arnefmeyer / lnpy Goto Github PK
View Code? Open in Web Editor NEWPython code for estimation of linear-nonlinear model parameters
License: GNU General Public License v2.0
Python code for estimation of linear-nonlinear model parameters
License: GNU General Public License v2.0
git clone https://github.com/arnefmeyer/lnpy.git
conda create -n lnpy_test python=3.7 numpy scipy cython matplotlib libgcc gcc_linux-64 gxx_linux-64
conda activate lnpy_test
cd lnpy
mv /tmp/1/gammatone/Gfb_analyze* ./lnpy/transform/src/gammatone # files already downloaded and unzipped into /tmp/1
python setup.py build
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "lnpy.transform.wrap_gtfb" sources
building extension "lnpy.multilinear.context.context_fast" sources
building extension "lnpy.learn.pyhelper" sources
building extension "lnpy.fast_tools" sources
build_src: building npy-pkg config files
running build_py
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/lnpy
copying lnpy/util.py -> build/lib.linux-x86_64-3.7/lnpy
copying lnpy/job.py -> build/lib.linux-x86_64-3.7/lnpy
copying lnpy/setup.py -> build/lib.linux-x86_64-3.7/lnpy
copying lnpy/simulate.py -> build/lib.linux-x86_64-3.7/lnpy
copying lnpy/__init__.py -> build/lib.linux-x86_64-3.7/lnpy
copying lnpy/plotting.py -> build/lib.linux-x86_64-3.7/lnpy
copying lnpy/base.py -> build/lib.linux-x86_64-3.7/lnpy
copying lnpy/metrics.py -> build/lib.linux-x86_64-3.7/lnpy
creating build/lib.linux-x86_64-3.7/lnpy/multilinear
copying lnpy/multilinear/util.py -> build/lib.linux-x86_64-3.7/lnpy/multilinear
copying lnpy/multilinear/setup.py -> build/lib.linux-x86_64-3.7/lnpy/multilinear
copying lnpy/multilinear/__init__.py -> build/lib.linux-x86_64-3.7/lnpy/multilinear
creating build/lib.linux-x86_64-3.7/lnpy/learn
copying lnpy/learn/sgd.py -> build/lib.linux-x86_64-3.7/lnpy/learn
copying lnpy/learn/setup.py -> build/lib.linux-x86_64-3.7/lnpy/learn
copying lnpy/learn/svm.py -> build/lib.linux-x86_64-3.7/lnpy/learn
copying lnpy/learn/glm.py -> build/lib.linux-x86_64-3.7/lnpy/learn
copying lnpy/learn/grid_search.py -> build/lib.linux-x86_64-3.7/lnpy/learn
copying lnpy/learn/__init__.py -> build/lib.linux-x86_64-3.7/lnpy/learn
copying lnpy/learn/base.py -> build/lib.linux-x86_64-3.7/lnpy/learn
creating build/lib.linux-x86_64-3.7/lnpy/lnb
copying lnpy/lnb/cbrf.py -> build/lib.linux-x86_64-3.7/lnpy/lnb
copying lnpy/lnb/__init__.py -> build/lib.linux-x86_64-3.7/lnpy/lnb
copying lnpy/lnb/base.py -> build/lib.linux-x86_64-3.7/lnpy/lnb
creating build/lib.linux-x86_64-3.7/lnpy/lnp
copying lnpy/lnp/setup.py -> build/lib.linux-x86_64-3.7/lnpy/lnp
copying lnpy/lnp/sta.py -> build/lib.linux-x86_64-3.7/lnpy/lnp
copying lnpy/lnp/glm.py -> build/lib.linux-x86_64-3.7/lnpy/lnp
copying lnpy/lnp/mid.py -> build/lib.linux-x86_64-3.7/lnpy/lnp
copying lnpy/lnp/__init__.py -> build/lib.linux-x86_64-3.7/lnpy/lnp
copying lnpy/lnp/base.py -> build/lib.linux-x86_64-3.7/lnpy/lnp
creating build/lib.linux-x86_64-3.7/lnpy/transform
copying lnpy/transform/modspec.py -> build/lib.linux-x86_64-3.7/lnpy/transform
copying lnpy/transform/setup.py -> build/lib.linux-x86_64-3.7/lnpy/transform
copying lnpy/transform/gammatone.py -> build/lib.linux-x86_64-3.7/lnpy/transform
copying lnpy/transform/__init__.py -> build/lib.linux-x86_64-3.7/lnpy/transform
copying lnpy/transform/gabor.py -> build/lib.linux-x86_64-3.7/lnpy/transform
copying lnpy/transform/base.py -> build/lib.linux-x86_64-3.7/lnpy/transform
copying lnpy/transform/spectrogram.py -> build/lib.linux-x86_64-3.7/lnpy/transform
creating build/lib.linux-x86_64-3.7/lnpy/linear
