Missing a package? Failed Install about python-blosc HOT 30 CLOSED

from python-blosc.

from python-blosc.

I'm fairly confident it's not anaconda to blame.

from python-blosc.

But did you actually try it? ;)

from python-blosc.

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

from python-blosc.

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.

from python-blosc.

Perhaps pip is caching the results of a previous compilation? Then try using the pip options that disable cache. --no-cache-dir is your friend.

from python-blosc.

Also, which version of pip are you using, pip --version will show that

from python-blosc.

I removed the cache:
sudo rm ~/.cache/pip

Ran:
sudo pip install blosc --ignore-installed

Output:
Collecting blosc
Downloading blosc-1.4.4.tar.gz (613kB)
100% |████████████████████████████████| 614kB 1.8MB/s
Installing collected packages: blosc
Running setup.py install for blosc ... done
Successfully installed blosc-1.4.4

and in ipython:
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

Is there a bug in setup.py?

My pip version:
pip 9.0.1

from python-blosc.

Hmmm:

esc@omnitech /tmp % virtualenv venv
Running virtualenv with interpreter /usr/bin/python2
New python executable in /tmp/venv/bin/python2
Also creating executable in /tmp/venv/bin/python
Installing setuptools, pkg_resources, pip, wheel...done.
esc@omnitech /tmp % source .venv/bin/activate
esc@omnitech /tmp % pip install blosc
Collecting blosc
  Using cached blosc-1.4.4.tar.gz
Building wheels for collected packages: blosc
  Running setup.py bdist_wheel for blosc ... done
  Stored in directory: /home/esc/.cache/pip/wheels/66/b5/8e/3e67ed59865256f2c3c5d5a914069e1b7f6ef61f4086e98c43
Successfully built blosc
Installing collected packages: blosc
Successfully installed blosc-1.4.4
pip install blosc  15,33s user 0,81s system 97% cpu 16,483 total
esc@omnitech /tmp % python -c "import blosc; print(blosc.__version__)"
1.4.4

It does work for me, so probably nothing to do with the setup.py

from python-blosc.

Here is one with an empty cache:

esc@omnitech /tmp % virtualenv venv
Running virtualenv with interpreter /usr/bin/python2
New python executable in /tmp/venv/bin/python2
Not overwriting existing python script /tmp/venv/bin/python (you must use /tmp/venv/bin/python2)
Installing setuptools, pkg_resources, pip, wheel...done.
esc@omnitech /tmp % source venv/bin/activate 
esc@omnitech /tmp % pip install -U pip
Requirement already up-to-date: pip in ./venv/lib/python2.7/site-packages
esc@omnitech /tmp % pip --version
pip 9.0.1 from /tmp/venv/local/lib/python2.7/site-packages (python 2.7)
esc@omnitech /tmp % pip install blosc
Collecting blosc
  Downloading blosc-1.4.4.tar.gz (613kB)
    100% |████████████████████████████████| 614kB 975kB/s 
Building wheels for collected packages: blosc
  Running setup.py bdist_wheel for blosc ... done
  Stored in directory: /home/esc/.cache/pip/wheels/66/b5/8e/3e67ed59865256f2c3c5d5a914069e1b7f6ef61f4086e98c43
Successfully built blosc
Installing collected packages: blosc
Successfully installed blosc-1.4.4
pip install blosc  15,96s user 0,80s system 94% cpu 17,706 total
esc@omnitech /tmp % python -c "import blosc; print(blosc.__version__)"
1.4.4

from python-blosc.

from python-blosc.

I figured it was the linking as well. I will try again from tar ball.

To answer your CMake question:
$ cmake --version
cmake version 3.5.1

from python-blosc.

