[maker-devel] MAKER installation debugging

[Jacqueline R M Doyle]

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_PK
>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_PK
>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
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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