copying lnpy/linear/sta.py -> build/lib.linux-x86_64-3.7/lnpy/linear
copying lnpy/linear/ridge.py -> build/lib.linux-x86_64-3.7/lnpy/linear
copying lnpy/linear/prior.py -> build/lib.linux-x86_64-3.7/lnpy/linear
copying lnpy/linear/asd.py -> build/lib.linux-x86_64-3.7/lnpy/linear
copying lnpy/linear/__init__.py -> build/lib.linux-x86_64-3.7/lnpy/linear
copying lnpy/linear/ald.py -> build/lib.linux-x86_64-3.7/lnpy/linear
copying lnpy/linear/ard.py -> build/lib.linux-x86_64-3.7/lnpy/linear
copying lnpy/linear/base.py -> build/lib.linux-x86_64-3.7/lnpy/linear
creating build/lib.linux-x86_64-3.7/lnpy/io
copying lnpy/io/hdf.py -> build/lib.linux-x86_64-3.7/lnpy/io
copying lnpy/io/__init__.py -> build/lib.linux-x86_64-3.7/lnpy/io
creating build/lib.linux-x86_64-3.7/lnpy/multilinear/context
copying lnpy/multilinear/context/setup.py -> build/lib.linux-x86_64-3.7/lnpy/multilinear/context
copying lnpy/multilinear/context/context.py -> build/lib.linux-x86_64-3.7/lnpy/multilinear/context
copying lnpy/multilinear/context/__init__.py -> build/lib.linux-x86_64-3.7/lnpy/multilinear/context
copying lnpy/multilinear/context/vb_dense.py -> build/lib.linux-x86_64-3.7/lnpy/multilinear/context
copying lnpy/multilinear/context/als_dense.py -> build/lib.linux-x86_64-3.7/lnpy/multilinear/context
running build_ext
customize UnixCCompiler
C compiler: /home/ajay/miniconda3/envs/lnpy_test/bin/x86_64-conda_cos6-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/ajay/miniconda3/envs/lnpy_test/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/ajay/miniconda3/envs/lnpy_test/include -fPIC
creating /tmp/tmplpkmrowm/tmp
creating /tmp/tmplpkmrowm/tmp/tmplpkmrowm
compile options: '-MMD -MF /tmp/tmplpkmrowm/file.c.d -c'
x86_64-conda_cos6-linux-gnu-cc: /tmp/tmplpkmrowm/file.c
customize UnixCCompiler using build_ext
customize UnixCCompiler
C compiler: /home/ajay/miniconda3/envs/lnpy_test/bin/x86_64-conda_cos6-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/ajay/miniconda3/envs/lnpy_test/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/ajay/miniconda3/envs/lnpy_test/include -fPIC
creating /tmp/tmpszjy380f/tmp
creating /tmp/tmpszjy380f/tmp/tmpszjy380f
compile options: '-MMD -MF /tmp/tmpszjy380f/file.c.d -c'
x86_64-conda_cos6-linux-gnu-cc: /tmp/tmpszjy380f/file.c
customize UnixCCompiler using build_ext
building 'lnpy.transform.wrap_gtfb' extension
compiling C sources
C compiler: /home/ajay/miniconda3/envs/lnpy_test/bin/x86_64-conda_cos6-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/ajay/miniconda3/envs/lnpy_test/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/ajay/miniconda3/envs/lnpy_test/include -fPIC
creating build/temp.linux-x86_64-3.7/lnpy
creating build/temp.linux-x86_64-3.7/lnpy/transform
creating build/temp.linux-x86_64-3.7/lnpy/transform/src
creating build/temp.linux-x86_64-3.7/lnpy/transform/src/gammatone
compile options: '-Ilnpy/transform/src/gammatone -I/home/ajay/miniconda3/envs/lnpy_test/lib/python3.7/site-packages/numpy/core/include -I/home/ajay/miniconda3/envs/lnpy_test/lib/python3.7/site-packages/numpy/core/include -I/home/ajay/miniconda3/envs/lnpy_test/include/python3.7m -c'
x86_64-conda_cos6-linux-gnu-cc: lnpy/transform/wrap_gtfb.c
x86_64-conda_cos6-linux-gnu-cc: lnpy/transform/src/gammatone/Gfb_analyze.c
In file included from lnpy/transform/src/gammatone/Gfb_analyze.c:36:0:
lnpy/transform/src/gammatone/Gfb_analyze.h:99:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void release_tables();
^~~~
lnpy/transform/src/gammatone/Gfb_analyze.c:135:6: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void release_tables()
