Install problems on Ubuntu #922
Comments
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Hello, Can you send me the output of these two commands?
Thanks. |
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Not sure which pip was used.
As I mentioned in the other thread, the graduate student that setup the workstation got caiman and mesmerized installed though it gives weird segmentation faults on closing. I will see if it runs through a dataset without issue.
Thanks for looking into the matter!
…-smb
$ which python
/opt/anaconda3/bin/python
$ pip
Command 'pip' not found, but there are 18 similar ones.
On Oct 1, 2021, at 7:32 PM, Pat Gunn ***@***.***> wrote:
Hello,
For some reason it looks like your build process is using the system version of the python development libraries rather than the conda ones.
Can you send me the output of these two commands?
which pip
and
which python
Thanks.
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If pip is not in your path, something is wrong with the conda environment (or perhaps no conda environment is active); a conda environment always has pip in its path. To really fix this, we'd want to recreate the install from scratch. |
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Yes, I think the installation is pretty wonky. We can close this out as I think it will run fine on a regular installation. Thanks for looking into it!
smb iPhone msg
… On Oct 2, 2021, at 10:35 AM, Pat Gunn ***@***.***> wrote:
If pip is not in your path, something is wrong with the conda environment (or perhaps no conda environment is active); a conda environment always has pip in its path. To really fix this, we'd want to recreate the install from scratch.
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For better support, please use the template below to submit your issue. When your issue gets resolved please remember to close it.
Sometimes errors while running CNMF occur during parallel processing which prevents the log to provide a meaningful error message. Please reproduce your error with setting
dview=None.If you need to upgrade CaImAn follow the instructions given in the documentation.
Operating system (Linux/macOS/Windows):
Python version (3.x):
Working environment (Python IDE/Jupyter Notebook/other):
Which of the demo scripts you're using for your analysis (if applicable):
CaImAn version*:
CaImAn installation process (
pip install ./pip install -e ./conda):*You can get the CaImAn version by creating a
paramsobject and then typingparams.data['caiman_version']. If the field doesn't exist, type N/A and consider upgrading)Describe the issue that you are experiencing
Copy error log below
Processing /home/serapio/Desktop/mesmer/CaImAn
DEPRECATION: A future pip version will change local packages to be built in-place without first copying to a temporary directory. We recommend you use --use-feature=in-tree-build to test your packages with this new behavior before it becomes the default.
pip 21.3 will remove support for this functionality. You can find discussion regarding this at Solving issues related to out-of-tree builds pypa/pip#7555.
Building wheels for collected packages: caiman
Building wheel for caiman (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /home/serapio/Desktop/mesmer/bin/python3.6 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-2qj5oqsr/setup.py'"'"'; file='"'"'/tmp/pip-req-build-2qj5oqsr/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-c1o3pq26
cwd: /tmp/pip-req-build-2qj5oqsr/
Complete output (105 lines):
running bdist_wheel
running build
running build_py
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/caiman
copying caiman/paths.py -> build/lib.linux-x86_64-3.6/caiman
copying caiman/init.py -> build/lib.linux-x86_64-3.6/caiman
copying caiman/summary_images.py -> build/lib.linux-x86_64-3.6/caiman
copying caiman/cluster.py -> build/lib.linux-x86_64-3.6/caiman
copying caiman/motion_correction.py -> build/lib.linux-x86_64-3.6/caiman
copying caiman/mmapping.py -> build/lib.linux-x86_64-3.6/caiman
copying caiman/components_evaluation.py -> build/lib.linux-x86_64-3.6/caiman
creating build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/init.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_tensorflow.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_pre_processing.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_demo.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_onacid.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_temporal.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/comparison_humans.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_deconvolution.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_memmapping.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/comparison_general.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/comparison_humans_online.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_movies.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_import.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_spatial.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_toydata.py -> build/lib.linux-x86_64-3.6/caiman/tests
creating build/lib.linux-x86_64-3.6/caiman/utils
copying caiman/utils/init.py -> build/lib.linux-x86_64-3.6/caiman/utils
copying caiman/utils/image_preprocessing_keras.py -> build/lib.linux-x86_64-3.6/caiman/utils
copying caiman/utils/nn_models.py -> build/lib.linux-x86_64-3.6/caiman/utils
copying caiman/utils/utils.py -> build/lib.linux-x86_64-3.6/caiman/utils
copying caiman/utils/visualization.py -> build/lib.linux-x86_64-3.6/caiman/utils
copying caiman/utils/unused.py -> build/lib.linux-x86_64-3.6/caiman/utils
