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

[Yarden Katz]

Hi Anke,

see below:

On Feb 24, 2012, at 9:22 PM, Anke Busch wrote:

> 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

It looks like you ran this again after initial compilation; do you mind deleting misopy/pysplicing and installing again, and sending me the full output?  

It's strange that this error comes up -- I'm using an almost identical setup to yours and have never run into this one.

  --Yarden

> 
> 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
> ******************************************
>