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flatironinstitute / CaImAn

Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
https://caiman.readthedocs.io
GNU General Public License v2.0
637 stars 370 forks source link

macOS Mojave 10.14.2 installation issue #439

Closed rem7101 closed 5 years ago

rem7101 commented 5 years ago
pgunn commented 5 years ago

Hi, As far as I can tell this relates to the version of the XCode command line tools you have installed; could you try upgrading that component and giving it another go?

(I think you can do this through the GUI or by issuing the xcode-select --install command from the terminal)

rem7101 commented 5 years ago

Hi, Using the xcode-select --install command in terminal did not update XCode, so I opened XCode separately and upon doing so, it installed additional components during the opening process. There are no other updates available in the App Store. It now says that I have XCode Version 10.1 (10B61). Then I reran the CaImAn install code, but I received the same error:

Last login: Tue Jan 29 12:33:11 on ttys000 macbook-pro:~ ninja7101$ xcode-select --install xcode-select: error: command line tools are already installed, use "Software Update" to install updates macbook-pro:~ ninja7101$ git clone https://github.com/flatironinstitute/CaImAn fatal: destination path 'CaImAn' already exists and is not an empty directory. macbook-pro:~ ninja7101$ cd CaImAn/ macbook-pro:CaImAn ninja7101$ conda env create -f environment.yml -n caiman

CondaValueError: prefix already exists: /Users/ninja7101/anaconda3/envs/caiman

macbook-pro:CaImAn ninja7101$ source activate caiman (caiman) macbook-pro:CaImAn ninja7101$ pip install . Processing /Users/ninja7101/CaImAn Building wheels for collected packages: caiman Building wheel for caiman (setup.py) ... error Complete output from command /Users/ninja7101/anaconda3/envs/caiman/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/wh/r3d_f4zj6gl3p_9qbq43s21m0000gn/T/pip-req-build-edczn7ug/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" bdist_wheel -d /private/var/folders/wh/r3d_f4zj6gl3p_9qbq43s21m0000gn/T/pip-wheel-1fpd3x0u --python-tag cp36: running bdist_wheel running build running build_py creating build creating build/lib.macosx-10.7-x86_64-3.6 creating build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/paths.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/components_evaluation.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/summary_images.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/motion_correction.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/mmapping.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/cluster.py -> build/lib.macosx-10.7-x86_64-3.6/caiman creating build/lib.macosx-10.7-x86_64-3.6/caiman/behavior copying caiman/behavior/behavior.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/behavior copying caiman/behavior/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/behavior creating build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_pre_processing.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_temporal.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_spatial.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_deconvolution.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_import.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/comparison_humans.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_general.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_toydata.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_demo.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/comparison_humans_online.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests creating build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/labelling.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/visualization.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/utils.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/stats.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/image_preprocessing_keras.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils creating build/lib.macosx-10.7-x86_64-3.6/caiman/gui copying caiman/gui/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/gui copying caiman/gui/caiman_gui.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/gui copying caiman/gui/gui.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/gui copying caiman/gui/gui_pyqtgraph.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/gui creating build/lib.macosx-10.7-x86_64-3.6/caiman/external copying caiman/external/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external copying caiman/external/cell_magic_wand.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external creating build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction copying caiman/source_extraction/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction creating build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/rois.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/movies.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/traces.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/timeseries.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base creating build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison copying caiman/tests/comparison/regen_main_gt.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison copying caiman/tests/comparison/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison copying caiman/tests/comparison/comparison.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison copying caiman/tests/comparison/create_gt.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison creating build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/demo_VST.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/regions.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/plotting.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/estimation.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/measures.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/stats.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/gat.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst creating build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/params.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/temporal.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/estimates.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/deconvolution.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/spatial.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/cnmf.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/initialization.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/cnmf_optional_outputs.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/map_reduce.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/utilities.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/pre_processing.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/merging.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/online_cnmf.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf running build_ext building 'caiman.source_extraction.cnmf.oasis' extension creating build/temp.macosx-10.7-x86_64-3.6 creating build/temp.macosx-10.7-x86_64-3.6/caiman creating build/temp.macosx-10.7-x86_64-3.6/caiman/source_extraction creating build/temp.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ninja7101/anaconda3/envs/caiman/include -arch x86_64 -I/Users/ninja7101/anaconda3/envs/caiman/include -arch x86_64 -I/Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include -I/Users/ninja7101/anaconda3/envs/caiman/include/python3.6m -c caiman/source_extraction/cnmf/oasis.cpp -o build/temp.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf/oasis.o warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found] In file included from caiman/source_extraction/cnmf/oasis.cpp:647: In file included from /Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822: /Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]