copying caiman/utils/stats.py -> build/lib.linux-x86_64-3.6/caiman/utils
copying caiman/utils/labelling.py -> build/lib.linux-x86_64-3.6/caiman/utils
creating build/lib.linux-x86_64-3.6/caiman/behavior
copying caiman/behavior/init.py -> build/lib.linux-x86_64-3.6/caiman/behavior
copying caiman/behavior/behavior.py -> build/lib.linux-x86_64-3.6/caiman/behavior
creating build/lib.linux-x86_64-3.6/caiman/external
copying caiman/external/init.py -> build/lib.linux-x86_64-3.6/caiman/external
copying caiman/external/cell_magic_wand.py -> build/lib.linux-x86_64-3.6/caiman/external
creating build/lib.linux-x86_64-3.6/caiman/source_extraction
copying caiman/source_extraction/init.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction
creating build/lib.linux-x86_64-3.6/caiman/base
copying caiman/base/init.py -> build/lib.linux-x86_64-3.6/caiman/base
copying caiman/base/rois.py -> build/lib.linux-x86_64-3.6/caiman/base
copying caiman/base/timeseries.py -> build/lib.linux-x86_64-3.6/caiman/base
copying caiman/base/traces.py -> build/lib.linux-x86_64-3.6/caiman/base
copying caiman/base/movies.py -> build/lib.linux-x86_64-3.6/caiman/base
creating build/lib.linux-x86_64-3.6/caiman/tests/comparison
copying caiman/tests/comparison/init.py -> build/lib.linux-x86_64-3.6/caiman/tests/comparison
copying caiman/tests/comparison/create_gt.py -> build/lib.linux-x86_64-3.6/caiman/tests/comparison
copying caiman/tests/comparison/comparison.py -> build/lib.linux-x86_64-3.6/caiman/tests/comparison
copying caiman/tests/comparison/regen_main_gt.py -> build/lib.linux-x86_64-3.6/caiman/tests/comparison
creating build/lib.linux-x86_64-3.6/caiman/external/houghvst
copying caiman/external/houghvst/init.py -> build/lib.linux-x86_64-3.6/caiman/external/houghvst
copying caiman/external/houghvst/plotting.py -> build/lib.linux-x86_64-3.6/caiman/external/houghvst
copying caiman/external/houghvst/estimation.py -> build/lib.linux-x86_64-3.6/caiman/external/houghvst
copying caiman/external/houghvst/measures.py -> build/lib.linux-x86_64-3.6/caiman/external/houghvst
copying caiman/external/houghvst/gat.py -> build/lib.linux-x86_64-3.6/caiman/external/houghvst
copying caiman/external/houghvst/regions.py -> build/lib.linux-x86_64-3.6/caiman/external/houghvst
copying caiman/external/houghvst/stats.py -> build/lib.linux-x86_64-3.6/caiman/external/houghvst
copying caiman/external/houghvst/demo_VST.py -> build/lib.linux-x86_64-3.6/caiman/external/houghvst
creating build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/init.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/params.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/merging.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/utilities.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/initialization.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/temporal.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/map_reduce.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/spatial.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/online_cnmf.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/deconvolution.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/pre_processing.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/cnmf_optional_outputs.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/cnmf.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/estimates.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
creating build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy
copying caiman/source_extraction/volpy/init.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy
copying caiman/source_extraction/volpy/utils.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy
copying caiman/source_extraction/volpy/volpy.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy
copying caiman/source_extraction/volpy/volpy_gui.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy
copying caiman/source_extraction/volpy/atm.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy
copying caiman/source_extraction/volpy/spikepursuit.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy
copying caiman/source_extraction/volpy/volparams.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy
creating build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy/mrcnn
copying caiman/source_extraction/volpy/mrcnn/init.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy/mrcnn
copying caiman/source_extraction/volpy/mrcnn/utils.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy/mrcnn
copying caiman/source_extraction/volpy/mrcnn/visualize.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy/mrcnn
copying caiman/source_extraction/volpy/mrcnn/neurons.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy/mrcnn
copying caiman/source_extraction/volpy/mrcnn/model.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy/mrcnn
copying caiman/source_extraction/volpy/mrcnn/config.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy/mrcnn
running build_ext
building 'caiman.source_extraction.cnmf.oasis' extension
/opt/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O2 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -I/home/serapio/Desktop/mesmer/lib/python3.6/site-packages/numpy/core/include -I/home/serapio/Desktop/mesmer/include -I/usr/include/python3.6m -c caiman/source_extraction/cnmf/oasis.cpp -o build/temp.linux-x86_64-3.6/caiman/source_extraction/cnmf/oasis.o
In file included from /usr/include/python3.6m/Python.h:8:0,
from caiman/source_extraction/cnmf/oasis.cpp:26:
/usr/include/python3.6m/pyconfig.h:3:12: fatal error: x86_64-linux-gnu/python3.6m/pyconfig.h: No such file or directory
include <x86_64-linux-gnu/python3.6m/pyconfig.h>
compilation terminated.
