fbrundu / pymrmr Goto Github PK
View Code? Open in Web Editor NEWPython3 binding to mRMR Feature Selection algorithm (currently not maintained)
License: MIT License
Python3 binding to mRMR Feature Selection algorithm (currently not maintained)
License: MIT License
Description:
I can't install pymrmr package using pip on my mac.
What I Did
Sudarshans-MacBook-Pro:~ Sudarshan$ pip install pymrmr
Collecting pymrmr
Using cached https://files.pythonhosted.org/packages/b3/ab/903712947a2f5cd1af249132885dbd81ae8bf8cfd30fb3b3f2beddab23e8/pymrmr-0.1.8.tar.gz
Requirement already satisfied: numpy>=1.12.0 in ./miniconda2/lib/python2.7/site-packages (from pymrmr) (1.15.4)
Building wheels for collected packages: pymrmr
Running setup.py bdist_wheel for pymrmr ... error
Complete output from command /Users/Sudarshan/miniconda2/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/74/q8y9smnn2td223yqvypdc1p00000gn/T/pip-install-7yhZcv/pymrmr/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/74/q8y9smnn2td223yqvypdc1p00000gn/T/pip-wheel-PplXhw --python-tag cp27:
running bdist_wheel
running build
running build_py
package init file 'pymrmr/init.py' not found (or not a regular file)
running egg_info
writing requirements to pymrmr.egg-info/requires.txt
writing pymrmr.egg-info/PKG-INFO
writing top-level names to pymrmr.egg-info/top_level.txt
writing dependency_links to pymrmr.egg-info/dependency_links.txt
reading manifest file 'pymrmr.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching 'pycache' found under directory ''
warning: no previously-included files matching '.py[co]' found under directory ''
warning: no files found matching '.jpg' under directory 'docs'
warning: no files found matching '.png' under directory 'docs'
warning: no files found matching '.gif' under directory 'docs'
writing manifest file 'pymrmr.egg-info/SOURCES.txt'
creating build
creating build/lib.macosx-10.6-x86_64-2.7
creating build/lib.macosx-10.6-x86_64-2.7/pymrmr
copying pymrmr/crank.cpp -> build/lib.macosx-10.6-x86_64-2.7/pymrmr
copying pymrmr/mrmr.cpp -> build/lib.macosx-10.6-x86_64-2.7/pymrmr
copying pymrmr/nrutil.cpp -> build/lib.macosx-10.6-x86_64-2.7/pymrmr
copying pymrmr/nrutil.h -> build/lib.macosx-10.6-x86_64-2.7/pymrmr
copying pymrmr/pbetai.cpp -> build/lib.macosx-10.6-x86_64-2.7/pymrmr
copying pymrmr/pymrmr.cpp -> build/lib.macosx-10.6-x86_64-2.7/pymrmr
copying pymrmr/pymrmr.pyx -> build/lib.macosx-10.6-x86_64-2.7/pymrmr
copying pymrmr/sort2.cpp -> build/lib.macosx-10.6-x86_64-2.7/pymrmr
running build_ext
skipping 'pymrmr/pymrmr.cpp' Cython extension (up-to-date)
building 'pymrmr' extension
creating build/temp.macosx-10.6-x86_64-2.7
creating build/temp.macosx-10.6-x86_64-2.7/pymrmr
clang-omp -fno-strict-aliasing -I/Users/Sudarshan/miniconda2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/Sudarshan/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/Users/Sudarshan/miniconda2/include/python2.7 -c pymrmr/pymrmr.cpp -o build/temp.macosx-10.6-x86_64-2.7/pymrmr/pymrmr.o -fopenmp -Ofast
unable to execute 'clang-omp': No such file or directory
error: command 'clang-omp' failed with exit status 1
Failed building wheel for pymrmr
Running setup.py clean for pymrmr
Failed to build pymrmr
Installing collected packages: pymrmr
Running setup.py install for pymrmr ... error
Complete output from command /Users/Sudarshan/miniconda2/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/74/q8y9smnn2td223yqvypdc1p00000gn/T/pip-install-7yhZcv/pymrmr/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/74/q8y9smnn2td223yqvypdc1p00000gn/T/pip-record-kralVI/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
package init file 'pymrmr/init.py' not found (or not a regular file)
running egg_info
writing requirements to pymrmr.egg-info/requires.txt
writing pymrmr.egg-info/PKG-INFO
writing top-level names to pymrmr.egg-info/top_level.txt
writing dependency_links to pymrmr.egg-info/dependency_links.txt
reading manifest file 'pymrmr.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching 'pycache' found under directory ''
warning: no previously-included files matching '.py[co]' found under directory ''
warning: no files found matching '.jpg' under directory 'docs'
warning: no files found matching '.png' under directory 'docs'
warning: no files found matching '.gif' under directory 'docs'
writing manifest file 'pymrmr.egg-info/SOURCES.txt'
creating build
creating build/lib.macosx-10.6-x86_64-2.7
creating build/lib.macosx-10.6-x86_64-2.7/pymrmr
copying pymrmr/crank.cpp -> build/lib.macosx-10.6-x86_64-2.7/pymrmr
copying pymrmr/mrmr.cpp -> build/lib.macosx-10.6-x86_64-2.7/pymrmr
copying pymrmr/nrutil.cpp -> build/lib.macosx-10.6-x86_64-2.7/pymrmr
copying pymrmr/nrutil.h -> build/lib.macosx-10.6-x86_64-2.7/pymrmr
copying pymrmr/pbetai.cpp -> build/lib.macosx-10.6-x86_64-2.7/pymrmr
copying pymrmr/pymrmr.cpp -> build/lib.macosx-10.6-x86_64-2.7/pymrmr
copying pymrmr/pymrmr.pyx -> build/lib.macosx-10.6-x86_64-2.7/pymrmr
copying pymrmr/sort2.cpp -> build/lib.macosx-10.6-x86_64-2.7/pymrmr
running build_ext
skipping 'pymrmr/pymrmr.cpp' Cython extension (up-to-date)
building 'pymrmr' extension
creating build/temp.macosx-10.6-x86_64-2.7
creating build/temp.macosx-10.6-x86_64-2.7/pymrmr
clang-omp -fno-strict-aliasing -I/Users/Sudarshan/miniconda2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/Sudarshan/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/Users/Sudarshan/miniconda2/include/python2.7 -c pymrmr/pymrmr.cpp -o build/temp.macosx-10.6-x86_64-2.7/pymrmr/pymrmr.o -fopenmp -Ofast
unable to execute 'clang-omp': No such file or directory
error: command 'clang-omp' failed with exit status 1
----------------------------------------
Command "/Users/Sudarshan/miniconda2/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/74/q8y9smnn2td223yqvypdc1p00000gn/T/pip-install-7yhZcv/pymrmr/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/74/q8y9smnn2td223yqvypdc1p00000gn/T/pip-record-kralVI/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/74/q8y9smnn2td223yqvypdc1p00000gn/T/pip-install-7yhZcv/pymrmr/
Sudarshans-MacBook-Pro:~ Sudarshan$
Hi,
I want to do mRMR with continuous variables. for example, one interested variable Y vs 10 attribute features.
Could you tell me how to set parameters in the code? I only see the example for discrete variables.
Thank you!
import pymrmr
pymrmr.mRMR(df,'MIQ',20)
I tried to run pymrmr in a data frame with size (3000, 1400) and show the top 30 features. "MaxRel features" was successful generated, while "mRMR features" crashed when outputing only one row.
Maybe when using data of small size, everything is well done, but large size goes wrong. Wondering how to fix this kind of problem. Could anyone give us a help?
*** MaxRel features ***
Program output:
Order Fea Name Score
1 1008 wavelet-HLL_glszm_LargeAreaLowGrayLevelEmphasis 0.911
2 1100 wavelet-HLH_glszm_LargeAreaHighGrayLevelEmphasis 0.911
3 913 wavelet-LHH_glszm_LargeAreaEmphasis 0.911
4 914 wavelet-LHH_glszm_LargeAreaHighGrayLevelEmphasis 0.911
5 1006 wavelet-HLL_glszm_LargeAreaEmphasis 0.911
6 1007 wavelet-HLL_glszm_LargeAreaHighGrayLevelEmphasis 0.911
7 820 wavelet-LHL_glszm_LargeAreaEmphasis 0.911
8 1101 wavelet-HLH_glszm_LargeAreaLowGrayLevelEmphasis 0.910
9 821 wavelet-LHL_glszm_LargeAreaHighGrayLevelEmphasis 0.910
10 1099 wavelet-HLH_glszm_LargeAreaEmphasis 0.910
11 915 wavelet-LHH_glszm_LargeAreaLowGrayLevelEmphasis 0.910
12 1287 wavelet-HHH_glszm_LargeAreaLowGrayLevelEmphasis 0.910
13 822 wavelet-LHL_glszm_LargeAreaLowGrayLevelEmphasis 0.910
14 729 wavelet-LLH_glszm_LargeAreaLowGrayLevelEmphasis 0.910
15 1194 wavelet-HHL_glszm_LargeAreaLowGrayLevelEmphasis 0.909
16 1192 wavelet-HHL_glszm_LargeAreaEmphasis 0.909
17 727 wavelet-LLH_glszm_LargeAreaEmphasis 0.909
18 728 wavelet-LLH_glszm_LargeAreaHighGrayLevelEmphasis 0.909
19 1286 wavelet-HHH_glszm_LargeAreaHighGrayLevelEmphasis 0.909
20 1285 wavelet-HHH_glszm_LargeAreaEmphasis 0.909
21 1193 wavelet-HHL_glszm_LargeAreaHighGrayLevelEmphasis 0.909
22 634 squareroot_glszm_LargeAreaEmphasis 0.907
23 76 original_glszm_LargeAreaEmphasis 0.907
24 448 logarithm_glszm_LargeAreaEmphasis 0.907
25 635 squareroot_glszm_LargeAreaHighGrayLevelEmphasis 0.906
26 449 logarithm_glszm_LargeAreaHighGrayLevelEmphasis 0.906
27 77 original_glszm_LargeAreaHighGrayLevelEmphasis 0.906
28 738 wavelet-LLH_glszm_ZoneVariance 0.905
29 450 logarithm_glszm_LargeAreaLowGrayLevelEmphasis 0.905
30 636 squareroot_glszm_LargeAreaLowGrayLevelEmphasis 0.905
*** mRMR features ***
Order Fea Name Score
1 1008 wavelet-HLL_glszm_LargeAreaLowGrayLevelEmphasis 0.911
Process finished with exit code -1073741819 (0xC0000005)
I tried to install pymrmr via pip install pymrmr
but that failed.
I'm working from an anaconda environment and the anaconda prompt for windows. I've installed cython via pip install cython
. Then, I received the error message, telling me I need a c++ distribution. I've followed the link from the error message, installed the following packages from visual studio build tools:
Then, I tried to install pymrmr again and received the following error message:
>pip install pymrmr
Collecting pymrmr
Using cached https://files.pythonhosted.org/packages/b3/ab/903712947a2f5cd1af249132885dbd81ae8bf8cfd30fb3b3f2beddab23e8/pymrmr-0.1.8.tar.gz
Requirement already satisfied: numpy>=1.12.0 in c:\users\[my-username]\.conda\envs\[my-conda-environment]\lib\site-packages (from pymrmr) (1.17.4)
Building wheels for collected packages: pymrmr
Building wheel for pymrmr (setup.py) ... /
[...]