On python-blosc-1.4.4.tar.gz I opened and ran:

python setup.py build_ext --inplace

python setup.py install
SSE2 detected
running install
running bdist_egg
running egg_info
creating blosc.egg-info
writing blosc.egg-info/PKG-INFO
writing top-level names to blosc.egg-info/top_level.txt
writing dependency_links to blosc.egg-info/dependency_links.txt
writing manifest file 'blosc.egg-info/SOURCES.txt'
reading manifest file 'blosc.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '.cpp' under directory 'c-blosc'
warning: no files found matching '.hpp' under directory 'c-blosc'
writing manifest file 'blosc.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
copying blosc/toplevel.py -> build/lib.linux-x86_64-2.7/blosc
copying blosc/init.py -> build/lib.linux-x86_64-2.7/blosc
copying blosc/test.py -> build/lib.linux-x86_64-2.7/blosc
copying blosc/version.py -> build/lib.linux-x86_64-2.7/blosc
running build_ext
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/blosc
copying build/lib.linux-x86_64-2.7/blosc/toplevel.py -> build/bdist.linux-x86_64/egg/blosc
copying build/lib.linux-x86_64-2.7/blosc/init.py -> build/bdist.linux-x86_64/egg/blosc
copying build/lib.linux-x86_64-2.7/blosc/blosc_extension.so -> build/bdist.linux-x86_64/egg/blosc
copying build/lib.linux-x86_64-2.7/blosc/test.py -> build/bdist.linux-x86_64/egg/blosc
copying build/lib.linux-x86_64-2.7/blosc/version.py -> build/bdist.linux-x86_64/egg/blosc
byte-compiling build/bdist.linux-x86_64/egg/blosc/toplevel.py to toplevel.pyc
byte-compiling build/bdist.linux-x86_64/egg/blosc/init.py to init.pyc
byte-compiling build/bdist.linux-x86_64/egg/blosc/test.py to test.pyc
byte-compiling build/bdist.linux-x86_64/egg/blosc/version.py to version.pyc
creating stub loader for blosc/blosc_extension.so
byte-compiling build/bdist.linux-x86_64/egg/blosc/blosc_extension.py to blosc_extension.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying blosc.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying blosc.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying blosc.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying blosc.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
zip_safe flag not set; analyzing archive contents...
creating dist
creating 'dist/blosc-1.4.4-py2.7-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing blosc-1.4.4-py2.7-linux-x86_64.egg
Copying blosc-1.4.4-py2.7-linux-x86_64.egg to /usr/local/anaconda/lib/python2.7/site-packages
Adding blosc 1.4.4 to easy-install.pth file

Installed /usr/local/anaconda/lib/python2.7/site-packages/blosc-1.4.4-py2.7-linux-x86_64.egg
Processing dependencies for blosc==1.4.4
Finished processing dependencies for blosc==1.4.4

Tried test.py:

python test.py
Traceback (most recent call last):
File "test.py", line 7, in
import blosc
File "/usr/local/anaconda/lib/python2.7/site-packages/blosc/init.py", line 13, in
from blosc.blosc_extension import (
ImportError: /usr/local/anaconda/lib/python2.7/site-packages/blosc/blosc_extension.so: undefined symbol: _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE9_M_appendEPKcm

from python-blosc.

from python-blosc.

cmake -DCMAKE_INSTALL_PREFIX="/usr/local"
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
Configuring for Blosc version: 1.11.1
-- Using LZ4 internal sources.
-- No snappy found. Using internal sources.
-- Found ZLIB: /usr/local/anaconda/lib/libz.so (found version "1.2.8")
-- No Zstd library found. Using internal sources.
-- No build type specified. Defaulting to 'Release'.
-- Building for system processor x86_64
-- Adding run-time support for SSE2
-- Adding run-time support for AVX2
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Configuring done
CMake Warning (dev) at blosc/CMakeLists.txt:191 (add_library):
Policy CMP0063 is not set: Honor visibility properties for all target
types. Run "cmake --help-policy CMP0063" for policy details. Use the
cmake_policy command to set the policy and suppress this warning.

Target "blosc_static" of type "STATIC_LIBRARY" has the following visibility
properties set for C:

C_VISIBILITY_PRESET

For compatibility CMake is not honoring them for this target.
This warning is for project developers. Use -Wno-dev to suppress it.

