[R-sig-phylo] Bug in bitsplits?

[Leonid Chindelevitch]

It looks like sometimes, the splits produced are not all distinct, namely:

> Tr=rtree(10,rooted=TRUE)
> Br=bitsplits(Tr)[[1]]
> Br
 [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,]   f3   fc   f0   f0   c0   e0   f0   f0
[2,]   c0   c0   c0   40   00   00   00   00

As you can see, the last two columns are identical. I unfortunately did not
save the tree which gave me this output, but I believe it should be
possible to test all the options that have those splits to find the
offender.

Thanks,

Leonid Chindelevitch

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Re: [R-sig-phylo] Bug in bitsplits?

[Leonid Chindelevitch]

Oops, sorry, my bad, just realized that the function assumes the tree is
unrooted, so this is not a bug!

Leonid

Leonid Chindelevitch,
Assistant Professor,
School of Computing Science,
Simon Fraser University.
Office: TASC 1 9425,
 University Avenue,
Burnaby, BC V5A 1S6.
Phone: 778-782-4973.

2016-11-12 15:29 GMT-08:00 Leonid Chindelevitch :

> It looks like sometimes, the splits produced are not all distinct, namely:
>
> > Tr=rtree(10,rooted=TRUE)
> > Br=bitsplits(Tr)[[1]]
> > Br
>  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
> [1,]   f3   fc   f0   f0   c0   e0   f0   f0
> [2,]   c0   c0   c0   40   00   00   00   00
>
> As you can see, the last two columns are identical. I unfortunately did
> not save the tree which gave me this output, but I believe it should be
> possible to test all the options that have those splits to find the
> offender.
>
> Thanks,
>
> Leonid Chindelevitch
>

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Re: [R-sig-phylo] error when using function read.GenBank in ape

[Eduardo Ascarrunz]

Hi Emmanuel,

Right! Sorry I misspoke.

Best,

Eduardo

2016-11-11 23:32 GMT+01:00 Emmanuel Paradis :

> Hi Eduardo & Ting-Wen,
>
> ape 4.0 is not yet released. The available version is 3.5-0.10 and, you
> are right Eduardo, it fixes this issue. The instructions to install this
> new version of ape is here:
>
> http://ape-package.ird.fr/ape_installation.html#versions
>
> The issue (not really a bug, strictly speaking) is because NCBI servers do
> not accept HTTP requests anymore like many web services. The new version of
> read.GenBank() uses HTTPS in place of HTTP. The relevant information from
> NCBI can be found there:
>
> https://www.ncbi.nlm.nih.gov/news/06-10-2016-ncbi-https/
>
> Best,
>
> Emmanuel
>
>
> Le 11/11/2016 à 09:22, Eduardo Ascarrunz a écrit :
>
>> Hi Ting-Wen.
>>
>> Are you using the latest version of ape? Emmanuel released ape v.4.0
>> yesterday with a bug fix for that function.
>>
>> Best,
>>
>> Eduardo
>>
>> 2016-11-11 0:35 GMT+01:00 Chen, Ting-Wen <
>> ting-wen.c...@biologie.uni-goettingen.de>:
>>
>> Dear all,
>>>
>>> recently I got an error when downloading sequences in R using MacOS 10.12
>>> (but no problem when using WIndows 7). I was using the function
>>> read.GenBank in package ape and pretty sure my laptop was connecting to
>>> the
>>> internet. Following is how the error looks like:
>>>
>>> R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
>>> Copyright (C) 2016 The R Foundation for Statistical Computing
>>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>> ...
>>> [R.app GUI 1.68 (7288) x86_64-apple-darwin13.4.0]
>>>
>>> library(ape)
 read.GenBank("U15717")

>>> Error in file(file, "r") : cannot open the connection
>>>
>>> Does anybody know how to solve this problem?
>>>
>>> All the best
>>> Ting-Wen
>>>
>>> --
>>> Ting-Wen Chen
>>> J.F. Blumenbach Institute of Zoology and Anthropology
>>> Georg August University Goettingen
>>> Berliner Str. 28
>>> D-37073 Goettingen, Germany
>>> Tel: +49-55139-10943
>>>
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>>
>>
>>

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