Missing a package? Failed Install #122
Comments
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Can you try with a regular virtualenv? Maybe anaconda is to blame?
…On 26 January 2017 19:11:10 CET, brianfm ***@***.***> wrote:
I just installed anaconda from a clean install and installed blosc
using pip install blosc. I am now having this import error:
In [1]: import blosc
---------------------------------------------------------------------------
ImportError Traceback (most recent call
last)
<ipython-input-1-d9d5f9fbfb2e> in <module>()
----> 1 import blosc
/usr/local/anaconda/lib/python2.7/site-packages/blosc/__init__.py in
<module>()
11
12 # Blosc C symbols that we want to export
---> 13 from blosc.blosc_extension import (
14 BLOSC_VERSION_STRING as VERSION_STRING,
15 BLOSC_VERSION_DATE as VERSION_DATE,
ImportError:
/usr/local/anaconda/lib/python2.7/site-packages/blosc/blosc_extension.so:
undefined symbol:
_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE9_M_appendEPKcm
I am running Linux Mint 18 Sarah 64-bit Kernel Linux 4.4.0-21-generic
x86_64 MATE 1.14.1
Am I missing a package when installing from pip? Thank you.
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#122
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Its not about a missing package from pip, something went wrong during compilation, I suppose.
…On 26 January 2017 19:11:10 CET, brianfm ***@***.***> wrote:
I just installed anaconda from a clean install and installed blosc
using pip install blosc. I am now having this import error:
In [1]: import blosc
---------------------------------------------------------------------------
ImportError Traceback (most recent call
last)
<ipython-input-1-d9d5f9fbfb2e> in <module>()
----> 1 import blosc
/usr/local/anaconda/lib/python2.7/site-packages/blosc/__init__.py in
<module>()
11
12 # Blosc C symbols that we want to export
---> 13 from blosc.blosc_extension import (
14 BLOSC_VERSION_STRING as VERSION_STRING,
15 BLOSC_VERSION_DATE as VERSION_DATE,
ImportError:
/usr/local/anaconda/lib/python2.7/site-packages/blosc/blosc_extension.so:
undefined symbol:
_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE9_M_appendEPKcm
I am running Linux Mint 18 Sarah 64-bit Kernel Linux 4.4.0-21-generic
x86_64 MATE 1.14.1
Am I missing a package when installing from pip? Thank you.
--
You are receiving this because you are subscribed to this thread.
Reply to this email directly or view it on GitHub:
#122
--
Sent from my Android device with K-9 Mail. Please excuse my brevity.
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I'm fairly confident it's not anaconda to blame. |
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But did you actually try it? ;) |
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I just tried it with the system python with the same error. pip is not compiling locally its just copying the so files into the site packages directory |
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That's fairly unlikely since there are no binary packages (i.e. no package that contains a *.so file) on PyPi: https://pypi.python.org/pypi/blosc/1.4.4 -- As you can see there is only a source package. This means the package must be compiled locally in order for you to obtain a *.so file. |
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Perhaps pip is caching the results of a previous compilation? Then try using the pip options that disable cache. |
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Also, which version of pip are you using, |
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I removed the cache: Ran: Output: and in ipython:
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Hmmm: It does work for me, so probably nothing to do with the setup.py |
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Here is one with an empty cache: |
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Brian,
That error indicates that probably what happened is the library was
compiled but not linked. I wonder if there's anything funny about your
import paths on your system? I've not had any trouble with blosc with
Anaconda 2.7/3.4/3.5 on Ubuntu 16.04, which is more-or-less equivalent to
Mint 18.
It might be better to download the tarball and run setup.py itself because
pip often hides a lot of important information when it comes to debugging a
setuptools problem.
Robert
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I figured it was the linking as well. I will try again from tar ball. To answer your CMake question: |
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On python-blosc-1.4.4.tar.gz I opened and ran: python setup.py build_ext --inplace python setup.py install Installed /usr/local/anaconda/lib/python2.7/site-packages/blosc-1.4.4-py2.7-linux-x86_64.egg Tried test.py: python test.py |
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warning: no files found matching '*.cpp' under directory 'c-blosc'
warning: no files found matching '*.hpp' under directory 'c-blosc'
Clearly it's not building the c-blosc backend at all, as the amount of
output would be far larger if it did. Could it be a problem with cmake or
gcc?
