[maker-devel] maker-2.23
Rodolfo Aramayo
raramayo at tamu.edu
Fri Feb 24 08:43:08 MST 2012
Thanks Carson,
So I did the following:
Deleted the Maker installation
Re-configure, re-compiled and re-installed mpich2
Re-installed CPAN and all the CPAN-modules required by Maker
Re-compiled and re-installed Maker
Re-installed Genemark
and now things work!
The question remains, why did this failed?
The only thing I can think of, the only thing I noticed, is the fact that
forks::shared and threads::shared were installed by CPAN as if they had not
been installed before??
But they were...so..perhaps CPAN modules got broken during a major MacPorts
upgrade I did over the weekend, where many, many MacPorts perl modules were
upgraded
Like they say: *No Good Deed Shall Go Unpunished!
*It is like I had to pay the Gods their tribute in pain over the fact that
I dared to upgrade the software*
*
Thanks for your help
--Rodolfo
On Thu, Feb 23, 2012 at 11:08, Carson Holt <carsonhh at gmail.com> wrote:
> Does it indicate at any level what the compilation error is?
>
> Could you pack up your job and send it to me? I'll just try it on a
> couple of system types. A malloc error with perl would normally happen at
> the C level, so it's a matter of identifying what module is being called.
>
> Thanks,
> Carson
>
> From: Rodolfo Aramayo <raramayo at tamu.edu>
> Date: Thu, 23 Feb 2012 11:00:37 -0600
>
> To: Carson Holt <carsonhh at gmail.com>
> Cc: MAKER <maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] maker-2.23
>
> 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.pm module 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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