ERROR: Command errored out with exit status 1:
command: 'C:\Users\[my-username]\.conda\envs\[my-conda-environment]\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\[my-username]\\AppData\\Local\\Temp\\pip-install-a9qm24d7\\pymrmr\\setup.py'"'"'; __file__='"'"'C:\\Users\\[my-username]\\AppData\\Local\\Temp\\pip-install-a9qm24d7\\pymrmr\\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 'C:\Users\[my-username]\AppData\Local\Temp\pip-wheel-gasidp6b' --python-tag cp37
cwd: C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\
Complete output (97 lines):
running bdist_wheel
running build
running build_py
package init file 'pymrmr\__init__.py' not found (or not a regular file)
running egg_info
writing pymrmr.egg-info\PKG-INFO
writing dependency_links to pymrmr.egg-info\dependency_links.txt
writing requirements to pymrmr.egg-info\requires.txt
writing top-level names to pymrmr.egg-info\top_level.txt
reading manifest file 'pymrmr.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
warning: no files found matching '*.jpg' under directory 'docs'
warning: no files found matching '*.png' under directory 'docs'
warning: no files found matching '*.gif' under directory 'docs'
writing manifest file 'pymrmr.egg-info\SOURCES.txt'
creating build
creating build\lib.win-amd64-3.7
creating build\lib.win-amd64-3.7\pymrmr
copying pymrmr\crank.cpp -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\mrmr.cpp -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\nrutil.cpp -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\nrutil.h -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\pbetai.cpp -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\pymrmr.cpp -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\pymrmr.pyx -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\sort2.cpp -> build\lib.win-amd64-3.7\pymrmr
running build_ext
skipping 'pymrmr\pymrmr.cpp' Cython extension (up-to-date)
building 'pymrmr' extension
creating build\temp.win-amd64-3.7
creating build\temp.win-amd64-3.7\Release
creating build\temp.win-amd64-3.7\Release\pymrmr
C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -IC:\Users\[my-username]\.conda\envs\[my-conda-environment]\lib\site-packages\numpy\core\include -IC:\Users\[my-username]\.conda\envs\[my-conda-environment]\include -IC:\Users\[my-username]\.conda\envs\[my-conda-environment]\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EHsc /Tppymrmr\pymrmr.cpp /Fobuild\temp.win-amd64-3.7\Release\pymrmr\pymrmr.obj -fopenmp -Ofast
cl : command line warning D9025 : "/Os" is replaced with "/Ot"
cl : command line warning D9002 : unknown option "-fopenmp" is ignored.
cl : command line warning D9002 : unknown option "-Of" is ignored.
cl : command line warning D9002 : unknown option "-Oa" is ignored.
pymrmr.cpp
C:\Users\[my-username]\.conda\envs\[my-conda-environment]\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(14) : Warning Msg: Using deprecated NumPy API, disable it with #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\pbetai.cpp(33): warning C4244: "return": conversion of "double" to "float", possible data loss
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\pbetai.cpp(47): warning C4244: "=": conversion of "double" to "float", possible data loss
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\pbetai.cpp(48): warning C4244: "=": conversion of "double" to "float", possible data loss
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\pbetai.cpp(50): warning C4244: "=": conversion of "double" to "float", possible data loss
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\pbetai.cpp(51): warning C4305: "=": conversion of "double" to "float"
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\pbetai.cpp(52): warning C4244: "=": conversion of "double" to "float", possible data loss
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\pbetai.cpp(57): warning C4244: "=": conversion of "double" to "float", possible data loss
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\pbetai.cpp(58): warning C4305: "=": conversion of "double" to "float"
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\pbetai.cpp(59): warning C4244: "=": conversion of "double" to "float", possible data loss
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\pbetai.cpp(60): warning C4305: "=": conversion of "double" to "float"
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\pbetai.cpp(61): warning C4244: "=": conversion of "double" to "float", possible data loss
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\pbetai.cpp(64): warning C4244: "=": conversion of "double" to "float", possible data loss
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\pbetai.cpp(65): warning C4305: "=": conversion of "double" to "float"
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\pbetai.cpp(66): warning C4244: "=": conversion of "double" to "float", possible data loss
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\pbetai.cpp(67): warning C4305: "=": conversion of "double" to "float"
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\pbetai.cpp(68): warning C4244: "=": conversion of "double" to "float", possible data loss
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\pbetai.cpp(90): warning C4244: "=": conversion of "double" to "float", possible data loss
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\pbetai.cpp(94): warning C4244: "argument": conversion of "double" to "float", possible data loss
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\pbetai.cpp(94): warning C4244: "return": conversion of "double" to "float", possible data loss
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\mrmr.cpp(189): warning C4267: "argument": conversion of "size_t" to "long", possible data loss
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\mrmr.cpp(205): warning C4267: "=": conversion of "size_t" to "unsigned long", possible data loss
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\mrmr.cpp(215): warning C4244: "=": conversion of "double" to "float", possible data loss
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\mrmr.cpp(216): warning C4244: "=": conversion of "unsigned long" in "float", possible data loss
C:\Users\[my-username]\AppData\Local\Temp\pip-install-a9qm24d7\pymrmr\pymrmr\mrmr.cpp(221): warning C4267: "argument": conversion of "size_t" to "unsigned long", possible data loss
pymrmr\pymrmr.cpp(5418): error C2197: "PyObject *(__cdecl *)(PyObject *,PyObject *const *,Py_ssize_t)": Too many arguments for coll.
pymrmr\pymrmr.cpp(5990): error C2039: "exc_type": Not an element of "_ts"
C:\Users\[my-username]\.conda\envs\[my-conda-environment]\include\pystate.h(212): note: See declaration of "_ts"
pymrmr\pymrmr.cpp(5991): error C2039: "exc_value": Not an element of "_ts"
C:\Users\[my-username]\.conda\envs\[my-conda-environment]\include\pystate.h(212): note: See declaration of "_ts"
pymrmr\pymrmr.cpp(5992): error C2039: "exc_traceback": Not an element of "_ts"
C:\Users\[my-username]\.conda\envs\[my-conda-environment]\include\pystate.h(212): note: See declaration of "_ts"
pymrmr\pymrmr.cpp(5999): error C2039: "exc_type": Not an element of "_ts"
C:\Users\[my-username]\.conda\envs\[my-conda-environment]\include\pystate.h(212): note: See declaration of "_ts"
pymrmr\pymrmr.cpp(6000): error C2039: "exc_value": Not an element of "_ts"
C:\Users\[my-username]\.conda\envs\[my-conda-environment]\include\pystate.h(212): note: See declaration of "_ts"
pymrmr\pymrmr.cpp(6001): error C2039: "exc_traceback": Not an element of "_ts"
C:\Users\[my-username]\.conda\envs\[my-conda-environment]\include\pystate.h(212): note: See declaration of "_ts"
pymrmr\pymrmr.cpp(6002): error C2039: "exc_type": Not an element of "_ts"
C:\Users\[my-username]\.conda\envs\[my-conda-environment]\include\pystate.h(212): note: See declaration of "_ts"
pymrmr\pymrmr.cpp(6003): error C2039: "exc_value": Not an element of "_ts"
C:\Users\[my-username]\.conda\envs\[my-conda-environment]\include\pystate.h(212): note: See declaration of "_ts"
pymrmr\pymrmr.cpp(6004): error C2039: "exc_traceback": Not an element of "_ts"
C:\Users\[my-username]\.conda\envs\[my-conda-environment]\include\pystate.h(212): note: See declaration of "_ts"
pymrmr\pymrmr.cpp(6059): error C2039: "exc_type": Not an element of "_ts"
C:\Users\[my-username]\.conda\envs\[my-conda-environment]\include\pystate.h(212): note: See declaration of "_ts"
pymrmr\pymrmr.cpp(6060): error C2039: "exc_value": Not an element of "_ts"
C:\Users\[my-username]\.conda\envs\[my-conda-environment]\include\pystate.h(212): note: See declaration of "_ts"
pymrmr\pymrmr.cpp(6061): error C2039: "exc_traceback": Not an element of "_ts"
C:\Users\[my-username]\.conda\envs\[my-conda-environment]\include\pystate.h(212): note: See declaration of "_ts"
pymrmr\pymrmr.cpp(6062): error C2039: "exc_type": Not an element of "_ts"
C:\Users\[my-username]\.conda\envs\[my-conda-environment]\include\pystate.h(212): note: See declaration of "_ts"
pymrmr\pymrmr.cpp(6063): error C2039: "exc_value": Not an element of "_ts"
C:\Users\[my-username]\.conda\envs\[my-conda-environment]\include\pystate.h(212): note: See declaration of "_ts"
pymrmr\pymrmr.cpp(6064): error C2039: "exc_traceback": Not an element of "_ts"
C:\Users\[my-username]\.conda\envs\[my-conda-environment]\include\pystate.h(212): note: See declaration of "_ts"
error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio\\2019\\BuildTools\\VC\\Tools\\MSVC\\14.24.28314\\bin\\HostX86\\x64\\cl.exe' failed with exit status 2
----------------------------------------
ERROR: Failed building wheel for pymrmr
Running setup.py clean for pymrmr
Failed to build pymrmr
Note, that my machine is set to German and I manually translated part of these messages to English.
I'm trying to run the below
n=10
pymrmr.mRMR(df.iloc[:, 1:], 'MIQ', n)
However, the error occurs as following.
TypeError: an integer is required
I'm searching the solution for the error but there is the solution working in Cython.
And, I have no knowledge on Cython. Also, I tried to add a code pymrmr.pyx but it didn't work
ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pymrmr.cpython-36m-darwin.so, 2): Library not loaded: /usr/local/opt/libiomp/lib/libiomp5.dylib
Referenced from: /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pymrmr.cpython-36m-darwin.so
Reason: image not found
I have installed libomp and llvm, but it does not work for me.
brew install libomp
brew install llvm
thanks in advance!
Failed to build pymrmr
DEPRECATION: Could not build wheels for pymrmr which do not use PEP 517. pip will fall back to legacy 'setup.py install' for these. pip 21.0 will remove support for this functionality. A possible replacement is to fix the wheel build issue reported above. You can find discussion regarding this at pypa/pip#8368.
