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

Tue Feb 28 15:08:10 EST 2012

Hi Yarden,

I'm not sure you got the email I sent on Saturday. I attached the output 
of my compilation of MISO. Since this was quite big, I got an email in 
reply saying that the email was too big and is waiting for approval. 
Since I haven't heard anything since then, I'm wondering whether my 
email might be lost?

Maybe let me quickly give you the main warnings that came up in the MISO 
compilation:

The following occurs over and over again:

pysplicing/include/f2c.h:183: warning: function declaration isn’t a 
prototype
pysplicing/include/f2c.h:184: warning: function declaration isn’t a 
prototype
pysplicing/include/f2c.h:185: warning: function declaration isn’t a 
prototype
pysplicing/include/f2c.h:186: warning: function declaration isn’t a 
prototype
pysplicing/include/f2c.h:187: warning: function declaration isn’t a 
prototype
pysplicing/include/f2c.h:187: warning: function declaration isn’t a 
prototype
pysplicing/include/f2c.h:188: warning: function declaration isn’t a 
prototype
pysplicing/include/f2c.h:189: warning: function declaration isn’t a 
prototype
pysplicing/include/f2c.h:190: warning: function declaration isn’t a 
prototype
pysplicing/include/f2c.h:191: warning: function declaration isn’t a 
prototype
pysplicing/include/f2c.h:192: warning: function declaration isn’t a 
prototype
pysplicing/include/f2c.h:193: warning: function declaration isn’t a 
prototype

Other warnings:

pysplicing/src/assignment.c: In function 
‘splicing_paired_assignment_matrix’:
pysplicing/src/assignment.c:391: warning: unused variable ‘elen’

pysplicing/src/lapack.c: In function ‘splicing_dgesdd’:
pysplicing/src/lapack.c:16: warning: unused variable ‘maxmn’

pysplicing/src/miso_paired.c: In function ‘splicing_score_iso_paired’:
pysplicing/src/miso_paired.c:95: warning: unused variable ‘isolen’

pysplicing/src/pysplicing.c: In function ‘pysplicing_to_gff’:
pysplicing/src/pysplicing.c:638: warning: implicit declaration of 
function ‘splicing_gff_reindex’
pysplicing/src/pysplicing.c: In function ‘initpysplicing’:
pysplicing/src/pysplicing.c:692: warning: implicit declaration of 
function ‘pysplicing_init_rng’
pysplicing/src/pysplicing.c: In function ‘pysplicing_to_gff’:
pysplicing/src/pysplicing.c:581: warning: ‘Ctype2’ may be used 
uninitialized in this function

pysplicing/src/lawson_hanson_nnls.c: In function ‘nnls_’:
pysplicing/src/lawson_hanson_nnls.c:343: warning: unused variable ‘io___33’

pysplicing/src/simulator.c: In function ‘splicing_create_gene’:
pysplicing/src/simulator.c:16: warning: unused variable ‘exlen’
pysplicing/src/simulator.c: In function ‘splicing_simulate_reads’:
pysplicing/src/simulator.c:76: warning: unused variable ‘p’

pysplicing/src/lapack/dlasq2.c: In function ‘splicingdlasq2_’:
pysplicing/src/lapack/dlasq2.c:205: warning: suggest parentheses around 
‘-’ inside ‘<<’
pysplicing/src/lapack/dlasq2.c:284: warning: suggest parentheses around 
‘+’ inside ‘<<’
pysplicing/src/lapack/dlasq2.c:285: warning: suggest parentheses around 
‘-’ inside ‘<<’
pysplicing/src/lapack/dlasq2.c:305: warning: suggest parentheses around 
‘-’ inside ‘<<’
pysplicing/src/lapack/dlasq2.c:319: warning: suggest parentheses around 
‘-’ inside ‘<<’
pysplicing/src/lapack/dlasq2.c:374: warning: suggest parentheses around 
‘-’ inside ‘<<’
pysplicing/src/lapack/dlasq2.c:448: warning: suggest parentheses around 
‘-’ inside ‘<<’
pysplicing/src/lapack/dlasq2.c:450: warning: suggest parentheses around 
‘+’ inside ‘<<’
pysplicing/src/lapack/dlasq2.c:452: warning: suggest parentheses around 
‘-’ inside ‘<<’
pysplicing/src/lapack/dlasq2.c:507: warning: suggest parentheses around 
‘-’ inside ‘<<’

