<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><font class="Apple-style-span" color="#070000">Hi Dan,</font><div><font class="Apple-style-span" color="#070000">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</font>(<span style="color: rgb(252, 24, 32); ">'gcc' failed with exit status 1</span>)<span class="Apple-style-span" style="color: rgb(7, 0, 0); ">. 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.</span></div><div><font class="Apple-style-span" color="#070000">Thanks again,</font></div><div><font class="Apple-style-span" color="#070000">Julia</font></div><div><font class="Apple-style-span" color="#FC1820"><br></font><div><div>On Oct 29, 2010, at 3:29 PM, Dan Yamins wrote:I </div><br class="Apple-interchange-newline"><blockquote type="cite"><br><br><div class="gmail_quote">On Fri, Oct 29, 2010 at 3:14 PM, Hui Zhao <span dir="ltr"><<a href="mailto:zhaoh@cbio.mskcc.org">zhaoh@cbio.mskcc.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; position: static; z-index: auto; "> <div style="word-wrap:break-word">Hi,<div>I upgraded python to python2.6 and got the error(<span style="color:rgb(252, 24, 32)">'gcc' failed with exit status 1</span>) 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?</div> </div></blockquote><div><br></div><div>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:</div> <div><br></div><div> A) build from source and put the python executable somewhere other than /usr/bin, or </div><div> B) use a special-purpose RPM for python26 which knows where to put the binaries. </div><div><br> </div><div>More details:</div><div>A) build from Source: get the python source code from <a href="http://python.org">python.org</a>. Follow the instructions in the install README, using the PREFIX option to install to your chosen location. </div> <div><br></div><div>B) Install using a package manager. EPEL provides high-quality RPMs for python2.6 on RHEL. This is the 64-bit:</div><div><br></div><div><a href="http://download.fedora.redhat.com/pub/epel/5/x86_64/repoview/python26.html">http://download.fedora.redhat.com/pub/epel/5/x86_64/repoview/python26.html</a></div> <div><br></div><div>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. </div> <div><br></div><div><br></div><div>Dan</div><div><br></div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div style="word-wrap:break-word"> <div># easy_install StarCluster</div><div>Searching for StarCluster</div><div>Best match: StarCluster 0.91.1</div><div>Processing StarCluster-0.91.1-py2.6.egg</div><div>StarCluster 0.91.1 is already the active version in easy-install.pth</div> <div>Installing starcluster script to /usr/bin</div><div><br></div><div>Using /usr/lib/python2.6/site-packages/StarCluster-0.91.1-py2.6.egg</div><div>Processing dependencies for StarCluster</div><div>Searching for pycrypto>=1.9</div> <div>Reading <a href="http://pypi.python.org/simple/pycrypto/" target="_blank">http://pypi.python.org/simple/pycrypto/</a></div><div>Reading <a href="http://pycrypto.sourceforge.net" target="_blank">http://pycrypto.sourceforge.net</a></div> <div>Reading <a href="http://www.pycrypto.org/" target="_blank">http://www.pycrypto.org/</a></div><div>Reading <a href="http://www.amk.ca/python/code/crypto" target="_blank">http://www.amk.ca/python/code/crypto</a></div><div> Best match: pycrypto 2.3</div><div>Downloading <a href="http://www.pycrypto.org/files/pycrypto-2.3.tar.gz" target="_blank">http://www.pycrypto.org/files/pycrypto-2.3.tar.gz</a></div><div>Processing pycrypto-2.3.tar.gz</div> <div>Running pycrypto-2.3/setup.py -q bdist_egg --dist-dir /tmp/easy_install-HgWIQJ/pycrypto-2.3/egg-dist-tmp-EjiFlb</div><div>warning: GMP library not found; Not building Crypto.PublicKey._fastmath.</div><div>src/MD2.c:31:20: error: Python.h: No such file or directory</div> <div>src/MD2.c:118: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token</div><div>In file included from src/MD2.c:134:</div><div>src/hash_template.c:42: error: expected specifier-qualifier-list before ‘PyObject_HEAD’</div> <div>src/hash_template.c:46: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘PyTypeObject’</div><div>src/hash_template.c: In function ‘newALGobject’:</div><div>src/hash_template.c:55: warning: implicit declaration of function ‘PyObject_New’</div> <div>src/hash_template.c:55: error: expected expression before ‘ALGobject’</div><div>src/hash_template.c:55: warning: assignment makes pointer from integer without a cast</div><div>src/hash_template.c: At top level:</div> <div>src/hash_template.c:62: error: expected ‘)’ before ‘*’ token</div><div>src/hash_template.c:77: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token</div><div>src/hash_template.c:96: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token</div> <div>src/hash_template.c:108: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token</div><div>src/hash_template.c:143: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token</div><div> src/hash_template.c:160: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘ALG_methods’</div><div>src/hash_template.c:169: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token</div><div>src/hash_template.c:178: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘ALGtype’</div> <div>src/hash_template.c:203: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token</div><div>src/hash_template.c:237: error: array type has incomplete element type</div><div>src/hash_template.c:238: error: ‘PyCFunction’ undeclared here (not in a function)</div> <div>src/hash_template.c:238: error: expected ‘}’ before ‘ALG_new’</div><div>src/hash_template.c: In function ‘initMD2’:</div><div>src/hash_template.c:254: error: ‘PyObject’ undeclared (first use in this function)</div><div> src/hash_template.c:254: error: (Each undeclared identifier is reported only once</div><div>src/hash_template.c:254: error: for each function it appears in.)