Installing collected packages: pymrmr
Running setup.py install for pymrmr ... error
ERROR: Command errored out with exit status 1:
command: /home/haihai/anaconda3/envs/tf2/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-9zmpkpdw/pymrmr/setup.py'"'"'; file='"'"'/tmp/pip-install-9zmpkpdw/pymrmr/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-mbilp0v7/install-record.txt --single-version-externally-managed --compile --install-headers /home/haihai/anaconda3/envs/tf2/include/python3.8/pymrmr
cwd: /tmp/pip-install-9zmpkpdw/pymrmr/
Complete output (251 lines):
running install
running build
running build_py
package init file 'pymrmr/init.py' not found (or not a regular file)
running egg_info
writing pymrmr.egg-info/PKG-INFO
writing dependency_links to pymrmr.egg-info/dependency_links.txt
writing requirements to pymrmr.egg-info/requires.txt
writing top-level names to pymrmr.egg-info/top_level.txt
reading manifest file 'pymrmr.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching 'pycache' found under directory ''
warning: no previously-included files matching '.py[co]' found under directory ''
warning: no files found matching '.jpg' under directory 'docs'
warning: no files found matching '.png' under directory 'docs'
warning: no files found matching '.gif' under directory 'docs'
writing manifest file 'pymrmr.egg-info/SOURCES.txt'
creating build
creating build/lib.linux-x86_64-3.8
creating build/lib.linux-x86_64-3.8/pymrmr
copying pymrmr/crank.cpp -> build/lib.linux-x86_64-3.8/pymrmr
copying pymrmr/mrmr.cpp -> build/lib.linux-x86_64-3.8/pymrmr
copying pymrmr/nrutil.cpp -> build/lib.linux-x86_64-3.8/pymrmr
copying pymrmr/nrutil.h -> build/lib.linux-x86_64-3.8/pymrmr
copying pymrmr/pbetai.cpp -> build/lib.linux-x86_64-3.8/pymrmr
copying pymrmr/pymrmr.cpp -> build/lib.linux-x86_64-3.8/pymrmr
copying pymrmr/pymrmr.pyx -> build/lib.linux-x86_64-3.8/pymrmr
copying pymrmr/sort2.cpp -> build/lib.linux-x86_64-3.8/pymrmr
running build_ext
skipping 'pymrmr/pymrmr.cpp' Cython extension (up-to-date)
building 'pymrmr' extension
creating build/temp.linux-x86_64-3.8
creating build/temp.linux-x86_64-3.8/pymrmr
gcc -pthread -B /home/haihai/anaconda3/envs/tf2/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/haihai/anaconda3/envs/tf2/lib/python3.8/site-packages/numpy/core/include -I/home/haihai/anaconda3/envs/tf2/include/python3.8 -c pymrmr/pymrmr.cpp -o build/temp.linux-x86_64-3.8/pymrmr/pymrmr.o -fopenmp -Ofast
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
In file included from /home/haihai/anaconda3/envs/tf2/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
from /home/haihai/anaconda3/envs/tf2/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/haihai/anaconda3/envs/tf2/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from pymrmr/pymrmr.cpp:455:
/home/haihai/anaconda3/envs/tf2/lib/python3.8/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 "
^~~~~~~
In file included from pymrmr/mrmr.cpp:23,
from pymrmr/pymrmr.cpp:457:
pymrmr/pbetai.cpp: In function ‘float betacf(float, float, float)’:
pymrmr/pbetai.cpp:74:72: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (m > MAXIT) nrerror("a or b too big, or MAXIT too small in betacf");
^
pymrmr/pbetai.cpp: In function ‘float betai(float, float, float)’:
pymrmr/pbetai.cpp:87:59: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (x < 0.0 || x > 1.0) nrerror("Bad x in routine betai");
^
In file included from pymrmr/sort2.cpp:3,
from pymrmr/mrmr.cpp:24,
from pymrmr/pymrmr.cpp:457:
pymrmr/nrutil.cpp: In function ‘float* vector(long int, long int)’:
pymrmr/nrutil.cpp:31:50: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!v) nrerror("allocation failure in vector()");
^
pymrmr/nrutil.cpp: In function ‘float* vector_phc(long int, long int)’:
pymrmr/nrutil.cpp:41:50: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!v) nrerror("allocation failure in vector()");
^
pymrmr/nrutil.cpp: In function ‘int* ivector(long int, long int)’:
pymrmr/nrutil.cpp:51:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!v) nrerror("allocation failure in ivector()");
^
pymrmr/nrutil.cpp: In function ‘unsigned char* cvector(long int, long int)’:
pymrmr/nrutil.cpp:61:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!v) nrerror("allocation failure in cvector()");
^
pymrmr/nrutil.cpp: In function ‘long unsigned int* lvector(long int, long int)’:
pymrmr/nrutil.cpp:71:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!v) nrerror("allocation failure in lvector()");
^
pymrmr/nrutil.cpp: In function ‘double* dvector(long int, long int)’:
pymrmr/nrutil.cpp:81:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!v) nrerror("allocation failure in dvector()");
^
pymrmr/nrutil.cpp: In function ‘float** matrix(long int, long int, long int, long int)’:
pymrmr/nrutil.cpp:93:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m) nrerror("allocation failure 1 in matrix()");
^
pymrmr/nrutil.cpp:99:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
^
pymrmr/nrutil.cpp: In function ‘double** dmatrix(long int, long int, long int, long int)’:
pymrmr/nrutil.cpp:117:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m) nrerror("allocation failure 1 in matrix()");
^
pymrmr/nrutil.cpp:123:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
^
pymrmr/nrutil.cpp: In function ‘int** imatrix(long int, long int, long int, long int)’:
pymrmr/nrutil.cpp:141:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m) nrerror("allocation failure 1 in matrix()");
^
pymrmr/nrutil.cpp:148:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
^
pymrmr/nrutil.cpp: In function ‘float** submatrix(float**, long int, long int, long int, long int, long int, long int)’:
pymrmr/nrutil.cpp:167:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m) nrerror("allocation failure in submatrix()");
^
pymrmr/nrutil.cpp: In function ‘float** convert_matrix(float*, long int, long int, long int, long int)’:
pymrmr/nrutil.cpp:189:58: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m) nrerror("allocation failure in convert_matrix()");
^
pymrmr/nrutil.cpp: In function ‘float*** f3tensor(long int, long int, long int, long int, long int, long int)’:
pymrmr/nrutil.cpp:208:54: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!t) nrerror("allocation failure 1 in f3tensor()");
^
pymrmr/nrutil.cpp:214:59: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!t[nrl]) nrerror("allocation failure 2 in f3tensor()");
^
pymrmr/nrutil.cpp:220:64: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!t[nrl][ncl]) nrerror("allocation failure 3 in f3tensor()");
^
In file included from pymrmr/mrmr.cpp:24,
from pymrmr/pymrmr.cpp:457:
pymrmr/sort2.cpp: In function ‘void sort2(long unsigned int, float*, float*)’:
pymrmr/sort2.cpp:68:61: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (jstack > NSTACK) nrerror("NSTACK too small in sort2.");
^
pymrmr/pymrmr.cpp: In function ‘PyObject* __Pyx_PyCFunction_FastCall(PyObject*, PyObject**, Py_ssize_t)’:
pymrmr/pymrmr.cpp:5418:69: error: too many arguments to function
return (((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL);
^
pymrmr/pymrmr.cpp: In function ‘void __Pyx__ExceptionSave(PyThreadState, PyObject**, PyObject**, PyObject**)’:
pymrmr/pymrmr.cpp:5990:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
type = tstate->exc_type;
^~~~~~~~
curexc_type
pymrmr/pymrmr.cpp:5991:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
value = tstate->exc_value;
^~~~~~~~~
curexc_value
pymrmr/pymrmr.cpp:5992:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
pymrmr/pymrmr.cpp: In function ‘void __Pyx__ExceptionReset(PyThreadState, PyObject, PyObject, PyObject*)’:
pymrmr/pymrmr.cpp:5999:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
tmp_type = tstate->exc_type;
^~~~~~~~
curexc_type
pymrmr/pymrmr.cpp:6000:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
pymrmr/pymrmr.cpp:6001:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
pymrmr/pymrmr.cpp:6002:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
tstate->exc_type = type;
^~~~~~~~
curexc_type
pymrmr/pymrmr.cpp:6003:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
tstate->exc_value = value;
^~~~~~~~~
curexc_value
pymrmr/pymrmr.cpp:6004:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
tstate->exc_traceback = tb;
^~~~~~~~~~~~~
curexc_traceback
pymrmr/pymrmr.cpp: In function ‘int __Pyx__GetException(PyThreadState*, PyObject**, PyObject**, PyObject**)’:
pymrmr/pymrmr.cpp:6059:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
tmp_type = tstate->exc_type;
^~~~~~~~
curexc_type
pymrmr/pymrmr.cpp:6060:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
pymrmr/pymrmr.cpp:6061:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
pymrmr/pymrmr.cpp:6062:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
tstate->exc_type = local_type;
^~~~~~~~
curexc_type
pymrmr/pymrmr.cpp:6063:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
tstate->exc_value = local_value;
^~~~~~~~~
curexc_value
pymrmr/pymrmr.cpp:6064:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
tstate->exc_traceback = local_tb;
^~~~~~~~~~~~~
curexc_traceback
In file included from pymrmr/nrutil.cpp:7,
from pymrmr/sort2.cpp:3,
from pymrmr/mrmr.cpp:24,
from pymrmr/pymrmr.cpp:457:
pymrmr/nrutil.h: At global scope:
pymrmr/nrutil.h:38:21: warning: ‘iminarg2’ defined but not used [-Wunused-variable]
static int iminarg1,iminarg2;
^~~~~~~~
pymrmr/nrutil.h:38:12: warning: ‘iminarg1’ defined but not used [-Wunused-variable]
static int iminarg1,iminarg2;
^~~~~~~~
pymrmr/nrutil.h:34:21: warning: ‘imaxarg2’ defined but not used [-Wunused-variable]
static int imaxarg1,imaxarg2;
^~~~~~~~
pymrmr/nrutil.h:34:12: warning: ‘imaxarg1’ defined but not used [-Wunused-variable]
static int imaxarg1,imaxarg2;
^~~~~~~~
pymrmr/nrutil.h:30:22: warning: ‘lminarg2’ defined but not used [-Wunused-variable]
static long lminarg1,lminarg2;
^~~~~~~~
pymrmr/nrutil.h:30:13: warning: ‘lminarg1’ defined but not used [-Wunused-variable]
static long lminarg1,lminarg2;
^~~~~~~~
pymrmr/nrutil.h:26:22: warning: ‘lmaxarg2’ defined but not used [-Wunused-variable]
static long lmaxarg1,lmaxarg2;
^~~~~~~~
pymrmr/nrutil.h:26:13: warning: ‘lmaxarg1’ defined but not used [-Wunused-variable]
static long lmaxarg1,lmaxarg2;
^~~~~~~~
pymrmr/nrutil.h:22:22: warning: ‘minarg2’ defined but not used [-Wunused-variable]
static float minarg1,minarg2;
^~~~~~~
pymrmr/nrutil.h:22:14: warning: ‘minarg1’ defined but not used [-Wunused-variable]
static float minarg1,minarg2;
^~~~~~~
pymrmr/nrutil.h:18:22: warning: ‘maxarg2’ defined but not used [-Wunused-variable]
static float maxarg1,maxarg2;
^~~~~~~
pymrmr/nrutil.h:18:14: warning: ‘maxarg1’ defined but not used [-Wunused-variable]
static float maxarg1,maxarg2;
^~~~~~~
pymrmr/nrutil.h:14:24: warning: ‘dminarg2’ defined but not used [-Wunused-variable]
static double dminarg1,dminarg2;
^~~~~~~~
pymrmr/nrutil.h:14:15: warning: ‘dminarg1’ defined but not used [-Wunused-variable]
static double dminarg1,dminarg2;
^~~~~~~~
pymrmr/nrutil.h:10:24: warning: ‘dmaxarg2’ defined but not used [-Wunused-variable]
static double dmaxarg1,dmaxarg2;
^~~~~~~~
pymrmr/nrutil.h:10:15: warning: ‘dmaxarg1’ defined but not used [-Wunused-variable]
static double dmaxarg1,dmaxarg2;
^~~~~~~~
pymrmr/nrutil.h:7:15: warning: ‘dsqrarg’ defined but not used [-Wunused-variable]
static double dsqrarg;
^~~~~~~
pymrmr/nrutil.h:4:14: warning: ‘sqrarg’ defined but not used [-Wunused-variable]
static float sqrarg;
^~~~~~
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /home/haihai/anaconda3/envs/tf2/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-9zmpkpdw/pymrmr/setup.py'"'"'; file='"'"'/tmp/pip-install-9zmpkpdw/pymrmr/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-mbilp0v7/install-record.txt --single-version-externally-managed --compile --install-headers /home/haihai/anaconda3/envs/tf2/include/python3.8/pymrmr Check the logs for full command output.
I followed the instructions using command `pip install numpy Cython` && `pip install pymrmr` in python 3.8. the error occur, I think maybe it's course by python version so I change to python3.7 in conda and it's the same
Hi,
i want to use mrmr for 1000 features and 10gb sized data, but it takes too long time, i got 32 core server ( can hire 64 core as well), but i see there is only 4 cores in use, does pymrmr run all cores? if so , how should i use it ?
Thanks in advance,
Regards,
Davut
While I was trying to install pymrmr with pip, installation was failed with the following error.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
gcc, build-essential, python-dev and python3.7-dev already installed in the system.
