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
>
>
>
Received on Fri Oct 29 2010 - 15:29:07 EDT