error: command '/opt/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc' failed with exit status 1
ERROR: Failed building wheel for caiman
Running setup.py clean for caiman
Failed to build caiman
Installing collected packages: caiman
Running setup.py install for caiman ... error
ERROR: Command errored out with exit status 1:
command: /home/serapio/Desktop/mesmer/bin/python3.6 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-2qj5oqsr/setup.py'"'"'; file='"'"'/tmp/pip-req-build-2qj5oqsr/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-qgbokyy_/install-record.txt --single-version-externally-managed --compile --install-headers /home/serapio/Desktop/mesmer/include/site/python3.6/caiman
cwd: /tmp/pip-req-build-2qj5oqsr/
Complete output (110 lines):
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/caiman
copying caiman/paths.py -> build/lib.linux-x86_64-3.6/caiman
copying caiman/init.py -> build/lib.linux-x86_64-3.6/caiman
copying caiman/summary_images.py -> build/lib.linux-x86_64-3.6/caiman
copying caiman/cluster.py -> build/lib.linux-x86_64-3.6/caiman
copying caiman/motion_correction.py -> build/lib.linux-x86_64-3.6/caiman
copying caiman/mmapping.py -> build/lib.linux-x86_64-3.6/caiman
copying caiman/components_evaluation.py -> build/lib.linux-x86_64-3.6/caiman
creating build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/init.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_tensorflow.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_pre_processing.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_demo.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_onacid.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_temporal.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/comparison_humans.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_deconvolution.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_memmapping.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/comparison_general.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/comparison_humans_online.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_movies.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_import.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_spatial.py -> build/lib.linux-x86_64-3.6/caiman/tests
copying caiman/tests/test_toydata.py -> build/lib.linux-x86_64-3.6/caiman/tests
creating build/lib.linux-x86_64-3.6/caiman/utils
copying caiman/utils/init.py -> build/lib.linux-x86_64-3.6/caiman/utils
copying caiman/utils/image_preprocessing_keras.py -> build/lib.linux-x86_64-3.6/caiman/utils
copying caiman/utils/nn_models.py -> build/lib.linux-x86_64-3.6/caiman/utils
copying caiman/utils/utils.py -> build/lib.linux-x86_64-3.6/caiman/utils
copying caiman/utils/visualization.py -> build/lib.linux-x86_64-3.6/caiman/utils
copying caiman/utils/unused.py -> build/lib.linux-x86_64-3.6/caiman/utils
copying caiman/utils/stats.py -> build/lib.linux-x86_64-3.6/caiman/utils
copying caiman/utils/labelling.py -> build/lib.linux-x86_64-3.6/caiman/utils
creating build/lib.linux-x86_64-3.6/caiman/behavior
copying caiman/behavior/init.py -> build/lib.linux-x86_64-3.6/caiman/behavior
copying caiman/behavior/behavior.py -> build/lib.linux-x86_64-3.6/caiman/behavior
creating build/lib.linux-x86_64-3.6/caiman/external
copying caiman/external/init.py -> build/lib.linux-x86_64-3.6/caiman/external
copying caiman/external/cell_magic_wand.py -> build/lib.linux-x86_64-3.6/caiman/external
creating build/lib.linux-x86_64-3.6/caiman/source_extraction
copying caiman/source_extraction/init.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction
creating build/lib.linux-x86_64-3.6/caiman/base
copying caiman/base/init.py -> build/lib.linux-x86_64-3.6/caiman/base
copying caiman/base/rois.py -> build/lib.linux-x86_64-3.6/caiman/base
copying caiman/base/timeseries.py -> build/lib.linux-x86_64-3.6/caiman/base
copying caiman/base/traces.py -> build/lib.linux-x86_64-3.6/caiman/base
copying caiman/base/movies.py -> build/lib.linux-x86_64-3.6/caiman/base
creating build/lib.linux-x86_64-3.6/caiman/tests/comparison
copying caiman/tests/comparison/init.py -> build/lib.linux-x86_64-3.6/caiman/tests/comparison
copying caiman/tests/comparison/create_gt.py -> build/lib.linux-x86_64-3.6/caiman/tests/comparison
copying caiman/tests/comparison/comparison.py -> build/lib.linux-x86_64-3.6/caiman/tests/comparison
copying caiman/tests/comparison/regen_main_gt.py -> build/lib.linux-x86_64-3.6/caiman/tests/comparison
creating build/lib.linux-x86_64-3.6/caiman/external/houghvst
copying caiman/external/houghvst/init.py -> build/lib.linux-x86_64-3.6/caiman/external/houghvst
copying caiman/external/houghvst/plotting.py -> build/lib.linux-x86_64-3.6/caiman/external/houghvst