python3.7 -m pip install pymrmr
Collecting pymrmr
Using cached https://files.pythonhosted.org/packages/b3/ab/903712947a2f5cd1af249132885dbd81ae8bf8cfd30fb3b3f2beddab23e8/pymrmr-0.1.8.tar.gz
Requirement already satisfied: numpy>=1.12.0 in ./.local/lib/python3.7/site-packages (from pymrmr) (1.15.0)
Building wheels for collected packages: pymrmr
Running setup.py bdist_wheel for pymrmr ... error
Complete output from command /usr/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-febd25wn/pymrmr/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 /tmp/pip-wheel-4_ly8i5r --python-tag cp37:
running bdist_wheel
running build
running build_py
package init file 'pymrmr/__init__.py' not found (or not a regular file)
running egg_info
writing pymrmr.egg-info/PKG-INFO
writing dependency_links to pymrmr.egg-info/dependency_links.txt
writing requirements to pymrmr.egg-info/requires.txt
writing top-level names to pymrmr.egg-info/top_level.txt
reading manifest file 'pymrmr.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
warning: no files found matching '*.jpg' under directory 'docs'
warning: no files found matching '*.png' under directory 'docs'
warning: no files found matching '*.gif' under directory 'docs'
writing manifest file 'pymrmr.egg-info/SOURCES.txt'
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/pymrmr
copying pymrmr/crank.cpp -> build/lib.linux-x86_64-3.7/pymrmr
copying pymrmr/mrmr.cpp -> build/lib.linux-x86_64-3.7/pymrmr
copying pymrmr/nrutil.cpp -> build/lib.linux-x86_64-3.7/pymrmr
copying pymrmr/nrutil.h -> build/lib.linux-x86_64-3.7/pymrmr
copying pymrmr/pbetai.cpp -> build/lib.linux-x86_64-3.7/pymrmr
copying pymrmr/pymrmr.cpp -> build/lib.linux-x86_64-3.7/pymrmr
copying pymrmr/pymrmr.pyx -> build/lib.linux-x86_64-3.7/pymrmr
copying pymrmr/sort2.cpp -> build/lib.linux-x86_64-3.7/pymrmr
running build_ext
skipping 'pymrmr/pymrmr.cpp' Cython extension (up-to-date)
building 'pymrmr' extension
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/pymrmr
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/ssec/.local/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -c pymrmr/pymrmr.cpp -o build/temp.linux-x86_64-3.7/pymrmr/pymrmr.o -fopenmp -Ofast
In file included from /home/ssec/.local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
from /home/ssec/.local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /home/ssec/.local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from pymrmr/pymrmr.cpp:455:
/home/ssec/.local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^~~~~~~
In file included from pymrmr/mrmr.cpp:23:0,
from pymrmr/pymrmr.cpp:457:
pymrmr/pbetai.cpp: In function ‘float betacf(float, float, float)’:
pymrmr/pbetai.cpp:74:72: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (m > MAXIT) nrerror("a or b too big, or MAXIT too small in betacf");
^
pymrmr/pbetai.cpp: In function ‘float betai(float, float, float)’:
pymrmr/pbetai.cpp:87:59: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (x < 0.0 || x > 1.0) nrerror("Bad x in routine betai");
^
In file included from pymrmr/sort2.cpp:3:0,
from pymrmr/mrmr.cpp:24,
from pymrmr/pymrmr.cpp:457:
pymrmr/nrutil.cpp: In function ‘float* vector(long int, long int)’:
pymrmr/nrutil.cpp:31:50: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!v) nrerror("allocation failure in vector()");
^
pymrmr/nrutil.cpp: In function ‘float* vector_phc(long int, long int)’:
pymrmr/nrutil.cpp:41:50: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!v) nrerror("allocation failure in vector()");
^
pymrmr/nrutil.cpp: In function ‘int* ivector(long int, long int)’:
pymrmr/nrutil.cpp:51:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!v) nrerror("allocation failure in ivector()");
^
pymrmr/nrutil.cpp: In function ‘unsigned char* cvector(long int, long int)’:
pymrmr/nrutil.cpp:61:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!v) nrerror("allocation failure in cvector()");
^
pymrmr/nrutil.cpp: In function ‘long unsigned int* lvector(long int, long int)’:
pymrmr/nrutil.cpp:71:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!v) nrerror("allocation failure in lvector()");
^
pymrmr/nrutil.cpp: In function ‘double* dvector(long int, long int)’:
pymrmr/nrutil.cpp:81:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!v) nrerror("allocation failure in dvector()");
^
pymrmr/nrutil.cpp: In function ‘float** matrix(long int, long int, long int, long int)’:
pymrmr/nrutil.cpp:93:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m) nrerror("allocation failure 1 in matrix()");
^
pymrmr/nrutil.cpp:99:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
^
pymrmr/nrutil.cpp: In function ‘double** dmatrix(long int, long int, long int, long int)’:
pymrmr/nrutil.cpp:117:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m) nrerror("allocation failure 1 in matrix()");
^
pymrmr/nrutil.cpp:123:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
^
pymrmr/nrutil.cpp: In function ‘int** imatrix(long int, long int, long int, long int)’:
pymrmr/nrutil.cpp:141:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m) nrerror("allocation failure 1 in matrix()");
^
pymrmr/nrutil.cpp:148:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
^
pymrmr/nrutil.cpp: In function ‘float** submatrix(float**, long int, long int, long int, long int, long int, long int)’:
pymrmr/nrutil.cpp:167:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m) nrerror("allocation failure in submatrix()");
^
pymrmr/nrutil.cpp: In function ‘float** convert_matrix(float*, long int, long int, long int, long int)’:
pymrmr/nrutil.cpp:189:58: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m) nrerror("allocation failure in convert_matrix()");
^
pymrmr/nrutil.cpp: In function ‘float*** f3tensor(long int, long int, long int, long int, long int, long int)’:
pymrmr/nrutil.cpp:208:54: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!t) nrerror("allocation failure 1 in f3tensor()");
^
pymrmr/nrutil.cpp:214:59: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!t[nrl]) nrerror("allocation failure 2 in f3tensor()");
^
pymrmr/nrutil.cpp:220:64: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!t[nrl][ncl]) nrerror("allocation failure 3 in f3tensor()");
^
In file included from pymrmr/mrmr.cpp:24:0,
from pymrmr/pymrmr.cpp:457:
pymrmr/sort2.cpp: In function ‘void sort2(long unsigned int, float*, float*)’:
pymrmr/sort2.cpp:68:61: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (jstack > NSTACK) nrerror("NSTACK too small in sort2.");
^
pymrmr/pymrmr.cpp: In function ‘PyObject* __Pyx_PyCFunction_FastCall(PyObject*, PyObject**, Py_ssize_t)’:
pymrmr/pymrmr.cpp:5418:69: error: too many arguments to function
return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL);
^
pymrmr/pymrmr.cpp: In function ‘void __Pyx__ExceptionSave(PyThreadState*, PyObject**, PyObject**, PyObject**)’:
pymrmr/pymrmr.cpp:5990:21: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
*type = tstate->exc_type;
^~~~~~~~
curexc_type
pymrmr/pymrmr.cpp:5991:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
*value = tstate->exc_value;
^~~~~~~~~
curexc_value
pymrmr/pymrmr.cpp:5992:19: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
*tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
pymrmr/pymrmr.cpp: In function ‘void __Pyx__ExceptionReset(PyThreadState*, PyObject*, PyObject*, PyObject*)’:
pymrmr/pymrmr.cpp:5999:24: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
tmp_type = tstate->exc_type;
^~~~~~~~
curexc_type
pymrmr/pymrmr.cpp:6000:25: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
pymrmr/pymrmr.cpp:6001:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
pymrmr/pymrmr.cpp:6002:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
tstate->exc_type = type;
^~~~~~~~
curexc_type
pymrmr/pymrmr.cpp:6003:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
tstate->exc_value = value;
^~~~~~~~~
curexc_value
pymrmr/pymrmr.cpp:6004:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
tstate->exc_traceback = tb;
^~~~~~~~~~~~~
curexc_traceback
pymrmr/pymrmr.cpp: In function ‘int __Pyx__GetException(PyThreadState*, PyObject**, PyObject**, PyObject**)’:
pymrmr/pymrmr.cpp:6059:24: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
tmp_type = tstate->exc_type;
^~~~~~~~
curexc_type
pymrmr/pymrmr.cpp:6060:25: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
pymrmr/pymrmr.cpp:6061:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
pymrmr/pymrmr.cpp:6062:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
tstate->exc_type = local_type;
^~~~~~~~
curexc_type
pymrmr/pymrmr.cpp:6063:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
tstate->exc_value = local_value;
^~~~~~~~~
curexc_value
pymrmr/pymrmr.cpp:6064:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
tstate->exc_traceback = local_tb;
^~~~~~~~~~~~~
curexc_traceback
In file included from pymrmr/nrutil.cpp:7:0,
from pymrmr/sort2.cpp:3,
from pymrmr/mrmr.cpp:24,
from pymrmr/pymrmr.cpp:457:
pymrmr/nrutil.h: At global scope:
pymrmr/nrutil.h:38:21: warning: ‘iminarg2’ defined but not used [-Wunused-variable]
static int iminarg1,iminarg2;
^~~~~~~~
pymrmr/nrutil.h:38:12: warning: ‘iminarg1’ defined but not used [-Wunused-variable]
static int iminarg1,iminarg2;
^~~~~~~~
pymrmr/nrutil.h:34:21: warning: ‘imaxarg2’ defined but not used [-Wunused-variable]
static int imaxarg1,imaxarg2;
^~~~~~~~
pymrmr/nrutil.h:34:12: warning: ‘imaxarg1’ defined but not used [-Wunused-variable]
static int imaxarg1,imaxarg2;
^~~~~~~~
pymrmr/nrutil.h:30:22: warning: ‘lminarg2’ defined but not used [-Wunused-variable]
static long lminarg1,lminarg2;
^~~~~~~~
pymrmr/nrutil.h:30:13: warning: ‘lminarg1’ defined but not used [-Wunused-variable]
static long lminarg1,lminarg2;
^~~~~~~~
pymrmr/nrutil.h:26:22: warning: ‘lmaxarg2’ defined but not used [-Wunused-variable]
static long lmaxarg1,lmaxarg2;
^~~~~~~~
pymrmr/nrutil.h:26:13: warning: ‘lmaxarg1’ defined but not used [-Wunused-variable]
static long lmaxarg1,lmaxarg2;
^~~~~~~~
pymrmr/nrutil.h:22:22: warning: ‘minarg2’ defined but not used [-Wunused-variable]
static float minarg1,minarg2;
^~~~~~~
pymrmr/nrutil.h:22:14: warning: ‘minarg1’ defined but not used [-Wunused-variable]
static float minarg1,minarg2;
^~~~~~~
pymrmr/nrutil.h:18:22: warning: ‘maxarg2’ defined but not used [-Wunused-variable]
static float maxarg1,maxarg2;
^~~~~~~
pymrmr/nrutil.h:18:14: warning: ‘maxarg1’ defined but not used [-Wunused-variable]
static float maxarg1,maxarg2;
^~~~~~~
pymrmr/nrutil.h:14:24: warning: ‘dminarg2’ defined but not used [-Wunused-variable]
static double dminarg1,dminarg2;
^~~~~~~~
pymrmr/nrutil.h:14:15: warning: ‘dminarg1’ defined but not used [-Wunused-variable]
static double dminarg1,dminarg2;
^~~~~~~~
pymrmr/nrutil.h:10:24: warning: ‘dmaxarg2’ defined but not used [-Wunused-variable]
static double dmaxarg1,dmaxarg2;
^~~~~~~~
pymrmr/nrutil.h:10:15: warning: ‘dmaxarg1’ defined but not used [-Wunused-variable]
static double dmaxarg1,dmaxarg2;
^~~~~~~~
pymrmr/nrutil.h:7:15: warning: ‘dsqrarg’ defined but not used [-Wunused-variable]
static double dsqrarg;
^~~~~~~
pymrmr/nrutil.h:4:14: warning: ‘sqrarg’ defined but not used [-Wunused-variable]
static float sqrarg;
^~~~~~
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
Failed building wheel for pymrmr
Running setup.py clean for pymrmr
Failed to build pymrmr
Installing collected packages: pymrmr
Running setup.py install for pymrmr ... error
Complete output from command /usr/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-febd25wn/pymrmr/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-j0lzuj61/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
package init file 'pymrmr/__init__.py' not found (or not a regular file)
running egg_info
writing pymrmr.egg-info/PKG-INFO
writing dependency_links to pymrmr.egg-info/dependency_links.txt
writing requirements to pymrmr.egg-info/requires.txt
writing top-level names to pymrmr.egg-info/top_level.txt
reading manifest file 'pymrmr.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
warning: no files found matching '*.jpg' under directory 'docs'
warning: no files found matching '*.png' under directory 'docs'
warning: no files found matching '*.gif' under directory 'docs'
