[miso-users] MISO aborts with error *** glibc detected *** python: free(): invalid pointer

[Anke Busch]

Hi Yarden,

I have the following versions installed:

pysam 0.6
samtools 0.1.18
gcc 4.4.3 (that's what "gcc --version" tells me)

/lib/libc.so.6 reports:
GNU C Library (Ubuntu EGLIBC 2.11.1-0ubuntu7.8) stable release version 
2.11.1, by Roland McGrath et al.
...
Compiled by GNU CC version 4.4.3.
Compiled on a Linux >>2.6.24-27-server<< system on 2011-01-21.
.....


The call "python setup.py install" reports the following:

/usr/lib/python2.6/distutils/dist.py:266: UserWarning: Unknown 
distribution option: 'install_requires'
   warnings.warn(msg)
running install
running build
running build_py
running build_ext
running build_scripts
running install_lib
running install_scripts
changing mode of /usr/local/bin/index_gff.py to 755
changing mode of /usr/local/bin/plot.py to 755
changing mode of /usr/local/bin/filter_events.py to 755
changing mode of /usr/local/bin/sam_to_bam.py to 755
changing mode of /usr/local/bin/module_availability.py to 755
changing mode of /usr/local/bin/run_events_analysis.py to 755
changing mode of /usr/local/bin/run_miso.py to 755
changing mode of /usr/local/bin/exon_utils.py to 755
changing mode of /usr/local/bin/pe_utils.py to 755
running install_data
running install_egg_info
Removing /usr/local/lib/python2.6/dist-packages/misopy-0.4.1.egg-info
Writing /usr/local/lib/python2.6/dist-packages/misopy-0.4.1.egg-info

I checked in the setup script what "install_requires" was and made sure 
I have all requirments.

Thanks a lot for your help.
Anke.


On 02/24/2012 05:53 PM, Yarden Katz wrote:
> Hi Anke,
>
> Could you please let me know the versions of pysam, samtools and gcc on your system?
>
> Also, can you please show me the trace of your compilation?  I.e. the call "python setup.py install"?
>
> Thanks.
>
> Best, --Yarden
>
>
> On Feb 24, 2012, at 6:03 PM, Anke Busch wrote:
>
>> Hello again,
>>
>> I updated all modules and packages (except I'm still using python2.6),
>> but nothing changed. Then I set
>>
>> export MALLOC_CHECK_=0
>>
>> which changed the output to the following:
>>
>> .....
>> .....
>> Computing Psi for 1 genes...
>>    - ENSMUSG00000019943
>>    - GFF filename:
>> /home/anke/Software/src/misopy-0.4.1/misopy/gff-events/mm9/genes/Atp2b1/indexed/chr10/ENSMUSG00000019943.pickle
>>    - BAM:
>> /home/anke/Software/src/misopy-0.4.1/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam
>>    - Outputting to:
>> /home/anke/Software/src/misopy-0.4.1/misopy/test-output/gene-psi-output
>> Loading BAM filename from:
>> /home/anke/Software/src/misopy-0.4.1/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam
>> Loading took 0.00 seconds
>> Segmentation fault
>> .
>> ----------------------------------------------------------------------
>> Ran 2 tests in 3.822s
>>
>> OK
>>
>> So at least something changed, but there's still a segmentation fault
>> which causes a crash.
>> Would be great, if anyone would have an idea on that...
>>
>> Thanks,
>> Anke.
>>
>> -- 
>> ******************************************
>>    Dr. Anke Busch
>>    Postdoctoral Researcher
>>    Department of Microbiology and Molecular Genetics
>>    Medical Sciences I, C290
>>    University of California, Irvine, USA
>>
>>    Email: abusch at uci.edu
>>    Phone: +1-949-824-2128
>> ******************************************
>>
>> _______________________________________________
>> miso-users mailing list
>> miso-users at mit.edu
>> http://mailman.mit.edu/mailman/listinfo/miso-users
>

-- 
******************************************
   Dr. Anke Busch
   Postdoctoral Researcher
   Department of Microbiology and Molecular Genetics
   Medical Sciences I, C290
   University of California, Irvine, USA

   Email: abusch at uci.edu
   Phone: +1-949-824-2128
******************************************