pysplicing/src/lapack/dlasq5.c: In function ‘splicingdlasq5_’:
pysplicing/src/lapack/dlasq5.c:109: warning: suggest parentheses around 
‘-’ inside ‘<<’
pysplicing/src/lapack/dlasq5.c:122: warning: suggest parentheses around 
‘-’ inside ‘<<’
pysplicing/src/lapack/dlasq5.c:140: warning: suggest parentheses around 
‘-’ inside ‘<<’
pysplicing/src/lapack/dlasq5.c:160: warning: suggest parentheses around 
‘-’ inside ‘<<’
pysplicing/src/lapack/dlasq5.c:176: warning: suggest parentheses around 
‘-’ inside ‘<<’
pysplicing/src/lapack/dlasq5.c:197: warning: suggest parentheses around 
‘-’ inside ‘<<’

pysplicing/src/lapack/dgesdd.c: In function ‘splicingdgesdd_’:
pysplicing/src/lapack/dgesdd.c:251: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/lapack/dgesdd.c:252: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/lapack/dgesdd.c:254: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/lapack/dgesdd.c:254: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/lapack/dgesdd.c:255: warning: suggest parentheses around 
‘&&’ within ‘||’

pysplicing/src/lapack/ilaenv.c: In function ‘splicingilaenv_’:
pysplicing/src/lapack/ilaenv.c:199: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/lapack/ilaenv.c:200: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/lapack/ilaenv.c:204: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/lapack/ilaenv.c:205: warning: suggest parentheses around 
‘&&’ within ‘||’

pysplicing/src/lapack/dbdsqr.c: In function ‘splicingdbdsqr_’:
pysplicing/src/lapack/dbdsqr.c:250: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/lapack/dbdsqr.c:254: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/lapack/dbdsqr.c:500: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/lapack/dbdsqr.c:533: warning: suggest parentheses around 
‘&&’ within ‘||’

pysplicing/src/lapack/lsame.c: In function ‘splicinglsame_’:
pysplicing/src/lapack/lsame.c:82: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/lapack/lsame.c:83: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/lapack/lsame.c:86: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/lapack/lsame.c:87: warning: suggest parentheses around 
‘&&’ within ‘||’

pysplicing/src/lapack/dorml2.c: In function ‘splicingdorml2_’:
pysplicing/src/lapack/dorml2.c:168: warning: suggest parentheses around 
‘&&’ within ‘||’

pysplicing/src/lapack/dormlq.c: In function ‘splicingdormlq_’:
pysplicing/src/lapack/dormlq.c:255: warning: suggest parentheses around 
‘&&’ within ‘||’

pysplicing/src/lapack/dlasq3.c: In function ‘splicingdlasq3_’:
pysplicing/src/lapack/dlasq3.c:212: warning: suggest parentheses around 
‘+’ inside ‘<<’
pysplicing/src/lapack/dlasq3.c:213: warning: suggest parentheses around 
‘-’ inside ‘<<’
pysplicing/src/lapack/dlasq3.c:275: warning: suggest parentheses around 
‘-’ inside ‘<<’
pysplicing/src/lapack/dlasq3.c:280: warning: suggest parentheses around 
‘-’ inside ‘<<’

pysplicing/src/lapack/dgemm.c: In function ‘splicingdgemm_’:
pysplicing/src/lapack/dgemm.c:218: warning: suggest parentheses around 
‘&&’ within ‘||’

pysplicing/src/lapack/dlascl.c: In function ‘splicingdlascl_’:
pysplicing/src/lapack/dlascl.c:141: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/lapack/dlascl.c:141: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/lapack/dlascl.c:154: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/lapack/dlascl.c:157: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/lapack/dlascl.c:157: warning: suggest parentheses around 
‘&&’ within ‘||’

pysplicing/src/lapack/dbdsdc.c: In function ‘splicingdbdsdc_’:
pysplicing/src/lapack/dbdsdc.c:244: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/lapack/dbdsdc.c:246: warning: suggest parentheses around 
‘&&’ within ‘||’

pysplicing/src/lapack/dlasdq.c: In function ‘splicingdlasdq_’:
pysplicing/src/lapack/dlasdq.c:208: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/lapack/dlasdq.c:212: warning: suggest parentheses around 
‘&&’ within ‘||’

pysplicing/src/lapack/dlasq6.c: In function ‘splicingdlasq6_’:
pysplicing/src/lapack/dlasq6.c:100: warning: suggest parentheses around 
‘-’ inside ‘<<’
pysplicing/src/lapack/dlasq6.c:124: warning: suggest parentheses around 
‘-’ inside ‘<<’
pysplicing/src/lapack/dlasq6.c:153: warning: suggest parentheses around 
‘-’ inside ‘<<’

pysplicing/src/lapack/dormqr.c: In function ‘splicingdormqr_’:
pysplicing/src/lapack/dormqr.c:253: warning: suggest parentheses around 
‘&&’ within ‘||’

