[maker-devel] MAKER installation debugging

[Jacqueline R M Doyle]

Hi Carson,

I am using MAKER 2.10 (I downloaded it so long ago I'd forgotten there were two options).  Would it be better for me to start over with 2.27?

Best wishes, Jackie

Department of Forestry and Natural Resources
Purdue University
West Lafayette, IN 47907 
Phone: 270-293-9486
E-mail: jmdoyle at purdue.edu

----- Original Message -----
From: Carson Holt <carsonhh at gmail.com>
To: Jacqueline R M Doyle <jmdoyle at purdue.edu>
Cc: maker-devel at yandell-lab.org
Sent: Tue, 07 May 2013 11:19:57 -0400 (EDT)
Subject: Re: [maker-devel] MAKER installation debugging

Which version of MAKER are you using.  Is it 2.10 or 2.27?

Thanks,
Carson



On 13-05-07 11:12 AM, "Jacqueline R M Doyle" <jmdoyle at purdue.edu> wrote:

>Hi Carson,
>
>Thanks for the quick reply!  I don't remember any errors during Blast
>installation, it appeared to install fine with the ./Build command.
>Augustus, Repeatmasker and SNAP were the programs I could not install
>with the ./Build commands, and instead installed manually.  I've attached
>the error messages I received when I tried to use the ./Build commands.
>I've tested out the three programs I installed manually and they seem to
>work fine on their own.
>
>I do have xcode installed.  How would I determine if I have "non-standard
>libraries via Mac ports"?
>
>Thanks again for your help with this.
>
>Best wishes, Jackie
>
>Department of Forestry and Natural Resources
>Purdue University
>West Lafayette, IN 47907
>Phone: 270-293-9486
>E-mail: jmdoyle at purdue.edu
>
>----- Original Message -----
>From: "Carson Holt" <carsonhh at gmail.com>
>To: "Jacqueline R M Doyle" <jmdoyle at purdue.edu>,
>maker-devel at yandell-lab.org
>Sent: Monday, May 6, 2013 10:02:52 AM
>Subject: Re: [maker-devel] MAKER installation debugging
>
>Most maker development and debugging actually happens on a Mac (OS X
>10.7.5).  Blast, Augustus, SNAP all install for me just fine with maker
>2.27.  What errors do you get during installation?  Do you by any chance
>have non-standard libraries via Mac ports for example.  Do you have xcode
>installed (it provides the appropriate 'make' command for compiling C)?
>
>Thanks,
>Carson
>
>
>On 13-05-05 7:55 AM, "Jacqueline R M Doyle" <jmdoyle at purdue.edu> wrote:
>
>>Hi!
>>
>>I've recently attempted to install MAKER (Mac OS X).  I installed blast
>>and exonerate using the ./Build blast and ./Build exonerate commands, and
>>I manually installed repeatmasker, snap and augustus (I couldn't get the
>>./Build commands to work).  I then attempted to test out maker following
>>the 2012 MAKER tutorial.  I received the blastx error message pasted
>>below, and there is additional information in the maker log I've attached
>>to this email.  I was wondering if anyone had any suggestions about
>>debugging, as I'm not quite sure where to begin...
>>
>>Best wishes and thanks, Jackie
>>
>>
>>#--------- command -------------#
>>Widget::formater:
>>/usr/local/maker/bin/../exe/blast/bin/makeblastdb -dbtype prot -in
>>/tmp/maker_0GBY28/te_proteins%2Efasta.mpi.10.0
>>#-------------------------------#
>>dyld: lazy symbol binding failed: Symbol not found:
>>__ZSt16__ostream_insertIcSt11char_traitsIcEERSt13basic_ostreamIT_T0_ES6_P
>>K
>>S3_i
>>  Referenced from: /usr/local/maker/bin/../exe/blast/bin/makeblastdb
>>  Expected in: flat namespace
>>
>>dyld: Symbol not found:
>>__ZSt16__ostream_insertIcSt11char_traitsIcEERSt13basic_ostreamIT_T0_ES6_P
>>K
>>S3_i
>>  Referenced from: /usr/local/maker/bin/../exe/blast/bin/makeblastdb
>>  Expected in: flat namespace
>>
>>ERROR: /usr/local/maker/bin/../exe/blast/bin/makeblastdb failed in
>>Widget::formater
>>
>>FATAL ERROR
>>ERROR: Failed while doing blastx repeats!!
>>
>>ERROR: Chunk failed at level 3
>>!!
>>FAILED CONTIG:contig-dpp-500-500
>>
>>
>>Department of Forestry and Natural Resources
>>Purdue University
>>West Lafayette, IN 47907
>>Phone: 270-293-9486
>>E-mail: jmdoyle at purdue.edu
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>
>