-- Generating done
-- Build files have been written to: ~/Downloads/python-blosc-1.4.4/c-blosc

~/Downloads/python-blosc-1.4.4/c-blosc $ cmake --build .
Scanning dependencies of target blosc_static
[ 1%] Building C object blosc/CMakeFiles/blosc_static.dir/blosc.c.o
[ 2%] Building C object blosc/CMakeFiles/blosc_static.dir/blosclz.c.o
[ 3%] Building C object blosc/CMakeFiles/blosc_static.dir/shuffle-generic.c.o
[ 4%] Building C object blosc/CMakeFiles/blosc_static.dir/bitshuffle-generic.c.o
[ 5%] Building C object blosc/CMakeFiles/blosc_static.dir/shuffle-sse2.c.o
[ 6%] Building C object blosc/CMakeFiles/blosc_static.dir/bitshuffle-sse2.c.o
[ 7%] Building C object blosc/CMakeFiles/blosc_static.dir/shuffle-avx2.c.o
[ 7%] Building C object blosc/CMakeFiles/blosc_static.dir/bitshuffle-avx2.c.o
[ 8%] Building C object blosc/CMakeFiles/blosc_static.dir/shuffle.c.o
[ 9%] Building C object blosc/CMakeFiles/blosc_static.dir//internal-complibs/lz4-1.7.2/lz4hc.c.o
[ 10%] Building C object blosc/CMakeFiles/blosc_static.dir//internal-complibs/lz4-1.7.2/lz4.c.o
[ 11%] Building CXX object blosc/CMakeFiles/blosc_static.dir//internal-complibs/snappy-1.1.1/snappy-c.cc.o
[ 12%] Building CXX object blosc/CMakeFiles/blosc_static.dir//internal-complibs/snappy-1.1.1/snappy-stubs-internal.cc.o
[ 13%] Building CXX object blosc/CMakeFiles/blosc_static.dir//internal-complibs/snappy-1.1.1/snappy.cc.o
[ 14%] Building CXX object blosc/CMakeFiles/blosc_static.dir//internal-complibs/snappy-1.1.1/snappy-sinksource.cc.o
[ 15%] Building C object blosc/CMakeFiles/blosc_static.dir//internal-complibs/zstd-1.0.0/common/fse_decompress.c.o
[ 16%] Building C object blosc/CMakeFiles/blosc_static.dir//internal-complibs/zstd-1.0.0/common/entropy_common.c.o
[ 17%] Building C object blosc/CMakeFiles/blosc_static.dir//internal-complibs/zstd-1.0.0/common/xxhash.c.o
[ 18%] Building C object blosc/CMakeFiles/blosc_static.dir//internal-complibs/zstd-1.0.0/common/zstd_common.c.o
[ 19%] Building C object blosc/CMakeFiles/blosc_static.dir//internal-complibs/zstd-1.0.0/compress/fse_compress.c.o
[ 20%] Building C object blosc/CMakeFiles/blosc_static.dir//internal-complibs/zstd-1.0.0/compress/huf_compress.c.o
[ 21%] Building C object blosc/CMakeFiles/blosc_static.dir//internal-complibs/zstd-1.0.0/compress/zstd_compress.c.o
[ 22%] Building C object blosc/CMakeFiles/blosc_static.dir//internal-complibs/zstd-1.0.0/compress/zbuff_compress.c.o
[ 23%] Building C object blosc/CMakeFiles/blosc_static.dir//internal-complibs/zstd-1.0.0/decompress/zstd_decompress.c.o
[ 24%] Building C object blosc/CMakeFiles/blosc_static.dir//internal-complibs/zstd-1.0.0/decompress/huf_decompress.c.o
[ 25%] Building C object blosc/CMakeFiles/blosc_static.dir//internal-complibs/zstd-1.0.0/decompress/zbuff_decompress.c.o
[ 26%] Linking CXX static library libblosc.a
[ 26%] Built target blosc_static
Scanning dependencies of target blosc_shared_testing
[ 27%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir/blosc.c.o
[ 28%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir/blosclz.c.o
[ 29%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir/shuffle-generic.c.o
[ 30%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir/bitshuffle-generic.c.o
[ 31%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir/shuffle-sse2.c.o
