Re: "starcluster help" error

From: Justin Riley <no email>
Date: Fri, 29 Oct 2010 15:34:38 -0400

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Hi Julia,

I would recommend not moving forward with py2.6 if it will put your
CentOS installation in danger.

I'm patching the code now to work with Python2.4 and will be releasing
0.91.2 today. I'll send an announcement when it's ready.

~Justin

On 10/29/2010 03:29 PM, Dan Yamins wrote:
>
>
> On Fri, Oct 29, 2010 at 3:14 PM, Hui Zhao <zhaoh_at_cbio.mskcc.org
> <mailto:zhaoh_at_cbio.mskcc.org>> wrote:
>
> 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?
>
>
> Julia -- I think there might be some danger in what you did (depending
> on how you did it). RHEL and centos rely on the system python
> installation for the yum package manager itself. That system python,
> which is version 2.4, CANNOT be updated to version 2.6 without breaking
> the package manager. If you upgraded on a CentOS system, you need
> to either:
>
> A) build from source and put the python executable somewhere other
> than /usr/bin, or
> B) use a special-purpose RPM for python26 which knows where to put
> the binaries.
>
> More details:
> A) build from Source: get the python source code from python.org
> <http://python.org>. Follow the instructions in the install README,
> using the PREFIX option to install to your chosen location.
>
> B) Install using a package manager. EPEL provides high-quality RPMs
> for python2.6 on RHEL. This is the 64-bit:
>
> http://download.fedora.redhat.com/pub/epel/5/x86_64/repoview/python26.html
>
> There is also corresponding i386 RPM, and some others. Note that this
> will create an executable called "python26" not "python". This is VERY
> important Whatever you do, make sure you use a reputable packaging
> that has been tested by others because you DO NOT WANT TO INTERFERE with
> the system python on centos systems.
>
>
> Dan
>
>
>
>
> # 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
>> <mailto: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
>> <mailto: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
>>
>> _______________________________________________
>> StarCluster mailing list
>> StarCluster_at_mit.edu <mailto:StarCluster_at_mit.edu>
>> http://mailman.mit.edu/mailman/listinfo/starcluster
>>
>>
>> _______________________________________________
>> StarCluster mailing list
>> StarCluster_at_mit.edu <mailto:StarCluster_at_mit.edu>
>> http://mailman.mit.edu/mailman/listinfo/starcluster
>
>

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Received on Fri Oct 29 2010 - 15:34:40 EDT