warning "Using deprecated NumPy API, disable it with " \

^ caiman/source_extraction/cnmf/oasis.cpp:651:10: fatal error: 'ios' file not found

include "ios"

       ^~~~~

2 warnings and 1 error generated. error: command 'gcc' failed with exit status 1

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 Complete output from command /Users/ninja7101/anaconda3/envs/caiman/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/wh/r3d_f4zj6gl3p_9qbq43s21m0000gn/T/pip-req-build-edczn7ug/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /private/var/folders/wh/r3d_f4zj6gl3p_9qbq43s21m0000gn/T/pip-record-4pwpux_5/install-record.txt --single-version-externally-managed --compile: running install running build running build_py creating build creating build/lib.macosx-10.7-x86_64-3.6 creating build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/paths.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/components_evaluation.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/summary_images.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/motion_correction.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/mmapping.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/cluster.py -> build/lib.macosx-10.7-x86_64-3.6/caiman creating build/lib.macosx-10.7-x86_64-3.6/caiman/behavior copying caiman/behavior/behavior.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/behavior copying caiman/behavior/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/behavior creating build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_pre_processing.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_temporal.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_spatial.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_deconvolution.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_import.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/comparison_humans.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_general.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_toydata.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_demo.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/comparison_humans_online.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests creating build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/labelling.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/visualization.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/utils.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/stats.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/image_preprocessing_keras.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils creating build/lib.macosx-10.7-x86_64-3.6/caiman/gui copying caiman/gui/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/gui copying caiman/gui/caiman_gui.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/gui copying caiman/gui/gui.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/gui copying caiman/gui/gui_pyqtgraph.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/gui creating build/lib.macosx-10.7-x86_64-3.6/caiman/external copying caiman/external/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external copying caiman/external/cell_magic_wand.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external creating build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction copying caiman/source_extraction/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction creating build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/rois.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/movies.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/traces.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/timeseries.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base creating build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison copying caiman/tests/comparison/regen_main_gt.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison copying caiman/tests/comparison/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison copying caiman/tests/comparison/comparison.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison copying caiman/tests/comparison/create_gt.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison creating build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/demo_VST.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/regions.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/plotting.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/estimation.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/measures.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/stats.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/gat.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst creating build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/params.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/temporal.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/estimates.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/deconvolution.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/spatial.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/cnmf.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/initialization.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/cnmf_optional_outputs.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/map_reduce.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/utilities.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/pre_processing.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/merging.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/online_cnmf.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf running build_ext building 'caiman.source_extraction.cnmf.oasis' extension creating build/temp.macosx-10.7-x86_64-3.6 creating build/temp.macosx-10.7-x86_64-3.6/caiman creating build/temp.macosx-10.7-x86_64-3.6/caiman/source_extraction creating build/temp.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ninja7101/anaconda3/envs/caiman/include -arch x86_64 -I/Users/ninja7101/anaconda3/envs/caiman/include -arch x86_64 -I/Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include -I/Users/ninja7101/anaconda3/envs/caiman/include/python3.6m -c caiman/source_extraction/cnmf/oasis.cpp -o build/temp.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf/oasis.o warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found] In file included from caiman/source_extraction/cnmf/oasis.cpp:647: In file included from /Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822: /Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]

warning "Using deprecated NumPy API, disable it with " \

 ^
caiman/source_extraction/cnmf/oasis.cpp:651:10: fatal error: 'ios' file not found
#include "ios"
         ^~~~~
2 warnings and 1 error generated.
error: command 'gcc' failed with exit status 1