[ 32%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir/bitshuffle-sse2.c.o
[ 33%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir/shuffle-avx2.c.o
[ 34%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir/bitshuffle-avx2.c.o
[ 35%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir/shuffle.c.o
[ 36%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir//internal-complibs/lz4-1.7.2/lz4hc.c.o
[ 37%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir//internal-complibs/lz4-1.7.2/lz4.c.o
[ 38%] Building CXX object blosc/CMakeFiles/blosc_shared_testing.dir//internal-complibs/snappy-1.1.1/snappy-c.cc.o
[ 39%] Building CXX object blosc/CMakeFiles/blosc_shared_testing.dir//internal-complibs/snappy-1.1.1/snappy-stubs-internal.cc.o
[ 39%] Building CXX object blosc/CMakeFiles/blosc_shared_testing.dir//internal-complibs/snappy-1.1.1/snappy.cc.o
[ 40%] Building CXX object blosc/CMakeFiles/blosc_shared_testing.dir//internal-complibs/snappy-1.1.1/snappy-sinksource.cc.o
[ 41%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir//internal-complibs/zstd-1.0.0/common/fse_decompress.c.o
[ 42%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir//internal-complibs/zstd-1.0.0/common/entropy_common.c.o
[ 43%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir//internal-complibs/zstd-1.0.0/common/xxhash.c.o
[ 44%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir//internal-complibs/zstd-1.0.0/common/zstd_common.c.o
[ 45%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir//internal-complibs/zstd-1.0.0/compress/fse_compress.c.o
[ 46%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir//internal-complibs/zstd-1.0.0/compress/huf_compress.c.o
[ 47%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir//internal-complibs/zstd-1.0.0/compress/zstd_compress.c.o
[ 48%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir//internal-complibs/zstd-1.0.0/compress/zbuff_compress.c.o
[ 49%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir//internal-complibs/zstd-1.0.0/decompress/zstd_decompress.c.o
[ 50%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir//internal-complibs/zstd-1.0.0/decompress/huf_decompress.c.o
[ 51%] Building C object blosc/CMakeFiles/blosc_shared_testing.dir//internal-complibs/zstd-1.0.0/decompress/zbuff_decompress.c.o
[ 52%] Linking CXX shared library libblosc_testing.so
[ 52%] Built target blosc_shared_testing
Scanning dependencies of target blosc_shared
[ 53%] Building C object blosc/CMakeFiles/blosc_shared.dir/blosc.c.o
[ 54%] Building C object blosc/CMakeFiles/blosc_shared.dir/blosclz.c.o
[ 55%] Building C object blosc/CMakeFiles/blosc_shared.dir/shuffle-generic.c.o
[ 56%] Building C object blosc/CMakeFiles/blosc_shared.dir/bitshuffle-generic.c.o
[ 57%] Building C object blosc/CMakeFiles/blosc_shared.dir/shuffle-sse2.c.o
[ 58%] Building C object blosc/CMakeFiles/blosc_shared.dir/bitshuffle-sse2.c.o
[ 59%] Building C object blosc/CMakeFiles/blosc_shared.dir/shuffle-avx2.c.o
[ 60%] Building C object blosc/CMakeFiles/blosc_shared.dir/bitshuffle-avx2.c.o
[ 61%] Building C object blosc/CMakeFiles/blosc_shared.dir/shuffle.c.o
[ 62%] Building C object blosc/CMakeFiles/blosc_shared.dir//internal-complibs/lz4-1.7.2/lz4hc.c.o
[ 63%] Building C object blosc/CMakeFiles/blosc_shared.dir//internal-complibs/lz4-1.7.2/lz4.c.o