pysplicing/src/f2c/wsne.c: In function ‘s_wsne’:
pysplicing/src/f2c/wsne.c:17: warning: suggest parentheses around 
assignment used as truth value

pysplicing/src/f2c/sue.c: In function ‘s_rsue’:
pysplicing/src/f2c/sue.c:38: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/sue.c: In function ‘s_wsue’:
pysplicing/src/f2c/sue.c:61: warning: suggest parentheses around 
assignment used as truth value

pysplicing/src/f2c/lwrite.c: In function ‘l_g’:
pysplicing/src/f2c/lwrite.c:141: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/lwrite.c:166: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/lwrite.c: In function ‘l_put’:
pysplicing/src/f2c/lwrite.c:190: warning: suggest parentheses around 
assignment used as truth value

pysplicing/src/f2c/wref.c: In function ‘wrt_E’:
pysplicing/src/f2c/wref.c:140: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/wref.c: In function ‘wrt_F’:
pysplicing/src/f2c/wref.c:236: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/wref.c:236: warning: suggest explicit braces to avoid 
ambiguous ‘else’
pysplicing/src/f2c/wref.c:286: warning: suggest parentheses around 
assignment used as truth value

pysplicing/src/f2c/uninit.c:62: warning: function declaration isn’t a 
prototype
pysplicing/src/f2c/uninit.c: In function ‘ieee0’:
pysplicing/src/f2c/uninit.c:262: warning: implicit declaration of 
function ‘fedisableexcept’
pysplicing/src/f2c/uninit.c:264: warning: implicit declaration of 
function ‘feenableexcept’

pysplicing/src/f2c/backspac.c: In function ‘f_back’:
pysplicing/src/f2c/backspac.c:47: warning: ignoring return value of 
‘fread’, declared with attribute warn_unused_result

pysplicing/src/f2c/wsfe.c: In function ‘s_wsfe’:
pysplicing/src/f2c/wsfe.c:55: warning: suggest parentheses around 
assignment used as truth value

pysplicing/src/f2c/dfe.c: In function ‘s_rdfe’:
pysplicing/src/f2c/dfe.c:104: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/dfe.c: In function ‘s_wdfe’:
pysplicing/src/f2c/dfe.c:126: warning: suggest parentheses around 
assignment used as truth value

pysplicing/src/f2c/iio.c: In function ‘s_rsfi’:
pysplicing/src/f2c/iio.c:91: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/iio.c: In function ‘s_wsfi’:
pysplicing/src/f2c/iio.c:123: warning: suggest parentheses around 
assignment used as truth value

pysplicing/src/f2c/wsle.c: In function ‘s_wsle’:
pysplicing/src/f2c/wsle.c:17: warning: suggest parentheses around 
assignment used as truth value

pysplicing/src/f2c/lread.c: In function ‘l_C’:
pysplicing/src/f2c/lread.c:294: warning: suggest explicit braces to 
avoid ambiguous ‘else’
pysplicing/src/f2c/lread.c:317: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/lread.c:329: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/lread.c: In function ‘nmL_getc’:
pysplicing/src/f2c/lread.c:356: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/lread.c: In function ‘l_L’:
pysplicing/src/f2c/lread.c:438: warning: suggest explicit braces to 
avoid ambiguous ‘else’
pysplicing/src/f2c/lread.c: In function ‘l_read’:
pysplicing/src/f2c/lread.c:693: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/lread.c:698: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/lread.c:709: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/lread.c:714: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/lread.c:717: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/lread.c: In function ‘s_rsle’:
pysplicing/src/f2c/lread.c:790: warning: suggest parentheses around 
assignment used as truth value

pysplicing/src/f2c/inquire.c: In function ‘f_inqu’:
pysplicing/src/f2c/inquire.c:67: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/f2c/inquire.c:66: warning: suggest explicit braces to 
avoid ambiguous ‘else’
pysplicing/src/f2c/inquire.c:70: warning: suggest explicit braces to 
avoid ambiguous ‘else’
pysplicing/src/f2c/inquire.c:75: warning: suggest parentheses around 
‘&&’ within ‘||’
pysplicing/src/f2c/inquire.c:74: warning: suggest explicit braces to 
avoid ambiguous ‘else’
pysplicing/src/f2c/inquire.c:78: warning: suggest explicit braces to 
avoid ambiguous ‘else’
pysplicing/src/f2c/inquire.c:83: warning: suggest explicit braces to 
avoid ambiguous ‘else’
pysplicing/src/f2c/inquire.c:87: warning: suggest explicit braces to 
avoid ambiguous ‘else’
pysplicing/src/f2c/inquire.c:91: warning: suggest explicit braces to 
avoid ambiguous ‘else’
pysplicing/src/f2c/inquire.c:95: warning: suggest explicit braces to 
avoid ambiguous ‘else’
pysplicing/src/f2c/inquire.c:99: warning: suggest explicit braces to 
avoid ambiguous ‘else’
pysplicing/src/f2c/inquire.c:103: warning: suggest explicit braces to 
avoid ambiguous ‘else’
pysplicing/src/f2c/inquire.c:112: warning: suggest explicit braces to 
avoid ambiguous ‘else’
pysplicing/src/f2c/inquire.c:30: warning: ‘x’ may be used uninitialized 
in this function