copying caiman/external/houghvst/estimation.py -> build/lib.linux-x86_64-3.6/caiman/external/houghvst
copying caiman/external/houghvst/measures.py -> build/lib.linux-x86_64-3.6/caiman/external/houghvst
copying caiman/external/houghvst/gat.py -> build/lib.linux-x86_64-3.6/caiman/external/houghvst
copying caiman/external/houghvst/regions.py -> build/lib.linux-x86_64-3.6/caiman/external/houghvst
copying caiman/external/houghvst/stats.py -> build/lib.linux-x86_64-3.6/caiman/external/houghvst
copying caiman/external/houghvst/demo_VST.py -> build/lib.linux-x86_64-3.6/caiman/external/houghvst
creating build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/init.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/params.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/merging.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/utilities.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/initialization.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/temporal.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/map_reduce.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/spatial.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/online_cnmf.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/deconvolution.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/pre_processing.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/cnmf_optional_outputs.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/cnmf.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
copying caiman/source_extraction/cnmf/estimates.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/cnmf
creating build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy
copying caiman/source_extraction/volpy/init.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy
copying caiman/source_extraction/volpy/utils.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy
copying caiman/source_extraction/volpy/volpy.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy
copying caiman/source_extraction/volpy/volpy_gui.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy
copying caiman/source_extraction/volpy/atm.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy
copying caiman/source_extraction/volpy/spikepursuit.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy
copying caiman/source_extraction/volpy/volparams.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy
creating build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy/mrcnn
copying caiman/source_extraction/volpy/mrcnn/init.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy/mrcnn
copying caiman/source_extraction/volpy/mrcnn/utils.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy/mrcnn
copying caiman/source_extraction/volpy/mrcnn/visualize.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy/mrcnn
copying caiman/source_extraction/volpy/mrcnn/neurons.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy/mrcnn
copying caiman/source_extraction/volpy/mrcnn/model.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy/mrcnn
copying caiman/source_extraction/volpy/mrcnn/config.py -> build/lib.linux-x86_64-3.6/caiman/source_extraction/volpy/mrcnn
running build_ext
building 'caiman.source_extraction.cnmf.oasis' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/caiman
creating build/temp.linux-x86_64-3.6/caiman/source_extraction
creating build/temp.linux-x86_64-3.6/caiman/source_extraction/cnmf
/opt/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O2 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -I/home/serapio/Desktop/mesmer/lib/python3.6/site-packages/numpy/core/include -I/home/serapio/Desktop/mesmer/include -I/usr/include/python3.6m -c caiman/source_extraction/cnmf/oasis.cpp -o build/temp.linux-x86_64-3.6/caiman/source_extraction/cnmf/oasis.o
In file included from /usr/include/python3.6m/Python.h:8:0,
from caiman/source_extraction/cnmf/oasis.cpp:26:
/usr/include/python3.6m/pyconfig.h:3:12: fatal error: x86_64-linux-gnu/python3.6m/pyconfig.h: No such file or directory
include <x86_64-linux-gnu/python3.6m/pyconfig.h>
compilation terminated.
error: command '/opt/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc' failed with exit status 1
ERROR: Command errored out with exit status 1: /home/serapio/Desktop/mesmer/bin/python3.6 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-2qj5oqsr/setup.py'"'"'; file='"'"'/tmp/pip-req-build-2qj5oqsr/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-qgbokyy_/install-record.txt --single-version-externally-managed --compile --install-headers /home/serapio/Desktop/mesmer/include/site/python3.6/caiman Check the logs for full command output.
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