[ 64%] Building CXX object blosc/CMakeFiles/blosc_shared.dir//internal-complibs/snappy-1.1.1/snappy-c.cc.o
[ 65%] Building CXX object blosc/CMakeFiles/blosc_shared.dir//internal-complibs/snappy-1.1.1/snappy-stubs-internal.cc.o
[ 66%] Building CXX object blosc/CMakeFiles/blosc_shared.dir//internal-complibs/snappy-1.1.1/snappy.cc.o
[ 67%] Building CXX object blosc/CMakeFiles/blosc_shared.dir//internal-complibs/snappy-1.1.1/snappy-sinksource.cc.o
[ 68%] Building C object blosc/CMakeFiles/blosc_shared.dir//internal-complibs/zstd-1.0.0/common/fse_decompress.c.o
[ 69%] Building C object blosc/CMakeFiles/blosc_shared.dir//internal-complibs/zstd-1.0.0/common/entropy_common.c.o
[ 70%] Building C object blosc/CMakeFiles/blosc_shared.dir//internal-complibs/zstd-1.0.0/common/xxhash.c.o
[ 71%] Building C object blosc/CMakeFiles/blosc_shared.dir//internal-complibs/zstd-1.0.0/common/zstd_common.c.o
[ 71%] Building C object blosc/CMakeFiles/blosc_shared.dir//internal-complibs/zstd-1.0.0/compress/fse_compress.c.o
[ 72%] Building C object blosc/CMakeFiles/blosc_shared.dir//internal-complibs/zstd-1.0.0/compress/huf_compress.c.o
[ 73%] Building C object blosc/CMakeFiles/blosc_shared.dir//internal-complibs/zstd-1.0.0/compress/zstd_compress.c.o
[ 74%] Building C object blosc/CMakeFiles/blosc_shared.dir//internal-complibs/zstd-1.0.0/compress/zbuff_compress.c.o
[ 75%] Building C object blosc/CMakeFiles/blosc_shared.dir//internal-complibs/zstd-1.0.0/decompress/zstd_decompress.c.o
[ 76%] Building C object blosc/CMakeFiles/blosc_shared.dir//internal-complibs/zstd-1.0.0/decompress/huf_decompress.c.o
[ 77%] Building C object blosc/CMakeFiles/blosc_shared.dir/__/internal-complibs/zstd-1.0.0/decompress/zbuff_decompress.c.o
[ 78%] Linking CXX shared library libblosc.so
[ 78%] Built target blosc_shared
Scanning dependencies of target test_shuffle_roundtrip_avx2
[ 79%] Building C object tests/CMakeFiles/test_shuffle_roundtrip_avx2.dir/test_shuffle_roundtrip_avx2.c.o
~/Downloads/python-blosc-1.4.4/c-blosc/tests/test_shuffle_roundtrip_avx2.c:25:4: warning: #warning AVX2 shuffle tests not enabled. [-Wcpp]
#warning AVX2 shuffle tests not enabled.
^
[ 80%] Linking C executable test_shuffle_roundtrip_avx2
[ 80%] Built target test_shuffle_roundtrip_avx2
Scanning dependencies of target test_shuffle_roundtrip_generic
[ 81%] Building C object tests/CMakeFiles/test_shuffle_roundtrip_generic.dir/test_shuffle_roundtrip_generic.c.o
[ 82%] Linking C executable test_shuffle_roundtrip_generic
~/Downloads/python-blosc-1.4.4/c-blosc/blosc/libblosc_testing.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)@GLIBCXX_3.4.21' ~/Downloads/python-blosc-1.4.4/c-blosc/blosc/libblosc_testing.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits, std::allocator >::resize(unsigned long, char)@GLIBCXX_3.4.21'
collect2: error: ld returned 1 exit status
tests/CMakeFiles/test_shuffle_roundtrip_generic.dir/build.make:94: recipe for target 'tests/test_shuffle_roundtrip_generic' failed
make[2]: *** [tests/test_shuffle_roundtrip_generic] Error 1
CMakeFiles/Makefile2:307: recipe for target 'tests/CMakeFiles/test_shuffle_roundtrip_generic.dir/all' failed
make[1]: *** [tests/CMakeFiles/test_shuffle_roundtrip_generic.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2