----------------------------------------

Command "/Users/ninja7101/anaconda3/envs/caiman/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/wh/r3d_f4zj6gl3p_9qbq43s21m0000gn/T/pip-req-build-edczn7ug/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /private/var/folders/wh/r3d_f4zj6gl3p_9qbq43s21m0000gn/T/pip-record-4pwpux_5/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/wh/r3d_f4zj6gl3p_9qbq43s21m0000gn/T/pip-req-build-edczn7ug/

pgunn commented 5 years ago

I've been reading up on this - apparently Mojave broke compile toolchains for a lot of packages.

This thread: https://stackoverflow.com/questions/52509602/cant-compile-c-program-on-a-mac-after-upgrade-to-mojave

goes deep into the issue. It suggests this might be a solution:

open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg

Give that a go and let us know the results of a pip install afterwards.

rem7101 commented 5 years ago

Thanks, In case it is helpful, here is the XCode page where it explains the issue: [https://developer.apple.com/documentation/xcode_release_notes/xcode_10_release_notes] Here they suggest '
To make sure that you're using the intended version of the command line tools, run xcode-select -s or xcode select -s /Library/Developer/CommandLineTools after installing.' after installing the package. I did not do this since I am not sure which option and path to use exactly.

I tried executing 'open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg' while in the caiman environment, but I got the same error as before. I also tried making a new environment called caiman2, then executed the open /.../...macOS_10.14.pkg command again before trying the pip install, but I also got the same error.

Thanks

pgunn commented 5 years ago

Hm. Did the open command itself give you an error or did it do nothing?

rem7101 commented 5 years ago

The open command worked - it brought up a standard gui installer window - all the steps seemed to complete ok.

pgunn commented 5 years ago

We're going to locally upgrade one of our systems to the new OS version to figure this out; it may take us a bit. Hopefully it won't be too long before we can get back to you.

rem7101 commented 5 years ago

Ok - thank you for the help.

epnev commented 5 years ago

@rem7101 Running CFLAGS='-libstd=libc++' pip install . (or pip install -e . depending on your preference) seems to fix the issue. Can you confirm? We're also testing this and will update the installer file accordingly.

rem7101 commented 5 years ago

Hi - thanks - just to make sure I understand before running in terminal: Should I run CFLAGS='-libstd=libc++' pip install . within my caiman environment on conda?

pgunn commented 5 years ago

@rem7101 Yes. Give that a go.

rem7101 commented 5 years ago

Ok - it did not seem to work for me:

MacBook-Pro:~ ninja7101$ source activate caiman (caiman) MacBook-Pro:~ ninja7101$ CFLAGS='-libstd=libc++' pip install . Directory '.' is not installable. Neither 'setup.py' nor 'pyproject.toml' found.

pgunn commented 5 years ago

You're going to want to do this in your caiman source directory (pip looks in the current directory for a setup.py)

pgunn commented 5 years ago

Testing #441 to make sure it doesn't break other platforms

rem7101 commented 5 years ago

I ran it again in the source directory, but it looks like I got the same error as yesterday:

