related to changes associated with R 3.4.0. Re-installing ape solved
the issue for me.

  Cheers,
  -- François

On Wed, Apr 26, 2017 at 11:01 PM, Simon Blomberg <s.blombe...@uq.edu.au> wrote:
> 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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> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
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