pymrmr
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install failed
- PymRMR version:0.1.8
- Python version: both 3.7 and 3.8
- Operating System:ubuntu 20.04
Description
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 https://github.com/pypa/pip/issues/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.
What I Did
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
I am not bringing any solution here, but the issue doesn't seem to come from the python version but from the compiler (gcc). I encounter the same problem on MacOS (mojave) Python 3.8 and clang-omp...
If someone has a solution...
Thank you :)