</div><div>src/hash_template.c:254: error: ‘m’ undeclared (first use in this function)</div> <div>src/hash_template.c:256: error: ‘ALGtype’ undeclared (first use in this function)</div><div>src/hash_template.c:256: error: ‘PyType_Type’ undeclared (first use in this function)</div><div>src/hash_template.c:257: warning: implicit declaration of function ‘Py_InitModule’</div> <div>src/hash_template.c:260: error: ‘o’ undeclared (first use in this function)</div><div>src/hash_template.c:260: warning: implicit declaration of function ‘PyInt_FromLong’</div><div>src/hash_template.c:260: warning: implicit declaration of function ‘PyDict_SetItemString’</div> <div>src/hash_template.c:260: warning: implicit declaration of function ‘PyModule_GetDict’</div><div>src/hash_template.c:260: warning: implicit declaration of function ‘Py_DECREF’</div><div>src/hash_template.c:263: warning: implicit declaration of function ‘PyErr_Occurred’</div> <div>src/hash_template.c:264: warning: implicit declaration of function ‘Py_FatalError’</div><div><font color="#FC1820">error: Setup script exited with error: command 'gcc' failed with exit status 1</font></div><div> <br></div><div>Thanks,</div><div>Julia</div><div> <br><div><div class="im"><div>On Oct 29, 2010, at 2:18 PM, Dan Yamins wrote:</div><br></div><div><div></div><div class="h5"><blockquote type="cite">What version of python are you running? I've had this problem with python 2.4. <div> <br></div><div>If you can upgrade to python >=2.5, do that. </div><div><br></div><div>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).</div> <div><br></div><div><br></div><div>Dan<br><div><br><div class="gmail_quote">On Fri, Oct 29, 2010 at 2:09 PM, Hui Zhao <span dir="ltr"><<a href="mailto:zhaoh@cbio.mskcc.org" target="_blank">zhaoh@cbio.mskcc.org</a>></span> wrote:<br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br> I just downloaded the latest version StarCluster-0.91.1.tar.gz and<br> installed it. But when I try to configure it, I got error shown as<br> below. Does anyone know what I am missing?<br> -bash-3.2$ starcluster help<br> StarCluster - (<a href="http://web.mit.edu/starcluster" target="_blank">http://web.mit.edu/starcluster</a>)<br> Software Tools for Academics and Researchers (STAR)<br> Please submit bug reports to <a href="mailto:starcluster@mit.edu" target="_blank">starcluster@mit.edu</a><br> <br> Traceback (most recent call last):<br> File "/usr/bin/starcluster", line 5, in ?<br> pkg_resources.run_script('StarCluster==0.91.1', 'starcluster')<br> File "/usr/lib/python2.4/site-packages/setuptools-0.6c11-py2.4.egg/<br> pkg_resources.py", line 489, in run_script<br> self.require(requires)[0].run_script(script_name, ns)<br> File "/usr/lib/python2.4/site-packages/setuptools-0.6c11-py2.4.egg/<br> pkg_resources.py", line 1214, in run_script<br> exec script_code in namespace, namespace<br> File "/usr/bin/starcluster", line 6, in ?<br> <br> File "build/bdist.linux-x86_64/egg/starcluster/cli.py", line 1070,<br> in main<br> File "build/bdist.linux-x86_64/egg/starcluster/cli.py", line 992,<br> in parse_subcommands<br> File "build/bdist.linux-x86_64/egg/starcluster/config.py", line<br> 283, in load<br> File "build/bdist.linux-x86_64/egg/starcluster/config.py", line<br> 177, in load_settings<br> File "build/bdist.linux-x86_64/egg/starcluster/config.py", line<br> 173, in config<br> File "build/bdist.linux-x86_64/egg/starcluster/config.py", line<br> 152, in __load_config<br> File "build/bdist.linux-x86_64/egg/starcluster/config.py", line<br> 107, in _get_fp<br> File "build/bdist.linux-x86_64/egg/starcluster/exception.py", line<br> 137, in __init__<br> TypeError: super() argument 1 must be type, not classobj<br> <br> <br> Thanks,<br> Julia<br> <br> _______________________________________________<br> StarCluster mailing list<br> <a href="mailto:StarCluster@mit.edu" target="_blank">StarCluster@mit.edu</a><br> <a href="http://mailman.mit.edu/mailman/listinfo/starcluster" target="_blank">http://mailman.mit.edu/mailman/listinfo/starcluster</a><br> </blockquote></div><br></div></div> _______________________________________________<br>StarCluster mailing list<br><a href="mailto:StarCluster@mit.edu" target="_blank">StarCluster@mit.edu</a><br><a href="http://mailman.mit.edu/mailman/listinfo/starcluster" target="_blank">http://mailman.mit.edu/mailman/listinfo/starcluster</a><br> </blockquote></div></div></div><br></div></div></blockquote></div><br> _______________________________________________<br>StarCluster mailing list<br><a href="mailto:StarCluster@mit.edu">StarCluster@mit.edu</a><br>http://mailman.mit.edu/mailman/listinfo/starcluster<br></blockquote></div><br></div></body></html>