writing manifest file 'pymrmr.egg-info/SOURCES.txt'
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/pymrmr
copying pymrmr/crank.cpp -> build/lib.linux-x86_64-3.7/pymrmr
copying pymrmr/mrmr.cpp -> build/lib.linux-x86_64-3.7/pymrmr
copying pymrmr/nrutil.cpp -> build/lib.linux-x86_64-3.7/pymrmr
copying pymrmr/nrutil.h -> build/lib.linux-x86_64-3.7/pymrmr
copying pymrmr/pbetai.cpp -> build/lib.linux-x86_64-3.7/pymrmr
copying pymrmr/pymrmr.cpp -> build/lib.linux-x86_64-3.7/pymrmr
copying pymrmr/pymrmr.pyx -> build/lib.linux-x86_64-3.7/pymrmr
copying pymrmr/sort2.cpp -> build/lib.linux-x86_64-3.7/pymrmr
running build_ext
skipping 'pymrmr/pymrmr.cpp' Cython extension (up-to-date)
building 'pymrmr' extension
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/pymrmr
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/ssec/.local/lib/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -c pymrmr/pymrmr.cpp -o build/temp.linux-x86_64-3.7/pymrmr/pymrmr.o -fopenmp -Ofast
In file included from /home/ssec/.local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
from /home/ssec/.local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /home/ssec/.local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from pymrmr/pymrmr.cpp:455:
/home/ssec/.local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^~~~~~~
In file included from pymrmr/mrmr.cpp:23:0,
from pymrmr/pymrmr.cpp:457:
pymrmr/pbetai.cpp: In function ‘float betacf(float, float, float)’:
pymrmr/pbetai.cpp:74:72: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (m > MAXIT) nrerror("a or b too big, or MAXIT too small in betacf");
^
pymrmr/pbetai.cpp: In function ‘float betai(float, float, float)’:
pymrmr/pbetai.cpp:87:59: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (x < 0.0 || x > 1.0) nrerror("Bad x in routine betai");
^
In file included from pymrmr/sort2.cpp:3:0,
from pymrmr/mrmr.cpp:24,
from pymrmr/pymrmr.cpp:457:
pymrmr/nrutil.cpp: In function ‘float* vector(long int, long int)’:
pymrmr/nrutil.cpp:31:50: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!v) nrerror("allocation failure in vector()");
^
pymrmr/nrutil.cpp: In function ‘float* vector_phc(long int, long int)’:
pymrmr/nrutil.cpp:41:50: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!v) nrerror("allocation failure in vector()");
^
pymrmr/nrutil.cpp: In function ‘int* ivector(long int, long int)’:
pymrmr/nrutil.cpp:51:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!v) nrerror("allocation failure in ivector()");
^
pymrmr/nrutil.cpp: In function ‘unsigned char* cvector(long int, long int)’:
pymrmr/nrutil.cpp:61:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!v) nrerror("allocation failure in cvector()");
^
pymrmr/nrutil.cpp: In function ‘long unsigned int* lvector(long int, long int)’:
pymrmr/nrutil.cpp:71:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!v) nrerror("allocation failure in lvector()");
^
pymrmr/nrutil.cpp: In function ‘double* dvector(long int, long int)’:
pymrmr/nrutil.cpp:81:51: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!v) nrerror("allocation failure in dvector()");
^
pymrmr/nrutil.cpp: In function ‘float** matrix(long int, long int, long int, long int)’:
pymrmr/nrutil.cpp:93:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m) nrerror("allocation failure 1 in matrix()");
^
pymrmr/nrutil.cpp:99:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
^
pymrmr/nrutil.cpp: In function ‘double** dmatrix(long int, long int, long int, long int)’:
pymrmr/nrutil.cpp:117:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m) nrerror("allocation failure 1 in matrix()");
^
pymrmr/nrutil.cpp:123:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
^
pymrmr/nrutil.cpp: In function ‘int** imatrix(long int, long int, long int, long int)’:
pymrmr/nrutil.cpp:141:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m) nrerror("allocation failure 1 in matrix()");
^
pymrmr/nrutil.cpp:148:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
^
pymrmr/nrutil.cpp: In function ‘float** submatrix(float**, long int, long int, long int, long int, long int, long int)’:
pymrmr/nrutil.cpp:167:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m) nrerror("allocation failure in submatrix()");
^
pymrmr/nrutil.cpp: In function ‘float** convert_matrix(float*, long int, long int, long int, long int)’:
pymrmr/nrutil.cpp:189:58: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!m) nrerror("allocation failure in convert_matrix()");
^
pymrmr/nrutil.cpp: In function ‘float*** f3tensor(long int, long int, long int, long int, long int, long int)’:
pymrmr/nrutil.cpp:208:54: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!t) nrerror("allocation failure 1 in f3tensor()");
^
pymrmr/nrutil.cpp:214:59: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!t[nrl]) nrerror("allocation failure 2 in f3tensor()");
^
pymrmr/nrutil.cpp:220:64: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (!t[nrl][ncl]) nrerror("allocation failure 3 in f3tensor()");
^
In file included from pymrmr/mrmr.cpp:24:0,
from pymrmr/pymrmr.cpp:457:
pymrmr/sort2.cpp: In function ‘void sort2(long unsigned int, float*, float*)’:
pymrmr/sort2.cpp:68:61: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
if (jstack > NSTACK) nrerror("NSTACK too small in sort2.");
^
pymrmr/pymrmr.cpp: In function ‘PyObject* __Pyx_PyCFunction_FastCall(PyObject*, PyObject**, Py_ssize_t)’:
pymrmr/pymrmr.cpp:5418:69: error: too many arguments to function
return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL);
^
pymrmr/pymrmr.cpp: In function ‘void __Pyx__ExceptionSave(PyThreadState*, PyObject**, PyObject**, PyObject**)’:
pymrmr/pymrmr.cpp:5990:21: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
*type = tstate->exc_type;
^~~~~~~~
curexc_type
pymrmr/pymrmr.cpp:5991:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
*value = tstate->exc_value;
^~~~~~~~~
curexc_value
pymrmr/pymrmr.cpp:5992:19: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
*tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
pymrmr/pymrmr.cpp: In function ‘void __Pyx__ExceptionReset(PyThreadState*, PyObject*, PyObject*, PyObject*)’:
pymrmr/pymrmr.cpp:5999:24: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
tmp_type = tstate->exc_type;
^~~~~~~~
curexc_type
pymrmr/pymrmr.cpp:6000:25: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
pymrmr/pymrmr.cpp:6001:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
pymrmr/pymrmr.cpp:6002:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
tstate->exc_type = type;
^~~~~~~~
curexc_type
pymrmr/pymrmr.cpp:6003:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
tstate->exc_value = value;
^~~~~~~~~
curexc_value
pymrmr/pymrmr.cpp:6004:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
tstate->exc_traceback = tb;
^~~~~~~~~~~~~
curexc_traceback
pymrmr/pymrmr.cpp: In function ‘int __Pyx__GetException(PyThreadState*, PyObject**, PyObject**, PyObject**)’:
pymrmr/pymrmr.cpp:6059:24: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
tmp_type = tstate->exc_type;
^~~~~~~~
curexc_type
pymrmr/pymrmr.cpp:6060:25: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
pymrmr/pymrmr.cpp:6061:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
pymrmr/pymrmr.cpp:6062:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
tstate->exc_type = local_type;
^~~~~~~~
curexc_type
pymrmr/pymrmr.cpp:6063:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
tstate->exc_value = local_value;
^~~~~~~~~
curexc_value
pymrmr/pymrmr.cpp:6064:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
tstate->exc_traceback = local_tb;
^~~~~~~~~~~~~
curexc_traceback
In file included from pymrmr/nrutil.cpp:7:0,
from pymrmr/sort2.cpp:3,
from pymrmr/mrmr.cpp:24,
from pymrmr/pymrmr.cpp:457:
pymrmr/nrutil.h: At global scope:
pymrmr/nrutil.h:38:21: warning: ‘iminarg2’ defined but not used [-Wunused-variable]
static int iminarg1,iminarg2;
^~~~~~~~
pymrmr/nrutil.h:38:12: warning: ‘iminarg1’ defined but not used [-Wunused-variable]
static int iminarg1,iminarg2;
^~~~~~~~
pymrmr/nrutil.h:34:21: warning: ‘imaxarg2’ defined but not used [-Wunused-variable]
static int imaxarg1,imaxarg2;
^~~~~~~~
pymrmr/nrutil.h:34:12: warning: ‘imaxarg1’ defined but not used [-Wunused-variable]
static int imaxarg1,imaxarg2;
^~~~~~~~
pymrmr/nrutil.h:30:22: warning: ‘lminarg2’ defined but not used [-Wunused-variable]
static long lminarg1,lminarg2;
^~~~~~~~
pymrmr/nrutil.h:30:13: warning: ‘lminarg1’ defined but not used [-Wunused-variable]
static long lminarg1,lminarg2;
^~~~~~~~
pymrmr/nrutil.h:26:22: warning: ‘lmaxarg2’ defined but not used [-Wunused-variable]
static long lmaxarg1,lmaxarg2;
^~~~~~~~
pymrmr/nrutil.h:26:13: warning: ‘lmaxarg1’ defined but not used [-Wunused-variable]
static long lmaxarg1,lmaxarg2;
^~~~~~~~
pymrmr/nrutil.h:22:22: warning: ‘minarg2’ defined but not used [-Wunused-variable]
static float minarg1,minarg2;
^~~~~~~
pymrmr/nrutil.h:22:14: warning: ‘minarg1’ defined but not used [-Wunused-variable]
static float minarg1,minarg2;
^~~~~~~
pymrmr/nrutil.h:18:22: warning: ‘maxarg2’ defined but not used [-Wunused-variable]
static float maxarg1,maxarg2;
^~~~~~~
pymrmr/nrutil.h:18:14: warning: ‘maxarg1’ defined but not used [-Wunused-variable]
static float maxarg1,maxarg2;
^~~~~~~
pymrmr/nrutil.h:14:24: warning: ‘dminarg2’ defined but not used [-Wunused-variable]
static double dminarg1,dminarg2;
^~~~~~~~
pymrmr/nrutil.h:14:15: warning: ‘dminarg1’ defined but not used [-Wunused-variable]
static double dminarg1,dminarg2;
^~~~~~~~
pymrmr/nrutil.h:10:24: warning: ‘dmaxarg2’ defined but not used [-Wunused-variable]
static double dmaxarg1,dmaxarg2;
^~~~~~~~
pymrmr/nrutil.h:10:15: warning: ‘dmaxarg1’ defined but not used [-Wunused-variable]
static double dmaxarg1,dmaxarg2;
^~~~~~~~
pymrmr/nrutil.h:7:15: warning: ‘dsqrarg’ defined but not used [-Wunused-variable]
static double dsqrarg;
^~~~~~~
pymrmr/nrutil.h:4:14: warning: ‘sqrarg’ defined but not used [-Wunused-variable]
static float sqrarg;
^~~~~~
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
Command "/usr/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-febd25wn/pymrmr/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-j0lzuj61/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-febd25wn/pymrmr/
Unable to install pymrmr onto my machine; I get the following error below
pip install numpy Cython
pip install pymrmr
Collecting pymrmr
Using cached pymrmr-0.1.8.tar.gz
Requirement already satisfied: numpy>=1.12.0 in /data/common/anaconda3/lib/python3.6/site-packages (from pymrmr)
Building wheels for collected packages: pymrmr
Running setup.py bdist_wheel for pymrmr ... error
Complete output from command /data/common/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-wtmeo0mi/pymrmr/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 /tmp/tmpsxq93q_8pip-wheel- --python-tag cp36:
running bdist_wheel
running build
running build_py
package init file 'pymrmr/__init__.py' not found (or not a regular file)
running egg_info
writing pymrmr.egg-info/PKG-INFO
writing dependency_links to pymrmr.egg-info/dependency_links.txt
writing requirements to pymrmr.egg-info/requires.txt
writing top-level names to pymrmr.egg-info/top_level.txt
warning: manifest_maker: standard file '-c' not found
reading manifest file 'pymrmr.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
warning: no files found matching '*.jpg' under directory 'docs'
warning: no files found matching '*.png' under directory 'docs'
warning: no files found matching '*.gif' under directory 'docs'
writing manifest file 'pymrmr.egg-info/SOURCES.txt'
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/pymrmr
copying pymrmr/crank.cpp -> build/lib.linux-x86_64-3.6/pymrmr
copying pymrmr/mrmr.cpp -> build/lib.linux-x86_64-3.6/pymrmr
copying pymrmr/nrutil.cpp -> build/lib.linux-x86_64-3.6/pymrmr
copying pymrmr/nrutil.h -> build/lib.linux-x86_64-3.6/pymrmr
copying pymrmr/pbetai.cpp -> build/lib.linux-x86_64-3.6/pymrmr
copying pymrmr/pymrmr.cpp -> build/lib.linux-x86_64-3.6/pymrmr
copying pymrmr/pymrmr.pyx -> build/lib.linux-x86_64-3.6/pymrmr
copying pymrmr/sort2.cpp -> build/lib.linux-x86_64-3.6/pymrmr
running build_ext
skipping 'pymrmr/pymrmr.cpp' Cython extension (up-to-date)
building 'pymrmr' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/pymrmr