^~~~~~~~~~~~~~
In file included from lnpy/transform/wrap_gtfb.c:432:0:
lnpy/transform/src/gammatone/Gfb_analyze.h:99:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void release_tables();
^~~~
In file included from /home/ajay/miniconda3/envs/lnpy_test/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0,
from /home/ajay/miniconda3/envs/lnpy_test/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/ajay/miniconda3/envs/lnpy_test/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from lnpy/transform/wrap_gtfb.c:436:
/home/ajay/miniconda3/envs/lnpy_test/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it with " \
^~~~~~~
lnpy/transform/wrap_gtfb.c: In function '__Pyx__ExceptionSave':
lnpy/transform/wrap_gtfb.c:5862:21: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
*type = tstate->exc_type;
^~~~~~~~
curexc_type
lnpy/transform/wrap_gtfb.c:5863:22: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
*value = tstate->exc_value;
^~~~~~~~~
curexc_value
lnpy/transform/wrap_gtfb.c:5864:19: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
*tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
lnpy/transform/wrap_gtfb.c: In function '__Pyx__ExceptionReset':
lnpy/transform/wrap_gtfb.c:5871:24: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
tmp_type = tstate->exc_type;
^~~~~~~~
curexc_type
lnpy/transform/wrap_gtfb.c:5872:25: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
lnpy/transform/wrap_gtfb.c:5873:22: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
lnpy/transform/wrap_gtfb.c:5874:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
tstate->exc_type = type;
^~~~~~~~
curexc_type
lnpy/transform/wrap_gtfb.c:5875:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
tstate->exc_value = value;
^~~~~~~~~
curexc_value
lnpy/transform/wrap_gtfb.c:5876:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
tstate->exc_traceback = tb;
^~~~~~~~~~~~~
curexc_traceback
lnpy/transform/wrap_gtfb.c: In function '__Pyx__GetException':
lnpy/transform/wrap_gtfb.c:5931:24: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
tmp_type = tstate->exc_type;
^~~~~~~~
curexc_type
lnpy/transform/wrap_gtfb.c:5932:25: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
lnpy/transform/wrap_gtfb.c:5933:22: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
lnpy/transform/wrap_gtfb.c:5934:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'; did you mean 'curexc_type'?
tstate->exc_type = local_type;
^~~~~~~~
curexc_type
lnpy/transform/wrap_gtfb.c:5935:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'; did you mean 'curexc_value'?
tstate->exc_value = local_value;
^~~~~~~~~
curexc_value
lnpy/transform/wrap_gtfb.c:5936:13: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'; did you mean 'curexc_traceback'?
tstate->exc_traceback = local_tb;
^~~~~~~~~~~~~
curexc_traceback
error: Command "/home/ajay/miniconda3/envs/lnpy_test/bin/x86_64-conda_cos6-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/ajay/miniconda3/envs/lnpy_test/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/ajay/miniconda3/envs/lnpy_test/include -fPIC -Ilnpy/transform/src/gammatone -I/home/ajay/miniconda3/envs/lnpy_test/lib/python3.7/site-packages/numpy/core/include -I/home/ajay/miniconda3/envs/lnpy_test/lib/python3.7/site-packages/numpy/core/include -I/home/ajay/miniconda3/envs/lnpy_test/include/python3.7m -c lnpy/transform/wrap_gtfb.c -o build/temp.linux-x86_64-3.7/lnpy/transform/wrap_gtfb.o -MMD -MF build/temp.linux-x86_64-3.7/lnpy/transform/wrap_gtfb.o.d" failed with exit status 1
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