I just built it with gcc 5.4.0 and cmake 3.5.1.
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cmake -DCMAKE_INSTALL_PREFIX="/usr/local" Target "blosc_static" of type "STATIC_LIBRARY" has the following visibility For compatibility CMake is not honoring them for this target. -- Generating done ~/Downloads/python-blosc-1.4.4/c-blosc $ cmake --build . (I confirmed using gcc 5.4.0 and cmake 3.5.1) |
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Ok, so we see the error now, and as suspected it didn't get linked after compilation. Somehow from the |
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From my .bashrc: export LD_LIBRARY_PATH=/usr/local/lib:/usr/bin:/usr/lib/gcc/x86_64-linux-gnu/5.4.0:$LD_LIBRARY_PATH ~/Downloads/python-blosc-1.4.4/c-blosc $ cmake . Target "blosc_static" of type "STATIC_LIBRARY" has the following visibility For compatibility CMake is not honoring them for this target. -- Generating done ~/Downloads/python-blosc-1.4.4/c-blosc $ cmake --build . |
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IIRC the setup.py will not invoke CMake (but might be mistaken) |
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Yeah, but CMake failing is an indication that something is not working properly in OP machine. As @robbmcleod said, this smells like an issue with the C++ libraries (which is quite strange). @brianfm could you try with disabling snappy (the only codec that needs C++) with: If that works, I suggest to comment this line and set |
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Hello - thank you all again for the help. I just ran: And it finished without error (Built target bench). Should I now cmake --build . --target install? Or go back, comment out the code you have set aside, and run from setup.py? Thank you. |
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Yes, you can do both. If you opt by installing the C library in the system, then you can tell the python installer where to find the library with: |
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cmake -DDEACTIVATE_SNAPPY=ON -DCMAKE_INSTALL_PREFIX="/usr/lib" . ctest: cmake --build . --target install python setup.py build_ext --blosc="/usr/local" python setup.py install Installed /usr/local/anaconda/lib/python2.7/site-packages/blosc-1.4.4-py2.7-linux-x86_64.egg python -c "import blosc; print(blosc.version)" |
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Mmh, you should either remove the old |
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That makes sense. I went out and deleted and cleared cache. After clearing cache, I ran: Output: File "build/bdist.linux-x86_64/egg/blosc/blosc_extension.py", line 7, in Why is it picking up on the cache again? Thank you again, I appreciate at all the help. |
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I am not sure how this cache works, but it looks like that the problem with shared libraries is appearing again. I am getting out of ideas, so not sure what to recommend. It might be a good idea to clean everything related with Blosc in your system and start anew. |
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Thank you for the help. I will try this on Monday and report back. |
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Thank you all for the help. |
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I am also facing this issue with Anaconda. On normal system it works fine. @brianfm did you solve it? |
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I was able to solve it - finally! This is what I did.
then: then:
From there I ran: Lastly, I set up my Library Path in .bashrc to point to: Once all of that was done, I was able to import blosc in python. I hope this helps. Took me a while to get it running. |
I just installed anaconda from a clean install and installed blosc using pip install blosc. I am now having this import error:
In [1]: import blosc
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
in ()
----> 1 import blosc
/usr/local/anaconda/lib/python2.7/site-packages/blosc/init.py in ()
11
12 # Blosc C symbols that we want to export
---> 13 from blosc.blosc_extension import (
14 BLOSC_VERSION_STRING as VERSION_STRING,
15 BLOSC_VERSION_DATE as VERSION_DATE,
ImportError: /usr/local/anaconda/lib/python2.7/site-packages/blosc/blosc_extension.so: undefined symbol: _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE9_M_appendEPKcm
I am running Linux Mint 18 Sarah 64-bit Kernel Linux 4.4.0-21-generic x86_64 MATE 1.14.1
Am I missing a package when installing from pip? Thank you.
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