<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">From [1] did you try:<div><br></div><div><pre style="overflow-x: auto; overflow-y: hidden; padding: 9.5px; font-family: Monaco, Menlo, Consolas, 'Courier New', monospace; font-size: 13px; color: rgb(51, 51, 51); border-top-left-radius: 4px; border-top-right-radius: 4px; border-bottom-right-radius: 4px; border-bottom-left-radius: 4px; margin-top: 0px; margin-bottom: 10px; line-height: 20px; word-break: break-all; word-wrap: break-word; white-space: pre-wrap; background-color: rgb(245, 245, 245); border: 1px solid rgba(0, 0, 0, 0.14902);">conda install --use-local simpleitk</pre><div>Brad</div><div><br></div><div>[1] <a href="http://conda.pydata.org/docs/build_tutorials/pkgs.html">http://conda.pydata.org/docs/build_tutorials/pkgs.html</a></div><div><br><div><div><div>On Sep 11, 2014, at 1:06 PM, Vishwa <<a href="mailto:vishwanath.somashekar@gmail.com">vishwanath.somashekar@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr">Hi All,<div>I think python PythonPackage/setup.py installed wasn't in the location that the recipe calls for. I manually went to the location and ran the command. It was in the following folder</div><div><br></div><div><p class="">/Users/dagarshali/anaconda/conda-bld/work/build/SimpleITK-build/Wrapping</p><p class="">After that when I checked for simpleITK in /Users/dagarshali/anaconda/lib/python2.7/site-packages, I found</p><div>
<br class="webkit-block-placeholder"></div><p class="">/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK</p><p class="">Now, when I try to import simpleitk, i get an error which is shown below. </p><p class="">>>> import SimpleITK as sitk</p><p class="">Traceback (most recent call last):</p><p class=""> File "<stdin>", line 1, in <module></p><p class=""> File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py", line 1, in <module></p><p class=""> from .SimpleITK import *</p><p class=""> File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 28, in <module></p><p class=""> _SimpleITK = swig_import_helper()</p><p class=""> File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 24, in swig_import_helper</p><p class=""> _mod = imp.load_module('_SimpleITK', fp, pathname, description)</p><p class="">ImportError: dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so, 2): Library not loaded: libjpeg.8.dylib</p><p class=""> Referenced from: /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so</p><p class=""> Reason: image not found</p><p class=""><br></p><p class="">I am guessing that's a progress from where I was. Any ideas to fix this one?</p><p class=""><br></p><p class="">Vishwa</p></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Sep 11, 2014 at 11:18 AM, Vishwa <span dir="ltr"><<a href="mailto:vishwanath.somashekar@gmail.com" target="_blank">vishwanath.somashekar@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi, <div>I looked in <span style="font-size:13.333333969116211px;font-family:arial,sans-serif">~/</span><span style="font-family:Menlo;font-size:11px">anaconda//lib/python2.7/site-packages and couldn't find the simpleitk directory. I ran the conda build again and saved the log file. I am attaching here for your reference. Hopefully, that should tell us something.</span></div><span class="HOEnZb"><font color="#888888"><div><span style="font-family:Menlo;font-size:11px"><br></span></div><div><span style="font-family:Menlo;font-size:11px">Vishwa</span></div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Sep 11, 2014 at 8:05 AM, Bradley Lowekamp <span dir="ltr"><<a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hello,<div><br></div><div>First I would look at the output of the conda build. What that OK? Did it give a successful output? Next I would look into the site packages directory in your anaconda installation ( e.g. ~/<span style="font-family:Menlo;font-size:11px">anaconda//lib/python2.7/site-packages) </span>for the SimpleITK directory.</div><div><br></div><div>Brad</div><div><div><div>On Sep 11, 2014, at 12:43 AM, Vishwa <<a href="mailto:vishwanath.somashekar@gmail.com" target="_blank">vishwanath.somashekar@gmail.com</a>> wrote:</div><br><blockquote type="cite"><div dir="ltr"><div class="gmail_quote"><br><br><div dir="ltr">I did install anaconda again and ran the conda build like you suggest. It ran without and problem. However, when I import simpleitk, it gives a error saying no module found. <div><br></div><div>Any ideas?</div><span><font color="#888888"><div><br></div><div>Vishwa</div></font></span></div><div class="gmail_extra"><br><div class="gmail_quote"><span>On Wed, Sep 10, 2014 at 10:10 AM, Bradley Lowekamp [via ITK Insight Users] <span dir="ltr"><<a href="mailto:ml-node+s2283740n7586186h92@n2.nabble.com" target="_blank">ml-node+s2283740n7586186h92@n2.nabble.com</a>></span> wrote:<br></span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span><span>