gcc -pthread -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/data/common/anaconda3/lib/python3.6/site-packages/numpy/core/include -I/data/common/anaconda3/include/python3.6m -c pymrmr/pymrmr.cpp -o build/temp.linux-x86_64-3.6/pymrmr/pymrmr.o -fopenmp -Ofast
unable to execute 'gcc': No such file or directory
error: command 'gcc' failed with exit status 1
----------------------------------------
Failed building wheel for pymrmr
Running setup.py clean for pymrmr
Failed to build pymrmr
Installing collected packages: pymrmr
Running setup.py install for pymrmr ... error
Complete output from command /data/common/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-wtmeo0mi/pymrmr/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-eodfh01f-record/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
package init file 'pymrmr/__init__.py' not found (or not a regular file)
running egg_info
writing pymrmr.egg-info/PKG-INFO
writing dependency_links to pymrmr.egg-info/dependency_links.txt
writing requirements to pymrmr.egg-info/requires.txt
writing top-level names to pymrmr.egg-info/top_level.txt
warning: manifest_maker: standard file '-c' not found
reading manifest file 'pymrmr.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
warning: no files found matching '*.jpg' under directory 'docs'
warning: no files found matching '*.png' under directory 'docs'
warning: no files found matching '*.gif' under directory 'docs'
writing manifest file 'pymrmr.egg-info/SOURCES.txt'
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/pymrmr
copying pymrmr/crank.cpp -> build/lib.linux-x86_64-3.6/pymrmr
copying pymrmr/mrmr.cpp -> build/lib.linux-x86_64-3.6/pymrmr
copying pymrmr/nrutil.cpp -> build/lib.linux-x86_64-3.6/pymrmr
copying pymrmr/nrutil.h -> build/lib.linux-x86_64-3.6/pymrmr
copying pymrmr/pbetai.cpp -> build/lib.linux-x86_64-3.6/pymrmr
copying pymrmr/pymrmr.cpp -> build/lib.linux-x86_64-3.6/pymrmr
copying pymrmr/pymrmr.pyx -> build/lib.linux-x86_64-3.6/pymrmr
copying pymrmr/sort2.cpp -> build/lib.linux-x86_64-3.6/pymrmr
running build_ext
skipping 'pymrmr/pymrmr.cpp' Cython extension (up-to-date)
building 'pymrmr' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/pymrmr
gcc -pthread -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/data/common/anaconda3/lib/python3.6/site-packages/numpy/core/include -I/data/common/anaconda3/include/python3.6m -c pymrmr/pymrmr.cpp -o build/temp.linux-x86_64-3.6/pymrmr/pymrmr.o -fopenmp -Ofast
unable to execute 'gcc': No such file or directory
error: command 'gcc' failed with exit status 1
----------------------------------------
Command "/data/common/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-wtmeo0mi/pymrmr/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-eodfh01f-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-wtmeo0mi/pymrmr/
When installing pymrmr, I downloaded project files and installed vc, mingw, cython but some errors occurs:
I run ' pip install pymrmr' in ./pymrmr-master/ and whole output is like:
----------------------------------------
Failed building wheel for pymrmr
Running setup.py clean for pymrmr
Failed to build pymrmr
Installing collected packages: pymrmr
Running setup.py install for pymrmr ... error
Complete output from command e:\anaconda3\envs\py35\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\ADMINI~1\\AppData\\Local\\Temp\\pip-install-hgwwn9as\\pymrmr\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\ADMINI~1\AppData\Local\Temp\pip-record-_oq9dut5\install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
package init file 'pymrmr\__init__.py' not found (or not a regular file)
running egg_info
writing top-level names to pymrmr.egg-info\top_level.txt
writing dependency_links to pymrmr.egg-info\dependency_links.txt
writing requirements to pymrmr.egg-info\requires.txt
writing pymrmr.egg-info\PKG-INFO
reading manifest file 'pymrmr.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
warning: no files found matching '*.jpg' under directory 'docs'
warning: no files found matching '*.png' under directory 'docs'
warning: no files found matching '*.gif' under directory 'docs'
writing manifest file 'pymrmr.egg-info\SOURCES.txt'
creating build
creating build\lib.win-amd64-3.5
creating build\lib.win-amd64-3.5\pymrmr
copying pymrmr\crank.cpp -> build\lib.win-amd64-3.5\pymrmr
copying pymrmr\mrmr.cpp -> build\lib.win-amd64-3.5\pymrmr
copying pymrmr\nrutil.cpp -> build\lib.win-amd64-3.5\pymrmr
copying pymrmr\nrutil.h -> build\lib.win-amd64-3.5\pymrmr
copying pymrmr\pbetai.cpp -> build\lib.win-amd64-3.5\pymrmr
copying pymrmr\pymrmr.cpp -> build\lib.win-amd64-3.5\pymrmr
copying pymrmr\pymrmr.pyx -> build\lib.win-amd64-3.5\pymrmr
copying pymrmr\sort2.cpp -> build\lib.win-amd64-3.5\pymrmr
running build_ext
error: [WinError 2] The system can not find the specified file.
----------------------------------------
Command "e:\anaconda3\envs\py35\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\ADMINI~1\\AppData\\Local\\Temp\\pip-install-hgwwn9as\\pymrmr\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\ADMINI~1\AppData\Local\Temp\pip-record-_oq9dut5\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in C:\Users\ADMINI~1\AppData\Local\Temp\pip-install-hgwwn9as\pymrmr\
I'm trying to install pymrmr. but:
Try to run this command from the system terminal. Make sure that you use the correct version of 'pip' installed for your Python interpreter located at 'C:\Users\Ali RB\AppData\Local\Programs\Python\Python39\python.exe'.
Collecting pymrmr
Using cached pymrmr-0.1.11.tar.gz (69 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'error'
Using cached pymrmr-0.1.9.tar.gz (77 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'error'
Using cached pymrmr-0.1.8.tar.gz (65 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'error'
Using cached pymrmr-0.1.7.tar.gz (65 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'error'
Using cached pymrmr-0.1.6.tar.gz (65 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'error'
Using cached pymrmr-0.1.5.tar.gz (65 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'error'
Using cached pymrmr-0.1.3.tar.gz (13 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'error'
Using cached pymrmr-0.1.2.tar.gz (13 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'error'
Using cached pymrmr-0.1.1.tar.gz (13 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'error'
WARNING: Discarding https://files.pythonhosted.org/packages/c0/67/2f1d7b7f24dc50ff2cfc8c6b7e8b163bda504b6979bb6a6936a907330493/pymrmr-0.1.1.tar.gz#sha256=1ada3ba549aced367774fd8f01035aaf02edafb2d52f382c74f7a5353f915673 (from https://pypi.org/simple/pymrmr/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
ERROR: Could not find a version that satisfies the requirement pymrmr (from versions: 0.1.4.macosx-10.12-x86_64, 0.1.1, 0.1.2, 0.1.3, 0.1.5, 0.1.6, 0.1.7, 0.1.8, 0.1.9, 0.1.11)
ERROR: No matching distribution found for pymrmr
I have an issue that seems to have been posted about here before. However, the fix suggested does not work for me.
When trying to import the package I get this:
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-d5e12a0062d7> in <module>()
14
15 # MRMR
---> 16 import pymrmr
17
ImportError: dlopen(/Users/kimrants/anaconda3/lib/python3.6/site-packages/pymrmr.cpython-36m-darwin.so, 2): Library not loaded: /usr/local/opt/libiomp/lib/libiomp5.dylib
Referenced from: /Users/kimrants/anaconda3/lib/python3.6/site-packages/pymrmr.cpython-36m-darwin.so
Reason: image not found
Hi, Sorry to bother you, your package helps me a lot, I am just wondering that the features (columns ) need to be normalized before the mrmr or not? My project is focus on regression problem not classification. Thank you in advance!
Jian
Paste the command(s) you ran and the output.
If there was a crash, please include the traceback here.
The Cython version used to create the pymrmr.pyx
in the current master
and in on pypi does not support python3.7.
This is the reason for the error reported here: #202
I am trying to "pip install pymrmr' however i have been running into issue as below [already installed: numpy Cython]:
error:
Collecting pymrmr
Using cached pymrmr-0.1.11.tar.gz (69 kB)
Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy>=1.19.5 in c:\users\dasss\appdata\local\programs\python\python311\lib\site-packages (from pymrmr) (1.24.1)
Building wheels for collected packages: pymrmr
Building wheel for pymrmr (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [33 lines of output]
running bdist_wheel
running build
running build_py
running egg_info
writing pymrmr.egg-info\PKG-INFO
writing dependency_links to pymrmr.egg-info\dependency_links.txt
writing requirements to pymrmr.egg-info\requires.txt
writing top-level names to pymrmr.egg-info\top_level.txt
reading manifest file 'pymrmr.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching 'pycache' found under directory ''
warning: no previously-included files matching '.py[co]' found under directory ''
warning: no files found matching '.jpg' under directory 'docs'
warning: no files found matching '.png' under directory 'docs'
warning: no files found matching '.gif' under directory 'docs'
adding license file 'LICENSE'
adding license file 'AUTHORS.rst'
writing manifest file 'pymrmr.egg-info\SOURCES.txt'
creating build
creating build\lib.win-amd64-cpython-311
creating build\lib.win-amd64-cpython-311\pymrmr
copying pymrmr\crank.cpp -> build\lib.win-amd64-cpython-311\pymrmr
copying pymrmr\mrmr.cpp -> build\lib.win-amd64-cpython-311\pymrmr
copying pymrmr\nrutil.cpp -> build\lib.win-amd64-cpython-311\pymrmr
copying pymrmr\nrutil.h -> build\lib.win-amd64-cpython-311\pymrmr
copying pymrmr\pbetai.cpp -> build\lib.win-amd64-cpython-311\pymrmr
copying pymrmr\pymrmr.cpp -> build\lib.win-amd64-cpython-311\pymrmr
copying pymrmr\pymrmr.pyx -> build\lib.win-amd64-cpython-311\pymrmr
copying pymrmr\sort2.cpp -> build\lib.win-amd64-cpython-311\pymrmr
running build_ext
skipping 'pymrmr\pymrmr.cpp' Cython extension (up-to-date)
building 'pymrmr' extension
error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pymrmr
Running setup.py clean for pymrmr
Failed to build pymrmr
Installing collected packages: pymrmr
Running setup.py install for pymrmr ... error
error: subprocess-exited-with-error
× Running setup.py install for pymrmr did not run successfully.
│ exit code: 1
╰─> [35 lines of output]
running install
C:\Users\dasss\AppData\Local\Programs\Python\Python311\Lib\site-packages\setuptools\command\install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_py
running egg_info
writing pymrmr.egg-info\PKG-INFO
writing dependency_links to pymrmr.egg-info\dependency_links.txt
writing requirements to pymrmr.egg-info\requires.txt
writing top-level names to pymrmr.egg-info\top_level.txt
reading manifest file 'pymrmr.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching 'pycache' found under directory ''
warning: no previously-included files matching '.py[co]' found under directory ''
warning: no files found matching '.jpg' under directory 'docs'
warning: no files found matching '.png' under directory 'docs'
warning: no files found matching '.gif' under directory 'docs'
adding license file 'LICENSE'
adding license file 'AUTHORS.rst'
writing manifest file 'pymrmr.egg-info\SOURCES.txt'
creating build
creating build\lib.win-amd64-cpython-311
creating build\lib.win-amd64-cpython-311\pymrmr
copying pymrmr\crank.cpp -> build\lib.win-amd64-cpython-311\pymrmr
copying pymrmr\mrmr.cpp -> build\lib.win-amd64-cpython-311\pymrmr
copying pymrmr\nrutil.cpp -> build\lib.win-amd64-cpython-311\pymrmr
copying pymrmr\nrutil.h -> build\lib.win-amd64-cpython-311\pymrmr
copying pymrmr\pbetai.cpp -> build\lib.win-amd64-cpython-311\pymrmr
copying pymrmr\pymrmr.cpp -> build\lib.win-amd64-cpython-311\pymrmr
copying pymrmr\pymrmr.pyx -> build\lib.win-amd64-cpython-311\pymrmr
copying pymrmr\sort2.cpp -> build\lib.win-amd64-cpython-311\pymrmr
running build_ext
skipping 'pymrmr\pymrmr.cpp' Cython extension (up-to-date)
building 'pymrmr' extension
error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure
× Encountered error while trying to install package.
