[maker-devel] MAKER installation debugging

[Carson Holt]

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