Hello,<div><br></div><div>You need to use the conda build environment. Look at the readme in this repo[1].</div><div><br></div><div>Basically you'll need to do the following:</div><div><br></div><div><div style="margin:0px;font-size:11px;font-family:Menlo">$ conda install conda-build</div></div><div>$ cd src</div><div>$ git clone <a href="https://github.com/thewtex/conda-recipes.git" rel="nofollow" link="external" target="_blank">https://github.com/thewtex/conda-recipes.git</a></div><div>$ git checkout simpleitk-clone-url</div><div>$ <span style="font-family:Menlo;font-size:11px">conda build simpleitk</span></div><div><br></div><div><br></div><div><br></div><div>[1] <a href="https://github.com/conda/conda-recipes" rel="nofollow" link="external" target="_blank">https://github.com/conda/conda-recipes</a></div></span></span><div><br><div><span><div>On Sep 10, 2014, at 11:01 AM, Vishwa <<a href="http://user/SendEmail.jtp?type=node&node=7586186&i=0" rel="nofollow" link="external" target="_blank">[hidden email]</a>> wrote:</div><br></span><blockquote style="border-left:2px solid #cccccc;padding:0 1em" type="cite"><span><span><div dir="ltr">Thanks very much for the information. I looked at the conda recipe. There are three files. <div>One is .sh file, the second is yaml file, and the third is just a test code. How am i to use that recipe to compile..</div><div><br></div><div>There are variables like Source_Dir in the .sh file. How do i get those. I am not familiar using it. </div><div><br></div><div>Am I to just copy the file build.sh into the SimpleITK source code directly and run sh ./build.sh? I tried that, and it ran for a while and gave an error. </div><div><br></div><div>Best regards,</div><div>Vishwa</div><div><br></div><div><br></div></div></span></span><div class="gmail_extra"><br><div class="gmail_quote"><span>On Wed, Sep 10, 2014 at 9:13 AM, Bradley Lowekamp <span dir="ltr"><<a href="http://user/SendEmail.jtp?type=node&node=7586186&i=1" rel="nofollow" link="external" target="_blank">[hidden email]</a>></span> wrote:<br></span><blockquote style="border-left:2px solid #cccccc;padding:0 1em" class="gmail_quote"><div style="word-wrap:break-word"><span><span>Hello,<div><br></div><div>This error message frequently happens when SimpleITK is compiled against a different version of Python than the runtime. This generally indicate there is something conflicting funny in your runtime environment.</div><div><br></div><div>I was easily able to use the build script from the conda-recipes repository. I would strongly recommend this approach when building for the anaconda enviroment as it does simplify some of there issue. Your CMake configuration does look correct.</div><div><br></div><div>You should look at you environment variables, such as PATH, DYLD_LIBRARY_PATH, and PYTHONPATH. Additionally look in you user install path [1]. You are looking for multiple copies of the SimpleITK module or library and or python runtime libraries which could confuse the linker.</div><div><br></div><div>Also you can inspect the runtime libraries:</div><div><br></div><div><div style="margin:0px;font-size:11px;font-family:Menlo"> otool -L /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so</div><div style="margin:0px;font-size:11px;font-family:Menlo">/Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so:</div><div style="margin:0px;font-size:11px;font-family:Menlo"><span style="white-space:pre-wrap"> </span>@loader_path/../../../libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0)</div><div style="margin:0px;font-size:11px;font-family:Menlo"><span style="white-space:pre-wrap"> </span>/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 855.17.0)</div><div style="margin:0px;font-size:11px;font-family:Menlo"><span style="white-space:pre-wrap"> </span>/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)</div><div style="margin:0px;font-size:11px;font-family:Menlo"><span style="white-space:pre-wrap"> </span>/usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 60.0.0)</div><div style="margin:0px;font-size:11px;font-family:Menlo"><span style="white-space:pre-wrap"> </span>/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 2577.0.0)</div></div><div><br></div><div>[1] <a href="https://docs.python.org/2/install/#alternate-installation-the-user-scheme" rel="nofollow" link="external" target="_blank">https://docs.python.org/2/install/#alternate-installation-the-user-scheme</a></div><div><br></div><div>Hope this helps,</div><div>Brad</div></span></span><span><span><span><div><br></div><div><div><div>On Sep 9, 2014, at 10:55 PM, Vishwa <<a href="http://user/SendEmail.jtp?type=node&node=7586186&i=2" rel="nofollow" link="external" target="_blank">[hidden email]</a>> wrote:</div><br><blockquote style="border-left:2px solid #cccccc;padding:0 1em" type="cite"><p style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">import SimpleITK as sitk</p><p style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Fatal Python error: PyThreadState_Get: no current thread</p><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><br></div><p style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Abort trap: 6</p></blockquote></div><br></div></span></span></span></div><span><br>_____________________________________<br>
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