<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear all,<div><br></div><div>a brief update, just in case this might help others:</div><div><br></div><div>I managed to install py25-pymvpa under leopard finally.</div><div><br></div><div><br></div><div>#shogun:</div><div>It appears that the current version of shogun in MacPorts (i.e., 0.9) is dependent on</div><div>python26, which caused MacPorts to additionally install python26 (see earlier mail in the</div><div>thread). This can be suppressed by installing shogun in the following way:</div><div><br></div><div><div>sudo port -v install shogun +no_python26 +python25</div></div><div><br></div><div>which makes installation of py25-pymvpa (sudo port install py25-pymvpa) possible.</div><div><br></div><div><br></div><div>#Deprecation warning: Some problems seem to persist:</div><div><br></div><div><div>>>> from mvpa.suite import *</div><div>/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/numerix/__init__.py:18: DeprecationWarning: </div><div>**********************************************************</div><div>matplotlib.numerix and all its subpackages are deprecated.</div><div>They will be removed soon. Please use numpy instead.</div><div>**********************************************************</div><div><br></div><div> warnings.warn(msg, DeprecationWarning)</div><div><br></div></div><div><br></div><div>Best, Christian</div><div><br></div><div><br><div><div>Am 10.12.2009 um 17:13 schrieb Christian Fiebach:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Thanks Anna, <div><br></div><div>installing as you suggested fully using py26 worked, with your commands given below. Thanks!!!</div><div><br></div><div>However, my first steps in pyMVPA continue to be difficult:</div><div><br></div><div>When I start python and try to follow the installation website or the getting started manual, </div><div>python produces either error messages or crashes:</div><div><br></div><div>From the installation web site: Deprecation Warning @ import and NameError for the very first command.</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">fiebach$ python</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">Python 2.6.4 (r264:75706, Dec 8 2009, 01:05:52) </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">[GCC 4.2.1 (Apple Inc. build 5646) (dot 1)] on darwin</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">Type "help", "copyright", "credits" or "license" for more information.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">>>> import mvpa</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/mvpa/base/verbosity.py:19: DeprecationWarning: the sets module is deprecated</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "> from sets import Set</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">>>> attr = SampleAttributes(os.path.join(pymvpa_dataroot, 'attributes.txt'))</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">Traceback (most recent call last):</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "> File "<stdin>", line 1, in <module></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">NameError: name 'SampleAttributes' is not defined</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">>>> </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><br></div></div><div><br></div><div>From the Getting Started section of the Manual: Deprecatin error and python crash</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">fiebach$ python</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">Python 2.6.4 (r264:75706, Dec 8 2009, 01:05:52) </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">[GCC 4.2.1 (Apple Inc. build 5646) (dot 1)] on darwin</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">Type "help", "copyright", "credits" or "license" for more information.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">>>> from mvpa.suite import *</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/mvpa/base/verbosity.py:19: DeprecationWarning: the sets module is deprecated</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "> from sets import Set</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">Python(673) malloc: *** error for object 0x7fff70e8b500: pointer being freed was not allocated</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">*** set a breakpoint in malloc_error_break to debug</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">Abort trap</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">fiebach$ </div><div><br></div><div><br></div><div>Just to make sure: My path seems to look fine. The export command is currently in .profile, </div><div>not in .bash_profile as suggested in the installation section:</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">fiebach$ echo $PATH</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin</div><div><br></div><div><br></div><div><br></div><div>Unfortunately, I am just starting to use python and therefore my debugging abilities</div><div>are not very advanced at present. I am greatful for any input you can give me right </div><div>now!</div><div><br></div><div>Thanks in advance,</div><div><br></div><div>Christian</div></div></div><div><br></div><div><br><div><div>Am 08.12.2009 um 14:57 schrieb Anna Manelis:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Christian,<br>I am not an expert, but I managed to install PYMVPA on my Snow Leopard by doing<br></div><div><span style="font-family: 'DejaVu Sans','Droid Sans',Verdana,sans-serif; font-size: 14px; color: rgb(68, 68, 68); line-height: 19px;"><pre style="border-top-width: 1px; border-right-width: 1px; border-bottom-width: 1px; border-left-width: 1px; border-top-style: solid; border-right-style: solid; border-bottom-style: solid; border-left-style: solid; border-top-color: rgb(221, 221, 221); border-right-color: rgb(221, 221, 221); border-bottom-color: rgb(221, 221, 221); border-left-color: rgb(221, 221, 221); padding-top: 0.25em; padding-right: 0.25em; padding-bottom: 0.25em; padding-left: 0.25em; background-color: rgb(246, 246, 246); color: rgb(102, 102, 102); font-family: 'DejaVu Sans Mono', 'Lucida Console', monospace; font-size: 11px; line-height: 1.25; white-space: pre-wrap; position: static; z-index: auto; ">sudo port install py26-pil py26-numpy py26-scipy py26-ipython py26-matplotlib +cairo+latex+tkinter py26-pyobjc2-cocoa python_select<br>sudo python_select python26</pre></span></div><div>And then <br></div><span style="font-family: 'Lucida Grande','Lucida Sans Unicode',Geneva,Verdana,sans-serif; font-size: 14px; line-height: 21px;"><pre style="border: 1px solid rgb(204, 204, 204); padding: 0.5em; font-family: Consolas,'Deja Vu Sans Mono','Bitstream Vera Sans Mono',monospace; font-size: 0.95em; letter-spacing: 0.015em; background-color: rgb(248, 248, 248); line-height: 15px;">sudo port install py26-pymvpa +scipy +pynifti +hcluster +libsvm <span style="font-family: arial,'Lucida Sans Unicode',Geneva,Verdana,sans-serif; font-size: small; line-height: normal; white-space: normal;"><span style="font-family: Consolas,'Deja Vu Sans Mono','Bitstream Vera Sans Mono',monospace; font-size: 13px; line-height: 15px; white-space: pre;">+matplotlib +pywavelet</span> </span></pre> </span>Although when I tried to install PYMVPA on Leopard, I encountered the same problem as you (the installation involves py26 even though I explicitly aske it to involve py25).<br><br>Good luck,<br>Anna.<br><br></blockquote></div><div apple-content-edited="true"><span class="Apple-style-span" style="font-size: 12px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><br class="khtml-block-placeholder"></div><div><br></div></span></div></span><br class="Apple-interchange-newline"> </div><br></div></div>_______________________________________________<br>Pkg-ExpPsy-PyMVPA mailing list<br><a href="mailto:Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org">Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org</a><br>http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa<br></blockquote></div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><br class="Apple-interchange-newline"><br class="khtml-block-placeholder"></div><div><br class="khtml-block-placeholder"></div><div>-------------------------------------------------------------</div><div>Prof. Dr. Christian Fiebach</div><div>Dept. of Psychology, University of Heidelberg</div><div>Hauptstr. 47-51; D-69117 Germany</div><div>Tel.: ++49-(0)6221-547371</div><div><a href="http://fimlab.uni-hd.de">http://fimlab.uni-hd.de</a></div><div>-------------------------------------------------------------</div><div><br></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"> </div><br></div></body></html>