[StarCluster] "starcluster help" error

Hui Zhao zhaoh at cbio.mskcc.org
Fri Oct 29 15:14:32 EDT 2010 

Hi,
I upgraded python to python2.6 and got the error('gcc' failed with  
exit status 1) during the installation which I solved before after  
install python-devel for python2.4. But I cannot find rpm for  
python2.6 Centos5.5. Did anyone have the same issue and how did you  
solve it?
# easy_install StarCluster
Searching for StarCluster
Best match: StarCluster 0.91.1
Processing StarCluster-0.91.1-py2.6.egg
StarCluster 0.91.1 is already the active version in easy-install.pth
Installing starcluster script to /usr/bin

Using /usr/lib/python2.6/site-packages/StarCluster-0.91.1-py2.6.egg
Processing dependencies for StarCluster
Searching for pycrypto>=1.9
Reading http://pypi.python.org/simple/pycrypto/
Reading http://pycrypto.sourceforge.net
Reading http://www.pycrypto.org/
Reading http://www.amk.ca/python/code/crypto
Best match: pycrypto 2.3
Downloading http://www.pycrypto.org/files/pycrypto-2.3.tar.gz
Processing pycrypto-2.3.tar.gz
Running pycrypto-2.3/setup.py -q bdist_egg --dist-dir /tmp/ 
easy_install-HgWIQJ/pycrypto-2.3/egg-dist-tmp-EjiFlb
warning: GMP library not found; Not building Crypto.PublicKey._fastmath.
src/MD2.c:31:20: error: Python.h: No such file or directory
src/MD2.c:118: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’  
before ‘*’ token
In file included from src/MD2.c:134:
src/hash_template.c:42: error: expected specifier-qualifier-list  
before ‘PyObject_HEAD’
src/hash_template.c:46: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or  
‘__attribute__’ before ‘PyTypeObject’
src/hash_template.c: In function ‘newALGobject’:
src/hash_template.c:55: warning: implicit declaration of function  
‘PyObject_New’
src/hash_template.c:55: error: expected expression before ‘ALGobject’
src/hash_template.c:55: warning: assignment makes pointer from integer  
without a cast
src/hash_template.c: At top level:
src/hash_template.c:62: error: expected ‘)’ before ‘*’ token
src/hash_template.c:77: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or  
‘__attribute__’ before ‘*’ token
src/hash_template.c:96: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or  
‘__attribute__’ before ‘*’ token
src/hash_template.c:108: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or  
‘__attribute__’ before ‘*’ token
src/hash_template.c:143: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or  
‘__attribute__’ before ‘*’ token
src/hash_template.c:160: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or  
‘__attribute__’ before ‘ALG_methods’
src/hash_template.c:169: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or  
‘__attribute__’ before ‘*’ token
src/hash_template.c:178: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or  
‘__attribute__’ before ‘ALGtype’
src/hash_template.c:203: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or  
‘__attribute__’ before ‘*’ token
src/hash_template.c:237: error: array type has incomplete element type
src/hash_template.c:238: error: ‘PyCFunction’ undeclared here (not in  
a function)
src/hash_template.c:238: error: expected ‘}’ before ‘ALG_new’
src/hash_template.c: In function ‘initMD2’:
src/hash_template.c:254: error: ‘PyObject’ undeclared (first use in  
this function)
src/hash_template.c:254: error: (Each undeclared identifier is  
reported only once
src/hash_template.c:254: error: for each function it appears in.)
src/hash_template.c:254: error: ‘m’ undeclared (first use in this  
function)
src/hash_template.c:256: error: ‘ALGtype’ undeclared (first use in  
this function)
src/hash_template.c:256: error: ‘PyType_Type’ undeclared (first use in  
this function)
src/hash_template.c:257: warning: implicit declaration of function  
‘Py_InitModule’
src/hash_template.c:260: error: ‘o’ undeclared (first use in this  
function)
src/hash_template.c:260: warning: implicit declaration of function  
‘PyInt_FromLong’
src/hash_template.c:260: warning: implicit declaration of function  
‘PyDict_SetItemString’
src/hash_template.c:260: warning: implicit declaration of function  
‘PyModule_GetDict’
src/hash_template.c:260: warning: implicit declaration of function  
‘Py_DECREF’
src/hash_template.c:263: warning: implicit declaration of function  
‘PyErr_Occurred’
src/hash_template.c:264: warning: implicit declaration of function  
‘Py_FatalError’
error: Setup script exited with error: command 'gcc' failed with exit  
status 1

Thanks,
Julia

On Oct 29, 2010, at 2:18 PM, Dan Yamins wrote:

> What version of python are you running?   I've had this problem with  
> python 2.4.
>
> If you can upgrade to python >=2.5, do that.
>
> If you can't -- try to pull starcluster source code from the git  
> repository, and install that instead.  I think the 2.4 compatibility  
> bug was fixed in the repo (though I could be wrong).
>
>
> Dan
>
> On Fri, Oct 29, 2010 at 2:09 PM, Hui Zhao <zhaoh at cbio.mskcc.org>  
> wrote:
> Hi,
> I just downloaded the latest version StarCluster-0.91.1.tar.gz and
> installed it. But when I try to configure it, I got error shown as
> below. Does anyone know what I am missing?
> -bash-3.2$ starcluster help
> StarCluster - (http://web.mit.edu/starcluster)
> Software Tools for Academics and Researchers (STAR)
> Please submit bug reports to starcluster at mit.edu
>
> Traceback (most recent call last):
>   File "/usr/bin/starcluster", line 5, in ?
>     pkg_resources.run_script('StarCluster==0.91.1', 'starcluster')
>   File "/usr/lib/python2.4/site-packages/setuptools-0.6c11-py2.4.egg/
> pkg_resources.py", line 489, in run_script
>     self.require(requires)[0].run_script(script_name, ns)
>   File "/usr/lib/python2.4/site-packages/setuptools-0.6c11-py2.4.egg/
> pkg_resources.py", line 1214, in run_script
>     exec script_code in namespace, namespace
>   File "/usr/bin/starcluster", line 6, in ?
>
>   File "build/bdist.linux-x86_64/egg/starcluster/cli.py", line 1070,
> in main
>   File "build/bdist.linux-x86_64/egg/starcluster/cli.py", line 992,
> in parse_subcommands
>   File "build/bdist.linux-x86_64/egg/starcluster/config.py", line
> 283, in load
>   File "build/bdist.linux-x86_64/egg/starcluster/config.py", line
> 177, in load_settings
>   File "build/bdist.linux-x86_64/egg/starcluster/config.py", line
> 173, in config
>   File "build/bdist.linux-x86_64/egg/starcluster/config.py", line
> 152, in __load_config
>   File "build/bdist.linux-x86_64/egg/starcluster/config.py", line
> 107, in _get_fp
>   File "build/bdist.linux-x86_64/egg/starcluster/exception.py", line
> 137, in __init__
> TypeError: super() argument 1 must be type, not classobj
>
>
> Thanks,
> Julia
>
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>
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