╰─> pymrmr
note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
I tried to get scores for each feature when using pymrmr.mRMR. What I expect is a score table as authors' example:
### *** MaxRel features ***
Order Fea Name Score
1 765 v765 0.375
2 1423 v1423 0.337
3 513 v513 0.321
4 249 v249 0.309
5 267 v267 0.304
6 245 v245 0.304
7 1582 v1582 0.280
8 897 v897 0.269
9 1771 v1771 0.269
10 1772 v1772 0.269
*** mRMR features ***
Order Fea Name Score
1 765 v765 0.375
2 1123 v1123 24.913
3 1772 v1772 3.984
4 286 v286 2.280
5 467 v467 1.979
6 377 v377 1.768
7 513 v513 1.803
8 1325 v1325 1.634
9 1972 v1972 1.741
10 1412 v1412 1.689
However, this code below only returned an ordered feature list.
pymrmr.mRMR(df, 'MIQ', 10)
Please help me to get score table.
Thank you very much.
My code as follows:
import pandas as pd
import pymrmr
df = pd.read_csv('mrmr_data_set.csv')
pymrmr.mRMR(df, 'MIQ', 20)
but it throws the following exception:
File "pymrmr/pymrmr.pyx", line 26, in pymrmr.mRMR (pymrmr\pymrmr.cpp:1790)
cdef vector[unsigned long] _feats = _mRMR(_data, _names, _method, nfeats)
MemoryError: bad array new length
my csv data is :
mrmr_data_set.txt
Hi,
I see in the project front page that the continuous data should be discretized. But:
1- When I give it continuous data I do not get any error.
2- If I want to discretize data, is it sufficient to just run for example sklearn's KBinsDiscretizer and give it the required number of bins with uniform strategy? This will not be the same as the strategy mentioned in the paper (i.e. considering mean+/-std and binning to -1, 0, and 1 accordingly) but I do not think that really matters. If the feature values are changed by a scale, why the feature selection mechanism should give us different results?
I hope to hear from you soon.
Best Regards
Shahriar
I am a bit confused why the mRMR table has one line more than the maxRel table - does it skip the least relevant feature in the first table, if you want to have ordered all of them?
And I do not understand the order in the second table - it does not seem to be ordered according to the actual score as you can see in this example.
*** mRMR features ***
Order Fea Name Score
1 887 a64345 0.99573
2 889 a8BYI6 0.99990
3 670 a9WVK4 0.99990
4 837 b11688 0.99990
5 006 a9WVJ3 0.99990
6 434 a9CaD1 0.99925
7 420 a9DBG3 0.99754
8 888 b08071 0.99699
9 326 b19157 0.99677
10 892 a810a5 0.99571
11 893 c09046 0.99238
12 270 a8BGG7 0.99077
13 232 b31324 0.98236
14 117 a9CRB6 0.97790
15 882 b55097 0.97712
16 868 a9CYN9 0.97711
17 023 a61503 0.97775
18 785 a6bB93 0.97892
19 165 a922B1 0.97849
20 683 a9JIK5 0.97918
PymRMR crashes in conversion when I want to execute with a correct dataset.
I read a dataset (it haven't NaN's or missing values), then I put the target on columns position 0. The dataset (included target) now have 10 variables. If I want to remove 1 variable, i.e. I want 8 predictors, I get the following error:
Traceback (most recent call last):
File "/home/.../preprocess_data.py", line 62, in <module>
pymrmr.mRMR(full_ds,'MIQ',8)
File "pymrmr/pymrmr.pyx", line 19, in pymrmr.mRMR (pymrmr/pymrmr.cpp:1666)
File "stringsource", line 53, in vector.from_py.__pyx_convert_vector_from_py_std_3a__3a_vector_3c_int_3e___ (pymrmr/pymrmr.cpp:4546)
File "stringsource", line 52, in vector.from_py.__pyx_convert_vector_from_py_int (pymrmr/pymrmr.cpp:4428)
OverflowError: value too large to convert to int
Describe what you were trying to get done.
Tell us what happened, what went wrong, and what you expected to happen.
pip install numpy Cython
pip install pymrmr
Collecting pymrmr
Using cached pymrmr-0.1.11.tar.gz (69 kB)
Requirement already satisfied: numpy>=1.19.5 in /opt/anaconda3/lib/python3.7/site-packages (from pymrmr) (1.20.1)
Building wheels for collected packages: pymrmr
Building wheel for pymrmr (setup.py) ... �[?25lerror
ERROR: Command errored out with exit status 1:
command: /opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/setup.py'"'"'; __file__='"'"'/private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/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/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-wheel-frxhfca6
cwd: /private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/
Complete output (38 lines):
/opt/anaconda3/lib/python3.7/site-packages/setuptools/dist.py:723: UserWarning: Module Cython was already imported from /opt/anaconda3/lib/python3.7/site-packages/Cython/__init__.py, but /private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/.eggs/Cython-3.0a6-py3.7.egg is being added to sys.path
pkg_resources.working_set.add(dist, replace=True)
running bdist_wheel
running build
running build_py
package init file 'pymrmr/__init__.py' not found (or not a regular file)
running egg_info
writing pymrmr.egg-info/PKG-INFO
writing dependency_links to pymrmr.egg-info/dependency_links.txt
writing requirements to pymrmr.egg-info/requires.txt
writing top-level names to pymrmr.egg-info/top_level.txt
reading manifest file 'pymrmr.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
warning: no files found matching '*.jpg' under directory 'docs'
warning: no files found matching '*.png' under directory 'docs'
warning: no files found matching '*.gif' under directory 'docs'
writing manifest file 'pymrmr.egg-info/SOURCES.txt'
creating build
creating build/lib.macosx-10.9-x86_64-3.7
creating build/lib.macosx-10.9-x86_64-3.7/pymrmr
copying pymrmr/crank.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
copying pymrmr/mrmr.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
copying pymrmr/nrutil.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
copying pymrmr/nrutil.h -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
copying pymrmr/pbetai.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
copying pymrmr/pymrmr.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
copying pymrmr/pymrmr.pyx -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
copying pymrmr/sort2.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
running build_ext
skipping 'pymrmr/pymrmr.cpp' Cython extension (up-to-date)
building 'pymrmr' extension
creating build/temp.macosx-10.9-x86_64-3.7
creating build/temp.macosx-10.9-x86_64-3.7/pymrmr
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/anaconda3/include -arch x86_64 -I/opt/anaconda3/include -arch x86_64 -I/opt/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/opt/anaconda3/include/python3.7m -c pymrmr/pymrmr.cpp -o build/temp.macosx-10.9-x86_64-3.7/pymrmr/pymrmr.o -fopenmp -Ofast
clang: error: unsupported option '-fopenmp'
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for pymrmr
nning setup.py clean for pymrmr
Failed to build pymrmr
Installing collected packages: pymrmr
Running setup.py install for pymrmr ... �[?25lerror
ERROR: Command errored out with exit status 1:
command: /opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/setup.py'"'"'; __file__='"'"'/private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/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/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-record-zrfq3baf/install-record.txt --single-version-externally-managed --compile --install-headers /opt/anaconda3/include/python3.7m/pymrmr
cwd: /private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/
Complete output (38 lines):
/opt/anaconda3/lib/python3.7/site-packages/setuptools/dist.py:723: UserWarning: Module Cython was already imported from /opt/anaconda3/lib/python3.7/site-packages/Cython/__init__.py, but /private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/.eggs/Cython-3.0a6-py3.7.egg is being added to sys.path
pkg_resources.working_set.add(dist, replace=True)
running install
running build
running build_py
package init file 'pymrmr/__init__.py' not found (or not a regular file)
running egg_info
writing pymrmr.egg-info/PKG-INFO
writing dependency_links to pymrmr.egg-info/dependency_links.txt
writing requirements to pymrmr.egg-info/requires.txt
writing top-level names to pymrmr.egg-info/top_level.txt
reading manifest file 'pymrmr.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
warning: no files found matching '*.jpg' under directory 'docs'
warning: no files found matching '*.png' under directory 'docs'
warning: no files found matching '*.gif' under directory 'docs'
writing manifest file 'pymrmr.egg-info/SOURCES.txt'
creating build
creating build/lib.macosx-10.9-x86_64-3.7
creating build/lib.macosx-10.9-x86_64-3.7/pymrmr
copying pymrmr/crank.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
copying pymrmr/mrmr.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
copying pymrmr/nrutil.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
copying pymrmr/nrutil.h -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
copying pymrmr/pbetai.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
copying pymrmr/pymrmr.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
copying pymrmr/pymrmr.pyx -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
copying pymrmr/sort2.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
running build_ext
skipping 'pymrmr/pymrmr.cpp' Cython extension (up-to-date)
building 'pymrmr' extension
creating build/temp.macosx-10.9-x86_64-3.7
creating build/temp.macosx-10.9-x86_64-3.7/pymrmr
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/anaconda3/include -arch x86_64 -I/opt/anaconda3/include -arch x86_64 -I/opt/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/opt/anaconda3/include/python3.7m -c pymrmr/pymrmr.cpp -o build/temp.macosx-10.9-x86_64-3.7/pymrmr/pymrmr.o -fopenmp -Ofast
clang: error: unsupported option '-fopenmp'
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/setup.py'"'"'; __file__='"'"'/private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/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/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-record-zrfq3baf/install-record.txt --single-version-externally-managed --compile --install-headers /opt/anaconda3/include/python3.7m/pymrmr Check the logs for full command output.
�[?25hNote: you may need to restart the kernel to use updated packages.
When I run ret = pymrmr.mRMR(df,'MIQ',36)
, which df = [y, X] with 7million row and 84 column. I have error of `Traceback (most recent call last):
File "", line 1, in
ret = pymrmr.mRMR(df,'MIQ',36)
File "pymrmr/pymrmr.pyx", line 20, in pymrmr.mRMR (pymrmr\pymrmr.cpp:1723)
AttributeError: 'numpy.int64' object has no attribute 'encode' `
Could you please help? Thanks!
Executed the "pip install pymrmr" and received error "gcc.exe' failed with exit status 1"
Below are the error logs:
error: command 'C:\Users\Jinee Goyal\Anaconda3\Library\mingw-w64\bin\gcc.exe' failed with exit status 1
Environment :
error traceback.txt
Paste the command(s) you ran and the output.
If there was a crash, please include the trace-back here.
I'm trying to install pymrmr via the jupyter terminal however it gives the warning "Failed building wheel for pymrmr". Please let me know how I can fix it, as I need to use it urgently. Thanks.
