[maker-devel] maker-2.23

Thu Feb 23 10:00:37 MST 2012

Carson,

Reinstalled storable, forks and forks::shared
Re-compiled maker
Same problem

Change from forks/forks::shared to threads/threads::shared in the compiled
executable and
Running maker gives me:

"Execution of /usr/local/bioinfosoft/maker-2.23/bin/maker aborted due to
compilation errors."

Ideas?

Thanks

--R

On Thu, Feb 23, 2012 at 09:26, Carson Holt <carsonhh at gmail.com> wrote:

> All MAKER versions after 2.2 use the CPAN forks.pm module rather than
> threads.pm.  forks.pm is just a drop in replacement for threads.pm so you
> can use the same syntax for forks as you do with threads.  Even if you have
> perl compiled with threads MAKER still uses forks.pm (I am referring to
> the about the module forks.pm and not forks themselves).  The place where
> you get the error suggests the problem is at the C level, so the forks.pmmodule from CPAN and Storable.pm are the  two most likely culprits.
>  Reinstalling both of those would be the first thing to do.  If you have
> threaded perl you can just change the 'use' statement at the start of
> MAKER, but if you don't have threaded perl, just reinstall forks.pm.
>  Don't worry about changing the perl installation.
>
> Thanks,
> Carson
>
> From: Rodolfo Aramayo <raramayo at tamu.edu>
> Date: Thu, 23 Feb 2012 09:17:36 -0600
> To: Carson Holt <carsonhh at gmail.com>
> Cc: MAKER <maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] maker-2.23
>
> Thanks Carson...please see below
>
> On Thu, Feb 23, 2012 at 08:56, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Try two things for me.  Install/Re-install the latest version of the CPAN
>> Storable module.  Install/Re-install forks and forks::shared from CPAN.
>>  Alternatively change 'use forks' to 'use threads' and 'use forks::shared'
>> to 'use threads::shared' in the MAKER executable.  Those modules are
>> supposed to be drop in replacements for each other.
>>
>
> which modules? I assume threads will be dropped, right?
> and if this is the case what are the advantages/disadvantages of using Perl
> 5, version 12, subversion 3 (v5.12.3) built for darwin-thread-multi-2level
> should I change to non-threads version?? or it does not matter
>
> Thanks
>
> --R
>
>
>> Thanks,
>> Carson
>>
>> From: Rodolfo Aramayo <raramayo at tamu.edu>
>> Date: Thu, 23 Feb 2012 08:47:32 -0600
>> To: MAKER <maker-devel at yandell-lab.org>
>> Subject: [maker-devel] maker-2.23
>>
>> I am running into an unusual problem
>> If I run Maker in the maker01 directory, say
>> "/Volumes/g0006/maker/maker01" things go well no problem so far...but if I
>> start a second maker inside the maker02 directory:
>> "/Volumes/g0006/maker/maker02"
>> the second maker quits with a: "[3]+  Abort trap              nohup
>> maker" and in the nohup file I see the following:
>>
>>
>> ##########################################################################################################
>> ...
>> ...
>> ...
>> ...
>> #-------------------------------#
>> re reading genemark report.
>>
>> /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_final_1000-10000.maker.output/SK4_01assembly_total_final_1000-10000_datastore/C6/70/NODE_2_length_2929_cov_50.101059//theVoid.NODE_2_length_2929_cov_50.101059/NODE_2_length_2929_cov_50%2E101059.all.Ralstonia_solanacearum%2Emod.genemark
>> running  genemark.
>> #--------- command -------------#
>> Widget::genemark:
>> /opt/local/bin/perl
>> /usr/local/bioinfosoft/maker-2.23/bin/../lib/Widget/genemark/gmhmm_wrap -m
>> /Volumes/a0003/bioinfodata/genemark/hmm/Ralstonia_solanacearum_plasmid_pGMI1000MP.mod
>> -g /usr/local/bioinfosoft/genemark/gmhmmp -p
>> /usr/local/bioinfosoft/genemark/probuild -o
>> /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_final_1000-10000.maker.output/SK4_01assembly_total_final_1000-10000_datastore/C6/70/NODE_2_length_2929_cov_50.101059//theVoid.NODE_2_length_2929_cov_50.101059/NODE_2_length_2929_cov_50%2E101059.all.Ralstonia_solanacearum_plasmid_pGMI1000MP%2Emod.genemark
>> /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_final_1000-10000.maker.output/SK4_01assembly_total_final_1000-10000_datastore/C6/70/NODE_2_length_2929_cov_50.101059//theVoid.NODE_2_length_2929_cov_50.101059/query.fasta
>> #-------------------------------#
>> formating database...
>> #--------- command -------------#
>> Widget::formater:
>> /usr/local/bin/makeblastdb -dbtype prot -in
>> /tmp/maker_hZ_8Uc/uniprot_sprot%2Efasta.mpi.10.0
>> #-------------------------------#
>> running  blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /usr/local/bin/blastx -db
>> /tmp/maker_hZ_8Uc/uniprot_sprot%2Efasta.mpi.10.0 -query
>> /tmp/maker_hZ_8Uc/rank0/NODE_2_length_2929_cov_50%2E101059.0
>> -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300
>> -searchsp 20000000 -num_threads 7 -seg yes -soft_masking true
>> -lcase_masking -show_gis -out
>> /Volumes/a0005/02SK4_01assembly_total_final_1000-10000/SK4_01assembly_total_final_1000-10000.maker.output/SK4_01assembly_total_final_1000-10000_datastore/C6/70/NODE_2_length_2929_cov_50.101059//theVoid.NODE_2_length_2929_cov_50.101059/NODE_2_length_2929_cov_50%2E101059.0.uniprot_sprot%2Efasta.blastx.temp_dir/uniprot_sprot%2Efasta.mpi.10.0.blastx
>> #-------------------------------#
>> deleted:97 hits
>> perl(12478) malloc: *** error for object 0x1033bada0: pointer being freed
>> was not allocated
>> *** set a breakpoint in malloc_error_break to debug
>> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum
>> for freed object - object was probably modified after being freed.
>> *** set a breakpoint in malloc_error_break to debug
>> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum
>> for freed object - object was probably modified after being freed.
>> *** set a breakpoint in malloc_error_break to debug
>> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum
>> for freed object - object was probably modified after being freed.
>> *** set a breakpoint in malloc_error_break to debug
>> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum
>> for freed object - object was probably modified after being freed.
>> *** set a breakpoint in malloc_error_break to debug
>> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum
>> for freed object - object was probably modified after being freed.
>> *** set a breakpoint in malloc_error_break to debug
>> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum
>> for freed object - object was probably modified after being freed.
>> *** set a breakpoint in malloc_error_break to debug
>> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum
>> for freed object - object was probably modified after being freed.
>> *** set a breakpoint in malloc_error_break to debug
>> perl(12478) malloc: *** error for object 0x1033b9c18: incorrect checksum
>> for freed object - object was probably modified after being freed.
>> *** set a breakpoint in malloc_error_break to debug
>>
>>
>> ##########################################################################################################
>>
>> I am using Maker 2.23
>>
>> I see this problem in Maker with and without mpich2 compilation
>> I am using:
>>
>> Perl 5, version 12, subversion 3 (v5.12.3) built for
>> darwin-thread-multi-2level
>>
>>
>> Any ideas?
>>
>> Thanks
>> _______________________________________________ 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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