Problems with special keys

[Leonardo Borges]

I have POY5 installed from source in a mac.

The program runs finely, but it is not recognizing special keys such as escape, arrows and control and life gets harder without then.

I am guessing the problem is with Ocaml, but I have no clue about how to fix it.

I would appreciate any ideas that may be of help, please

Leonardo

[Nicholas Lucaroni]

The OCaml toplevel does not have line editing by default. You will have to install either ncurses or readline. We detect them automatically if they exist but to specify that one should be used configure with,

./configure --enable-interface=readline

and it will force readline to be used, or throw an error that you don't have it.


Also, just a heads up, the PDF tutorial you've downloaded may not be correct in some of the commands as they've changed in POY5.


Regards,
Nick

[Ward Wheeler]

 I'm going to update that this week. 

W

Sent from mobile

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[Leonardo Borges]

New tutorial = nice

Nick, that means I will have to reinstall it all over?

Thanks!

Leo

aquitemcaqui.com

[Ashish Agarwal]

I would recommend the new utop instead of the normal ocaml toplevel. Utop is really nice. Just do `opam install utop`.

--

[Nicholas Lucaroni]

Actually no.

I believe readline comes with rlwrap that will wrap readline around any application. This should be sufficient for your use --although I've not tried it.

nick

[Nicholas Lucaroni]

I will be giving that a shot, thanks.

nick

[Ward C Wheeler]

Hello,

I checked the POY 4.0 tutorial by Andres and Megan, and the issues I was concerned with--basically

the transform (tcm:(blah, blah)) type commands--are fine.  So looks like that tutorial is good to go.

If you find any other problems, please tell me and I'll work to fix them.

W

On Sep 10, 2013, at 11:08 PM, Nicholas Lucaroni <nicholas....@gmail.com>

Ward Wheeler

Division of Invertebrate Zoology

American Museum of Natural History

Central Park West at 79th Street

New York, NY 10024-5192

USA

whe...@amnh.org

http://www.amnh.org/our-research/staff-directory/ward-wheeler

http://www.amnh.org/our-research/computational-sciences/research/projects/systematic-biology/poy/download

http://www.wiley.com/WileyCDA/WileyTitle/productCd-047067170X.html

[Leonardo Borges]

I am going through it without problems for now, but if I find anything, I will let you guys know!

Thanks ;)

Leonardo

aquitemcaqui.com

[Leonardo Borges]

I installed readline, but it did not work until I recompiled POY5. Everything is fine now.

I saw utop as a potential option but did not tryed it. Looks nice.

Leonardo

aquitemcaqui.com

[Cyrille D'Haese]

Hi Ward,

just a little snag (if I'm correct?) with the tree parser.
When I ask branch length (report ("file.trees", trees:(branches,total))), some branches have length in the form: -1.61061e+09 (see an example attached).
The problem is when I want to read these trees with POY5 (for fusing for instance), POY5 crashes and retuns this:
Fatal error: exception Tree.Parse.Illegal_tree_format("Unexpected Char +")
No problem with integer-branch length though

Cyrille

Le 11/09/13 15:17, Ward C Wheeler a écrit :

-- 
Cyrille D'Haese

UMR 7205 CNRS
Origine, Structure et Evolution de la Biodiversite
Departement Systematique et Evolution
Museum National d'Histoire Naturelle
CP50 - Entomologie
45 rue Buffon, 75231 Paris cedex 05, FRANCE

Voice: +33 (0)1 40 79 57 36
Fax: +33 (0)1 40 79 56 79
e-mail: dha...@mnhn.fr

[Nicholas Lucaroni]

Thanks Cyrille.

The tree parser works with e-09, but not e+09. I'll resolve that. In the mean time, you can remove the + symbol from the file and it will read the tree in correctly.

Nick

http://www.amnh.org/our-research/staff-directory/ward-wheeler

http://www.amnh.org/our-research/computational-sciences/research/projects/systematic-biology/poy/download

http://www.wiley.com/WileyCDA/WileyTitle/productCd-047067170X.html

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[dha...@mnhn.fr]

Thanks a lot, that's an easy one.

Cyrille

Nicholas Lucaroni <nicholas....@gmail.com> a �crit�:

> Thanks Cyrille.
>
> The tree parser works with e-09, but not e+09. I'll resolve that. In the
> mean time, you can remove the + symbol from the file and it will read the
> tree in correctly.
>
> Nick
>
> On Friday, September 13, 2013 3:56:56 AM UTC-4, Cyrille wrote:
>>
>> Hi Ward,
>>
>> just a little snag (if I'm correct?) with the tree parser.
>> When I ask branch length (report ("file.trees", trees:(branches,total))),
>> some branches have length in the form: -1.61061e+09 (see an example
>> attached).
>> The problem is when I want to read these trees with POY5 (for fusing for
>> instance), POY5 crashes and retuns this:
>> Fatal error: exception Tree.Parse.Illegal_tree_format("Unexpected Char +")
>> No problem with integer-branch length though
>>
>> Cyrille
>>

>> Le 11/09/13 15:17, Ward C Wheeler a �crit :

>>
>> Hello,
>> I checked the POY 4.0 tutorial by Andres and Megan, and the issues I was
>> concerned with--basically
>> the transform (tcm:(blah, blah)) type commands--are fine. So looks like
>> that tutorial is good to go.
>>
>> If you find any other problems, please tell me and I'll work to fix them.
>> W
>>
>> On Sep 10, 2013, at 11:08 PM, Nicholas Lucaroni

>> <nicholas....@gmail.com<javascript:>

>> email to poy4+uns...@googlegroups.com <javascript:>.
>> To post to this group, send email to po...@googlegroups.com <javascript:>.

>> Visit this group at http://groups.google.com/group/poy4.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>>
>> Ward Wheeler
>> Division of Invertebrate Zoology
>> American Museum of Natural History
>> Central Park West at 79th Street
>> New York, NY 10024-5192
>> USA
>> http://www.amnh.org/our-research/staff-directory/ward-wheeler
>>
>>
>> http://www.amnh.org/our-research/computational-sciences/research/projects/systematic-biology/poy/download
>>
>>

>> http://www.wiley.com/WileyCDA/WileyTitle/productCd-047067170X.html
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "POY - Phylogenetic Analysis Software" group.
>> To unsubscribe from this group and stop receiving emails from it, send an

>> email to poy4+uns...@googlegroups.com <javascript:>.
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>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>>
>> --
>> Cyrille D'Haese
>>
>> UMR 7205 CNRS
>> Origine, Structure et Evolution de la Biodiversite
>> Departement Systematique et Evolution
>> Museum National d'Histoire Naturelle
>> CP50 - Entomologie
>> 45 rue Buffon, 75231 Paris cedex 05, FRANCE
>>
>> Voice: +33 (0)1 40 79 57 36
>> Fax: +33 (0)1 40 79 56 79

>> e-mail: dha...@mnhn.fr <javascript:>

>>
>>
>
> --
> You received this message because you are subscribed to the Google
> Groups "POY - Phylogenetic Analysis Software" group.
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>



--
Cyrille D'Haese

UMR 7205 CNRS

"Origine, Structure et Evolution de la Biodiversit�"
D�partement Syst�matique et Evolution
Mus�um National d'Histoire Naturelle