error: command 'C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.16.27023\bin\H
ostX86\x64\cl.exe' failed with exit status 2
I simply run the command pip install pymrmr and this is how it executed:
Collecting pymrmr
Using cached https://files.pythonhosted.org/packages/b3/ab/903712947a2f5cd1af249132885dbd81ae8bf8cfd30fb3b3f2beddab23e8/p
ymrmr-0.1.8.tar.gz
Requirement already satisfied: numpy>=1.12.0 in c:\programdata\anaconda3\lib\site-packages (from pymrmr) (1.18.5)
Building wheels for collected packages: pymrmr
Building wheel for pymrmr (setup.py) ... error
Complete output from command C:\ProgramData\Anaconda3\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\
MYPC~1\\AppData\\Local\\Temp\\pip-install-2qskcm1m\\pymrmr\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.re
ad().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d C:\Users\MYPC~1\AppData\Local\Te
mp\pip-wheel-ni2izhkx --python-tag cp37:
running bdist_wheel
running build
running build_py
package init file 'pymrmr\__init__.py' not found (or not a regular file)
running egg_info
writing pymrmr.egg-info\PKG-INFO
writing dependency_links to pymrmr.egg-info\dependency_links.txt
writing requirements to pymrmr.egg-info\requires.txt
writing top-level names to pymrmr.egg-info\top_level.txt
reading manifest file 'pymrmr.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
warning: no files found matching '*.jpg' under directory 'docs'
warning: no files found matching '*.png' under directory 'docs'
warning: no files found matching '*.gif' under directory 'docs'
writing manifest file 'pymrmr.egg-info\SOURCES.txt'
creating build
creating build\lib.win-amd64-3.7
creating build\lib.win-amd64-3.7\pymrmr
copying pymrmr\crank.cpp -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\mrmr.cpp -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\nrutil.cpp -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\nrutil.h -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\pbetai.cpp -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\pymrmr.cpp -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\pymrmr.pyx -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\sort2.cpp -> build\lib.win-amd64-3.7\pymrmr
running build_ext
skipping 'pymrmr\pymrmr.cpp' Cython extension (up-to-date)
building 'pymrmr' extension
creating build\temp.win-amd64-3.7
creating build\temp.win-amd64-3.7\Release
creating build\temp.win-amd64-3.7\Release\pymrmr
C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.16.27023\bin\HostX86\x64\cl.exe /c /nologo
/Ox /W3 /GL /DNDEBUG /MD -IC:\ProgramData\Anaconda3\lib\site-packages\numpy\core\include -IC:\ProgramData\Anaconda3\includ
e -IC:\ProgramData\Anaconda3\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.16.2
7023\ATLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.16.27023\include" "-
IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.6.1\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.1776
3.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\
include\10.0.17763.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\winrt" "-IC:\Program Files (x86)\Wi
ndows Kits\10\include\10.0.17763.0\cppwinrt" /EHsc /Tppymrmr\pymrmr.cpp /Fobuild\temp.win-amd64-3.7\Release\pymrmr\pymrmr.o
bj -fopenmp -Ofast
cl : Command line warning D9025 : overriding '/Os' with '/Ot'
cl : Command line warning D9002 : ignoring unknown option '-fopenmp'
cl : Command line warning D9002 : ignoring unknown option '-Of'
cl : Command line warning D9002 : ignoring unknown option '-Oa'
pymrmr.cpp
c:\programdata\anaconda3\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(14) : Warning Msg: Using dep
recated NumPy API, disable it with #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(33): warning C4244: 'return': conversion
from 'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(47): warning C4244: '=': conversion from
'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(48): warning C4244: '=': conversion from
'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(50): warning C4244: '=': conversion from
'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(51): warning C4305: '=': truncation from
'double' to 'float'
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(52): warning C4244: '=': conversion from
'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(57): warning C4244: '=': conversion from
'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(58): warning C4305: '=': truncation from
'double' to 'float'
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(59): warning C4244: '=': conversion from
'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(60): warning C4305: '=': truncation from
'double' to 'float'
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(61): warning C4244: '=': conversion from
'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(64): warning C4244: '=': conversion from
'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(65): warning C4305: '=': truncation from
'double' to 'float'
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(66): warning C4244: '=': conversion from
'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(67): warning C4305: '=': truncation from
'double' to 'float'
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(68): warning C4244: '=': conversion from
'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(90): warning C4244: '=': conversion from
'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(94): warning C4244: 'argument': conversio
n from 'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(94): warning C4244: 'return': conversion
from 'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\mrmr.cpp(189): warning C4267: 'argument': conversion
from 'size_t' to 'long', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\mrmr.cpp(205): warning C4267: '=': conversion from '
size_t' to 'unsigned long', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\mrmr.cpp(215): warning C4244: '=': conversion from '
double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\mrmr.cpp(216): warning C4244: '=': conversion from '
unsigned long' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\mrmr.cpp(221): warning C4267: 'argument': conversion
from 'size_t' to 'unsigned long', possible loss of data
pymrmr\pymrmr.cpp(5418): error C2197: 'PyObject *(__cdecl *)(PyObject *,PyObject *const *,Py_ssize_t)': too many argument
s for call
pymrmr\pymrmr.cpp(5990): error C2039: 'exc_type': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(5991): error C2039: 'exc_value': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(5992): error C2039: 'exc_traceback': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(5999): error C2039: 'exc_type': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6000): error C2039: 'exc_value': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6001): error C2039: 'exc_traceback': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6002): error C2039: 'exc_type': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6003): error C2039: 'exc_value': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6004): error C2039: 'exc_traceback': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6059): error C2039: 'exc_type': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6060): error C2039: 'exc_value': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6061): error C2039: 'exc_traceback': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6062): error C2039: 'exc_type': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6063): error C2039: 'exc_value': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6064): error C2039: 'exc_traceback': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio\\2017\\Community\\VC\\Tools\\MSVC\\14.16.27023\\bin\\Hos
tX86\\x64\\cl.exe' failed with exit status 2
----------------------------------------
Failed building wheel for pymrmr
Running setup.py clean for pymrmr
Failed to build pymrmr
Installing collected packages: pymrmr
Running setup.py install for pymrmr ... error
Complete output from command C:\ProgramData\Anaconda3\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users
\\MYPC~1\\AppData\\Local\\Temp\\pip-install-2qskcm1m\\pymrmr\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.
read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\MYPC~1\AppData\Loca
l\Temp\pip-record-tv804p8d\install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
package init file 'pymrmr\__init__.py' not found (or not a regular file)
running egg_info
writing pymrmr.egg-info\PKG-INFO
writing dependency_links to pymrmr.egg-info\dependency_links.txt
writing requirements to pymrmr.egg-info\requires.txt
writing top-level names to pymrmr.egg-info\top_level.txt
reading manifest file 'pymrmr.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
warning: no files found matching '*.jpg' under directory 'docs'
warning: no files found matching '*.png' under directory 'docs'
warning: no files found matching '*.gif' under directory 'docs'
writing manifest file 'pymrmr.egg-info\SOURCES.txt'
creating build
creating build\lib.win-amd64-3.7
creating build\lib.win-amd64-3.7\pymrmr
copying pymrmr\crank.cpp -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\mrmr.cpp -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\nrutil.cpp -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\nrutil.h -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\pbetai.cpp -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\pymrmr.cpp -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\pymrmr.pyx -> build\lib.win-amd64-3.7\pymrmr
copying pymrmr\sort2.cpp -> build\lib.win-amd64-3.7\pymrmr
running build_ext
skipping 'pymrmr\pymrmr.cpp' Cython extension (up-to-date)
building 'pymrmr' extension
creating build\temp.win-amd64-3.7
creating build\temp.win-amd64-3.7\Release
creating build\temp.win-amd64-3.7\Release\pymrmr
C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.16.27023\bin\HostX86\x64\cl.exe /c /nolo
go /Ox /W3 /GL /DNDEBUG /MD -IC:\ProgramData\Anaconda3\lib\site-packages\numpy\core\include -IC:\ProgramData\Anaconda3\incl
ude -IC:\ProgramData\Anaconda3\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.16
.27023\ATLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.16.27023\include"
"-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.6.1\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17
763.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\shared" "-IC:\Program Files (x86)\Windows Kits\1
0\include\10.0.17763.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\winrt" "-IC:\Program Files (x86)\
Windows Kits\10\include\10.0.17763.0\cppwinrt" /EHsc /Tppymrmr\pymrmr.cpp /Fobuild\temp.win-amd64-3.7\Release\pymrmr\pymrmr
.obj -fopenmp -Ofast
cl : Command line warning D9025 : overriding '/Os' with '/Ot'
cl : Command line warning D9002 : ignoring unknown option '-fopenmp'
cl : Command line warning D9002 : ignoring unknown option '-Of'
cl : Command line warning D9002 : ignoring unknown option '-Oa'
pymrmr.cpp
c:\programdata\anaconda3\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(14) : Warning Msg: Using d
eprecated NumPy API, disable it with #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(33): warning C4244: 'return': conversio
n from 'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(47): warning C4244: '=': conversion fro
m 'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(48): warning C4244: '=': conversion fro
m 'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(50): warning C4244: '=': conversion fro
m 'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(51): warning C4305: '=': truncation fro
m 'double' to 'float'
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(52): warning C4244: '=': conversion fro
m 'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(57): warning C4244: '=': conversion fro
m 'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(58): warning C4305: '=': truncation fro
m 'double' to 'float'
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(59): warning C4244: '=': conversion fro
m 'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(60): warning C4305: '=': truncation fro
m 'double' to 'float'
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(61): warning C4244: '=': conversion fro
m 'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(64): warning C4244: '=': conversion fro
m 'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(65): warning C4305: '=': truncation fro
m 'double' to 'float'
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(66): warning C4244: '=': conversion fro
m 'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(67): warning C4305: '=': truncation fro
m 'double' to 'float'
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(68): warning C4244: '=': conversion fro
m 'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(90): warning C4244: '=': conversion fro
m 'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(94): warning C4244: 'argument': convers
ion from 'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\pbetai.cpp(94): warning C4244: 'return': conversio
n from 'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\mrmr.cpp(189): warning C4267: 'argument': conversi
on from 'size_t' to 'long', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\mrmr.cpp(205): warning C4267: '=': conversion from
'size_t' to 'unsigned long', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\mrmr.cpp(215): warning C4244: '=': conversion from
'double' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\mrmr.cpp(216): warning C4244: '=': conversion from
'unsigned long' to 'float', possible loss of data
c:\users\my pc\appdata\local\temp\pip-install-2qskcm1m\pymrmr\pymrmr\mrmr.cpp(221): warning C4267: 'argument': conversi
on from 'size_t' to 'unsigned long', possible loss of data
pymrmr\pymrmr.cpp(5418): error C2197: 'PyObject *(__cdecl *)(PyObject *,PyObject *const *,Py_ssize_t)': too many argume
nts for call
pymrmr\pymrmr.cpp(5990): error C2039: 'exc_type': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(5991): error C2039: 'exc_value': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(5992): error C2039: 'exc_traceback': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(5999): error C2039: 'exc_type': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6000): error C2039: 'exc_value': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6001): error C2039: 'exc_traceback': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6002): error C2039: 'exc_type': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6003): error C2039: 'exc_value': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6004): error C2039: 'exc_traceback': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6059): error C2039: 'exc_type': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6060): error C2039: 'exc_value': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6061): error C2039: 'exc_traceback': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6062): error C2039: 'exc_type': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6063): error C2039: 'exc_value': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
pymrmr\pymrmr.cpp(6064): error C2039: 'exc_traceback': is not a member of '_ts'
c:\programdata\anaconda3\include\pystate.h(212): note: see declaration of '_ts'
error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio\\2017\\Community\\VC\\Tools\\MSVC\\14.16.27023\\bin\\H
ostX86\\x64\\cl.exe' failed with exit status 2
----------------------------------------
Command "C:\ProgramData\Anaconda3\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\MYPC~1\\AppData\\Local
\\Temp\\pip-install-2qskcm1m\\pymrmr\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '
\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\MYPC~1\AppData\Local\Temp\pip-record-tv804p
8d\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in C:\Users\MYPC~1\AppData\Lo
cal\Temp\pip-install-2qskcm1m\pymrmr\
If I call the method with the 3rd parameter > 1 I get the error:
File "pymrmr/pymrmr.pyx", line 26, in pymrmr.mRMR (pymrmr/pymrmr.cpp:1790)
MemoryError: std::bad_array_new_length
For the mRMR features.
E.g. call with 3rd parameter = 2:
*** MaxRel features ***
Order Fea Name Score
1 12 HitStatisticsValues.z_travel 0.429
2 18 LineFit_TT.z 0.392
*** mRMR features ***
Order Fea Name Score
1 12 HitStatisticsValues.z_travel 0.429
Traceback (most recent call last):
File "select_attributes.py", line 99, in
test = pymrmr.mRMR(data, 'MID', 2)
File "pymrmr/pymrmr.pyx", line 26, in pymrmr.mRMR (pymrmr/pymrmr.cpp:1790)
MemoryError: std::bad_array_new_length
I am trying to pip install pymrmr however i have been running into issue as below :
error: command 'C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\x86_amd64\cl.exe' failed with exit status 2
----------------------------------------
Command "C:\Users\jieya\Anaconda2\envs\python3\python.exe -u -c "import setuptools, tokenize;file='C:\Users\jieya\AppData\Local\Temp\pip-build-x9k46uvy\pymrmr\setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record C:\Users\jieya\AppData\Local\Temp\pip-zwgj7n1d-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in C:\Users\jieya\AppData\Local\Temp\pip-build-x9k46uvy\pymrmr\
not too sure if its windows problem or there isnt any wheel built for this library for python 3.6
Getting import error while importing pymrmr
Traceback (most recent call last):
File "", line 1, in
ImportError: /home/saif/anaconda3/lib/python2.7/site-packages/pymrmr.so: undefined symbol: __log_finite
I've been trying to run a quick Python program, but it seems that the pymrmr code cannot find libiomp5. I'm not sure what that is, I didn't see it listed in the dependencies here.
> python3 gene_selection.py
Traceback (most recent call last):
File "gene_selection.py", line 8, in <module>
import pymrmr
ImportError: dlopen(/usr/local/lib/python3.6/site-packages/pymrmr.cpython-36m-darwin.so, 2): Library not loaded: /usr/local/opt/libiomp/lib/libiomp5.dylib
Referenced from: /usr/local/lib/python3.6/site-packages/pymrmr.cpython-36m-darwin.so
Reason: image not found
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