[ITK] [ITK-users] Issue installing SimpleITK via conda-recipe

Bradley Lowekamp blowekamp at mail.nih.gov
Thu Oct 23 09:57:01 EDT 2014 

Hello,

Thank you for sending me the file off list. I asked that just because of the potential size of the file. It's best to keep the conversation on the list so that all can benefit.

It does appear that there is a problem with the SimpleITK using system libraries not picking up the anaconda dependencies but instead the system ones. For example here in the ITK CMakeCache.txt file we have:


TIFF_INCLUDE_DIR:PATH=/usr/include/x86_64-linux-gnu

TIFF_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libtiff.so

PNG_PNG_INCLUDE_DIR:PATH=/usr/include

and simular things for jpeg and zlib.

I'd recommend turning them all off until a better solution is found. I have a pull request for this change here:
https://github.com/conda/conda-recipes/pull/201

Thanks,
Brad

On Oct 23, 2014, at 9:21 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:

> Hello,
> 
> Yes, Changing the problematic USE_SYSTEM cmake options to OFF should fix this issue.
> 
> Unfortunately, the variables I was looking for were not in that CMakeCache.txt file. They would be in the CMakeCache.txt file in the ITK-buiild subdirectory. Could you please e-mail that one off list?
> 
> Thanks,
> Brad
> 
> On Oct 23, 2014, at 9:00 AM, Guillaume Lemaître <g.lemaitre58 at gmail.com> wrote:
> 
>> Hi Brad,
>> 
>> Find attached the CMakeCache.txt from ./anaconda/conda-bld/work/build
>> In this file it seems that,
>> ITK_USE_SYSTEM_TIFF:BOOL=ON
>> 
>> Does it mean that the TIFF used is from the anaconda "system"? I assume that I have to try to put the boolean to OFF to use the one of ITK.
>> 
>> Thanks,
>> 
>> On 23 October 2014 14:52, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>> Hello,
>> 
>> Can you please send me you CMakeCache.txt file from the build directory.
>> 
>> The simplest thing to do may be to remote using the anaconda "system" tiff library and just use the one ITK has. This can be done by modifying the conda recipe build script here [1].
>> 
>> Most likely there is some confusion which occurs during the CMake configuration about which tiff library to use.
>> 
>> Brad
>> 
>> [1] https://github.com/conda/conda-recipes/blob/master/simpleitk/build.sh#L35
>> 
>> On Oct 23, 2014, at 4:43 AM, Guillaume Lemaître <g.lemaitre58 at gmail.com> wrote:
>> 
>>> Hi all,
>>> 
>>> First, I am a newbie in Python and anaconda and sorry in advance if things seems trivial
>>> I tried to install SimpleITK through conda-recipe. The installation by itself seems to be fined but the test is failling:
>>> 
>>> ==== testing package: simpleitk-0.8.0.post29-py27_0 =====
>>> import: u'SimpleITK'
>>> Traceback (most recent call last):
>>>   File "/home/lemaitre/anaconda/conda-bld/test-tmp_dir/run_test.py", line 25, in <module>
>>>     import SimpleITK
>>>   File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/__init__.py", line 1, in <module>
>>>     from .SimpleITK import *
>>>   File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 28, in <module>
>>>     _SimpleITK = swig_import_helper()
>>>   File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 24, in swig_import_helper
>>>     _mod = imp.load_module('_SimpleITK', fp, pathname, description)
>>> ImportError: /home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: symbol TIFFFieldDataType, version LIBTIFF_4.0 not defined in file libtiff.so.5 with link time reference
>>> TESTS FAILED: simpleitk-0.8.0.post29-py27_0
>>> 
>>> I got that the issue is linked with the libtiff but I believed that anaconda would manage the installation of the dependencies needed.
>>> 
>>> My system is:
>>> Ubuntu 14.04
>>> Python 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Aug 21 2014, 18:22:21) 
>>> [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
>>> 
>>> Cheers,
>>> 
>>> -- 
>>> LEMAÎTRE Guillaume
>>> PhD Candiate
>>> MSc Erasmus Mundus ViBOT (Vision-roBOTic)
>>> MSc Business Innovation and Technology Management
>>> 
>>> g.lemaitre58 at gmail.com
>>> 
>>> 
>>> ViCOROB - Computer Vision and Robotic Team
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>> 
>> 
>> 
>> 
>> -- 
>> LEMAÎTRE Guillaume
>> PhD Candiate
>> MSc Erasmus Mundus ViBOT (Vision-roBOTic)
>> MSc Business Innovation and Technology Management
>> 
>> g.lemaitre58 at gmail.com
>> 
>> 
>> ViCOROB - Computer Vision and Robotic Team
>> Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona
>> Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 
>> http://vicorob.udg.es/
>> LE2I - Le Creusot
>> IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot
>> Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 
>> http://le2i.cnrs.fr
>>         
>> https://sites.google.com/site/glemaitre58/
>> Vice - Chairman of A.S.C. Fours UFOLEP
>> Chairman of A.S.C. Fours FFC
>> Webmaster of http://ascfours.free.fr
>> <CMakeCache.txt>
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
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