(I confirmed using gcc 5.4.0 and cmake 3.5.1)

from python-blosc.

Ok, so we see the error now, and as suspected it didn't get linked after compilation. Somehow glibcxx.3.4.21.lib isn't being linked to. I suspect either your system environment variables have been overwritten at some point, or one of your library files has been corrupted. Try:

export LD_LIBRARY_PATH=" /usr/lib/gcc/x86_64-linux-gnu/5.4.0:$LD_LIBRARY_PATH"
cmake .

from the python-blosc-1.4.4/c-blosc directory? I don't have Mint so that path may not be correct, verify that it exists first.

from python-blosc.

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 .
Configuring for Blosc version: 1.11.1
-- Using LZ4 internal sources.
-- No snappy found. Using internal sources.
-- No Zstd library found. Using internal sources.
-- Building for system processor x86_64
-- Adding run-time support for SSE2
-- Adding run-time support for AVX2
-- Configuring done
CMake Warning (dev) at blosc/CMakeLists.txt:191 (add_library):
Policy CMP0063 is not set: Honor visibility properties for all target
types. Run "cmake --help-policy CMP0063" for policy details. Use the
cmake_policy command to set the policy and suppress this warning.

Target "blosc_static" of type "STATIC_LIBRARY" has the following visibility
properties set for C:

C_VISIBILITY_PRESET

For compatibility CMake is not honoring them for this target.
This warning is for project developers. Use -Wno-dev to suppress it.

-- Generating done
-- Build files have been written to: ~/Downloads/python-blosc-1.4.4/c-blosc

~/Downloads/python-blosc-1.4.4/c-blosc $ cmake --build .
[ 26%] Built target blosc_static
[ 52%] Built target blosc_shared_testing
[ 78%] Built target blosc_shared
[ 80%] Built target test_shuffle_roundtrip_avx2
[ 81%] Linking C executable test_shuffle_roundtrip_generic
~/Downloads/python-blosc-1.4.4/c-blosc/blosc/libblosc_testing.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)@GLIBCXX_3.4.21' ~/Downloads/python-blosc-1.4.4/c-blosc/blosc/libblosc_testing.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits, std::allocator >::resize(unsigned long, char)@GLIBCXX_3.4.21'
collect2: error: ld returned 1 exit status
tests/CMakeFiles/test_shuffle_roundtrip_generic.dir/build.make:94: recipe for target 'tests/test_shuffle_roundtrip_generic' failed
make[2]: *** [tests/test_shuffle_roundtrip_generic] Error 1
CMakeFiles/Makefile2:307: recipe for target 'tests/CMakeFiles/test_shuffle_roundtrip_generic.dir/all' failed
make[1]: *** [tests/CMakeFiles/test_shuffle_roundtrip_generic.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2

from python-blosc.

IIRC the setup.py will not invoke CMake (but might be mistaken)

from python-blosc.

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:

cmake -DDEACTIVATE_SNAPPY=ON .

If that works, I suggest to comment this line and set HAVE_SNAPPY=0 in this other line?

from python-blosc.

Hello - thank you all again for the help.

I just ran:
cmake -DDEACTIVATE_SNAPPY=ON .
cmake --build .

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.

from python-blosc.

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:

$ python setup.py build_ext --blosc=installed_blosc_dir

from python-blosc.

cmake -DDEACTIVATE_SNAPPY=ON -DCMAKE_INSTALL_PREFIX="/usr/lib" .

ctest:
100% tests passed, 0 tests failed out of 1613
Total Test time (real) = 93.00 sec

cmake --build . --target install
[ 24%] Built target blosc_static
[ 49%] Built target blosc_shared_testing
[ 74%] Built target blosc_shared
[ 76%] Built target test_shuffle_roundtrip_avx2
[ 78%] Built target test_shuffle_roundtrip_generic
[ 80%] Built target test_shuffle_roundtrip_sse2
[ 82%] Built target test_nolock
[ 84%] Built target test_getitem
[ 87%] Built target test_maxout
[ 89%] Built target test_noinit
[ 91%] Built target test_compressor
[ 93%] Built target test_nthreads
[ 95%] Built target test_api
[ 97%] Built target test_compress_roundtrip
[100%] Built target bench
Install the project...
-- Install configuration: "Release"
-- Up-to-date: /usr/local/include/blosc.h
-- Up-to-date: /usr/local/include/blosc-export.h
-- Up-to-date: /usr/local/lib/libblosc.so.1.11.1
-- Up-to-date: /usr/local/lib/libblosc.so.1
-- Up-to-date: /usr/local/lib/libblosc.so
-- Up-to-date: /usr/local/lib/libblosc.a

