[Seqinr-forum] bug in dist,alignment

[Jean Lobry]

I was able to reproduce this behaviour (cf. crash.png)
with :

 > sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: 
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_3.5.1 tools_3.5.1

Le 10/02/2020 à 05:56, Russell J Gray a écrit :
> Hi there,
> 
> I'm trying to use the seqinr package for some ITS sequence analysis and 
> when I run the first basic functions of the package it automatically 
> crashes R. I've attached my FASTA text file, and have copied my code 
> here....
> Once you run the line "*D <- dist.alignment(dna, matrix = 
> "similarity")*" if you try to view the dna data, or if R autocompletes a 
> function, or you try to do anything further, R runs the "Fatal Error" 
> window and says it cannot connect to the server.
> 
> 
> *library(seqinr)*
> *library(adegenet)*
> *library(ape)*
> *library(ggtree)*
> *
> *
> *
> *
> *dna <- read.alignment("Amanita.txt", format = "fasta")*
> *D <- dist.alignment(dna, matrix = "similarity")*
> *
> *
> 
> Any help is appreciated!
> 
> Best regards
> 
> -RG
> 
> 
> *--*
> *Russell J. Gray*
> Wildlife Ecology & Conservation Consultant
> 
> 0934581341 | rgrayherpetology at gmail.com <mailto:rgrayherpetology at gmail.com>
> 
> https://www.rjgrayecology.com/
> 
> 705 alligator ranch rd. New Smyrna Beach, FL, USA. 32168
> 
> 
> 
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