MacBook-Pro:~ ninja7101$ cd CaImAn/ MacBook-Pro:CaImAn ninja7101$ source activate caiman (caiman) MacBook-Pro:CaImAn ninja7101$ CFLAGS='-libstd=libc++' pip install . Processing /Users/ninja7101/CaImAn Building wheels for collected packages: caiman Building wheel for caiman (setup.py) ... error Complete output from command /Users/ninja7101/anaconda3/envs/caiman/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/wh/r3d_f4zj6gl3p_9qbq43s21m0000gn/T/pip-req-build-jayraq1a/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" bdist_wheel -d /private/var/folders/wh/r3d_f4zj6gl3p_9qbq43s21m0000gn/T/pip-wheel-ixmkqqsx --python-tag cp36: running bdist_wheel running build running build_py creating build creating build/lib.macosx-10.7-x86_64-3.6 creating build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/paths.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/components_evaluation.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/summary_images.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/motion_correction.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/mmapping.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/cluster.py -> build/lib.macosx-10.7-x86_64-3.6/caiman creating build/lib.macosx-10.7-x86_64-3.6/caiman/behavior copying caiman/behavior/behavior.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/behavior copying caiman/behavior/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/behavior creating build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_pre_processing.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_temporal.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_spatial.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_deconvolution.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_import.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/comparison_humans.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_general.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_toydata.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_demo.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/comparison_humans_online.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests creating build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/labelling.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/visualization.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/utils.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/stats.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/image_preprocessing_keras.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils creating build/lib.macosx-10.7-x86_64-3.6/caiman/gui copying caiman/gui/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/gui copying caiman/gui/caiman_gui.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/gui copying caiman/gui/gui.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/gui copying caiman/gui/gui_pyqtgraph.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/gui creating build/lib.macosx-10.7-x86_64-3.6/caiman/external copying caiman/external/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external copying caiman/external/cell_magic_wand.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external creating build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction copying caiman/source_extraction/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction creating build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/rois.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/movies.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/traces.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/timeseries.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base creating build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison copying caiman/tests/comparison/regen_main_gt.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison copying caiman/tests/comparison/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison copying caiman/tests/comparison/comparison.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison copying caiman/tests/comparison/create_gt.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison creating build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/demo_VST.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/regions.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/plotting.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/estimation.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/measures.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/stats.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/gat.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst creating build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/params.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/temporal.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/estimates.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/deconvolution.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/spatial.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/cnmf.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/initialization.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/cnmf_optional_outputs.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/map_reduce.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/utilities.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/pre_processing.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/merging.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/online_cnmf.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf running build_ext building 'caiman.source_extraction.cnmf.oasis' extension creating build/temp.macosx-10.7-x86_64-3.6 creating build/temp.macosx-10.7-x86_64-3.6/caiman creating build/temp.macosx-10.7-x86_64-3.6/caiman/source_extraction creating build/temp.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -libstd=libc++ -I/Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include -I/Users/ninja7101/anaconda3/envs/caiman/include/python3.6m -c caiman/source_extraction/cnmf/oasis.cpp -o build/temp.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf/oasis.o clang: warning: -libstd=libc++: 'linker' input unused [-Wunused-command-line-argument] warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found] In file included from caiman/source_extraction/cnmf/oasis.cpp:647: In file included from /Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822: /Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]

warning "Using deprecated NumPy API, disable it with " \

^ caiman/source_extraction/cnmf/oasis.cpp:651:10: fatal error: 'ios' file not found

include "ios"

