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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy bugs >> Bad Binary Operator Placement: http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1322494245 Message started by DavidW on Nov 28^th, 2011 at 7:30am

Title: Bad Binary Operator Placement:
Post by DavidW on Nov 28^th, 2011 at 7:30am

Hi

On running a GARD analysis, I get an error:

Bad Binary Operator Placement:+?siteDifferenceCount

which crashes the analysis very early on (it definitely starts and accepts the commands I give it). I found a wiki entry about something similar: hyphywiki/index.php/Trouble:Bad_Binary_Operator_Placement
but it doesn't seem to be exactly the same issue and there doesn't seem to be a solution . .

Has anyone solved something similar?

Thanks.

David

Title: Re: Bad Binary Operator Placement:
Post by Sergei on Nov 28^th, 2011 at 2:20pm

Hi David,

Are you running the most recent version of HyPhy (should be version 2.10xxxx?)
The error you are seeing indicates to me that you may be running a version of HyPhy which does not understand the '+=' operator added about 9 months ago.

Sergei

Title: Re: Bad Binary Operator Placement:
Post by DavidW on Nov 28^th, 2011 at 4:33pm

Thanks Sergei

That is almost certainly the case. I shall send a request to my cluster administrator.

David

Title: Re: Bad Binary Operator Placement:
Post by Sergei on Nov 28^th, 2011 at 4:34pm

Hi David,

You can also install HyPhy in your home directory and bypass the admin to speed things up.

Sergei

Title: Re: Bad Binary Operator Placement:
Post by DavidW on Nov 29^th, 2011 at 6:07pm

Part of the problem was that I was getting the source code with:

svn co XXXXXXXdatam0nk3y.org/svn/hyphy (!) (censored with XXX so I can post the link)

It seems this could be obsolete now (2.00xxx) but will still give out source code if asked.

The other problem was that I was feeding it the wrong file ::)

The latest github code (2.1020111129beta(MP) for Linux on x86_64) seems to be working.

. . . actually, this time GARDProcessor.bf fitted a single-tree, multiple partition model, printed 30 trees to the screen but then quit with:

Fitting a mutilple tree, multiple partition model Error: Unbalanced Parentheses in Expression:]? Function call stack 1 : Build Tree tree_1 from string ] ------- 2 : ExecuteCommands in string "Tree tree_"+pccounter+" = "+partLines[pccounter*2+3]+";" using basepath /home/play/Work/Apps/hyphy/lib/hyphy/TemplateBatchFiles/. -------

Title: Re: Bad Binary Operator Placement:
Post by Sergei on Nov 30^th, 2011 at 1:08pm

Hi David,

Please be sure to supply the .splits file when prompted -- the error you see is suggesting to me that HyPhy is trying to read the NEXUS file as a list of Newick strings and coordinate ranges (which is what is in the .splits file). Take a look at page 7 in Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to