pysplicing/src/f2c/rsne.c: In function ‘hash’:
pysplicing/src/f2c/rsne.c:86: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rsne.c: In function ‘mk_hashtab’:
pysplicing/src/f2c/rsne.c:107: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rsne.c: In function ‘nl_init’:
pysplicing/src/f2c/rsne.c:159: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rsne.c:165: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rsne.c: In function ‘getname’:
pysplicing/src/f2c/rsne.c:188: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rsne.c: In function ‘getdimen’:
pysplicing/src/f2c/rsne.c:243: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rsne.c:247: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rsne.c:251: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rsne.c: In function ‘x_rsne’:
pysplicing/src/f2c/rsne.c:349: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rsne.c:401: warning: suggest parentheses around ‘&&’ 
within ‘||’
pysplicing/src/f2c/rsne.c:404: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rsne.c:429: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rsne.c:445: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rsne.c:457: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rsne.c:476: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rsne.c:511: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rsne.c:531: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rsne.c:542: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rsne.c:549: warning: suggest explicit braces to avoid 
ambiguous ‘else’
pysplicing/src/f2c/rsne.c: In function ‘s_rsne’:
pysplicing/src/f2c/rsne.c:603: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rsne.c: In function ‘mk_hashtab’:
pysplicing/src/f2c/rsne.c:106: warning: ‘x0’ may be used uninitialized 
in this function
pysplicing/src/f2c/rsne.c: In function ‘x_rsne’:
pysplicing/src/f2c/rsne.c:311: warning: ‘dn’ may be used uninitialized 
in this function
pysplicing/src/f2c/rsne.c:311: warning: ‘dn0’ may be used uninitialized 
in this function

pysplicing/src/f2c/lbitbits.c: In function ‘lbit_cshift’:
pysplicing/src/f2c/lbitbits.c:47: warning: suggest parentheses around 
‘-’ inside ‘>>’
pysplicing/src/f2c/lbitbits.c:51: warning: suggest parentheses around 
‘-’ inside ‘<<’
pysplicing/src/f2c/lbitbits.c:60: warning: suggest parentheses around 
‘-’ inside ‘>>’
pysplicing/src/f2c/lbitbits.c:60: warning: suggest parentheses around 
arithmetic in operand of ‘|’
pysplicing/src/f2c/lbitbits.c:64: warning: suggest parentheses around 
‘-’ inside ‘<<’
pysplicing/src/f2c/lbitbits.c:64: warning: suggest parentheses around 
arithmetic in operand of ‘|’

pysplicing/src/f2c/due.c: In function ‘s_rdue’:
pysplicing/src/f2c/due.c:40: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/due.c: In function ‘s_wdue’:
pysplicing/src/f2c/due.c:53: warning: suggest parentheses around 
assignment used as truth value

pysplicing/src/f2c/endfile.c: In function ‘f_end’:
pysplicing/src/f2c/endfile.c:46: warning: suggest parentheses around 
assignment used as truth value

pysplicing/src/f2c/rdfmt.c: In function ‘rd_Z’:
pysplicing/src/f2c/rdfmt.c:39: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rdfmt.c:42: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/rdfmt.c:71: warning: suggest parentheses around ‘+’ 
inside ‘>>’
pysplicing/src/f2c/rdfmt.c:93: warning: suggest parentheses around ‘-’ 
inside ‘<<’
pysplicing/src/f2c/rdfmt.c:93: warning: suggest parentheses around 
arithmetic in operand of ‘|’

pysplicing/src/f2c/open.c: In function ‘f_open’:
pysplicing/src/f2c/open.c:246: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/open.c:256: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/open.c:258: warning: suggest parentheses around 
assignment used as truth value
pysplicing/src/f2c/open.c:270: warning: suggest explicit braces to avoid 
ambiguous ‘else’

I hope, the email is not too big this time.
Thanks again for your help.
Anke.

On 02/25/2012 11:48 AM, Yarden Katz wrote:
> 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
>> ******************************************
>>
>
>

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

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