Well. Just check that you use the latest version of ape (2.7-1). If yes, can
you send me your data (privately)?
Cheers,
Emmanuel
-Original Message-
From: alfredo tello
Date: Tue, 7 Jun 2011 14:22:19
To:
Cc: ; Carl Boettiger;
Subject: Re: [R-sig-phylo] ape Crashes & latest version do
I have rerun the analysis using "nj" instead of "bionj" and no longer get
problems. Perhaps my distances are too big (¿?¿?).
Any comments would be appreciated.
Best,
A
On Tue, Jun 7, 2011 at 2:18 PM, alfredo tello wrote:
> Hi Emmanuel,
>
> I'm a bit new to phylogenetics, but I believe my distan
Hi Emmanuel,
I'm a bit new to phylogenetics, but I believe my distances are way below
100. A histogram of my distances (K80) shows they are between 0 and 0.25.
Does this make sense?
A
On Tue, Jun 7, 2011 at 2:07 PM, Emmanuel Paradis wrote:
> Hi Alfredo,
>
> I recently fixed a bug in bionj() whi
Hi Alfredo,
I recently fixed a bug in bionj() which makes R crash if some distances are too
large(> 100). Is that your case? (I guess not since you analyse DNA with K80.)
Cheers,
Emmanuel
-Original Message-
From: alfredo tello
Sender: r-sig-phylo-boun...@r-project.org
Date: Tue, 7 Jun
Here is another error message. They appear when I run "boot.phylo". I tried
using set.seed to see if that worked, but it didn't.
> boot.eryth<-boot.phylo(eryth.bionj,erythSeq,function(x){bionj(dist.dna(x,
model = "K80"))})
*** caught segfault ***
address 0x38, cause 'memory not mapped'
Tracebac
Hi Carl,
Thanks for your reply. These ape crashes seem rather random to me, but below
is an error message I just got:
> boot.amp<-boot.phylo(amp.bionj,ampSeq,function(x){bionj(dist.dna(x, model
= "K80"))})
*** caught bus error ***
address 0x1168f2000, cause 'non-existent physical address'
Trac
