Re: "starcluster help" error

From: Dan Yamins <no email>
Date: Fri, 29 Oct 2010 16:05:29 -0400

There's also a python26-devel repo from EPEL

http://download.fedora.redhat.com/pub/epel/5/i386/repoview/python26-devel.html

On Fri, Oct 29, 2010 at 4:01 PM, Hui Zhao <zhaoh_at_cbio.mskcc.org> wrote:

> Hi Dan,
> Thank you very much for the help. I did use EPEL repo to install python2.6
> and made a link to python2.6. The problem is I cannot find python-devel2.6
> for centos5.5 to solve the error('gcc' failed with exit status 1). Do you
> know if there is other cause for this error? Hopefully the new version of
> starcluster will solve all of the problems I am having.
> Thanks again,
> Julia
>
> On Oct 29, 2010, at 3:29 PM, Dan Yamins wrote:I
>
>
>
> On Fri, Oct 29, 2010 at 3:14 PM, Hui Zhao <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. 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> 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
>>>
>>> _______________________________________________
>>> StarCluster mailing list
>>> StarCluster_at_mit.edu
>>> http://mailman.mit.edu/mailman/listinfo/starcluster
>>>
>>
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>> http://mailman.mit.edu/mailman/listinfo/starcluster
>>
>>
>>
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>
Received on Fri Oct 29 2010 - 16:05:34 EDT