       ^~~~~

2 warnings and 1 error generated. error: command 'gcc' failed with exit status 1

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 Complete output from command /Users/ninja7101/anaconda3/envs/caiman/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/wh/r3d_f4zj6gl3p_9qbq43s21m0000gn/T/pip-req-build-jayraq1a/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /private/var/folders/wh/r3d_f4zj6gl3p_9qbq43s21m0000gn/T/pip-record-xtcqv542/install-record.txt --single-version-externally-managed --compile: running install running build running build_py creating build creating build/lib.macosx-10.7-x86_64-3.6 creating build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/paths.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/components_evaluation.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/summary_images.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/motion_correction.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/mmapping.py -> build/lib.macosx-10.7-x86_64-3.6/caiman copying caiman/cluster.py -> build/lib.macosx-10.7-x86_64-3.6/caiman creating build/lib.macosx-10.7-x86_64-3.6/caiman/behavior copying caiman/behavior/behavior.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/behavior copying caiman/behavior/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/behavior creating build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_pre_processing.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_temporal.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_spatial.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_deconvolution.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_import.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/comparison_humans.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_general.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_toydata.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/test_demo.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests copying caiman/tests/comparison_humans_online.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests creating build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/labelling.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/visualization.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/utils.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/stats.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils copying caiman/utils/image_preprocessing_keras.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/utils creating build/lib.macosx-10.7-x86_64-3.6/caiman/gui copying caiman/gui/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/gui copying caiman/gui/caiman_gui.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/gui copying caiman/gui/gui.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/gui copying caiman/gui/gui_pyqtgraph.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/gui creating build/lib.macosx-10.7-x86_64-3.6/caiman/external copying caiman/external/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external copying caiman/external/cell_magic_wand.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external creating build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction copying caiman/source_extraction/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction creating build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/rois.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/movies.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/traces.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base copying caiman/base/timeseries.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/base creating build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison copying caiman/tests/comparison/regen_main_gt.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison copying caiman/tests/comparison/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison copying caiman/tests/comparison/comparison.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison copying caiman/tests/comparison/create_gt.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/tests/comparison creating build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/demo_VST.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/regions.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/plotting.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/estimation.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/measures.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/stats.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst copying caiman/external/houghvst/gat.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/external/houghvst creating build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/params.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/temporal.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/estimates.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/deconvolution.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/init.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/spatial.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/cnmf.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/initialization.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/cnmf_optional_outputs.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/map_reduce.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/utilities.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/pre_processing.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/merging.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf copying caiman/source_extraction/cnmf/online_cnmf.py -> build/lib.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf running build_ext building 'caiman.source_extraction.cnmf.oasis' extension creating build/temp.macosx-10.7-x86_64-3.6 creating build/temp.macosx-10.7-x86_64-3.6/caiman creating build/temp.macosx-10.7-x86_64-3.6/caiman/source_extraction creating build/temp.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -libstd=libc++ -I/Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include -I/Users/ninja7101/anaconda3/envs/caiman/include/python3.6m -c caiman/source_extraction/cnmf/oasis.cpp -o build/temp.macosx-10.7-x86_64-3.6/caiman/source_extraction/cnmf/oasis.o clang: warning: -libstd=libc++: 'linker' input unused [-Wunused-command-line-argument] warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found] In file included from caiman/source_extraction/cnmf/oasis.cpp:647: In file included from /Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822: /Users/ninja7101/anaconda3/envs/caiman/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]

warning "Using deprecated NumPy API, disable it with " \

 ^
caiman/source_extraction/cnmf/oasis.cpp:651:10: fatal error: 'ios' file not found
#include "ios"
         ^~~~~
2 warnings and 1 error generated.
error: command 'gcc' failed with exit status 1

----------------------------------------

Command "/Users/ninja7101/anaconda3/envs/caiman/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/wh/r3d_f4zj6gl3p_9qbq43s21m0000gn/T/pip-req-build-jayraq1a/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /private/var/folders/wh/r3d_f4zj6gl3p_9qbq43s21m0000gn/T/pip-record-xtcqv542/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/wh/r3d_f4zj6gl3p_9qbq43s21m0000gn/T/pip-req-build-jayraq1a/

j-friedrich commented 5 years ago

Can you please try CFLAGS='-stdlib=libc++' pip install . i.e. stdlib instead libstd

rem7101 commented 5 years ago

I think it worked that time - just as an fyi, this was the same environment where I ran the open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg yesterday. I will try running the demo file later today. Thanks! Please find the terminal read-out below:

MacBook-Pro:~ ninja7101$ cd CaImAn/ MacBook-Pro:CaImAn ninja7101$ source activate caiman (caiman) MacBook-Pro:CaImAn ninja7101$ CFLAGS='-stdlib=libc++' pip install . Processing /Users/ninja7101/CaImAn Building wheels for collected packages: caiman Building wheel for caiman (setup.py) ... done Stored in directory: /private/var/folders/wh/r3d_f4zj6gl3p_9qbq43s21m0000gn/T/pip-ephem-wheel-cache-to8p9203/wheels/72/88/92/c81ff69de5f1770bbc4063afbb1f59821ce0e82a05f8b159e6 Successfully built caiman Installing collected packages: caiman Successfully installed caiman-1.0

pgunn commented 5 years ago

Fixed in dev with 441.

epnev commented 5 years ago

@pgunn I'll do some testing and merge with master tomorrow.