python setup.py build_ext --blosc="/usr/local"
running build_ext

python setup.py install
SSE2 detected
running install
running bdist_egg
running egg_info
writing blosc.egg-info/PKG-INFO
writing top-level names to blosc.egg-info/top_level.txt
writing dependency_links to blosc.egg-info/dependency_links.txt
reading manifest file 'blosc.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.hpp' under directory 'c-blosc'
writing manifest file 'blosc.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
copying blosc/version.py -> build/lib.linux-x86_64-2.7/blosc
running build_ext
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/blosc
copying build/lib.linux-x86_64-2.7/blosc/toplevel.py -> build/bdist.linux-x86_64/egg/blosc
copying build/lib.linux-x86_64-2.7/blosc/init.py -> build/bdist.linux-x86_64/egg/blosc
copying build/lib.linux-x86_64-2.7/blosc/blosc_extension.so -> build/bdist.linux-x86_64/egg/blosc
copying build/lib.linux-x86_64-2.7/blosc/test.py -> build/bdist.linux-x86_64/egg/blosc
copying build/lib.linux-x86_64-2.7/blosc/version.py -> build/bdist.linux-x86_64/egg/blosc
byte-compiling build/bdist.linux-x86_64/egg/blosc/toplevel.py to toplevel.pyc
byte-compiling build/bdist.linux-x86_64/egg/blosc/init.py to init.pyc
byte-compiling build/bdist.linux-x86_64/egg/blosc/test.py to test.pyc
byte-compiling build/bdist.linux-x86_64/egg/blosc/version.py to version.pyc
creating stub loader for blosc/blosc_extension.so
byte-compiling build/bdist.linux-x86_64/egg/blosc/blosc_extension.py to blosc_extension.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying blosc.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying blosc.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying blosc.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying blosc.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
zip_safe flag not set; analyzing archive contents...
creating 'dist/blosc-1.4.4-py2.7-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing blosc-1.4.4-py2.7-linux-x86_64.egg
Removing /usr/local/anaconda/lib/python2.7/site-packages/blosc-1.4.4-py2.7-linux-x86_64.egg
Copying blosc-1.4.4-py2.7-linux-x86_64.egg to /usr/local/anaconda/lib/python2.7/site-packages
blosc 1.4.4 is already the active version in easy-install.pth

Installed /usr/local/anaconda/lib/python2.7/site-packages/blosc-1.4.4-py2.7-linux-x86_64.egg
Processing dependencies for blosc==1.4.4
Finished processing dependencies for blosc==1.4.4

python -c "import blosc; print(blosc.version)"
Traceback (most recent call last):
File "", line 1, in
File "blosc/init.py", line 13, in
from blosc.blosc_extension import (
ImportError: blosc/blosc_extension.so: undefined symbol: _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE9_M_appendEPKcm

from python-blosc.

Mmh, you should either remove the old blosc/blosc_extension.so or go out from the python-blosc/ source dir before trying to import it.

from python-blosc.

That makes sense. I went out and deleted and cleared cache. After clearing cache, I ran:
python -c "import blosc; print(blosc.version)"

Output:
Traceback (most recent call last):
File "", line 1, in
File "build/bdist.linux-x86_64/egg/blosc/init.py", line 13, in

File "build/bdist.linux-x86_64/egg/blosc/blosc_extension.py", line 7, in
File "build/bdist.linux-x86_64/egg/blosc/blosc_extension.py", line 6, in bootstrap
ImportError: /home/bmccarthy/.cache/Python-Eggs/blosc-1.4.4-py2.7-linux-x86_64.egg-tmp/blosc/blosc_extension.so: undefined symbol: _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE9_M_appendEPKcm

Why is it picking up on the cache again?

Thank you again, I appreciate at all the help.

from python-blosc.

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.

from python-blosc.

Thank you for the help. I will try this on Monday and report back.

from python-blosc.

Thank you all for the help.

from python-blosc.

I am also facing this issue with Anaconda. On normal system it works fine. @brianfm did you solve it?

from python-blosc.

I was able to solve it - finally! This is what I did.

1. I grep'ed to find any instance of blosc or cblosc on my machine (and corresponding files) from previous attempts and deleted them all.

2. I installed cblosc from scratch first. https://github.com/Blosc/c-blosc/releases
   From there I moved to the folder to run cmake:

   cmake -DDEACTIVATE_SNAPPY=ON -DCMAKE_INSTALL_PREFIX="/usr/lib" .

then:
ctest

then:
cmake --build . --target install

3. I downloaded python blosc from scratch:
   https://github.com/Blosc/python-blosc/releases/tag/v1.5.1

From there I ran:
python setup.py build_ext --blosc="/usr/local"
python setup.py install

Lastly, I set up my Library Path in .bashrc to point to:
libblosc.so.1

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.

from python-blosc.